Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_072295
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 825163
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:12528 original size:21 final size:21
Alignment explanation
Indices: 12491--12558 Score: 111
Period size: 21 Copynumber: 3.2 Consensus size: 21
12481 CGTTTATAGC
*
12491 GCTT-ATGGCCAGTGGGGTCAT
1 GCTTGATGGCCA-AGGGGTCAT
12512 GCTTGATGGCCAAGGGGTCAT
1 GCTTGATGGCCAAGGGGTCAT
12533 GCTTGATGGCCAAGGGGTCAT
1 GCTTGATGGCCAAGGGGTCAT
12554 GCTTG
1 GCTTG
12559 TATGTTAGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
21 38 0.84
22 7 0.16
ACGTcount: A:0.16, C:0.19, G:0.38, T:0.26
Consensus pattern (21 bp):
GCTTGATGGCCAAGGGGTCAT
Left flanking sequence: Indices 11991 -- 12490
AATAGCTACCTTTTAAGGAATTGAAAAAGAATGAAATGCTATTCTCTTCGATCGCTCTATTCAAA
AATCAAAAACGAAGGGTGGGGAAGGAGCGAGCAGAAAGAGGCTCCTCATAGTAAGAAGAAGAAGC
TCACAGCCTGGGCTAGACCAAATGGCGAGGTTTCGTATCTTGTAGAGGGCCTTTGCTTGGATTCG
TCATTCATTACTTTATAGTTACCACGAGGATGGAGCCCATTAGCTAGCATAATTTGAAGACAGAG
ATGAATCCCCCTTATGAAAACAGAAATGCCGGCCGAGCTGAACGAACAGGGCGTGCTTTGGAATC
ATAAATCATTTACCGCCGAGACAGATTCTCTATGGATGGGGAATAACCTCTATTGGGAATAACTA
GGACATAGGGGTCTCCATGGGGATAGGACATCGGGGAATACTCCAAGTGTAGTGTCTAATATCAT
AAGCTAGTTTTCGTGTCTTTACCTGCCTGCTTTCCCGTTTATAGC
Right flanking sequence: Indices 12559 -- 13058
TATGTTAGTTGATTTTTTATTTCTTATTCTTTTTCTTATTTATTTGTATACGAGTTCCCATTCCG
AAGCTTGAGCTGGGCTAGATTCTTTATGCCAATGTTTGTTACCGGGAAACACCTACTCTAAAGGG
GGCTTGTCGTGCTTGACTTATTTCTTACCCAGGGCTGCGAAATGCCTCTGCTATGGGCTCCCCTC
GGGGGGCTCTTGTTGTCTACCCAATCTATGGTGGGCTCAAGCTATGGCTAAGGCAATGATGGGAT
CGATCTAGCGAGGGTACATTCTGGGATCGATTTGTCTCTTGGCTCTCCTAACCGTGCCTTGAATC
CTATTTAGCCACCCACTAGCAGGTCGGTTGCCCTCGTTGCTTCGGTGTTTTGCCCTAATGATAAA
TAATGGTTATGAAATCCAAGGCTACTACGGGAAGGTCCCTCCATGAATCGGATTTGGAAAAGGAT
GCGTACCAGGAGCGGTTTCTGGACCAGCCGTTGTTTGCTTTGAAG
Found at i:100791 original size:23 final size:25
Alignment explanation
Indices: 100765--100817 Score: 65
Period size: 28 Copynumber: 2.1 Consensus size: 25
100755 ATGGAAGCTG
100765 CCGTGGT-AG-CCTTGTTAGGCAGT
1 CCGTGGTGAGTCCTTGTTAGGCAGT
100788 CCGTGGTGGGGAGTCCTTGTTAGGCAGT
1 CCGTGGT---GAGTCCTTGTTAGGCAGT
100816 CC
1 CC
100818 AGAGAATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 7 0.28
27 2 0.08
28 16 0.64
ACGTcount: A:0.11, C:0.23, G:0.38, T:0.28
Consensus pattern (25 bp):
CCGTGGTGAGTCCTTGTTAGGCAGT
Left flanking sequence: Indices 100265 -- 100764
GCAGGACTTCGTAAATAGGCATAAATCCATCAATCGAATGGGTGTATGGAATCCCGTGTAGCTAG
CCTGCTTATCAGGATAAAGAAAACAAGATATTAAGAAAGTCTGCCCCCAAGAGATGAACTCCTAC
GGCCCTGTTCTCCTAGCTGCAACCGGTAGTCTGTTAGCTGGACTTCCTTCATGCGCTTGTAGCTC
TATAAGGGAGGATGCTCCCCCGTCTCTAGTAGGTAGGCTGTTCCTATTAGCTTCTTGTTCTTGTC
TGTAGGAGTATGGAGCCTAATGCCTTTCATATCCTGCAAGCTCCTAAGGAAGTTAGCTCTTGCCC
TATGGGCGTTCCTCGCTAGCTACCTAATAGAAAGTCTATCCTGAGGTAAGTAGCTCCCTGAATCT
GGATGCTAGACGACGAGCTGAGTAGGATAAAGAATCTGTCTTCTTGTTAGGACTAGCATTCCCTT
CCTTCCCCGACCTGTTGATCCTCGTACCTAGCTTTATGGAAGCTG
Right flanking sequence: Indices 100818 -- 101317
AGAGAATCTCTTCCCTGCTCTGTCTGCTCGGGTTTCCCTGGGCTAGTTACGTTGGGGTGTAGGCG
AGAGAGAAAGGAATCTCCCTCTTCCCGGCCCCTCCCATGCAATCGAAAAAAGAATCGGTATCCAA
GTTCGAATCGTATGTGTTAAGCAACGAATGCGAATGACTGACCGATCCCGTTTTCCTAGTACCCA
CTTTTCTTTCTTTTCCCGGTATGGAGTTCTTCGCCGCATAGCATTTTCGGGCAACTTCACTCCCC
CGATTTCTCCCTATCGTTTCCGCAAGGGGGGATTATGAAGAAAAAAATCCAGTGTCGTAAGTCCC
ACCAGTCAAGGCCAAAGTATGAGGGTGAGACAGCCATCGTCTTGGATTTGATTAATGACCGCCTT
CTTGTCTTCCTCCTGTTCTGGCTGAGTCCTGGAGTTCCAACCCGTAATTTCCAGCACGGGCACTG
AGGTGATCCTCAACCAGGGGTATTATTGGGCAAGCCAGATCATAG
Found at i:100816 original size:14 final size:14
Alignment explanation
Indices: 100774--100817 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
100764 GCCGTGGTAG
100774 CCTTGTTAGGCAGT
1 CCTTGTTAGGCAGT
* * * *
100788 CCGTGGTGGGGAGT
1 CCTTGTTAGGCAGT
100802 CCTTGTTAGGCAGT
1 CCTTGTTAGGCAGT
100816 CC
1 CC
100818 AGAGAATCTC
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.11, C:0.23, G:0.36, T:0.30
Consensus pattern (14 bp):
CCTTGTTAGGCAGT
Left flanking sequence: Indices 100274 -- 100773
CGTAAATAGGCATAAATCCATCAATCGAATGGGTGTATGGAATCCCGTGTAGCTAGCCTGCTTAT
CAGGATAAAGAAAACAAGATATTAAGAAAGTCTGCCCCCAAGAGATGAACTCCTACGGCCCTGTT
CTCCTAGCTGCAACCGGTAGTCTGTTAGCTGGACTTCCTTCATGCGCTTGTAGCTCTATAAGGGA
GGATGCTCCCCCGTCTCTAGTAGGTAGGCTGTTCCTATTAGCTTCTTGTTCTTGTCTGTAGGAGT
ATGGAGCCTAATGCCTTTCATATCCTGCAAGCTCCTAAGGAAGTTAGCTCTTGCCCTATGGGCGT
TCCTCGCTAGCTACCTAATAGAAAGTCTATCCTGAGGTAAGTAGCTCCCTGAATCTGGATGCTAG
ACGACGAGCTGAGTAGGATAAAGAATCTGTCTTCTTGTTAGGACTAGCATTCCCTTCCTTCCCCG
ACCTGTTGATCCTCGTACCTAGCTTTATGGAAGCTGCCGTGGTAG
Right flanking sequence: Indices 100818 -- 101317
AGAGAATCTCTTCCCTGCTCTGTCTGCTCGGGTTTCCCTGGGCTAGTTACGTTGGGGTGTAGGCG
AGAGAGAAAGGAATCTCCCTCTTCCCGGCCCCTCCCATGCAATCGAAAAAAGAATCGGTATCCAA
GTTCGAATCGTATGTGTTAAGCAACGAATGCGAATGACTGACCGATCCCGTTTTCCTAGTACCCA
CTTTTCTTTCTTTTCCCGGTATGGAGTTCTTCGCCGCATAGCATTTTCGGGCAACTTCACTCCCC
CGATTTCTCCCTATCGTTTCCGCAAGGGGGGATTATGAAGAAAAAAATCCAGTGTCGTAAGTCCC
ACCAGTCAAGGCCAAAGTATGAGGGTGAGACAGCCATCGTCTTGGATTTGATTAATGACCGCCTT
CTTGTCTTCCTCCTGTTCTGGCTGAGTCCTGGAGTTCCAACCCGTAATTTCCAGCACGGGCACTG
AGGTGATCCTCAACCAGGGGTATTATTGGGCAAGCCAGATCATAG
Found at i:150155 original size:12 final size:12
Alignment explanation
Indices: 150138--150162 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
150128 TCTGGAGGTA
150138 GTTCCTGTGCCT
1 GTTCCTGTGCCT
150150 GTTCCTGTGCCT
1 GTTCCTGTGCCT
150162 G
1 G
150163 AGGGAAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.32, G:0.28, T:0.40
Consensus pattern (12 bp):
GTTCCTGTGCCT
Left flanking sequence: Indices 149638 -- 150137
ATCAACTAAACAAAAAGCTTCTACCACGATATTTCACGCAGCAGAAATCTGTTTCATGTAGCTTG
GCAAGGAAATTTTGAGTCATGGGTACAGGACCCTTTACATGTAAGGCCTATTGCTCATGCAATTT
GGGATCCTCATTTTGGTCAACCGGCTGTGGAAGCTTTTACTCGAGGGGGTGCTCTTGGCCCAGTG
AATATCTCCTTAAGCGTTGAGGGGACAACTGATTCGTTGTGAGGACCATTAACTGAGATTTTCAC
TTCTTGTCTTGCAAATGCTGGTAGATCCGTGTTCATTGTTCTTACCGGAGGGAATCAACAATAGT
AGCCCAGTCAACCTCCTGTCAAATCAAGACCTTAAAGAAAAAGAGTAATCTATATGGAACAGCGG
TAAACTCTCGAGAATTGGTCCGCTAAAGGAATTCCATCTTTTGCTTTGGGCTCAACTCAAAAGTC
TAGCTGGAGCAGGTTTGAGCAAGTGTTGAAAGCAGTCTGGAGGTA
Right flanking sequence: Indices 150163 -- 150662
AGGGAAGGAAAAGACAGTCAAGTCAAGATGAAGGGGGGAGCTCTAGTCAAGTCAAGTTCTAATCA
AAGTCGTAAGTCCTCACCGCGTGAAAATGGAGTGATCGGCAGAAGGAATGAAAGTAGTTGAATAG
GAGGAAGTGAGCAAGTGTTGAAAGCTTCAGTCTTCAGTGATCCATTGGAACCGAAGATAACAAGT
AGAGTCTGCCCAATAGGTCACCAGGCTTGAAGTAACTTCGTGACTGATGGAGGTGGCCATTCCAC
GTTTGCTTTGTTCGTGAAGGGAGATCCTAAGCTCTGTGATATGACGTCCCCACCTGGTTGGTCTC
ATAGTTGTGCGAAAGCGGGACATGTGGACCACCGTTTAAGGGGATAGCTTTTAGTTAGCCGTTGA
AGGAGAAGGGGAAGTCAAGAAAAGCTCAAGATCTCATTAGTCAGGACAGAATCCGCTTTCAAGCT
TCAGTTAGAAAGGCAATCAATCAATCGAATTCGTCAGTCTGACGA
Found at i:178401 original size:21 final size:21
Alignment explanation
Indices: 178377--178418 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
178367 GATCCACTTG
*
178377 ACCAGTCATCCAGAGCTTGGA
1 ACCAGTAATCCAGAGCTTGGA
*
178398 ACCAGTAATTCAGAGCTTGGA
1 ACCAGTAATCCAGAGCTTGGA
178419 CAGTTAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (21 bp):
ACCAGTAATCCAGAGCTTGGA
Left flanking sequence: Indices 177877 -- 178376
ATAGTATTGACATAAGAGGAAAGATTCTGATCGCTGCATTTACGGTGCTAATATCTTTACTCTTA
CCGGGAATTCCTTGGTCGAAGCCTAGTTGACGAGCGACGAAGATTGGCTTGTAAGCAAGCACGAA
GAATCTCTCTGCTTCTCTTTTTTCGATCTTGAATCCAATCAAAGCGCTGGGAAGTGTAGAAATGC
ATGCAGAAATCGATGATTGGAGCGGGTAATCTAAAGAATCCGGATTGGCCGGTCGTCAAAAGGGA
AATGAACCCAATCCTCCAGAGGTGTTTGCTCTTTTTTCTCCCTACGTTCTTTCATTCCTTACGCT
CTATTTCATTTGAGCAGGGATCCCCGAAACCATCTCCCATCTACGCGCTACAGTTTATACCCTAT
CCACCAGCCCAAGAAGAGGTTCCGCTTGACTCATACTTTCCTGATCTATTTCTTCCGAATATGCC
TGCGATCCTACTCTTGATTGGAATCTCGAATGAAAGATCCACTTG
Right flanking sequence: Indices 178419 -- 178918
CAGTTAGTTGGGTAAGCATGGTCAGACCTCTTATCGACCGCTTCTCCTCTTTCAGTTACAGTACT
ACGGGGGGTGTGTTTGGGGAAAACGACCTAAAAGACCATAAAAAAGCTTTTTAAGCCACTTTTTA
GGTGGGATAACATCCTGCCTTGGCTGAAAGAGAAGTTAACGATGTCTCTCCCGCGGATCGCTTGA
GAAAGGTTACTAGAAACTATCGTGGTTCTCCTTCCACTTTGACTTCGACTATTGTTACTTCTTCG
ACCCGACCCCGAGATCTCGAATTCTTAACAGACAGAGACAGCCTCCACTTCTTTCAGATTCTTCT
TTTGAGCTTGAAGTCCACCCAAGAGAGTTCCCCGGCTTCTCGTGATGAGCGCAGCGCAGCAAAGG
GTGTTTGCGCCAGAGGACACGTTGGACCAGATGCAACTGCAAGGAAGATCTTGTTAGCTGGACTA
TACTAGGGGACACTTTGAACATACGTTCAAGAGGTTGTTAGAAGT
Found at i:182297 original size:16 final size:16
Alignment explanation
Indices: 182274--182317 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
182264 GAGAACTCCT
182274 TCTATGATCGGAATGT-
1 TCTATGATCGGAAT-TC
* *
182290 TGTATGATTGGAATTC
1 TCTATGATCGGAATTC
182306 TCTATGATCGGA
1 TCTATGATCGGA
182318 GATTGATTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (16 bp):
TCTATGATCGGAATTC
Left flanking sequence: Indices 181774 -- 182273
CATCTGTCTAATGTTTGCATTTTGAGAACTACGTGCGACCTGATCTGTATGTACGAGAATGAAAA
GAAGGAAGATCTATCTGACAGGACAAAGAAATAGGAAGGGAGGGTTCTTGATATCATCAATCAGG
ATAAGGAGAGTCCTAAAGCGTCAAGGAAAAAAATAAGAATAATATTTACCAATGAGTTGACTGCC
TTCATCCTACTAGAGTCCTTCACAAGCTGGAGGCTTAACCGCTTGGCCTCCTCTCCCGCTAAAGG
AAGGAAGGTATGTTTTGTTGATCAAGCCGTCGAGTTCTGAGTTCGAGCTGGGAGTTAAGAGTTTA
AGACAGTTTATAAAGAAGTGACGATAACAATGTCACTTCCTCACATCGTCACTTCTTTGACTTCC
CTTCCTTTCTCATCGTTGTTCGTTCCTCGGTCACAGCTCTGGGCCATTCCTGAAGTTAGGCCGAA
TATGTGTGGGAACATACTATAGGGAACACCGGGAAGAGAACTCCT
Right flanking sequence: Indices 182318 -- 182817
GATTGATTCAATACATCAAACATTTATTGCGCATAGCCAGTCCATTCTCCAACCTGAATGAGAAA
TCTGACCCGTTGTTCTGCCTACTTCTCTACTCGCTTCATATTACCTACTCATCCTGGATACACTT
CCGGACGCTAGCTATATGCTTAACACATGCACGTCGAGAACTACCGCGATTTGCTTACATGCTTG
TTATAAAGGTTGGAACAGGGGACACCACCCCTCTTATCTGGATCTGGATTCTCGTACATACATTT
CTAGGCAGCAGGATAGGAAGACTGTCTCCTTGCTTGTATGTAGTTGCGGTGCTATCCTTTATTTG
AATACCCACCTACGAGAAAGAATGGAAGAGAAAGCATACTGCTCTCTCTATCTCGGCTGCTTTCT
CTACGACGCAGCTGCAACATCTTCATCTTAACGTCTTCTCGTCTACCAGATTCGGTCGTGTCCCA
TGTAACACGCTGTCCTTTCGTTCCCTTCATTTTGACAGGGGACCT
Found at i:228481 original size:13 final size:13
Alignment explanation
Indices: 228463--228489 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
228453 CCGAGTTTGA
228463 GTTCGAGTTCCTC
1 GTTCGAGTTCCTC
228476 GTTCGAGTTCCTC
1 GTTCGAGTTCCTC
228489 G
1 G
228490 ATTTCCGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.30, G:0.26, T:0.37
Consensus pattern (13 bp):
GTTCGAGTTCCTC
Left flanking sequence: Indices 227963 -- 228462
TTTGATTGTTGGACGATGTGAATGAGCATGCCATTCATTCTGAGCAGGGAACTGAATAGGGTTTG
TCTTTTGCAATCGCGGGCGGAGACGAGTCAAGTTGGCGAAAGCCAAGGACGACATCGGAGGGCGA
TTAGCCTCTATGTTCAAGTAAGGTAAGCATTGACTGACCTCATGAGAGTGAGCAAGAACGAGAGT
CACAGGGTTCATGGGTTCTGAGTTGTCAAAAAAGACAAAACCACCGACATGACTTTCGTAGAGAT
CGGGATTAGCAGACTCCTCGGTGATCGTAGCAGTGGTCTTGATGTCGGGGAGAACCCGAATGAGT
ACGTCTTCCCTTTCCAGCAGCTCGTCCACTGACTCCTCGGCGGAAGTTGCGTCAAGTGATTGCAT
GGCTCCATGCAACGTCTCAATTGTAGATACGAGGGACCCATTTCGGATAAGGAAGGTTTCCTGGA
AGGGAGAAGGGGGCGGAAAGGAGGGGGAAGGGCTTCCGAGTTTGA
Right flanking sequence: Indices 228490 -- 228989
ATTTCCGGTCGGTGAACGAACAAGCCCGGTGGAGAGCCCAAGTTCCTCGCGTTCTTCTTCTTGTC
TTCCCTTCCGGCTAGACTGGCTATCCTAGCTAGCAGTTCTCTTAGCAGTAGGAGGCCGTAGTCCG
AGCCCGATCCCAAGTCCGAGTTCGAGTTCGGGTCTTCCTCGAATGGCTGAGTTAAGGTAAGCGCT
AGCTTTGCTCTCCTGCTTAACGCACCTAACCCTCGGGTTTGCTTCGTCTCCATTTGTGTATTGCT
TAAATCGATCTTTTGAAGCCAAAAATACGGGGTTTTGAGAATCAATTGCACATAGATTCAGACCT
TCGTCTTCTCGGCTGGTTCTGGACTGGAACCGCTTAGTCAATCCAGAAGTTAGAAGTTGTTAGAA
GTTAGGTCCAAGAGAAAGAAAGGGCTACTCCCCGAATTATGGAAAATAGATGAAGCGCCCTAGGT
CTAAAAGGTGGGGATCAATTTCTTAAAAGAAAGCGACCAATTATA
Found at i:373023 original size:32 final size:31
Alignment explanation
Indices: 372939--373024 Score: 75
Period size: 36 Copynumber: 2.6 Consensus size: 31
372929 CTTCTAGTAG
* *
372939 GTAGAGTAGCCTACCCTTGAGTAGGTCTGTCT
1 GTAGAGTAGCTTACCCTTGAGTAGGTCTGT-A
*
372971 GTAGAGTAGCTAACCAACCCTAT-AGTAGGTCTGTA
1 GTAGAGTAGCT----TACCCT-TGAGTAGGTCTGTA
373006 GATAGAGTAGCTTACCCTT
1 G-TAGAGTAGCTTACCCTT
373025 ACCTTTCAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
31 1 0.02
32 15 0.34
35 1 0.02
36 26 0.59
37 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (31 bp):
GTAGAGTAGCTTACCCTTGAGTAGGTCTGTA
Left flanking sequence: Indices 372439 -- 372938
ATGCGAGTTGGTGAACTGCACCACTGCTTCGAAGGAACAAGGGACTCTCAAACAAAGACTCCCAA
GTCCTACTGTGGAATGGATCGCTTTCTTGTTCACCTGTACGAGATTGCTTTCTGTGCGCGTACGG
ATCGACAGAGATACGTCGTAAGTCAGATTGAATTTCCAGTAACCAATCAATCACGATAAGAGGAT
GTTCTCCAAAACCACAAGGGGAAGGGTATTACAGCTTCGATTCGATCCTTATTTAGCGTAGTTGC
TACGTAAACCTCGTTGGTACAACTATAGATGAGATTAAGCTTTCACCAGTCAAATGTCAATGGTG
CGGCACGTACTTCATTGACCTTAGTGCCTGTAGTTGGCCTACAGTTAGGTTAGGTTAGATAGGTG
CCTTAGTGGGATTGTCGATAAGCAAGACCTTGCAAAGATTAGCTTCTAAGGCTCTCGAGCGCTCA
CTGACACCTACTAGATAGATATTCCGCTGCTTTGTCTTCTAGTAG
Right flanking sequence: Indices 373025 -- 373524
ACCTTTCAATAAGGAGTTCTTCTGAGGGCTGTCGATTAGCAACAAGACGCAAGTAGTTGTTCTTC
TTTTAAGGTTTCCTTGCGAGTTCTTTCTTCTCGACAAGTAGAGCAGGTCAGTACAGTTGTCTCAC
TTTAGCAAGTGTATCGCTATAGCTGCTCTATTGCTGTTGTATCGCTTTGATAGCTGCGTTTAGGA
GTTGTGTATTTGTATGCGTTGGGAGTTGTCTTGCTATAATAGATGCTATAGAGCTGCTATTATAG
CAGTTGTATAACTATCCTAGCTATAGGTAGTTCATAGGACAAGTAGGTATGGGTAGCCTCAACGC
TGTAGGTATAGGTTTCCTCAACGCACAAGTCGGTAGCGGAAAGTTGTTCTTTTAGTAGTAGCTAA
GTAGTAGCTGTCTAGTGCTTTTATTCGTAGCTACCGAGGAGCTGTATACGCAAGGTCAACGCTTC
CTTTACAGAAGTCTTTAGCGCAAAGCTACACCCTCCCTCTCTCTT
Found at i:373355 original size:24 final size:24
Alignment explanation
Indices: 373327--373373 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
373317 CATAGGACAA
*
373327 GTAGGTATGGGTAGCCTCAACGCT
1 GTAGGTATAGGTAGCCTCAACGCT
**
373351 GTAGGTATAGGTTTCCTCAACGC
1 GTAGGTATAGGTAGCCTCAACGC
373374 ACAAGTCGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (24 bp):
GTAGGTATAGGTAGCCTCAACGCT
Left flanking sequence: Indices 372827 -- 373326
TGCCTTAGTGGGATTGTCGATAAGCAAGACCTTGCAAAGATTAGCTTCTAAGGCTCTCGAGCGCT
CACTGACACCTACTAGATAGATATTCCGCTGCTTTGTCTTCTAGTAGGTAGAGTAGCCTACCCTT
GAGTAGGTCTGTCTGTAGAGTAGCTAACCAACCCTATAGTAGGTCTGTAGATAGAGTAGCTTACC
CTTACCTTTCAATAAGGAGTTCTTCTGAGGGCTGTCGATTAGCAACAAGACGCAAGTAGTTGTTC
TTCTTTTAAGGTTTCCTTGCGAGTTCTTTCTTCTCGACAAGTAGAGCAGGTCAGTACAGTTGTCT
CACTTTAGCAAGTGTATCGCTATAGCTGCTCTATTGCTGTTGTATCGCTTTGATAGCTGCGTTTA
GGAGTTGTGTATTTGTATGCGTTGGGAGTTGTCTTGCTATAATAGATGCTATAGAGCTGCTATTA
TAGCAGTTGTATAACTATCCTAGCTATAGGTAGTTCATAGGACAA
Right flanking sequence: Indices 373374 -- 373873
ACAAGTCGGTAGCGGAAAGTTGTTCTTTTAGTAGTAGCTAAGTAGTAGCTGTCTAGTGCTTTTAT
TCGTAGCTACCGAGGAGCTGTATACGCAAGGTCAACGCTTCCTTTACAGAAGTCTTTAGCGCAAA
GCTACACCCTCCCTCTCTCTTGAAAACTTATATATCCCCTGTAAGCAAGCGCGATGAATTCCAGA
TAGCTTGAGGTTGTTAGCTAGAGCTAGCTACAATACAGCTACGCGGTTGGCTTACTTTCCCTACC
CTTGTCTTAAGCATAACACATTGCAGTAAATCGCTTACTAGGAACTGTTCTTAGTACGAGGTATA
GTAATAGCCGTATCTCTCCGCAGTTCCCTTTAGGTTTTATAGTTTCTTCTTTCTTTTCCGTCGGC
TTTCTTCCCAAAGCGGTCGAGTCCTGGCACTTAGATATATATCGATCGTAACCGAGACCGATCTA
CAACTCTATCTAAAACAGAGTTTTGGTAGTTGAGTACCTTCTTTC
Found at i:407130 original size:17 final size:18
Alignment explanation
Indices: 407103--407136 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
407093 CAGGAAAGGA
407103 TTTCATTACTGACTTTCC
1 TTTCATTACTGACTTTCC
*
407121 TTTC-TTACTGCCTTTC
1 TTTCATTACTGACTTTC
407137 AGTTTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.29, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTCATTACTGACTTTCC
Left flanking sequence: Indices 406603 -- 407102
CTAAGACAAGCTTTCGCTTGCCTCTCTTTATGGAAAAAAGCTACCAATGCTATGGTGTCCAACCT
AACGCTTTCCGAGCCAACCTAAGACCCCTAACACTTTCCTCTCACTGGAGTTTAAGCCAAATCAG
GCTAGGCTTTCCTGACTTTGCCGACCTTCTAATTCATATCTCTTTGTTTTCAATTTCGCACTTTA
TGTAATGTACTGAAAATTTCTTTCATCAATAAATCCCAGGAAAATGAAAGTATTCGACTTCTTTC
TTTTGGCACTCTTTAGAGTCAAATCGGTCTAATGCCCCGCCCTATATAGTCAGGGGAAAGGATTC
TACTTTTTTTGATCTCCATCTCCCTTTAGCCTTGGCCGCCTCTCGTTAAAGAGTGAATTCATGAA
CATTGAGTAAAGATAGGCAAGACGTGACTTCTTACATTACACGGGTTTGGCTTGAAGACAGGGAT
CTGTCCCTATATCTTTTCTTTTACGAAGGGATATCCAGGAAAGGA
Right flanking sequence: Indices 407137 -- 407636
AGTTTATAATAGATTCGATCTTGCTTCCCGGCGCGTGTAGTAATAAAAACCTCACCTTCCGTACC
GTAGGCTTCTCACCGGCTGTCTTTCCTGGATCAACTGGTGCATTCTTCTAGCTCTAGTTAACCTG
TCGCGGGAGATTAAATGGAACGAGATTGAACCTTCTTTATCTCGCGAGCATGCACAGGAAGATAA
AGAAGTGGGGGCTATCTTAAGATCATCTAATACGAATTCTGTTCTTTACCTCTCTTATCTTCTTG
GTCTTGCGAGTGATCGCTCTTAGTCGCCAGGCTTTCTTCTCCCAAAGACGGAATGACCAAGCGCT
TCTTCTCTTCCTTATCTTATCCCGATCCCTTCTTCCGTCCGAACGTACTTATCGTTTTCAAGGGA
AGGGGGAAATGAATTCAAATAATGTATTCTATGAAGGCGGATATAAAAGAATGTCTTCAAAAGAG
AAGCTTCAATCCCCTCATAGGCAGGAACTAATGCTTAGCTTAATT
Found at i:408190 original size:15 final size:17
Alignment explanation
Indices: 408160--408195 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
408150 TGACCCGAAA
408160 GACTTTGAGCTTGCTTT
1 GACTTTGAGCTTGCTTT
408177 GACTTTG-G-TTGCTTT
1 GACTTTGAGCTTGCTTT
408192 -ACTT
1 GACTT
408196 AGTAGGGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 7 0.37
16 1 0.05
17 7 0.37
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (17 bp):
GACTTTGAGCTTGCTTT
Left flanking sequence: Indices 407660 -- 408159
GGACAAAGATTCAAGCCCCGTCCGATCGGTTAAAGATTCTATTCACTCCCCTACTAAGTCAAGGG
GGATCGAGATTCAAGTAATCGTAATTTCCTATCACTCACTCAAGCTAATTGCATTTCCTCAGTTA
AGCTCTTCTAAATCGGTTTGGCACCTCGATATTGGCTCTTCTCCACCTGGGGCTGGCTGTACTAT
GTTCCAAGGAAAAGAATTTTCTTACTTACTCCCCTCCTCTCCTTAACAGTCGAGTCTCCTTCGGA
CCCTGACTTAAGAGCTTTAGGGGATTAGCTCATCTTCGGTCGCCGTCTTGGTTGGTCGACAAGAG
GGGTTGGGAATAGGAATAGTTTAAGAGCGAAGCAAACCTCCGGTGAAGGAGAGGAACCTTCGAAC
TTCAAAGTCAGAGCGAGGAGGAAGAAAAGAAAAGGCCATTTACTATAGATAGTCTGCCAGAAAAG
ATTCATGATTTGGAAGCCCCTATACTGAGAAAGCCTGACCCGAAA
Right flanking sequence: Indices 408196 -- 408695
AGTAGGGGAGGAAAGCGACCCTCAGAATATGGTCTACCTTACCCCGTCTCGGGCTTTCTAGATCC
CTAAGAACATAGTCTTTCCAGCCTTTCCGGAGGTTACGAACCTATGAGATTTCACCGGTCTTTCT
TTTGTGAACTCTTTCGGTACTGCCCCACTGGCTCTTGATCGTCGAAGGTGTGCTGGCTGATGAAT
CTCTTTCTGGGTTCTCTCTATCTGCCTTTCCTGGGTCCTGAAGTTCATTCTAGTCTGGCAAGGAT
GGAGGTTGAAGGAGAGTTGAACGAAGGGTCTACTCAAGCGAATGAGAGCGAGCAGAATAACAATA
AGAGAATAGCCGTCCAATGGGTCTTTCACTTTCAAATCGATATGAGATCCGAAGCCTTCATAAAA
TAGGGCATTCCTTAGCTTGACTTTAGAAGAGAAGGTAACCATATTCAAAGACGCAGCCATAGAGC
ATGAGCCTTCGTTGCTACTCTACTACTTATTTATAGCTATAGTTA
Found at i:436587 original size:19 final size:19
Alignment explanation
Indices: 436559--436597 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
436549 TCTGAGCTCA
* *
436559 ACCAATAAAGGAAAGTAAG
1 ACCAAGAAAGGAAAGGAAG
*
436578 ACCAAGAAAGTAAAGGAAG
1 ACCAAGAAAGGAAAGGAAG
436597 A
1 A
436598 GAGTCGTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.10, G:0.23, T:0.08
Consensus pattern (19 bp):
ACCAAGAAAGGAAAGGAAG
Left flanking sequence: Indices 436059 -- 436558
CGTCCCATGCAGGGGTTACCGTAGGTTTGGAACCCTCCGAACTCAGAAATATTCTCAAACGGCGA
AGCCTCGCTCAGTACCACGGGGTATTCTCAAACGTCTTCCCGGATCAATGGATCGGTCGAGCAAA
GCTAGCGCTTACCTTAACTGCACTGCCCGACTGAAACTGCGAGCGCTAGAGCAGGGTTCCCCCGG
GGGTAGTTACATCCGTCCTACCCAAGATCAACTAGCTTACCAACCACAGATGATGCGGGAGCGAA
GTAGCCGTATTTTATAATGCGGGTCACGATATCTGACAAAAATGCCACCCTCAGGAAACCATGGG
TTTAGAGCTCCTCGAGTTAGAGCTCTAAATTTTGCAATCCAGCGCTTTTTATCCCACAAAAAGCA
TTTCAGATGTTCCCGCGCATCATCTAAAATCCTTCGGGGCAACCGAAAAAGTAATCTAAAAACAC
TTCCTCTTCTACGCTAAAACCTCCTAATAAAGAGTTCTGAGCTCA
Right flanking sequence: Indices 436598 -- 437097
GAGTCGTTTCTATTCCGGAGAGTATCCTCGGAGGAGGGGAGAAGCCGAGCTGCAGAGTCACGTTC
TTTTTAAATTGAATAGTCGTCCACCGTCCACTCTGATCTGTCTCACAACGTCTCCTCTTCACACC
CATGTAACAGAATTTTAGAGACGCTTGTCTCCAAGCTCCCCCTGTCCTGTTCCCCCAATTGCTGG
AGTAATTCCAATTGGTTTTGACCCCATTGTAGGTTTTTCTCTCCCATAAGAAAGATAGGCATGAT
CCTTTTTTTGTTCTCCCACCCTCCCTTCTCGATGGTGACTGTAGCGAGTGGCCAGCTAGCGTGAT
CCATCTTATCCGGATCGTCGTATCTATAGATGCCCACCTGCGCCTCCTTTATTCGTTTGAATAGT
TTGATTGTTGTCACAGTCTTCGTTTCACCTCCCATTTGCAGTTCCACCTGGGATATCCTGCTATT
TTGGGTTGGTTTCTTTCGAAACGGATTTCGAAAAAGGGGCTGGGG
Found at i:440403 original size:14 final size:14
Alignment explanation
Indices: 440384--440413 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
440374 TCGTCCGCTA
*
440384 GATAGGATAGATAG
1 GATAGGATAAATAG
440398 GATAGGATAAATAG
1 GATAGGATAAATAG
440412 GA
1 GA
440414 ACTCAAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (14 bp):
GATAGGATAAATAG
Left flanking sequence: Indices 439884 -- 440383
CCTATCGTCCTCTTGCTATAGATAGAATAGCAACGATTAGCTAGCGCTAAGAAGAAAAACCTGCC
TTTACTAAGTACACTATAAAAATGCCTTTTGCTCTCTATCTCCTAATGCCAACTGCAATCTAACA
TCTGCAGCGTCAATGCATAGTATAATAGGTGGCAGCCGCTCTCTATGTACTTGTAGTTGAGTAAG
GACTGTAAGCTTCAAGTCCCTTCTTATCTTCTTTTAGTTCCAACAGGAGGCTGGGTGTAACTCAG
GGAAGATAGTTATATCTTCTCATCCTAGTGCTTCTCTTTCCCCTATCTATAGGACTCTCCTCTTT
TCTGTATTATCAGAAGGTCTGTCTCTTTCCCTCGTCCTGTAGTTTCTCTTTTGAAGGTTATACCG
GACTCTTATCTGACATAACTATAGTAGTAGTTGTATCGTCCTCTTGTATTATATGAATTAAGAAG
ATCCCTTTCATAGTAGTTGTTATCTATAGTCCGCATCGTCCGCTA
Right flanking sequence: Indices 440414 -- 440913
ACTCAAAACAAGCTACTAGGCAAGAAGAGCTACCATCTAGCAACTCGGTTCGGATAGGACTACTA
GCTGCTAAGACTAAATGGTAGTACAGTACGAAGACAGACAGGGCTTTCCCTGAAATGGAACTTGA
ATGCTGGAGCAAGAAGACGCATGAAAGTCGATCTAGTACGACCAGCGCGGTTGTTCTTATTTCAT
TTTCTTCTTCCAAGCCCTTAAACGAAAGCACTCACTGAGTTACTTACGGTCTTCAGCAGGCATGG
TTGAACTGACGGCTACGCACTTCCCTTTTGCCCTCCGTTAGTCTTCTACGGACTTCTTTGTGGAA
GGCACTCCTATAGGAGTTCGCACGAAGATCGTCCAAGATAGCAAAGATATCTTGGACTTTTTCTT
CTAGGGAAGTGGGGGCACCGCGTTCATCCCACTCCATAACCTCTTCCATTACCTGATTGGAGGTG
GCGTGAATTTTGTCACCATCAGGCAATGGCTCCTCCTGCACCTGC
Found at i:475484 original size:39 final size:39
Alignment explanation
Indices: 475430--475508 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
475420 AGATTTTCTA
*
475430 TTCACTCATGATCTGGCCTGGTCGACCCGATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
475469 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
475508 T
1 T
475509 GAAGGATGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.32
Consensus pattern (39 bp):
TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
Left flanking sequence: Indices 474930 -- 475429
CCCACACCTGTGTAGAGTAGATCGTTCAACACCTGCGGCACAAACCCATTTTGGACTACGTTAAA
CCTAGTATCATAGGCGACCGAACGGCCGCCCCCTAATTACTAGACCGACCTGCTATAATAATTCC
ATAAACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATGTTCGGATCTGACAATACCA
TACCATAATCAAAAGGTACAACGGCCCGAGCGACCAGACTTAACATAAATGTAGCCACTGGAGCC
ATTCTAAAAAGGGAGAAATTTGCACTACTTGGTGAAATAGGTTCTTTTAGAATCAATTTCAAACC
ATCTGCTAGAGGTTGTAACAATCCAAACGATCCAACTACATCAGGACCCTTTCGACGTTGCACAA
AAGCCATTACTTTACGTTCAGCTAGCACTAAAAAGGCTACTCCTAGTAGAAGTGGTAGAATTATT
CCAAGTATTTCCGCAGGAACAGCTATGTACATTTTAGATTTTCTA
Right flanking sequence: Indices 475509 -- 476008
GAAGGATGGGACCTTTTCTCGAAAAACCCCACGTTAGCCCCAAGACGTTGGTCTCTAACTAGAAA
AGTAAATGCTTGATGGCCAACTTTCTTCATCCCTCAAATATCCCCTCAAATCAAAAAAGCAACTC
ACACATCGTCATTCTGAGGAAGAGCCCCTCCGCTTTCTTTGAGTGCTATGGGGGTCTTCTTCCTT
TGATTATTTGAAATCAATCCTCTGGTTGCCTTTTTCTCTGCCTTTTGTTCTCAGGCGCGAAGCCC
TATCGTTGACGAATACTTCGTCATCTGAAAACAACCGTTCTTCTCGTCTATCACTCAACCTTCTT
TATCTTGCTTTTCTTCCAAGATCTGTTGCAAACGAACTGATCTGTCTTTCTGGCTTCTGGCCTAC
TCAACTGTGGCAGGAAGTATAATCAGTCCTTCCCTGCTATAGGTCGGGATGGCCACGTTCTCTCT
CTCAAGGATATCAGTGTACTCCTTCCAAGCGTCAACTAGACCGCA
Found at i:523078 original size:17 final size:18
Alignment explanation
Indices: 523056--523092 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
523046 CAACTTGGTG
523056 GAAAAATA-AAGAAATAT
1 GAAAAATATAAGAAATAT
523073 GAAAAATATAAGAAATAT
1 GAAAAATATAAGAAATAT
523091 GA
1 GA
523093 TAATATGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (18 bp):
GAAAAATATAAGAAATAT
Left flanking sequence: Indices 522556 -- 523055
CCTGCTGCTCCGCGGAGAATTCCCCTCGCGGATGGGGGATCGACGCTCGCTCTACGATGCTATCG
AGTTCCCTCTTAGGTAGTCGCTCTACGATGCTATCGAGTTCCCCCCTTTCCGGAAAAACATCAGC
AACTACAGGCGCTTGCTGGCTTCCTACTAATGGTGGGGCCGGCCGGTCATCCACCTTCGGTGGCG
CCAGAGTCAAATCTAAATCAACATCATCCCCATCTGGAATGGGCTGACCAAGGACCAACTCAAAA
TTGAGCCCTGATGGAGCTTCCATATAGAGAATTGGAAAAATACTAGTCCATACGGCTACAGCTGG
AAAAAGAATCCTATTCAAAATGAAGTATACTAAAATAAGCATTTTCATAATTTGAAGAAAAGTAC
GAAAATCTTTATTTTTTATAAAAAAGAGAAAAATGCGTTGCTCGAAAGAAGATAAGACTTCCCGA
AGGTGAATGGGGTGAAAACTTGAATTACGCACATACAACTTGGTG
Right flanking sequence: Indices 523093 -- 523592
TAATATGGAAAATTTGGAATGTGAAAATAAGATTGAACATGTGGGAGGATCCGAACAATTTCTTT
CTTTCATTTCCAATTAAGGAGAGCACTGAGTTACTTACGTTATAGCACAGTCAGGCAGGCTTATA
CCATTACGCTCACGAGCAGAATCTTTGAAATGGAAATTGATTCACCGGGCTTGGACCATGTCTCC
CGAACAATCTCAGTACATATGGCGCAAGACGATTCCACATATCGAGGTCGGAATGGGATCGGGTG
TTTTCACGTCTCACCGTAGTGCCCGGTTTGTCTTGATTTCCGATTGATGAACAAGAAGGAAAATG
GAACTATTGGATTTGATGACTCGCCCCCGGCTACGTGTCCTTTGGACGCCCGCCCGCCACCAGTG
GAAGCAAGCTAGCCCAGCTTCAAAAGAAGGCGCTAGCGCCCTTACTAATCGATAGGCTAGCGCGC
AAGGGCTTTTTTGAAGCCAGCTAAAAAACGGATGCGCGCTACTAG
Found at i:544536 original size:16 final size:17
Alignment explanation
Indices: 544504--544549 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
544494 CTTGGCTTGG
544504 GGTTAGTTCATTCTCTT
1 GGTTAGTTCATTCTCTT
*
544521 GGTTAGTTGA-TCTCTT
1 GGTTAGTTCATTCTCTT
* *
544537 GCTTAGTTTATTC
1 GGTTAGTTCATTC
544550 CATTTACTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (17 bp):
GGTTAGTTCATTCTCTT
Left flanking sequence: Indices 544004 -- 544503
GTATGCGCGAGTTGCAGGGCTTCAAGCTGCTTTGACATATCGGGTGCAGGATGTGCTTCTATCCC
CTTACCGAATTCCCTGTCATTTTCTTTAATATGTTGTGTTGTAAGATGTTGTAATAAATGTTATA
GTTGAAAGACACCTCCTCCTTTTTTTATCATCCCTTAGCTCTTTGATGAGCTCTGAGAGAGTAAT
TAAATAGGCGTAGGCTCATGACTCTTGAAAGTGAATATCGCTCGCAATGGCCGCCCTGATAGTTG
AAGCCTTCAACGGGGAATTTCGTATGCTAGCTCCAATGAGTAGTAGAGGAAAGCTCGGCCTCAGT
GCGTCCCACTTGTGTCGTGTTTTAAGCCTGCTATGCATCCTTGCTTCATCTACCATTCCTGACAA
TCCATTTCTGGTATGCCCGCTGCTTCGTTCACAATTACTGACAATCCATCCTATCTTTATTGGGA
TCATACCCCCTTGGACTTGAAATCCGAGATCATCCCTTGGCTTGG
Right flanking sequence: Indices 544550 -- 545049
CATTTACTGCCCCTCTTTTGCTTGATGAAAGACATCCTGGCAAAGGCCGATTAGTAAAAAAAGGG
GACTTTCATGGGTCCGATGGCTCTTTGACTGGTGTGCCTTAAAATGTTATTGATAAATGGGCGAA
ACTCGATTTGTCGCTTAAAGAGGTATTGTCTCCGCCTTTGAAAGTAGGGATCATCTCTCTTCTCT
TATGATCCTCCATTGCTGTTCGGTAGTGGCCTAAGGCTCAATGATTGATCTTCTGCGCTAAGGCT
AGCATCTTATCCCATCTTTCATCTTATTGCTTCGAGCTCTCTTCGGGAAAGTGTAAAAGTGTAAC
CTCTTGCTCCTTGATTTCACATAAACAACTGAGTGCCTTCTGCTCCTTTTGGTCTTCTCTTCCTG
TGTCTATTGATCTCCTGCCCACTCACATGATCTTTATCAAATCCTTGACGGCGGATAGGACTACT
CCTGCTTGCTCTTGGCCTTGGCTGCTTAGAGACATCCCTGTAGTT
Found at i:586085 original size:14 final size:15
Alignment explanation
Indices: 586061--586090 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
586051 CGGTACCTGC
586061 CCTTATCCCTATCTG
1 CCTTATCCCTATCTG
586076 CCTT-TCCCTATCTG
1 CCTTATCCCTATCTG
586090 C
1 C
586091 AGTAGCCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.10, C:0.43, G:0.07, T:0.40
Consensus pattern (15 bp):
CCTTATCCCTATCTG
Left flanking sequence: Indices 585561 -- 586060
AGTAGCAAGCGTTCCAGTTGAGGGCATGACTCCTCAAACGGTACCGCTGAGTTACTTTCTCCAGC
TAAAAGAGAGTCCAAGATCTCACCAAGATGTTTGGCAATTTTCTGGCAGCACAGTCCCATTCTTC
ACAACCGCTTGTATCACCCAACCAGAGCCAGACCACTCAAGTTACAAGTCAGCCCTTCCTGCGAG
GATACCCGCTAGGATCGTAGCACTAGCATCGGGAACTGGAACTCCTAACTCGAGCTCCTAACTCC
CCTCGCGCCACTCGAACTCATAGTATTCGTTCGCTTTTCTATATTTATACTTTGTACGAGGAGGA
GCCTGCCCTCACATCTAGGAACCGGCCGAGCTAGCTGGCTCGGCTATCGCTACCTTGCTTTCTTT
CATTTGGTGGCGGAATCTTCCTTGTGCAGGAATCCCTTTACTTTATCTCTCCCTGGTAGTACCCC
CGGTACTAAGAGATGTGAAGGATAATCCCTTTCATCGGTACCTGC
Right flanking sequence: Indices 586091 -- 586590
AGTAGCCTTGTCATCAGCATCGAAGAATCTCCTATCAAGATCGTAAGAGCAGGCTGCCTTATCTC
CTTATCTCGAAGTCGGAAGCTACTTATCTGTACCTCCGTGGCAACCGCCTAGCATCACCGTTACT
CCTCGCTTCAGTAACTCCCTTTGTTCCCCCGCTCCAACTCGACTGTCTCCTTACCTCGGGCAAGG
TCCTTTCCTTGTGTTGACGCGGGCCTGCTGTCCGCCTCGAATGCTTTCTCTTCTCTTTACAAATG
GGTAGGAGATCCACTTGGGTAACTACCAGCAGCCGGAACAAGAGCAGACTGGCATTCCTTCGAAC
AACAGGGAAAACTTCATTACAAAGAGGACGAAGACGATTGGGGAAGAAGATTTGCAAGAACATCT
TATTTAGAATCTACTGCTTGAACTCTGTAAAGCAGTAGATTCTTAGAAGTGGATTCGTACTTTCT
TTAAGAATCTAATATTCTTCCTTGATTGAAGAAGATTCCTCGTAT
Found at i:680460 original size:15 final size:15
Alignment explanation
Indices: 680440--680471 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
680430 AGAAAGCGAC
*
680440 TATTCACGTTAGTAG
1 TATTCACGTCAGTAG
680455 TATTCACGTCAGTAG
1 TATTCACGTCAGTAG
680470 TA
1 TA
680472 GAGGTTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (15 bp):
TATTCACGTCAGTAG
Left flanking sequence: Indices 679940 -- 680439
ACTTGCTACTGATTGAGCATGAAAACAGTCTGCTTTTCACATTAATGAGACGTGCTATTAGAGAA
GGGAGAAATTGTTCTTTGTTCAAGCTAACTAATTAGAAAATGTTCATTCACATCTTCGAATATGC
TTAACACATGCAAGTCGAAAACGTTGAGGAAGCAGACGATATGCATTTACTTTTAAGCTGCTGGT
CTGCTAGTCGAATAGCTATTCCAACTACGTCTAGCTGCTAGGGCAGGAACTCCAAGTACTAGCTC
GTACAAATAAATAAATAATAATAAGGCTTCCAACTGCTTTTCTTATTCCAATATAAGAAAAATAA
GGAAGGAAAGCCCACGGAAAGATATAAGTTTCCCAAATCCTTATTTTCAATACACAGGCGAATAA
ACTATTAGCTTATATAAGGTAAAGGAAATCGATGAAATGTCGGCAAGAGTTCCTTGACTTTGGCC
GGTCACCGATTGATAGTAGAGCTGTTACAAGTCCAAGAAAGCGAC
Right flanking sequence: Indices 680472 -- 680971
GAGGTTGTTGTAGTTGATGTAATTGATTTCATTGTTTGATTTTCTTTGTTGAGATTGGGTTGGTG
TTCCGTGTACTAAGGTACAAGATCTCTAATAATGCATTGGATGGATGCCCGGGCATTGAGAAGGA
AGGACGCTTTCAGAGGCGAAAGGCCATGGGGAGATACCGTCTGTGATCCATGGATCTCCGATCGG
GAAACCGTATCCAAGCTCCGTGGCTAGTCTGCGCTCTTTGGACTTTTCAAACTTAGCGAACTGAA
ACATCTGAGTAGCTAAAGGAAAGGAAATCAACCGAGACCCCGTTAGTAGCGGCGAGCGAGAGCGG
GTTGGGGGTTTGAAGAAAAACAAAGACGAAGCCCTCTTTCCGAGGGTTAGGTGCGTTAAGCAGTC
GAGCATCTTCAAACCTCAGCTTCGTGTTCACTTCTTTTTCGCCAGGTTTCATTCGATTTGTTGTG
GATGATGGAAAAACCAGCAAGCTACGGCTTCAAAGCAACCCTTAT
Found at i:731741 original size:14 final size:14
Alignment explanation
Indices: 731722--731750 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
731712 AAAATACCAA
731722 TTGCAAGAATAAAT
1 TTGCAAGAATAAAT
731736 TTGCAAGAATAAAT
1 TTGCAAGAATAAAT
731750 T
1 T
731751 CAATTGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (14 bp):
TTGCAAGAATAAAT
Left flanking sequence: Indices 731222 -- 731721
TTAATCAAAGGTCCAACTGATCACCACGTCTGTATTGTAAATATGCAGTTACGAATAATCCAGCC
AAAGTAATAGGAATTAGACCTAACACGATTCCAAATAGAAAAACTTCAATCATTTCAATTTGTTT
GAAAGGAAAAAAAGAGGTAATATCTATAATTAAATATTAATACGAATTGCCATGAATCTCAATGA
TCAAGAATTGGCAATTGATACGGTAAGTCATTATAGAATACGCAGAATACTACATAAAGATTTCT
TTTTATGAATTGTTGATTTCATTCATTTCAAATATGAATTTCAAATAAGTCGTATCTTGCTCAGA
CCAATAAAGAGAGCTGAGGTTATAGTTAAAGCCGCTAGTAAAAAACCGAAATAACTAGTTATAGT
AGGCATGAAGAAGCTAAATGAAATATATTCGTTTTATACATATGTTTATAAAGCACTTACCTAAG
TTAGTTTCCATTTTTGCAAAATAGGAGGATAAGCAAAAATACCAA
Right flanking sequence: Indices 731751 -- 732250
CAATTGAAAGTTTTTGATTCATCAATCATTATAGACAGCATTAAAAAAGCAAAGATAAAGTGACA
AGCGTATAAAAAAAAGAAATTGATTCATCATTTTTGACATCTATCTATACTTTAATTCCAATCAA
CAGATTCATTGAACAACTCTTGAGTAAACTATAAAGTTATAAAGTAATAATAAGAACTATGTCGT
GTAACTTTATTCAAAAATGAAACTCTTTTTGAATCATTCTATAATTAGAAAATTCTTTCTATTTT
TTTGATCATTTCTTTTATTTTTTAATTGTATCGAATCCATTTTTTCTATTTTAAAATAAATAGTA
ACTTTATAAAACTTTTGACTTTATGTTAATTTTAACTCATTAGATTCAATAGTAAGTTCAGTCAC
ATAATATCTTGAATGAATGAGAAGAAAAAAGTTATTACACGATCACCCTAAATTGGTCCAAAACT
AGTAATTCCTATTATCTTTTCTTTTTTTTATAGGTTCTACGTTTT
Found at i:732464 original size:29 final size:29
Alignment explanation
Indices: 732431--732488 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
732421 GCTGATCTTA
732431 CTTGTTACTACTAACCAATTCCCTAAAAT
1 CTTGTTACTACTAACCAATTCCCTAAAAT
*
732460 CTTGTTACTATTAACCAATTCCCTAAAAT
1 CTTGTTACTACTAACCAATTCCCTAAAAT
732489 AAAAAAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
CTTGTTACTACTAACCAATTCCCTAAAAT
Left flanking sequence: Indices 731931 -- 732430
TAAGAACTATGTCGTGTAACTTTATTCAAAAATGAAACTCTTTTTGAATCATTCTATAATTAGAA
AATTCTTTCTATTTTTTTGATCATTTCTTTTATTTTTTAATTGTATCGAATCCATTTTTTCTATT
TTAAAATAAATAGTAACTTTATAAAACTTTTGACTTTATGTTAATTTTAACTCATTAGATTCAAT
AGTAAGTTCAGTCACATAATATCTTGAATGAATGAGAAGAAAAAAGTTATTACACGATCACCCTA
AATTGGTCCAAAACTAGTAATTCCTATTATCTTTTCTTTTTTTTATAGGTTCTACGTTTTATCTT
TCCATATTATAAAGCCTTATCTTTGTGGTTAGGTCAAGAAAGAACCTTTGAATCTCGATCTAATA
CAACAATGCATGCATTATGAATATTGATTACAATTCTTTTATTCTTTGTTCTCTTTCTTTCATCG
AATACTATGAATACTATCTACTATTGTTACTTCTTGCTGATCTTA
Right flanking sequence: Indices 732489 -- 732988
AAAAAAGAATTCCAACAAAACAAAAAGCGCTTCTACTATGAAAAGAAGATTTCTAGATCTCGCAT
CCTACTTAAATTGTGGGAATATGAGAATCCCTTTCATGAATTATTAGAAACTAACTTGGCAGATT
CCCATTTTACTGGATCTTCAGTTTCTAGCCCGAAGCTAATAATGGCGAAAAATAAAATATACTAT
TTTTAATAATTTTCTATTGAGTGGGACGTCGTTTTATATCGACAAGTAAAGAAAGAAAGAAATTA
TCTAGTACTTTCTTTCACTATTGATTGAAATTGCGTTGCTGTGTCAGAAGAAGGATAGCTATACT
GATTCGGTATACTCTAAAGACGCCCTCGGTACTATATTGACGATCTTACAAAGATTAAATTTCAG
TCAATTTCCATTTACTGATCTCATCTTTTACGGAATCGATCCCCTTTTGACTGTACAAGAATATG
TGGAGCTCAGCATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTG
Found at i:787584 original size:13 final size:14
Alignment explanation
Indices: 787553--787585 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
787543 TCATACCCAA
787553 AAGTTGCAGAGATGC
1 AAGTTGCAGAGA-GC
787568 AAGTTGCAGAG-GC
1 AAGTTGCAGAGAGC
787581 AAGTT
1 AAGTT
787586 CCAACCGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
15 11 0.61
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.21
Consensus pattern (14 bp):
AAGTTGCAGAGAGC
Left flanking sequence: Indices 787053 -- 787552
CTCCGACGATTCTACGGCCGGAAAGAGAGAGAGCAGTGTGATTGGCTCTATAATTTCAATAATGG
AAATGCTCTGTCGTAGAGCTTCGCTAGCAGTGTCGAGCTTTGCTCGCGATTCGACTGGAACTAAG
GACCTGAATGGAATTGAAGAGCTCTCACGCTGCTATCTAAAGAATGAAGAAACCACTACTGAACG
AGAGCGAGTGAAGTGAGTAAGCCTCTGACGAGATAGGGGCGAGCCAAAGAGAAGTTGTAGCAAGG
AGCTACTAAGGAGTGACTGTGTTGAAGCTTCAAACGTAGAGCTCGCGACGACTTCGAGCGAACGG
AGCGAGTGTGCCGAAAAAGACTAAATAAAAAGAATCTGCGTTCAGTAAATCGCAATTCTTTTTGT
GTGTCGGGCAGCGCGCGTTAAGATTCGCCGCGTGATTGTCCGGGCGAGGTATAAAGCCAAAACAA
GTTGGAGTTCCCCGCCTCGCCTAGATACGGGGGCTTCATACCCAA
Right flanking sequence: Indices 787586 -- 788085
CCAACCGAGGTAGGAGATCCATCATATCCATACGAACAAACCAGCACAGGTAGCAGTGGTTGCCT
TTACGTTTATAGGGGGCTCGACTTTCCCCTTTGTCACTATCTCGCCCAGCATATCTGCCGAGAGC
AGGAGCATATCCAAGTCTCATATGAAGTTGAATCAGATCTAGCAGCGCTCGCAGCGCTCACTACT
GAGACGAAAGAAAGGAGCAAGATACGACGGCCAAAAAGCCGGAGATTCTCGCGCAGGAACAAGCG
TAGGCCTGTAGCGCGCCCTTCACCCAAAAATTCTTTTCTTGGCGAAGCGAGGAAGCACAGTTGCG
CGCCTCTCCATAGCCCCTCTATACTCTATAGGCTATTAGTACCAAGCGCAAGCGCCTGATTTGGA
AGCTTGCTGTGTAATTGAATAAAGAAAGAAAAGTGTGTGAACTTCAGCGAGTCCGGATTTCAAAC
TAGCCTCCTAGACTGAACCGACCTTTTTTATAGGGTATAACTATC
Found at i:816120 original size:20 final size:21
Alignment explanation
Indices: 816060--816126 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
816050 CGTTTATAGC
*
816060 GCTT-ATGGCCAGTGGGGTCAT
1 GCTTGATGGCCA-AGGGGTCAT
816081 GCTTGATGGCCAAGGGGTCAT
1 GCTTGATGGCCAAGGGGTCAT
816102 GCTTGATGGCCAA-GGGTCAT
1 GCTTGATGGCCAAGGGGTCAT
816122 GCTTG
1 GCTTG
816127 TATGTTAGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
20 12 0.27
21 25 0.57
22 7 0.16
ACGTcount: A:0.16, C:0.19, G:0.37, T:0.27
Consensus pattern (21 bp):
GCTTGATGGCCAAGGGGTCAT
Left flanking sequence: Indices 815560 -- 816059
AATAGCTACCTTTTAAGGAATTGAAAAAGAATGAAATGCTATTCTCTTCGATCGCTCTATTCAAA
AATCAAAAACGAAGGGTGGGGAAGGAGCGAGCAGAAAGAGGCTCCTCATAGTAAGAAGAAGAAGC
TCACAGCCTGGGCTAGACCAAATGGCGAGGTTTCGTATCTTGTAGAGGGCCTTTGCTTGGATTCG
TCATTCATTACTTTATAGTTACCACGAGGATGGAGCCCATTAGCTAGCATAATTTGAAGACAGAG
ATGAATCCCCCTTATGAAAACAGAAATGCCGGCCGAGCTGAACGAACAGGGCGTGCTTTGGAATC
ATAAATCATTTACCGCCGAGACAGATTCTCTATGGATGGGGAATAACCTCTATTGGGAATAACTA
GGACATAGGGGTCTCCATGGGGATAGGACATCGGGGAATACTCCAAGTGTAGTGTCTAATATCAT
AAGCTAGTTTTCGTGTCTTTACCTGCCTGCTTTCCCGTTTATAGC
Right flanking sequence: Indices 816127 -- 816626
TATGTTAGTTGATTTTTTATTTCTTATTCTTTTTCTTATTTATTTGTATACGAGTTCCCATTCCG
AAGCTTGAGCTGGGCTAGATTCTTTATGCCAATGTTTGTTACCGGGAAACACCTACTCTAAAGGG
GGCTTGTCGTGCTTGACTTATTTCTTACCCAGGGCTGCGAAATGCCTCTGCTATGGGCTCCCCTC
GGGGGGCTCTTGTTGTCTACCCAATCTATGGTGGGCTCAAGCTATGGCTAAGGCAATGATGGGAT
CGATCTAGCGAGGGTACATTCTGGGATCGATTTGTCTCTTGGCTCTCCTAACCGTGCCTTGAATC
CTATTTAGCCACCCACTAGCAGGTCGGTTGCCCTCGTTGCTTCGGTGTTTTGCCCTAATGATAAA
TAATGGTTATGAAATCCAAGGCTACTACGGGAAGGTCCCTCCATGAATCGGATTTGGAAAAGGAT
GCGTACCAGGAGCGGTTTCTGGACCAGCCGTTGTTTGCTTTGAAG
Found at i:819380 original size:12 final size:12
Alignment explanation
Indices: 819363--819388 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
819353 GAACACTGAC
819363 TTTTTTTGGTTG
1 TTTTTTTGGTTG
819375 TTTTTTTGGTTG
1 TTTTTTTGGTTG
819387 TT
1 TT
819389 GACCTGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (12 bp):
TTTTTTTGGTTG
Left flanking sequence: Indices 818863 -- 819362
TCGAAAGCCTGCTCCCAATAGCAACTATGAAATCCACACTCTAAAAGGTTAGAGTAGACATCAGA
TAGATAAGATGGGTCTAGCACCTCCTCTTCCCCAATCACCATCCGGGTAAATTCTTCGGGAGACC
AGTTGGATGGCAAGTCCGCTCCTATTTCCTCTATCTTTCCTTGAAAGAAACGAGAAAGATCATCA
AAGTTTTCACTAAGATCTGGAGAAGAAGAAGGCAGCTCATTTCGGACCCCAGTGGATGCCTCAGA
AGCGGAACTATTGGAATGAGCACGGCTAGCCAAATTACTCGTTTCATATGCGAGATCAGAGATAG
AATTAGAAAGTTCGATCAAATCACCTTGTTCCATAGTTCGCGGGTCAAGGTTCGACCCATACTGA
AAAATGGATAAACGCTGTTGAGGCATTCTTGATTGAGACAAAGAAATTCCCTCCAGACAGCTTAA
CTCCGTCAAGCCTGTAGGAGTAGTGAAGAAGGATAGAACACTGAC
Right flanking sequence: Indices 819389 -- 819888
GACCTGAATGACTTGATCGATCGTACTAGATAGATAGTCTAAGATAGACCATACACCTTTCATAC
GGATCCATTCATTAATGCGCAAGAGAAAGATCCATCAGATAGAGGGAAGTTGGTCTTTCTCCAGA
AGGAGAATGTACTTTTAAACAGAAACTGGAACATCATAAGAAGACGAATGAAATCAACAGAATCC
GATTATCGACCACTAAAGGACCGAGACATATCTCAAAATCTGACTTTCAACCCTGAGAATAGTAC
TTGTATTCGGGAACCAATCGCAGAGAAGATGAGATCCCATCAAGGGGTACAAGAATGGCTTTTGA
CCAGAACTGATTGCCCTAATAAGGCAAGGTTTAGAATCCTAATGAAGCGTACTCCCAGCACAGGC
TGGTGAGAACAGGATTGAATGCACCTGTCTCCTATGCTATACCCACCGCCCTTACTCGCTTCATT
TTTCTTTCTTCTCGACAAGCTGAAGAAGAAATCCTCTTCAGTATC
Done.