Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_045228
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: 434980
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:526 original size:24 final size:24
Alignment explanation
Indices: 494--546 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
484 AAGGCGTCGG
494 TCCGCGCGATTTGTTCTTCCCCGA
1 TCCGCGCGATTTGTTCTTCCCCGA
518 TCCGCGCGATTTGTTCTTCCCCGA
1 TCCGCGCGATTTGTTCTTCCCCGA
*
542 CCCGC
1 TCCGC
547 CGGAGCTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.08, C:0.42, G:0.21, T:0.30
Consensus pattern (24 bp):
TCCGCGCGATTTGTTCTTCCCCGA
Left flanking sequence: Indices 1 -- 493
AGACCAATTACCAGATCCGCCTATCATCGCCGGCATAACCATAAAAAAGATCATTAAAAAAGCGT
GAGCCGTTATTAAAACATTATAAAGTTGATGATTACCACCAAGAATTTGATCGCCGGGTCGTGCT
AATTCCATACGAATCAGTACTGAGAAGCATGTGCCCATCACTCCAGCAATAGCACCGAAGATGAA
ATATAGAGTCCCTGTATCCTTGTGGTTAGTGGAGAACAGCCATCGTGTCATAAAATTGAGATTAT
TTCTGTATTTCCTTGTCAGAGAGGGGCCCTTAGGGAGCGGGGCTTTTTTATTATTGTCCTACCAC
CGGAAGCAGCTTTTGGTATTAAATTGCCACCGCATCCGGCCATTTTCCGTTTGCAATTCCGTTTC
CAACGCCGTGATGCGAGAATAGTCCGCATCACGTTGCTGTTGGTACTGGGACACTGCCCGTTCCC
GCGCTTGATCTAGCTCTTTGGGTAGATCAAGGCGTCGG
Right flanking sequence: Indices 547 -- 1046
CGGAGCTCTTCTTCGACCCTCTCGAGCTCGTCGAATAGCACTCTCTGGAGCGCCGCGCTCTCCCG
CCGACGAATTTCCTCCAGTGGGACTAGTGCAATCATTCCCTTCCTAACAGCGCCTTCTTCTTCTT
CATCACCAGGAGTTGATTCAATTGCTAAGAAGGCATTTACCCCAGTTCTTACCAACCTCCGGTGT
GTAATCGACATGTTGCTAGCTTCAACTCGGTTGAATAAGAATCATTGATTACCTATGCTGTCCAT
TTATTATTCATTCAGGGCGCTCGGACGAAGAACCGGCAAATCGAGTATGGAATTAGAGCTCGGGC
GGGGCATCAACCACAGCACAGGTTGCGGACCTATCGAGATGCTTCCTTGCAGAACCCAACAAGGG
CTGTAACTCAATAGAGTGAGTGGGAAACCTTGTAAACGCGAGCAGGAGAATAGAGATCGGTCTGT
CTTGTCTTAGACCAGCCCTACTCCACCCATCTTGACTATCTTGAG
Found at i:36044 original size:15 final size:16
Alignment explanation
Indices: 36002--36044 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
35992 TCCTACCTTA
36002 ACAGTCGATCATGCGCTC
1 ACAGTCGATCATGCG--C
*
36020 ACACTCGATCATGCG-
1 ACAGTCGATCATGCGC
36035 ACAGTCGATC
1 ACAGTCGATC
36045 TGTCCATCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 9 0.39
18 14 0.61
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (16 bp):
ACAGTCGATCATGCGC
Left flanking sequence: Indices 35502 -- 36001
TTGCATGAAAAAACTCAAAAAAGAATAGGTGATCGTAGGTCAGCCCGTGGGTAAGTTCCGGGCTT
TCATTGATATTTTCTCGTTCATGATCTCTAATCCTTTGAGTAGATTGGGCAGGGGTAAGACTATG
CACATAGCTTCGGTTCCGTCTTGTTTGCCAAGGAGATATGGTTGCTTTTCCTTCTTCAGTAGGCT
TTCCCGCGGGTTCGGTTACAGATAGGATACACGGGTCAAAGGGAAGGCTTGAGTTCAGAGACGAA
GTTGGCTTTGAAGGTACAAACTTTCAGACAGTTCCTTACTTTCTATTCTCTAATCTCGTATGGCA
GCTTTCAGTCCCATCTTCAGTTTCGGGATATTGCTCCTATGCCTCTTCGAAGTGAAGCCCTTATA
TCGAATGATTCAAGACATTTGATTTTATAATAGAAATGAGAGGACAGCCGAATTGACAGAAAATA
GTCTGAATTTGTTGATCAACTCTCTTTGTTGAAGGTCCTACCTTA
Right flanking sequence: Indices 36045 -- 36544
TGTCCATCCGACTACATTCACTGGGGGGTGAGGTTGTCCAATTTCAATTATGTGCCGCTCGTTGA
CATCTAGTTTCCATTGCCGGTGTGAGAGATCTTCCTTCGGTTCTAGTTAAGTATGGCAGCTTGAG
GTCTCCTATTTAACTTTCACCAGCCATTGGGAACTCAAATAAACTTTCATTTAACGGCAGGCGAG
AAAGGTTCTAAAAGAAAGAAAGGTAGAAGGGGGGTTTTCTCCCGTTTCGGGGTTCTCTTGTGGAC
TGGCTGTTGACTGGCCGGGAGAAAACCGGTGCTTTTAGCTTAAACGGATTTTCACTGGATCGGAG
CCTTTCGGAAATCCTCCCCTTTTGGCTTCACTTGAGCGGTTGACGCAATCCAAGAGGAAGAGGAA
GCTAAACCCGTGCTGACGAATAACCAAACCCCTTAATTCGTCGAGTAAAGTAAATAGGGAAGGTA
TAGGTTTGTTATGAATGACCCCGTATCGAATACAGGTAATAATAT
Found at i:44597 original size:39 final size:39
Alignment explanation
Indices: 44543--44621 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
44533 CGATTTTCTA
* *
44543 TTCACTCATGATCTGGCCTGGTCGACCCGATCATGATAT
1 TTCACTCATGATCTGGCCCGGTCGACCCAATCATGATAT
44582 TTCACTCATGATCTGGCCCGGTCGACCCAATCATGATAT
1 TTCACTCATGATCTGGCCCGGTCGACCCAATCATGATAT
44621 T
1 T
44622 GAAGGATGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (39 bp):
TTCACTCATGATCTGGCCCGGTCGACCCAATCATGATAT
Left flanking sequence: Indices 44043 -- 44542
GCCCACACCTGTGTAGAGTAGATCGTTCAACACCTGCGGCACAAACCCATTTTTGACCTATTGGT
CCTAGTATCATAGGCGACCGAACGGCCGCCCCCTAATTACTAGACCAACCTGCTATAATAATTCC
ATAAACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATGTTCGAATCTGACAATACCA
TACCATAATCAAAAGGTACAACGGCCCGAGCAACCAGACTTAACATAAATGTAGTCACTGGAGCC
ATTCTAAAAAGGGAGAAATTAGCACTACTTGGTGAAATAGGTTCTTTTAGAATCAATTTCAAACC
ATCTGCTAGAGGTTGTAACAATCCGAACGATCCCACTACATCAGGACCCTTTCGACGTTGCACAA
AAGCCATTACTTTACGTTCAGCTAGCACTAAAAAGGCTACTCCTAGTAGAAGTGGTAGAATTATT
CCAAGTATTTCGGCTGGAACTGCTATGTACGTTTTCGATTTTCTA
Right flanking sequence: Indices 44622 -- 45121
GAAGGATGGGACCTTTTCTCGAAAAACTCCGGATCCAGAGAAGAGTTGAAGATGGTGCAACATCG
AATCCTGTCACCTTACTTCGAATGGAATCTTAGCCCGCCTCACTTGCTTTCTGTACTGCATAAGG
GCCATAAGGGCATAAGCGAAGTCAAGGGATTTCCTTCTAACTAGTGGCTGAGAGTAAGCAAGCTA
CCTTCATTCAACAGATTTGTGGTTGAGTCAATAACATGCTCTGGGTCGGGAATCTTTGCTCTTCT
CTTTTGCATTTCCGCTGCCTGCGTTCTTCTTCGTGTCCGTCCGTATCGCAAAGCTGGTCGACGCC
AGCTGTAATGGTTGAAAATAGGGGGCCAACCAAGACCCTACCCTAATAAAGCTTTGTTCGATAAA
GCAAACGATTCGTTCCGACAACTTCGGACCAGATTAACCCTTTTGAATTAGCCGATCTTACAAAA
TGGATCGGGCGGGCTGGTTGGGAAGGGGTGATTTGCGGAGAAAAG
Found at i:80940 original size:13 final size:13
Alignment explanation
Indices: 80922--80947 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
80912 CCCCGCCCTA
80922 TAGAATGAATAAG
1 TAGAATGAATAAG
80935 TAGAATGAATAAG
1 TAGAATGAATAAG
80948 GAGAGGCCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (13 bp):
TAGAATGAATAAG
Left flanking sequence: Indices 80422 -- 80921
TGTCCAGCGGTGTTGTCCACCAGAACATCGATGTGCGGAAGAGAAAAAGAATCTTTTCGGCTTGC
CTTGTTTAGGGTCTTTTGACTCACGGAACCTGCTTTATGAGGGAAAAACCGTTCTCGAAAAGCGT
GACCATCCCGTTGAATCTCGTTACCCTCCCGTGTGGTTATGGGGGCGCGCCCGCTTTCCACTATT
ATGGAGCCGGGCCGCAAGCAAGTGAATGCGATCCCGCCCTCCATCAGCCGGTGTGTGTGAGCTTC
GCTCCTTATAGCTCTACACCGCCGCCGGCCACTTTAGCTCCTCTACCATATGATTCATTCTTTGG
AAGTTAGGCACGTGACTCGATAGCGCAGGCACAAGACCTTTGAATGCAAACAAAGAATGGCGAGA
CCGCATATAGTTTGGAACCCAAGCTTACCTTATTATTATTCAAAGGGGAAGGTTTGATAAAGGAG
CTTTTAAGCCCTTTTGCTGAATTGTTGGTCCGCAGCCCCGCCCTA
Right flanking sequence: Indices 80948 -- 81447
GAGAGGCCTGTTGATGACCGAGCCACTCTTATACTACTCCTTACCTCACCCCCCCCCTTGTCACT
TAAAGGGCGAAGTCGCTGAAGCGAGTCTAAAGGCCAAAGAGTGATCTTTGAACGCTACTACGCAT
CCTTACTAATAGTATAGTGTAAGGTAGGTTTGGGTATAGCAGGACTTGAACCTGCGACCATTAGG
TTAAAAGCCCAATGCTCTACCAACTGAGCTATACACCCCCAAAATATATAGTAAAAAATAAGGAT
TGGTGCGGAAAAAAAAGGGGGCAGCCGCGGTCGAACTCTAATTCTGGAAAAAAGTCGGGGCCCCT
TTTCCAAGTCTACCAGATAGAAGATGATAGAGGGCCATATCGTTGCGTTGGACAAGACGGCGCCG
TCTCACTTCGAGTTCCTTCCTTCGTAGTAAAATCAGATGATACGCTTCGGCGATGTTACCTACCA
AATTTAAGGCCTGCTAGGTGATCGAAATTGCTCAGGTCAGTGAGG
Found at i:99529 original size:21 final size:21
Alignment explanation
Indices: 99505--99556 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
99495 TATACCTATC
99505 AATGATCCCCCTTTCAATCCA
1 AATGATCCCCCTTTCAATCCA
99526 AATGATCCCCCTTTCAATCCA
1 AATGATCCCCCTTTCAATCCA
99547 AATGATCCCC
1 AATGATCCCC
99557 AACCTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.38, G:0.06, T:0.27
Consensus pattern (21 bp):
AATGATCCCCCTTTCAATCCA
Left flanking sequence: Indices 99005 -- 99504
CGTGGATAGCTCTTTAAAGAAAAGGTTCTAGTTCGATCCACTAGCAGACAAAGAATAACATAGAT
AGAGGAGAGGTGTACCAGATTGTGACACTTCCCGGTTCGTCATGATTAGGTCGGTGTTCAGTGTA
CCTGTTGAAGACCTTAACGTAAGTAACTTAGTGCAAAAAAAAGTGGCGGAGATCCACAAAGGTAA
CCGGATGCCTGGGGCTTAGGACAAGGAGCGTCCGGAGTCTCTTAAGAAAGGAAAGAAAAAAAGTT
ATCATGAAGATACCTAGGTTCCGTCACATTTTCTATCAAATATTTCATTCTATGATCATCTTCTT
CTTAGGTAGACCACTCGTTAGGCTTGGGTTCGCTTACTTTTATTTGGTTTTGTGGAATTGGCTTT
TGGTAAACGCACCTTTTGCTGACATCGATCTTATGCATTTTTTTTCGGACTCTTTGGCCGTGAAC
TCTGGCTCCATCGCAGATTCCAATTCTATTCATAATATACCTATC
Right flanking sequence: Indices 99557 -- 100056
AACCTTTAAATAATCCAATACCTCTCGACGTTGTCGATCAATTTCGTATACTCAACCAAGAGACG
GAATTGGAACTCTTTGCTCGGATACGACTTCTCGAGAACCGTTTGATTGACGGCTTGCCACCGCA
AATGAACTTTGGCGAGTACGAAGCCTTAGTCAGAGGGTTTCTCGATGACACCCTGACCATTGGAC
ACTACCGTAATGTCCTGAGCAATGAGCTCTTCGATCTTCGCCTGTTAGAGTTTAAGGCGAATCTC
TTAGAGCAACTCGTAAATTTGTTAATGAGCGAAACAACTGAGCGGCTCACTCAAATATTGGCAGA
CTCGCCCTTTCGAGAGGGTGCCATAAGGACCGAAGCTCTTTCATTTATAAACGACTTTATGAGTC
GTTTAAATCTGACGGACCCCCAGTCCCATTTTGATAAAAGATTGGTTGAAGCTATGCTGCGGTAC
TGGATCCAAGATGCCCAGCAAAACGGGAATCTCTCCGCCGTGTAT
Found at i:101288 original size:15 final size:15
Alignment explanation
Indices: 101270--101305 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
101260 GGACTATAAT
101270 AAGGAGAAGTATTTA
1 AAGGAGAAGTATTTA
101285 AAGGAGAAGTATTTA
1 AAGGAGAAGTATTTA
101300 AAGGAG
1 AAGGAG
101306 GACGATAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (15 bp):
AAGGAGAAGTATTTA
Left flanking sequence: Indices 100770 -- 101269
AACTCAAAAGGTTATAATTGACCAGTGCAAAACTCTTTTTTTTTCGAAAGAAGATTCGAACTTGT
TTATTCCTGAATTCTACTTTGATGTTATGGTTAGTGCATTGTTAGAACAACTCAACGTAGAATTT
AATCAACCAGCACTCTCGAGCATTCTCATGTCTCTCTCCACCGATGAGCACCACGCCCCGTTCTA
CGCAGAGCTCTTAAATTCGGAGCTGTATACTTCTTTTTGGAACGAACATAAAGCGAAGGAAGAAG
CGGAGTCTCGGAGTTATTTGAAGTACCAGGAGTATCTTTCACTAGAGGACAGGGGCCGCGTGCTC
CGGGCCGAACGCGATTCGTTGTTGCGTCAGTTAAGCCGGCACCGGGGCTAGGGATCACATATTTC
TTAAAGTAGGACGAGGCCCGCTACGAAGAACCTAATAGAACTATCCAGAAAAAGGTGAAAAGACA
GGATGTATTCCGACGAAATGCTATTGATTTTAGGAGGACTATAAT
Right flanking sequence: Indices 101306 -- 101805
GACGATAGACCCACTCACGATCTACTAAAAGGCAAGTAGCTTGATATTGGTTCAAATCCAATTCG
TGAGAAGAAGCGTCAAATGATTTGGACAGTTGTCGCGCTGGCGGAGCGGGGAGCCTACAGGGAAG
ATTGGGGCAATGAGGAGCTCGACGAGTATCTGCAGACCCTCTACCCCATCGACTACATCTATCGC
TGAACCAACTTCCGAACCGACTTCCTTTGTTGATTGAGCTGCTCCGACGAACCTTGCCGATGAGT
CCATTAGCCTTGCAACTAAGCTCTTTGGCCCGAGTTGAGAATCTATAGTGGATGCTTCCTCCGCT
AATAGGCCCCTTGAACACAAGTCAGGCTGGGGCAAAGCCCTATCCATTGAATCTCGCAAACGGCC
GTCAAAGGGCAGGCTCGGAATTGGGGAATACCAATATAGAAGGTTTCTCCATGCTTTTCCCCATA
CCGCTCAATCACGTAGAGAGGCTAACCGCTCTCTAATCGATCGAA
Found at i:132609 original size:8 final size:8
Alignment explanation
Indices: 132596--132635 Score: 53
Period size: 8 Copynumber: 4.6 Consensus size: 8
132586 AAATAATAGA
132596 TATATAAT
1 TATATAAT
132604 TATATAAT
1 TATATAAT
132612 AGATATATAAT
1 ---TATATAAT
132623 TATATAAT
1 TATATAAT
132631 TATAT
1 TATAT
132636 CTATAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 21 0.72
11 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (8 bp):
TATATAAT
Left flanking sequence: Indices 132096 -- 132595
CAGCCTTAACCTGTCCCCAGACAGCCAGCCCTCACCAGGCTGCTGGAATTGCTAAATGCTCCGCC
ACGAAGCAAGCTCTCCCGATCCCGAAGACGACAGATGCGGAAGTGGCTAAAGAAGTCGGAGGAAG
AAAGTTGTTGGGCAATTGTATGCGCGAGGGTACATTATAAGTATTCTGAGAATTGGCAACATTGA
CAGAAAGGGGAAGAAAAGGGGGTAGGAATAAACTTTTTTAGGTGTAGCTATACTAAAGTAAGTAG
TCGGCCTAACCTTCGGTTCCCGTAACCAAGTTTTTCTTTCTCACTCCTTATGTTATGTACTTTTT
CTTACTTAATCCATACTTTTTTACCTTTTCTGAAGTGTGGGGCAAAGGGTGCCCTCTACTTATAC
TTCTAACTAAAGGCGAACTGCAGGCATTGCAAGCAAACAAAGCGCCCCCGCCCGTTTGAGTCGCG
AAGGGGCCGCTTGCTTAAAAAATTTATTTTATATAAAATAATAGA
Right flanking sequence: Indices 132636 -- 133135
CTATAAACTAAGAAAATCCGTTTTTTTTATCCAATTGTTCATTCCCGGGAAGAGGAAGAAGCAGA
TAGAGCAAAGGCCTCCTCTTTCCTTCCGTCCGCTCTTCCCGAAGTGGGCGAATTGCATGTAGAGA
TCCGCAGGGGCTTATAGTTTAATTGGTTGAAACGTACCGCTCATAACGGTTATATTGTAGGTTCG
AGCCCTACTAAGCCTACCACCCCCTTCTCTGCACCCGATACAAGGCAGTCGAAGTCCTCGCCACC
CTGCAGATCTCAATCTAGCGACGGCACCTGGAACCGCACAGCTTCCGCTGCCCTTCGGGCACGCC
TCCTACGCTCTTGCGGCATGCCCCCTTCGGGCAATACGGCTTTCGTGAGTAATACGCGAAGCAGC
TGAGCGATAGCTCTCTTCGATCGCTATATTCTTGCGATAGCGAAGGCGTAGTTCATCCTCTAAGA
GAGAGTAGATGCGAAGATTCGGATCGAAGATCTTCGCTTGGGCCG
Found at i:132612 original size:19 final size:19
Alignment explanation
Indices: 132588--132630 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
132578 TTTATATAAA
132588 ATAATAGATATATAATTAT
1 ATAATAGATATATAATTAT
132607 ATAATAGATATATAATTAT
1 ATAATAGATATATAATTAT
132626 ATAAT
1 ATAAT
132631 TATATCTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
ATAATAGATATATAATTAT
Left flanking sequence: Indices 132088 -- 132587
AGCAGGCCCAGCCTTAACCTGTCCCCAGACAGCCAGCCCTCACCAGGCTGCTGGAATTGCTAAAT
GCTCCGCCACGAAGCAAGCTCTCCCGATCCCGAAGACGACAGATGCGGAAGTGGCTAAAGAAGTC
GGAGGAAGAAAGTTGTTGGGCAATTGTATGCGCGAGGGTACATTATAAGTATTCTGAGAATTGGC
AACATTGACAGAAAGGGGAAGAAAAGGGGGTAGGAATAAACTTTTTTAGGTGTAGCTATACTAAA
GTAAGTAGTCGGCCTAACCTTCGGTTCCCGTAACCAAGTTTTTCTTTCTCACTCCTTATGTTATG
TACTTTTTCTTACTTAATCCATACTTTTTTACCTTTTCTGAAGTGTGGGGCAAAGGGTGCCCTCT
ACTTATACTTCTAACTAAAGGCGAACTGCAGGCATTGCAAGCAAACAAAGCGCCCCCGCCCGTTT
GAGTCGCGAAGGGGCCGCTTGCTTAAAAAATTTATTTTATATAAA
Right flanking sequence: Indices 132631 -- 133130
TATATCTATAAACTAAGAAAATCCGTTTTTTTTATCCAATTGTTCATTCCCGGGAAGAGGAAGAA
GCAGATAGAGCAAAGGCCTCCTCTTTCCTTCCGTCCGCTCTTCCCGAAGTGGGCGAATTGCATGT
AGAGATCCGCAGGGGCTTATAGTTTAATTGGTTGAAACGTACCGCTCATAACGGTTATATTGTAG
GTTCGAGCCCTACTAAGCCTACCACCCCCTTCTCTGCACCCGATACAAGGCAGTCGAAGTCCTCG
CCACCCTGCAGATCTCAATCTAGCGACGGCACCTGGAACCGCACAGCTTCCGCTGCCCTTCGGGC
ACGCCTCCTACGCTCTTGCGGCATGCCCCCTTCGGGCAATACGGCTTTCGTGAGTAATACGCGAA
GCAGCTGAGCGATAGCTCTCTTCGATCGCTATATTCTTGCGATAGCGAAGGCGTAGTTCATCCTC
TAAGAGAGAGTAGATGCGAAGATTCGGATCGAAGATCTTCGCTTG
Found at i:138328 original size:24 final size:24
Alignment explanation
Indices: 138296--138348 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
138286 AAGGCGTCGG
138296 TCCGCGCGATTTGTTCTTCCCCGA
1 TCCGCGCGATTTGTTCTTCCCCGA
138320 TCCGCGCGATTTGTTCTTCCCCGA
1 TCCGCGCGATTTGTTCTTCCCCGA
*
138344 CCCGC
1 TCCGC
138349 CGGAGCTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.08, C:0.42, G:0.21, T:0.30
Consensus pattern (24 bp):
TCCGCGCGATTTGTTCTTCCCCGA
Left flanking sequence: Indices 137796 -- 138295
TCGGAACAGACCAATTACCAGATCCGCCTATCATCGCCGGCATAACCATAAAAAAGATCATTAAA
AAAGCGTGAGCCGTTATTAAAACATTATAAAGTTGATGATTACCACCAAGAATTTGATCGCCGGG
TCGTGCTAATTCCATACGAATCAGTACTGAGAAGCATGTGCCCATCACTCCAGCAATAGCACCGA
AGATGAAATATAGAGTCCCTGTATCCTTGTGGTTAGTGGAGAACAGCCATCGTGTCATAAAATTG
AGATTATTTCTGTATTTCCTTGTCAGAGAGGGGCCCTTAGGGAGCGGGGCTTTTTTATTATTGTC
CTACCACCGGAAGCAGCTTTTGGTATTAAATTGCCACCGCATCCGGCCATTTTCCGTTTGCAATT
CCGTTTCCAACGCCGTGATGCGAGAATAGTCCGCATCACGTTGCTGTTGGTACTGGGACACTGCC
CGTTCCCGCGCTTGATCTAGCTCTTTGGGTAGATCAAGGCGTCGG
Right flanking sequence: Indices 138349 -- 138848
CGGAGCTCTTCTTCGACCCTCTCGAGCTCGTCGAATAGCACTCTCTGGAGCGCCGCGCTCTCCCG
CCGACGAATTTCCTCCAGTGGGACTAGTGCAATCATTCCCTTCCTAACAGCGCCTTCTTCTTCTT
CATCACCAGGAGTTGATTCAATTGCTAAGAAGGCATTTACCCCAGTTCTTACCAACCTCCGGTGT
GTAATCGACATGTTGCTAGCTTCAACTCGGTTGAATAAGAATCATTGATTACCTATGCTGTCCAT
TTATTATTCATTCAGGGCGCTCGGACGAAGAACCGGCAAATCGAGTATGGAATTAGAGCTCGGGC
GGGGCATCAACCACAGCACAGGTTGCGGACCTATCGAGATGCTTCCTTGCAGAACCCAACAAGGG
CTGTAACTCAATAGAGTGAGTGGGAAACCTTGTAAACGCGAGCAGGAGAATAGAGATCGGTCTGT
CTTGTCTTAGACCAGCCCTACTCCACCCATCTTGACTATCTTGAG
Found at i:160271 original size:21 final size:20
Alignment explanation
Indices: 160242--160283 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
160232 CAAAGATTGC
*
160242 CCACTTCACTTCGCTTCACTT
1 CCACCTCACTTCG-TTCACTT
*
160263 CCACCTCACTTCGTTTACTT
1 CCACCTCACTTCGTTCACTT
160283 C
1 C
160284 GTAACCTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.14, C:0.43, G:0.05, T:0.38
Consensus pattern (20 bp):
CCACCTCACTTCGTTCACTT
Left flanking sequence: Indices 159742 -- 160241
CAGCCTCGTGAATACAACCGTTAGGCTGCGAAGCAGATCTTGTGCAATCAATAAAAAAAAAAGAA
TGAAGGAGCGGAACCTTCCTCTGACTCACTTCGGTGGCAGGAGATTCCGGAATTACTACGCAAGA
TAAGGGGACTCTGTCAAAGAGGCACACTCATCTCGATGGCTTGACGGAACACGGCCGCACACCCC
TTTGTTGTCAACGCGACTGAAACGAAAGAGTGGCGCCTCGGCCACTGCTTTGTATTGAAAGTGGT
GCTCCTCGTCATGCTTGCCGTGGGAGGGGATGATTACAAACCATCCCTCTTGCCAGTCCCCGTCT
CCCTGACTCGTCCGGGGATCCCTCGTATCATTCCGTCATTTCACAGATGTAGGGTCCGTAAGGGC
GACGAAAGGTAGGATGCCCCTGTTTGGCTTTTGTTTTCCAAACAGGGTTTGCCGCTAAGCCAACC
CTCCATATCTGGACGCTGGTTCAAGTCAACAGTGGCAAAGATTGC
Right flanking sequence: Indices 160284 -- 160783
GTAACCTCATGTTTACACAAAATGTTGTTGTTAAGGAATTCCCACTATGGTCTCGAGAGAACAAT
CCTAACCCAAAGCTTGGAAAACTTTTCATAATCCTGCCTTCGATCTCCGCAAGCGGAGGGTTTCG
CACTCAACCAGCGGGAGATTGCTCGACCATACCATTAGGGAGAGGGGATTGAGACGATCTTGAGC
GTCAGGCGAAGCCGAGACACATCCATACTAGAAGCCATTCGAACTTCCAGCAAAAGGACTCGGGG
GTGACCTAACCGAGTCCATCTTGTTCCCCCGTACCATCCCAATGTGATTAAGATCAATCCGAAGC
CCAGACGTTTCGAGCTCTGTCTCGATCAGATGCATCAGAGGCGCCAAAGGCGTGAGGGGAGGCTT
GAAAAACTGCCGGAATGGTCCTACGGGTATCTTTTCCCATCGGAGGTAGTGCCCAACGGGAGAAG
GGGCCGAAATGGGGTTTCTATTACCAGAAAGCGTCCATTCAGATG
Found at i:165441 original size:30 final size:30
Alignment explanation
Indices: 165405--165503 Score: 101
Period size: 30 Copynumber: 3.1 Consensus size: 30
165395 GCGATTTTAA
165405 TTCCTTTTCTAGTTGTAATTTTAATAGCTT
1 TTCCTTTTCTAGTTGTAATTTTAATAGCTT
* **
165435 TTCCTTTTCGAGTTGTAATTCTATTTCTA-CTTTT
1 TTCCTTTTCTAGTTGTAA-T-T-TTAATAGC--TT
165469 AATTCCTTTTCTAGTTGTAATTTTAATAGCTT
1 --TTCCTTTTCTAGTTGTAATTTTAATAGCTT
165501 TTC
1 TTC
165504 TAGTTTTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
30 20 0.36
31 1 0.02
32 4 0.07
33 8 0.15
34 4 0.07
35 1 0.02
36 17 0.31
ACGTcount: A:0.19, C:0.15, G:0.09, T:0.57
Consensus pattern (30 bp):
TTCCTTTTCTAGTTGTAATTTTAATAGCTT
Left flanking sequence: Indices 164905 -- 165404
TGGATTTTTTTTATAGTGGAAATGCCATAAAGCGCGAACCAAGATCCGTGATACGAAAACCAAAA
TCAGAATGAGGAAGAAAAAGATATCGTGATGTAAGTCCATTATTCCTTGCATCATAGGTGTTGCT
GCGTCTTGAAATCCTAATTGCCATGGTTCCGCTGCATCACAAGGAACAATTGTGAGGAATAGCCA
TTCTAGAACAATCATTTGGGTTGGTTCATTCTTTAACTGCTCCGCCCCCCCCAAAAAAAAGAAGA
GAGACTTGTTCTTGCTCTCCCAATTCAGGAAGACGGAAGTCGCCGGTTGGGCTTTTCCAACCAAG
AAAAACATGGGACTTTTGGGCATTTTCTTCTCTTACGCTACGCAATTTCTATTTATTATTTTTGA
ATAGAAATCTAACTTTATATTAGATATTTGGAAGGGATATTTCTATTCGAGATGCTACTTACTTA
CATATGATGTTTTCTTTCACAAGGCAGCGACTCAAGCGATTTTAA
Right flanking sequence: Indices 165504 -- 166003
TAGTTTTAATAGCTTTTCCTTTTCTAGTTGCTTTTCCTTTTCGAGTTGTAATTCTATTTCTACTT
GTAATAGCAAAATCTGTTCCTGGGTCATAAAATTGGGATTTACGTCATTTTGATTCCCTCCAGAA
AAAAAGTAGTTCTTACCTTCCTGTACGAGTAGTGAAGAATTATAGTGAGTTGTGGTTGGTTGTTG
ACCAACGGAAAGCATGGGAGTCTTTGGGCATAGGAGGTTCTCTCTCTCTCTTACGATATAAATAA
GTCCGGGAATGAGCTATCATATGCCTTCTGTTTGAAAGGCTAATTTCCTTTTACTCAATGAAGAA
AGCTAAAACTAAAAGAGTAGGACATAGATTGTATTATAAAAGTTTAATGAGAGATGCGAATCATA
GCGTATCCAAAGTAGTACTTCTGTTTTGTTTTCAAGGCAATTAAATTCTTACTGTCCGGTAAGGC
AAGGAAAGGCTTTTTCCCCTAAGGGCGAACTTAACCGGGCATGGA
Found at i:165470 original size:42 final size:42
Alignment explanation
Indices: 165423--165533 Score: 102
Period size: 42 Copynumber: 2.6 Consensus size: 42
165413 CTAGTTGTAA
*
165423 TTTTAATAGCTTTTCCTTTTCGAGTTGTAAT-TCTATTTCTAC
1 TTTTAATAGCTTTTCCTTTTCGAGTTGTAATAGCT-TTTCTAC
** * * * *
165465 TTTTAATTCCTTTT-CTAGTT-GTAATTTTAATAGCTTTTCTAG
1 TTTTAATAGCTTTTCCT-TTTCG-AGTTGTAATAGCTTTTCTAC
*
165507 TTTTAATAGCTTTTCCTTTTCTAGTTG
1 TTTTAATAGCTTTTCCTTTTCGAGTTG
165534 CTTTTCCTTT
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
41 3 0.06
42 44 0.86
43 4 0.08
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (42 bp):
TTTTAATAGCTTTTCCTTTTCGAGTTGTAATAGCTTTTCTAC
Left flanking sequence: Indices 164923 -- 165422
GAAATGCCATAAAGCGCGAACCAAGATCCGTGATACGAAAACCAAAATCAGAATGAGGAAGAAAA
AGATATCGTGATGTAAGTCCATTATTCCTTGCATCATAGGTGTTGCTGCGTCTTGAAATCCTAAT
TGCCATGGTTCCGCTGCATCACAAGGAACAATTGTGAGGAATAGCCATTCTAGAACAATCATTTG
GGTTGGTTCATTCTTTAACTGCTCCGCCCCCCCCAAAAAAAAGAAGAGAGACTTGTTCTTGCTCT
CCCAATTCAGGAAGACGGAAGTCGCCGGTTGGGCTTTTCCAACCAAGAAAAACATGGGACTTTTG
GGCATTTTCTTCTCTTACGCTACGCAATTTCTATTTATTATTTTTGAATAGAAATCTAACTTTAT
ATTAGATATTTGGAAGGGATATTTCTATTCGAGATGCTACTTACTTACATATGATGTTTTCTTTC
ACAAGGCAGCGACTCAAGCGATTTTAATTCCTTTTCTAGTTGTAA
Right flanking sequence: Indices 165534 -- 166033
CTTTTCCTTTTCGAGTTGTAATTCTATTTCTACTTGTAATAGCAAAATCTGTTCCTGGGTCATAA
AATTGGGATTTACGTCATTTTGATTCCCTCCAGAAAAAAAGTAGTTCTTACCTTCCTGTACGAGT
AGTGAAGAATTATAGTGAGTTGTGGTTGGTTGTTGACCAACGGAAAGCATGGGAGTCTTTGGGCA
TAGGAGGTTCTCTCTCTCTCTTACGATATAAATAAGTCCGGGAATGAGCTATCATATGCCTTCTG
TTTGAAAGGCTAATTTCCTTTTACTCAATGAAGAAAGCTAAAACTAAAAGAGTAGGACATAGATT
GTATTATAAAAGTTTAATGAGAGATGCGAATCATAGCGTATCCAAAGTAGTACTTCTGTTTTGTT
TTCAAGGCAATTAAATTCTTACTGTCCGGTAAGGCAAGGAAAGGCTTTTTCCCCTAAGGGCGAAC
TTAACCGGGCATGGAAGGCAACTCTATCAAGTAAAGCTAGTCGTC
Found at i:165479 original size:18 final size:18
Alignment explanation
Indices: 165435--165490 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
165425 TTAATAGCTT
* *
165435 TTCCTTTTCGAGTTGTAA
1 TTCCTTTTCTACTTGTAA
*
165453 TT-CTATTTCTACTTTTAA
1 TTCCT-TTTCTACTTGTAA
*
165471 TTCCTTTTCTAGTTGTAA
1 TTCCTTTTCTACTTGTAA
165489 TT
1 TT
165491 TTAATAGCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 2 0.06
18 27 0.87
19 2 0.06
ACGTcount: A:0.18, C:0.16, G:0.09, T:0.57
Consensus pattern (18 bp):
TTCCTTTTCTACTTGTAA
Left flanking sequence: Indices 164935 -- 165434
AGCGCGAACCAAGATCCGTGATACGAAAACCAAAATCAGAATGAGGAAGAAAAAGATATCGTGAT
GTAAGTCCATTATTCCTTGCATCATAGGTGTTGCTGCGTCTTGAAATCCTAATTGCCATGGTTCC
GCTGCATCACAAGGAACAATTGTGAGGAATAGCCATTCTAGAACAATCATTTGGGTTGGTTCATT
CTTTAACTGCTCCGCCCCCCCCAAAAAAAAGAAGAGAGACTTGTTCTTGCTCTCCCAATTCAGGA
AGACGGAAGTCGCCGGTTGGGCTTTTCCAACCAAGAAAAACATGGGACTTTTGGGCATTTTCTTC
TCTTACGCTACGCAATTTCTATTTATTATTTTTGAATAGAAATCTAACTTTATATTAGATATTTG
GAAGGGATATTTCTATTCGAGATGCTACTTACTTACATATGATGTTTTCTTTCACAAGGCAGCGA
CTCAAGCGATTTTAATTCCTTTTCTAGTTGTAATTTTAATAGCTT
Right flanking sequence: Indices 165491 -- 165990
TTAATAGCTTTTCTAGTTTTAATAGCTTTTCCTTTTCTAGTTGCTTTTCCTTTTCGAGTTGTAAT
TCTATTTCTACTTGTAATAGCAAAATCTGTTCCTGGGTCATAAAATTGGGATTTACGTCATTTTG
ATTCCCTCCAGAAAAAAAGTAGTTCTTACCTTCCTGTACGAGTAGTGAAGAATTATAGTGAGTTG
TGGTTGGTTGTTGACCAACGGAAAGCATGGGAGTCTTTGGGCATAGGAGGTTCTCTCTCTCTCTT
ACGATATAAATAAGTCCGGGAATGAGCTATCATATGCCTTCTGTTTGAAAGGCTAATTTCCTTTT
ACTCAATGAAGAAAGCTAAAACTAAAAGAGTAGGACATAGATTGTATTATAAAAGTTTAATGAGA
GATGCGAATCATAGCGTATCCAAAGTAGTACTTCTGTTTTGTTTTCAAGGCAATTAAATTCTTAC
TGTCCGGTAAGGCAAGGAAAGGCTTTTTCCCCTAAGGGCGAACTT
Found at i:165480 original size:24 final size:24
Alignment explanation
Indices: 165453--165513 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
165443 CGAGTTGTAA
* * *
165453 TTCTATTTCTACTTTTAATTCCTT
1 TTCTAGTTCTAATTTTAATACCTT
* *
165477 TTCTAGTTGTAATTTTAATAGCTT
1 TTCTAGTTCTAATTTTAATACCTT
*
165501 TTCTAGTTTTAAT
1 TTCTAGTTCTAAT
165514 AGCTTTTCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.07, T:0.59
Consensus pattern (24 bp):
TTCTAGTTCTAATTTTAATACCTT
Left flanking sequence: Indices 164953 -- 165452
TGATACGAAAACCAAAATCAGAATGAGGAAGAAAAAGATATCGTGATGTAAGTCCATTATTCCTT
GCATCATAGGTGTTGCTGCGTCTTGAAATCCTAATTGCCATGGTTCCGCTGCATCACAAGGAACA
ATTGTGAGGAATAGCCATTCTAGAACAATCATTTGGGTTGGTTCATTCTTTAACTGCTCCGCCCC
CCCCAAAAAAAAGAAGAGAGACTTGTTCTTGCTCTCCCAATTCAGGAAGACGGAAGTCGCCGGTT
GGGCTTTTCCAACCAAGAAAAACATGGGACTTTTGGGCATTTTCTTCTCTTACGCTACGCAATTT
CTATTTATTATTTTTGAATAGAAATCTAACTTTATATTAGATATTTGGAAGGGATATTTCTATTC
GAGATGCTACTTACTTACATATGATGTTTTCTTTCACAAGGCAGCGACTCAAGCGATTTTAATTC
CTTTTCTAGTTGTAATTTTAATAGCTTTTCCTTTTCGAGTTGTAA
Right flanking sequence: Indices 165514 -- 166013
AGCTTTTCCTTTTCTAGTTGCTTTTCCTTTTCGAGTTGTAATTCTATTTCTACTTGTAATAGCAA
AATCTGTTCCTGGGTCATAAAATTGGGATTTACGTCATTTTGATTCCCTCCAGAAAAAAAGTAGT
TCTTACCTTCCTGTACGAGTAGTGAAGAATTATAGTGAGTTGTGGTTGGTTGTTGACCAACGGAA
AGCATGGGAGTCTTTGGGCATAGGAGGTTCTCTCTCTCTCTTACGATATAAATAAGTCCGGGAAT
GAGCTATCATATGCCTTCTGTTTGAAAGGCTAATTTCCTTTTACTCAATGAAGAAAGCTAAAACT
AAAAGAGTAGGACATAGATTGTATTATAAAAGTTTAATGAGAGATGCGAATCATAGCGTATCCAA
AGTAGTACTTCTGTTTTGTTTTCAAGGCAATTAAATTCTTACTGTCCGGTAAGGCAAGGAAAGGC
TTTTTCCCCTAAGGGCGAACTTAACCGGGCATGGAAGGCAACTCT
Found at i:165536 original size:18 final size:18
Alignment explanation
Indices: 165515--165551 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
165505 AGTTTTAATA
*
165515 GCTTTTCCTTTTCTAGTT
1 GCTTTTCCTTTTCGAGTT
165533 GCTTTTCCTTTTCGAGTT
1 GCTTTTCCTTTTCGAGTT
165551 G
1 G
165552 TAATTCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.05, C:0.22, G:0.16, T:0.57
Consensus pattern (18 bp):
GCTTTTCCTTTTCGAGTT
Left flanking sequence: Indices 165015 -- 165514
CTTGCATCATAGGTGTTGCTGCGTCTTGAAATCCTAATTGCCATGGTTCCGCTGCATCACAAGGA
ACAATTGTGAGGAATAGCCATTCTAGAACAATCATTTGGGTTGGTTCATTCTTTAACTGCTCCGC
CCCCCCCAAAAAAAAGAAGAGAGACTTGTTCTTGCTCTCCCAATTCAGGAAGACGGAAGTCGCCG
GTTGGGCTTTTCCAACCAAGAAAAACATGGGACTTTTGGGCATTTTCTTCTCTTACGCTACGCAA
TTTCTATTTATTATTTTTGAATAGAAATCTAACTTTATATTAGATATTTGGAAGGGATATTTCTA
TTCGAGATGCTACTTACTTACATATGATGTTTTCTTTCACAAGGCAGCGACTCAAGCGATTTTAA
TTCCTTTTCTAGTTGTAATTTTAATAGCTTTTCCTTTTCGAGTTGTAATTCTATTTCTACTTTTA
ATTCCTTTTCTAGTTGTAATTTTAATAGCTTTTCTAGTTTTAATA
Right flanking sequence: Indices 165552 -- 166051
TAATTCTATTTCTACTTGTAATAGCAAAATCTGTTCCTGGGTCATAAAATTGGGATTTACGTCAT
TTTGATTCCCTCCAGAAAAAAAGTAGTTCTTACCTTCCTGTACGAGTAGTGAAGAATTATAGTGA
GTTGTGGTTGGTTGTTGACCAACGGAAAGCATGGGAGTCTTTGGGCATAGGAGGTTCTCTCTCTC
TCTTACGATATAAATAAGTCCGGGAATGAGCTATCATATGCCTTCTGTTTGAAAGGCTAATTTCC
TTTTACTCAATGAAGAAAGCTAAAACTAAAAGAGTAGGACATAGATTGTATTATAAAAGTTTAAT
GAGAGATGCGAATCATAGCGTATCCAAAGTAGTACTTCTGTTTTGTTTTCAAGGCAATTAAATTC
TTACTGTCCGGTAAGGCAAGGAAAGGCTTTTTCCCCTAAGGGCGAACTTAACCGGGCATGGAAGG
CAACTCTATCAAGTAAAGCTAGTCGTCAGTCAGGGTTGAGACAGT
Found at i:262238 original size:30 final size:30
Alignment explanation
Indices: 262144--262239 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
262134 AAGTAATCTC
262144 AAGGAATTATTATCGCTTAGCGCTTGTGCT
1 AAGGAATTATTATCGCTTAGCGCTTGTGCT
* * * **
262174 AAGGTAGT-TTACTTGCTTA---CTTGTTAGAGG
1 AAGGAATTATTA-TCGCTTAGCGCTTG-T-G-CT
262204 AAGGAATTATTATCGCTTAGCGCTTGTGCT
1 AAGGAATTATTATCGCTTAGCGCTTGTGCT
262234 AAGGAA
1 AAGGAA
262240 GAGCTTTTAG
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
27 4 0.08
28 1 0.02
29 4 0.08
30 30 0.62
31 4 0.08
32 1 0.02
33 4 0.08
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (30 bp):
AAGGAATTATTATCGCTTAGCGCTTGTGCT
Left flanking sequence: Indices 261644 -- 262143
CAATTGTAGTACGAATCGCAGTAATTTGAATCCCTTATATATTAAAAAAAAAAGTGAAAGATGGA
GGTAGGTTTTGCCTACCAAAAGAATGGGAAAGGGAAACGAAACATTCTATTTCAAAACGGAGGAA
AAAGATTCTACTACTTTATCTATCCTACTGCGCTTAATCTTCATTCTTTATTAGAAGAGCAAGAA
AGAAGAAACATTTCTATTCTTTGTTACGTTATTTCAATTTCTTGATTTCTATTTCTTTTACGCAA
TCTCGATTTTGATTCTACGTAATCTCTATTCTACGTTATTTGAGAGGTGAAGCAGGTTCTGTTCT
GAGCCAGAAGTAGTCTCTTAGTTTTCGTATGAATAGATTGGGTCATAGCAAGGTGAACCAAATTG
ATCGAAAACATAGCCCGACCCGCGTATGTTAAGCATATAGCTAATCCTTCTTAACGCTTAGCTAC
TGCGTATAAGCTTCACCCAGCTCTTACAAGAAAGTAAGTAATCTC
Right flanking sequence: Indices 262240 -- 262739
GAGCTTTTAGGGAAAGATTATTGGGCTAGGGTGCTTGAGCAATTTGCCATTCTTCCAATTCAACG
ACTAGGCGTATGCTCAGAACGAGCAAACTGGAGGAAAGCTGGGATTGTGAATGAAAACAACCGTC
AGCTGCCCGAGAGAGCTCATTTCATTCAGGGATTGCCTCAAGAGAGGACTTCAAAGGCTTGGCTT
GAGGTTGCGTCTGCTGCTTGAGATGGAAGGTCTTCCGTAGCTTGGTTGCTTAGCCGTCAATCGTC
GTTCGAGAGGTCAGTAAGGTTTGGGACCTTCTGGCAGCTAAAAGCAAATTTCTTATTAAAGAAAG
ATGGCCGTCTAATAGATTTCCTTCTATCTTGCTGTTGTTCACTGTAAGGTAAGAATAGATTATAC
CGGGTATGAATGTATTAGATTGGGCAGTAAGGGTCGGAGAAGGGCAATCACTCATTCTTAAAACC
AGCGTTCTTAAGACCAAAGAGTCGGGCGGAAAAGGGGGTAAACTC
Found at i:284293 original size:18 final size:18
Alignment explanation
Indices: 284272--284314 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
284262 CAACCTTGTT
284272 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
284290 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
284308 GACTATG
1 GACTATG
284315 GCAGGGCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 283772 -- 284271
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 284315 -- 284814
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTTAGG
TCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCATAGGGCGACCGGGCCAGGC
CGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAGGGGAAGAGGGG
GCAGCCCTCGGCCCGATCATCCAATTCGCTCCAACAGATAGGCATGGTTCTGTAGTCAAAGCAAC
TTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTCGGGGGTTCCTTAGGGACCGATTCACT
CTGCGTAGATTGACTGAACGCAGAAAGCCTTCCACTGGCAGGCGATCGTGTTTTTCACAGGATTT
CTCGTTACTCATGTCAGCATTCTCACTTCTGATATCTCCAGGTGTTGTCACCAAAAACCTTCCCC
GATTGACAGAACGTTCCGCTACTGACACTTGAAAAAGAAGCTTTC
Found at i:293815 original size:17 final size:17
Alignment explanation
Indices: 293793--293829 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
293783 GCACAGATTC
293793 CCTATAAAGAAAAATTT
1 CCTATAAAGAAAAATTT
* *
293810 CCTATAAAGACAGATTT
1 CCTATAAAGAAAAATTT
293827 CCT
1 CCT
293830 CTCTTCCCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (17 bp):
CCTATAAAGAAAAATTT
Left flanking sequence: Indices 293293 -- 293792
ACTCCTAGTAGGCCACGAACTCCCTTTCAAGCTTTAACCGACCCGAATCAAATCCAGATGCCTCA
CCAGATAGTTCTCCTTTCATCTGTCCGATCAGGCAGCCAATTCTATGCCACTAAAGCTTCATGCC
ATTGAAGACTGGTCCCGAAAGCGATTAGAAAGCGAACTAGGATCTGCAAGATTCGACTTTGATCC
GCCTATGAACCTTGGTTCACGCTCTACGTATCTTATTCTTTCAAGCTTTCTCGAGTCACCCTAAC
GTAACGGCTAAGAGAACTTGGCTAACTTCGATCAATTCCACGACTTTCCATCCTTCTTGTGTTGT
GGGATGTGAGTCATCAGTTCTTTCCTCCGCCTGATAGTTTATTCTCGAGGATCACTGAACTTGGC
TTACTTCTTACTGAATGCCGTACTTAGCACTCGGGGCGAGCTCTTAGCGATTAGTCAGTCCGGGT
CCAGCTAGTCTTGCACTTTCAGACCCAAACAAAGGGCACAGATTC
Right flanking sequence: Indices 293830 -- 294329
CTCTTCCCGAATGCTTTCCTTAGCTAATACTGATTGATTCACCGCATCTTCTCCATTAGGAGATC
TAACCAAGCACTCGAAATGCGACATTGACTAAAGAAGGTAGACAAAAAGGCAAACTAGAGAAAAA
GCCAAGCTGACTGAATTGAATCTTTCAGTGGAATTGGGGCTTACCTTATATCATATCCTCTCTCT
TTCAAGCACAGTTGAATGAAAAAAGCGTACCTTCGAAGGCATGATTGCTGCGATCAAGAGCTGCT
TAACATCATTGAGAACAGGAGCTCAGAAGATTTGGTGGAGGATAAAAAGTGAACCAACACTGGGA
TCCGATCATAGCCGCAGTGAAGTGTTGGGATGCAAAGACGATGGTTTTTAGATTCGGCAAACATG
AGATGTGTCCCACACTTGAAGAAGTACATCGAATTTTGGAGATATCCCGTAAATTCCTTTTTGTA
CCTAGAGAAGGACGACCGAGAAAAAAAGGCTTCGCGTTCTCCAAG
Found at i:340469 original size:20 final size:20
Alignment explanation
Indices: 340444--340481 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
340434 TCTTGTTTTA
340444 GTAGCTAAGGAGTT-CTAGTT
1 GTAGCT-AGGAGTTGCTAGTT
340464 GTAGCTAGGAGTTGCTAG
1 GTAGCTAGGAGTTGCTAG
340482 CAGCTATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.11, G:0.34, T:0.32
Consensus pattern (20 bp):
GTAGCTAGGAGTTGCTAGTT
Left flanking sequence: Indices 339944 -- 340443
ATTCTTTTTCTCCAACCTTCGATGATCCTCCTGCAGGCAAATCATCGAAGTCAAGAAGAAGTGAT
GGGCCAGGCAGCAATGCTAGGTCCGAGGAAGAGACCTGTAGGTTTGGAAAGCCTGTCGATCCATC
CTGATTAACTTACGCAATTTCTGACTAGAGAGAGGACTTAGATCGGAGAGGAGCAGCTCTTTTCT
TTTTAACAGAAAGCAGTGATGAATGGGACAGAGCTGCTACAATAGCTTCAAGCTGGAGCTGCTTT
ATGTATTGGAGCAGAGGTGGCAGTTCAGACAGCAGCAGGAGCAGGACCAGCAACTAGGGTTGTTT
TGTTCACAGAGCAGCCGTCTTTCCCTCTCAAGCGGAGAAGACTGGTTACATGTCCGATCCGGTAG
GGATGGTTCTTCTCGACAGATTAAGCTACTTACTATAGTTAGGGTATTGAACAACGGGTGGCAAC
TTGCCCAATAAGAAAAGTCGCCCGAGTGAAAGAGCTCTTGTTTTA
Right flanking sequence: Indices 340482 -- 340981
CAGCTATGAGTTCCGAGTTGACGAGATCATAAACAAATCTGTCTGGGACTGGTGACACCTGTACC
ACACTCTATGGCACACACCCCTCGTTGTAGTAGACGAAGATGGTCACCTAGGATAGGCAGACAAC
CCTGAACCTTAGAAAGTCGCCGGCGGAGACGCTACGGGAGAACCGCCTAGGATGGCGTAAGAGAC
TCGAGCATCTCTTTCTTCAATTTGGGTTTGTGCATTTGTCTTTCAAATAGGTCAAGGGTTCAGAC
AGGAGATGTGCTTTAGCCAAAGAAGCTTGGGCACCTGCTCCAATAAAGCTAAGAGGACTAGCTAC
GGTGTGGGCACCAGATCCACTCAGTGAGGCCGGGCAAGACTTTACGTCCGATATAGTAGTGTCAG
ACATTTGTCATACTTAAGCAGTGGGATAGACTCCTTCAAATGGAAAGATAGGAGATGTTTAGCCA
GTACAAGCTGTGTTTGTGGCACCCATCCGGGTGGAGTAGCCAGGA
Found at i:351415 original size:18 final size:18
Alignment explanation
Indices: 351392--351426 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
351382 GAAAAGCTGT
351392 TAGCCTTTTATGCCCTAC
1 TAGCCTTTTATGCCCTAC
351410 TAGCCTTTTATGCCCTA
1 TAGCCTTTTATGCCCTA
351427 GCCTTCCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.40
Consensus pattern (18 bp):
TAGCCTTTTATGCCCTAC
Left flanking sequence: Indices 350892 -- 351391
TCACTCCTTTTGGTCCGGGTATCTGCCCTCTGATTCGGTGGAGTAACTGCCCGCCCTGTATCTGG
TGGTGCCTGTCTGGCTGGCTTCGGCTTGCTGAACGTTGTTATTATTCTTTTTAGGGTCTGGTGGT
CTTGCTGCAGTCAGCGCTCGCCTCATTCAATCCCCACCTCTCTGTATTGCTAGCACAGAAGGCTC
TCTCTGTTCTTACTACCTACGGGATAAAGCCAAGCCATGGCCTCCAGGGTTGGTTGTCTTACTCG
AGGTTCTGCCCGCTCCATCGATATCTTTCTTACTACTTTCCTTGCCTTGGCAAAGTCTACCTGTA
CGTTACGATTTCAAGCCTTTCCGAACGCCCGTTAGAACTGAACTTTGAAACCGGTAGCTTTGATG
CCCGACGCTTCGTCATGCCAACCTTGAGCCCCTTTATTTAGCCCTGTACTGTGGTGAAACCGGAA
CTTATGGCTGAGTGTTTTTAGCCGCTTTTGACTCGGAAAAGCTGT
Right flanking sequence: Indices 351427 -- 351926
GCCTTCCCTAGCCTTGAAAACGATTATGCTTTCGTAATTAGTTCCAGCTTAGCTTCGTCATGCCC
ACCGGAAGGAACGCCTTCACTCACGCCAACAACAACAACAACCTCTGCTTAAGCAGCCTACCTTG
AACCAGCGAAAGTTAAAATCACATTTCTTTGCCTGAGAGAGAAGAGCGTCAGCCCGCACGGTCCC
TGTGAGCAGCGGATTGCTTCCGCGTTGAGCCCTTGGCACTGACCTTTGAGACATCGTTCCCGTAG
CACCTTATACCTGACCTTGGAATGTCACTCTGCCTCACAAAGATCGTCTCTCTGGCACTTCCGCT
TCCGGGGTTGGGTCAAAGCTATCGGTCGATCTCGTGGCGAGCCTTCCCCACCTACCTTACCTGGA
CCACCGTTAGCCCACCAACTTCCTTTGCAACCTGAACGCCCAACAACTTCCACTTCCACTGGGAC
TTGACCACCAACAGGCACTGGCTCACCTCACTACGCTCCGAAAGC
Found at i:375269 original size:22 final size:23
Alignment explanation
Indices: 375236--375289 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
375226 GGAGGTTACT
375236 CTCGT-CCTACACTAG-GTCACC
1 CTCGTCCCTACACTAGCGTCACC
* *
375257 CTCGTCCCTACACTAGCTTCTCC
1 CTCGTCCCTACACTAGCGTCACC
375280 CTC-TCCCTAC
1 CTCGTCCCTAC
375290 GGTCGAGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.17
22 17 0.59
23 7 0.24
ACGTcount: A:0.15, C:0.48, G:0.09, T:0.28
Consensus pattern (23 bp):
CTCGTCCCTACACTAGCGTCACC
Left flanking sequence: Indices 374736 -- 375235
GCTCCTCCGGCCGCCTATGGAAGTAGTAGAGCCACCTAAAGTGCTTTATAGAAAGTAGTCCCATG
CATTCCTACAAATGTAAATGGTATCGCTAGACGGTAAGGAAAGAGAAAGGGCCTTTCAGCCTCTG
CTTGAGTTCCTCTTTTTTATGTTTATGGTCTTTCTCGAGGCGCTGCCTACCTACAAGGCAAGATC
AATTGAACCTTCACCTTAAACTGCGACCGGTCTAAATGCAGGCGCTTCGGGCACAGTAGTTGTTA
TAGATCAATCCATGGGAGTCTCCGACTTGCTACCCCTTCTCCAGAGCTGCAAAAGAGTTTGACTT
CTATTATCTTACGTATAATTTCTAGCAATACTCTTAGTAACTCTCTTTTTATAAGATATTATAAA
AAGTCTTTTGGCATACCAATCAGTGAAACTCTAAGCTATCACAGCTACATCCACTCATAAATGCT
CCGCTGCTCGGGGAACACTCGTTACGAAGAAAAGGGGAGGTTACT
Right flanking sequence: Indices 375290 -- 375789
GGTCGAGTTGCCCCGCCCATTTCCTCTCAGACAAGCACGTAACCATCCCCAGTCGAGCTAGCGGC
TCTATCTTCTACTGATATCGAGCTAGGTCCAGATAGCTAAATTGATTGTATGACCATTTCTGGAC
GTTTCTACGGTTTATGGCCAGGGATGCAATCCTATCGATCGATTTCCCTATAGCTTTTTGCCCTC
TCGGCGTAAGATTTTGATTGGAAGATTGGGTGAAGCCTAGCTTCTTTCTTTCTTGCCTCTGCCAA
AACCAATAGGAATTGGAGCTCCTTCTGAGTAGAATGAGGAGAGTGCAGACGCTTTCACAGATGCC
CGGTATCTTCCGGAGCTGTAATCTTTACACACTAAGTAAGCAAGCTTTGGTTGGCTCTATTAACT
CAAGATATCCATCATCCCGCGCTATACGGATCGAAGCCTTCCACTTTAGGAATAGGTTTAATTGT
TTAATGTGAACGCTAAGGAAGAGAAATCCTTACCGGAAAGCCGGG
Found at i:404295 original size:13 final size:14
Alignment explanation
Indices: 404262--404295 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
404252 CAGAAGCTAG
*
404262 AGGACAGTATTCGT
1 AGGACGGTATTCGT
404276 AGGACGGTATTCGT
1 AGGACGGTATTCGT
404290 -GGACGG
1 AGGACGG
404296 ATGAGCGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.24
Consensus pattern (14 bp):
AGGACGGTATTCGT
Left flanking sequence: Indices 403762 -- 404261
TAGATACGTGATAACACTTGTGGTTTCGGCGAATCGCCTTCACTCTCGGGGTTCAGTACCCGCCT
CTTGGTGTCCAATACCCAGTGATGGGAGAAGGAGTGGGAGACGAAGAGAGAGAAGATGGTTGCTT
AGCAGCGGAAGCTGGGGATCGAGAAGCGGAGGGAGAGCTTAGGCTTGAAATGGAGCTGGGATACC
GGTATTTTTCCCTCCCTGGATCCGAGTCTTTCTCTTCTCCTGGACCGAGCACCGAGACCGAGGAA
AGAGAGGCTGGATACGAGTCTGATGAGATCAGAGCCAGTGAAGAGAAGAGGGAAGGCTTACTCTG
CTAGGCTGGCTTGCTTGTTCGACTAGAGCACATAAATAAGGTAGCTTGCTTACTTAGTGCGAAAC
GCTAAGGCCAATTAAGCAACGTTAATGGACCGCTCCCCATTACAGACGCTTTCACAGGGCTTCTT
TTTAGATAAAATAGGCCATAGAAATTCACTCATAACAGAAGCTAG
Right flanking sequence: Indices 404296 -- 404795
ATGAGCGATTGGACCGCCTATAGGACAGTTACTGGACAGATGCGACCGTTACCAGTTGACAGATG
ACAGGCAGAAGAGCGGGAAGTCGCTCTATTTAAAGGACGGGAATTGCACATTAAAGGAAGGGAAT
CGTGTACTGAGCTAGCCTGCCTTGAACTTGAAGTAGGTAGTCTCTCCTATATCTGATAGCTTTAA
CTGGCCACTACAAAGAAATTGCCATAGATCGAAACTTATTCCAGGCTTAGTATCCCCGGATAGAC
CCTATAAAAGAAGACGAGTCATAAAGGCAAATATCTAACAATTTCAGGGGGGCACATCCTAACTG
AATAGTACTCGCAGGTTCTCTTTTCCATATGTTCTTCCCGATGCCCTATCCGACAGCCGTTAACT
GCCTTGCAGGGAATTCCTTACTCAAAAGTATGAGAGTGCGGCATAGCAAGAGTGAATCCTCCCAC
CTCCCTCTAACGCTTATCTCTTTTCTTGCTTCCTTGCTTTAATCC
Done.