Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_062588
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: 422985
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Found at i:952 original size:16 final size:17
Alignment explanation
Indices: 931--962 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
921 TAGTGAGGTT
931 GTAATCCA-TAACCTAG
1 GTAATCCAGTAACCTAG
947 GTAATCCAGTAACCTA
1 GTAATCCAGTAACCTA
963 AAAGACCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (17 bp):
GTAATCCAGTAACCTAG
Left flanking sequence: Indices 431 -- 930
AGTAAGCAACAGGTCATATTCGTACCTTAGTAAAAATGGCTTTTTAAGCTTTTCCAGCGGAAATA
GCTCGAGTGATAACGATAGGGGGAGAATCAAAAGTGTTTTAAGTCGCTCCGTTTGGAAGAAGATA
AAGTCGTTTACTATTAACGGTATTCAATCAAGTCTAGCTAACCGCTTAACCCACTTGGGTCAATA
TGTTTCACTCCTGGTTGACCCCGGCACTTAGGCTTTGGAAAGCCCTTCTTTCGGACATTGTGACC
ATTCCCTGAACTATCTGATGGGAAGCCTAACGACGTAGCATGAAGTTCTTATTCTTATTTCCGAA
TTCTCATTTACTATGAAAATAGATACTCGACTGGCAATTCGTTTACTCGGCTTAAATGCGCTTAT
TTTCTCTGTTTTGAATGAGGTTATACCGGTATAACTGTCATTCTCTACTCCCGTTAACAATTAGT
TGCGGGCGGAAAGTAGACATCCCCTATTGACATATTAGTGAGGTT
Right flanking sequence: Indices 963 -- 1462
AAAGACCGTTTGACATAGTTTATCTTGTAATAGAGTTGTTCATAGAAAGGGTTCCACTTGGCATG
GGGCTACTAGCAACTAATTGACTAGTTATACTAGGGGTACTACGGACAGTCGACTTACCTTTGAC
ATAGTTTAGTGAGAGATGTCAATCTTGTTATTTCTTTTACATTGAAGAAGCTGAAAGATGCCTAT
CAATCATATGTCAATCATAGTTGGTTATGGATTAGCCCGTACAACCGTTCATAGGCTGTGTCAAT
CAGTGACGCTCATAGATAGTTGGTTAGTTAACAATGACTTGGTTATGTGGAATCCTTTCTATCAC
TAAGATGTGTGCTTACAGATAGTGAATGGTGTGCCACATGAAAGGTATTCATTTACCTCAGTTGA
ATTCATGCTTTCTATCAATCCCTATGTCTATCATAGATAGTTGGTTATGGATTACACGGGACTAA
TATGTCAATCCCTAACGACTAATTGACTTGCATTCACTACTAGTT
Found at i:58137 original size:18 final size:18
Alignment explanation
Indices: 58114--58150 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
58104 TCATATCATA
58114 AACGGGTCTACCCTCAAG
1 AACGGGTCTACCCTCAAG
58132 AACGGGTCTACCCTCAAG
1 AACGGGTCTACCCTCAAG
58150 A
1 A
58151 GCAGGTAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.32, G:0.22, T:0.16
Consensus pattern (18 bp):
AACGGGTCTACCCTCAAG
Left flanking sequence: Indices 57614 -- 58113
TTCATTCTAGTTACGAGAATACTGGCAAAAGTGCCTGATAACGTCGAAAAAGACCTGGGAGTTCC
TTCCGCAAAGAATCGAATAATGAGAAAGATTGATATCATTGGTAGCTAAACCATATCCATACCGG
TGGAGCGTAAAGCGAACACTCTCCTCGAAAATGCTGCGGTTAGCTGCCGGAAAGAAGTATGGTTC
TTTTGAATATATATCCCACAAGATTTCTAGCACAGCACGTGTGTTAAATTTGCTTTCTTCTACAT
TAATGAAAAAGTCAAGTTTTTCTCGGAGTGAGACCGCTGCGGTCCGGTCCTGTTCTTGTTGGATT
GCAAGACTGTATGCCGGGTTCAGCTCCTGGTTTAAGTCTTCGAAAAAGAGGATATAGCCATTTAG
TTTCCCCAATTTTTCTAGAGTAGAGATGTCTGAAATCTAATTTGGCACGTGTAAAAGAGTTAGAA
AGTATAAGGCTTGGGCTGGAGTCCCCCATACCCCTTCATATCATA
Right flanking sequence: Indices 58151 -- 58650
GCAGGTAGCCCTTCAATGGAAGCGTTTGGAAAAACGGCGCACGCGCCAGAAAAAACGAAAGGTGA
TAGGATTCTATCTAGACACCAGAGGATGGGAGAAATGATTTTCATATATATATAAGCAAATAAGC
AATGAAATAAGGAATCTGAATAGCAAAATAAGATATTTTTTTTCTTTTTTAATAAAAATAAACAT
TTCCAGCAGATTTTTTTTCCGCCAATGTGATGGAGAATGCTATGAGGTGTTCGAAAATGGTTGAA
GTAGTTGAATAGGAGGATCACTATGACTATAGCCCTTGGTAAATTTACCAAAGACCAAAAGGATT
TTTTTTTAATTATGGATGACTGGTTACGGAGGGATCGTTTCGTTTTTGTAGGTTGGTCTGACCTA
TTGCTCTTTCCTTGTGCCTATTTCGCTTTAGGGGGTTGGTTCACAGGTACACCCTTTGTAACTTC
ATGGTATACCCATGGATTAGCAAGTTCCTATTTGGAAGGCTGTAA
Found at i:68577 original size:36 final size:36
Alignment explanation
Indices: 68527--68597 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
68517 TCCAACAACT
*
68527 GACAGTATCGGTTGTGTAGTTAATACAGCCGTATTG
1 GACAGTATCCGTTGTGTAGTTAATACAGCCGTATTG
68563 GACAGTATCCGTTGTGTAGTTAATACAGCCGTATT
1 GACAGTATCCGTTGTGTAGTTAATACAGCCGTATT
68598 TACATCCCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (36 bp):
GACAGTATCCGTTGTGTAGTTAATACAGCCGTATTG
Left flanking sequence: Indices 68027 -- 68526
TTGTTGTTTAATGGCTCAATTTGTATTGGATTGGGATAAGGGTATAATTGTAATTGCCATGTTAA
GGCGGGTAGCAAATAGGCTTTTATTGGGTAAGAGAGTTAGTTTGTTGTTGCTGCCGTCAAACCCT
CTTAGTGAGCTGCTGTGAAACTGCTGCTGCTGTCTAGCCTTTGTAAACCCTCTCTTTGTTAGTGG
ATTTCCTTCTCCCTGCTGCTCCGTGGACGTAGGCAATTGCCGAACCACGTTAAATCCTTTGTGTT
CTTCTTTCTTTGTCTTTCTGGCTTTGTTTTGGTCTGTGGCATTCTCCCCGCAGTAAATCCTTTCT
CCCCGCAGTAGCTCCTTGTTCATCTGTCGCTGCAGGTTATTTGGTGCTCTGAGCACAACATGCTT
AACCCACCCAAAAGGAGAACTACTGGGAGTCAAGAAAGAAAGCATTAAGGGGGAGTGTTGAGTGA
GCTGCTCCATTCAAGCTGCAAATCTAGACTACTGCTCCAACAACT
Right flanking sequence: Indices 68598 -- 69097
TACATCCCTTTGTATCATCTTTCATACTGTGCTCTTAGCTTCTTCTTGTAAGCTACTTTCACGAC
AAAAGATTCAATGGCATCCTCCAAATCATAAGCAGCTTCTCTAATAATATTAACCCATAACCAAG
AAGTAATTAGTGAACCTATCCTAGGTATCGGTATTTGTTTTTTACTGAGATTGTATTCGACCCTA
ATGGCAAACGTAACTATCTTAATAGTCGTAACTATCTTAATAGTAAGGAATCCCACAACTACATC
ATAATACAAAGGATCAGTTTCAATACCACATATCAAGACCAGCCGTAGTGTCAATCGTGATCCTT
GTCCTTCCCTCTATTCTCGTTTTAGTTTCAATTCTTTGATTCAATCTTCATTCCACTCCGTCATC
CATAGGGACCCTGCAGCACCCAGCGCGCACCCTGCAGCACCCAGCACCCTGCCTCATCTCTGGTG
CCTCCTGCTCCCTCAACACATCACATGCGAACTCGGCTCCAAGAT
Found at i:68824 original size:18 final size:18
Alignment explanation
Indices: 68801--68836 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
68791 TAATGGCAAA
68801 CGTAACTATCTTAATAGT
1 CGTAACTATCTTAATAGT
68819 CGTAACTATCTTAATAGT
1 CGTAACTATCTTAATAGT
68837 AAGGAATCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (18 bp):
CGTAACTATCTTAATAGT
Left flanking sequence: Indices 68301 -- 68800
TTTCTGGCTTTGTTTTGGTCTGTGGCATTCTCCCCGCAGTAAATCCTTTCTCCCCGCAGTAGCTC
CTTGTTCATCTGTCGCTGCAGGTTATTTGGTGCTCTGAGCACAACATGCTTAACCCACCCAAAAG
GAGAACTACTGGGAGTCAAGAAAGAAAGCATTAAGGGGGAGTGTTGAGTGAGCTGCTCCATTCAA
GCTGCAAATCTAGACTACTGCTCCAACAACTGACAGTATCGGTTGTGTAGTTAATACAGCCGTAT
TGGACAGTATCCGTTGTGTAGTTAATACAGCCGTATTTACATCCCTTTGTATCATCTTTCATACT
GTGCTCTTAGCTTCTTCTTGTAAGCTACTTTCACGACAAAAGATTCAATGGCATCCTCCAAATCA
TAAGCAGCTTCTCTAATAATATTAACCCATAACCAAGAAGTAATTAGTGAACCTATCCTAGGTAT
CGGTATTTGTTTTTTACTGAGATTGTATTCGACCCTAATGGCAAA
Right flanking sequence: Indices 68837 -- 69336
AAGGAATCCCACAACTACATCATAATACAAAGGATCAGTTTCAATACCACATATCAAGACCAGCC
GTAGTGTCAATCGTGATCCTTGTCCTTCCCTCTATTCTCGTTTTAGTTTCAATTCTTTGATTCAA
TCTTCATTCCACTCCGTCATCCATAGGGACCCTGCAGCACCCAGCGCGCACCCTGCAGCACCCAG
CACCCTGCCTCATCTCTGGTGCCTCCTGCTCCCTCAACACATCACATGCGAACTCGGCTCCAAGA
TGGCATTGTTCGGCCCGCACCGATGGCACTGTAAAGTATCCCATCCCTAAAGCTCTTCTCTCTGT
TATTAATTCCATGGAACCCACTTGTTATACTCAGGCTGTTAAAGATGCAAATTGGAGAGCAGCCA
TGACTGAGTAAATGAATGCCTTGTTGAAGAATGGTCCCTTGTTGAAGAATGGTACTTGGTCTCTA
ATTCCTCACTCTCCATCTCAACATGTTGTGGGCTGTAAATGGCTG
Found at i:69268 original size:18 final size:18
Alignment explanation
Indices: 69245--69279 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
69235 TAAATGAATG
69245 CCTTGTTGAAGAATGGTC
1 CCTTGTTGAAGAATGGTC
69263 CCTTGTTGAAGAATGGT
1 CCTTGTTGAAGAATGGT
69280 ACTTGGTCTC
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:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (18 bp):
CCTTGTTGAAGAATGGTC
Left flanking sequence: Indices 68745 -- 69244
ATCCTAGGTATCGGTATTTGTTTTTTACTGAGATTGTATTCGACCCTAATGGCAAACGTAACTAT
CTTAATAGTCGTAACTATCTTAATAGTAAGGAATCCCACAACTACATCATAATACAAAGGATCAG
TTTCAATACCACATATCAAGACCAGCCGTAGTGTCAATCGTGATCCTTGTCCTTCCCTCTATTCT
CGTTTTAGTTTCAATTCTTTGATTCAATCTTCATTCCACTCCGTCATCCATAGGGACCCTGCAGC
ACCCAGCGCGCACCCTGCAGCACCCAGCACCCTGCCTCATCTCTGGTGCCTCCTGCTCCCTCAAC
ACATCACATGCGAACTCGGCTCCAAGATGGCATTGTTCGGCCCGCACCGATGGCACTGTAAAGTA
TCCCATCCCTAAAGCTCTTCTCTCTGTTATTAATTCCATGGAACCCACTTGTTATACTCAGGCTG
TTAAAGATGCAAATTGGAGAGCAGCCATGACTGAGTAAATGAATG
Right flanking sequence: Indices 69280 -- 69779
ACTTGGTCTCTAATTCCTCACTCTCCATCTCAACATGTTGTGGGCTGTAAATGGCTGTTTCGTAT
TAAGCGTAACCCGGATGGTTCAGTAGAGCGCTACAAGGCACGCCTTCTTGCAAAGGGATTTCATC
AACAGCATGGCATCGATTATGGTGAAACTTTCAGTCCTGTGATCAAGCCAGCTACAATTCGCACT
GTTCTTTGTCTTGCTGTGTCCGCCTCTTCGCCAATCGGACTACTTTCCTTCCATACCCATTAGAC
GTCAAAAATGCCTTTCTTCATGGCTATCTTCAAGAGGATGTCTACATGACCCAACCTCTAGGCTT
TACCGATCCCTCTCGGCCTTCCTTGCAAGCTCCACAAGTTCCTTTTTACGGCTTCGATTGGCTGT
CGAGCTCTTTCTTTCTATGTGGATAGTCACTAAGATAGCTATATAAAGAATGACTAGACCGTAAG
ACACTCATGAAGACATGTCAATCTTGTTCTCTATCCATTGGTGTT
Found at i:70015 original size:20 final size:20
Alignment explanation
Indices: 69990--70029 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
69980 GTACCAATGT
*
69990 CGTATTTGTAATGTGTTTCC
1 CGTATTTGTAATGTCTTTCC
70010 CGTATTTGTAATGTCTTTCC
1 CGTATTTGTAATGTCTTTCC
70030 ATGGGCCAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.50
Consensus pattern (20 bp):
CGTATTTGTAATGTCTTTCC
Left flanking sequence: Indices 69490 -- 69989
GTGTCCGCCTCTTCGCCAATCGGACTACTTTCCTTCCATACCCATTAGACGTCAAAAATGCCTTT
CTTCATGGCTATCTTCAAGAGGATGTCTACATGACCCAACCTCTAGGCTTTACCGATCCCTCTCG
GCCTTCCTTGCAAGCTCCACAAGTTCCTTTTTACGGCTTCGATTGGCTGTCGAGCTCTTTCTTTC
TATGTGGATAGTCACTAAGATAGCTATATAAAGAATGACTAGACCGTAAGACACTCATGAAGACA
TGTCAATCTTGTTCTCTATCCATTGGTGTTACCATGGTGGCCAAGACCACTTCCTAAACTAGCCA
TTTCTGTTGGCTAGCTACTAGCTAGCTAAACTACCATGTTTTCCTTTTCTCTTGTTGCTCTTGTG
GCCGCACAAGTCATCTTTGTAATTGTCATTTTAACCGGTTATAAAGGTTTGCCGTCCCTATTTGC
CTTCATCGAACGCAACTACTCTTGCGCACTTTCCTGTACCAATGT
Right flanking sequence: Indices 70030 -- 70529
ATGGGCCAGGTAAATACCGTCATGAATGATATAGCAACCAGTACTACGCACTTTGAAATAGATTA
TATCCACATCATTCGGGTACAAAGTTAAACGAATCACACAATGAGATGGTTGTTGAGAAACTTCA
GGGGGTTGTGGATGTTTACTCACTGTTTTTAAAGCGGATCCAAGATGATCATCATCTGTCAACTC
CCAAACCATAAGATCAACCTCCCAGCTACGGTAGGTCACAATATGCAGACGCCCTTGGCGCACAC
ATATATCCATGACGTTACCAAATGATCGAATACAACCTGCATCAACGAGTCGGAATTGGTAATGA
TCATCGTCAACAGTCTCACCGCCACTGCCGATCACAAAAGGATCCAACGCAACTAGACCGTTCTG
GTAAGCCATCTCATCATATGCCTCATATGCCCAGTACAAGATTCCATTGTGAGCAAGGCTATTAC
TTCTAGTAGCGTCTGCAAACCTGAGACTTCGTCGGGATGATACAA
Found at i:125140 original size:18 final size:18
Alignment explanation
Indices: 125117--125159 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
125107 CCACCTTGTT
125117 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
125135 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
125153 GACTATG
1 GACTATG
125160 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 124617 -- 125116
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCATGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCCACCTTGTT
Right flanking sequence: Indices 125160 -- 125659
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGAGTAAAGGCCCCTTAGG
TCGCCAAACTACGACGAGAGTTTCGTCTTTTGAAGCGCCAGTCGCGTAGGGCGACCGGGCCAGGC
CGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAGGGGAAGAGGAA
GCAAAGCTCGGCCCGATCATTCAATTCGCTCCAACAGACAGGCATGGTTCTGTAGTCAAAGCAAC
TTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTCGGGGGTTCCTTAGGGACCGATTCACT
CTGCGTAGATTGACTGAACGCAGAAAGCCTTCCACTGGCAGGCGATCGTGTTTTTCACAGGATTT
ATCGTTACTCATGTCAGCATTCTCACTTCTGATATCTCCAGGTGTTGTCACCAAAAACCTTCCCC
GATTGACAGAACGTTCCGCTACTGACACTTGAAAAAAAGCTTTCA
Found at i:129801 original size:32 final size:32
Alignment explanation
Indices: 129760--129821 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
129750 GCATATTTCG
* *
129760 TTGAATCAGTCTTTTTCGCTACATCGGGGCTA
1 TTGAATCAGTCTTTTTCGCCACATCAGGGCTA
129792 TTGAATCAGTCTTTTTCGCCACATCAGGGC
1 TTGAATCAGTCTTTTTCGCCACATCAGGGC
129822 GTCAATATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (32 bp):
TTGAATCAGTCTTTTTCGCCACATCAGGGCTA
Left flanking sequence: Indices 129260 -- 129759
ATTTTTTCAACTGATATTTCGATATAGAAAGATCTCCTTATTTCTTCACCGCGGATTCTCGCGTC
ATTTTCTTGAAAAAATATTAGATCAGCGTGGGACACTTTTAAATGAGTAATGCTTACCATTCCAT
TATTCACACAAACCCTTCGATGACTTATCGGCTGCCTTGCTTGAGGAATAGTTTCACAAAAATGG
AGACGAACCGGAATAACGTCCGATCTTGTTTCTGGATTGAGTGGAAAAGGGATATATGAAGTTCG
CTCTGTTCCTCTGTGCATCTCTGTGATGGGTAAATCCCCATGAAAAAGGGGCAACTTTCGTGTAG
TTTGTGATTGGATGTAACTGTTAAGATTTTTTCTCGGATAAATCTTTCTCTTAATAGATCTCTTC
TTGTTTCTCAATCTTCGGAGAATGCGGCGTTGTATTATTGTAAGTTCTCTGTTCCGAACATTTCC
TGAAAGTAGACGACAAGTTTTAAATCTTAATGCAGGCATATTTCG
Right flanking sequence: Indices 129822 -- 130321
GTCAATATGATATTTGCATAGGTTTTTCGTTAGAAAAAAAGAAAGGTTAACTCGGCTCAAGCAAT
GAGGAATTAGCTCAAGGAGTACTAAAAAAGGTGTTAACGGCGAGGTTCGCCTTTCAGCAGCCGCC
GTAGCGCTTCATTCTTTTCCTCGAGAATGCGTATTTTTCCGAGCAGATTAGAACACTCCGCTGCT
TCCGCTTCGTGGTAATCTCGGACCGAAGCTTTTATTTGATCATTTAGATCTTCGGCCGCCCTGGC
CTGTTGCTCCATTTTCTTCAGGTGGAGCAACATGTTACGCCTTTCCTCTTCGCAGGCGGCGGAAT
AGACCGGATCCATGTCCCTAGAATCGATTTGGGAAAGTCCCTCTAGAACCTCCGCCTCTAGCGAC
ATCCGCTTTTGGCGGAGCTCTTCGATTTTTCGGAGCAGCTCGTCGGAGGTTTGGTGCGCCCTGTG
AGAGGGCCCCGCTTGCTCCCCCCCCCTTACGGTTGGTTGAGAAGT
Found at i:135366 original size:19 final size:19
Alignment explanation
Indices: 135342--135379 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
135332 CCCAACCCGA
135342 TACCGACCGAAAGAGTAGT
1 TACCGACCGAAAGAGTAGT
135361 TACCGACCGAAAGAGTAGT
1 TACCGACCGAAAGAGTAGT
135380 AAACACAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (19 bp):
TACCGACCGAAAGAGTAGT
Left flanking sequence: Indices 134842 -- 135341
GAATAGTGAAGCCCGGGAGAGAGGCCCATGATTCTTCGCCAATACCACAAAGAAGGAGTTAGACT
AAACTTACTTGATTAACCACACATCCAGAGTGGTCATCGTTGTTTGTAGCCCTTGGGCAAAGAGG
AAGCTTCAGAAGCAGAATCGTCGCAACAAAAGCAGGATTCGAGGCCTCAGCAAAACCGCCTTAAG
GCAATTCCTAACTTTTACATATTAGTAATCGAAAGACTGTTTATCGAGCCGCTGTTGACGCGGCA
ACACCATAAGCACCTGAGATAGTGAATGGGGGAACGGGAAACCTGTTGTTAGGAGGACGGCTAGC
TAACCAGTTGTCAGGAGAAAGGCTAACCCAGTTGTTGCCATGCCTTGATTGGTCCATTGATAGAA
TTCGCTGATAACAGTAAGTGAGTGAGAGAGAGAGCGAGAGAGTGGGGTTTACGATTTCTGGGTGT
AAAGCGGAAGGGAAGTAACCGAGGGCAGTCGGAAGCCCAACCCGA
Right flanking sequence: Indices 135380 -- 135879
AAACACAAGGGGCAGCATGTAGGGGGAGGCGTCAGTTGTTGCCATGGCTTGATTGGTATAGGCAG
GGGTTGCAGCCGCAGCCTTCTTCTTCTCCGTGACACATGGTTCCTCGTTCAAAGGGATTCTCTCT
CATATTATAGTACGGGATTCTCTCTCATATTAGTACAACTTAGGGTCACCCTAGGAATCTGTACT
GATAAAAGAGAAGGGCGGCTCGAAGCCAATTTAGTATTTCCCTCCGCATATAAGTATCTAACAAT
CGCTATGTCAATTGAATCACATGCATTGGTAAGACTCTTATGCTATTTCGTGCTATTTCGAGTTT
GATCGAGGGTTCTCCTAAAAGCAGCCTTTCTCTTATATACGATGAGGAAGACGGGAGTTTATAAC
CTCTCTCTGACTAACTCAACACAGAACAAATATGAATACCCTCACAGCCGATCGAATGCCAATCT
CACAGAGGAAAGGAAACTCTCAGGCCTTGGATAAGATCGAATGTT
Found at i:168252 original size:39 final size:39
Alignment explanation
Indices: 168195--168273 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
168185 CCTATCCTTC
* *
168195 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
168234 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
168273 A
1 A
168274 TAGAAAATCG
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:0.33, C:0.19, G:0.27, T:0.22
Consensus pattern (39 bp):
AATATCATGATCGAGTCGACCAGGCCAGATCATGAGTGA
Left flanking sequence: Indices 167695 -- 168194
GGTATGTTATTTAAGGAAGAACTGGGTATTTCGGTTATTTCTTTATAGAGAAAAGAGAAAGGACA
AAAATCGTTGATCTCATTAAACTTTACCTTTTGTCTGTGGTGAGGGTGACCTTGTTCAAAAATGG
TTTGGTGTGCCCTTTCCTATGGTGTCTCTTCTGTGCTAGCTAGTATAAGTCTTGGTGCTTTTGTT
TTAGTAAGGCCAATAGGAGAGGATTCAATGGATTAAAAATGTTTGTACACCATGATATTAATGGG
GTCATGGATCCTGTCTATACTCGTGGGCTCCAATCGGAATTGGACCAAACTCCTGCGGAATCCCT
CCCGGAAAAGCTCGACTTTATGATGCATAGGGAGTACGCGTGGTTTAACCTCCCGCTGCACGACA
AGGGAGGAAGTTCCGCGGACTAAGATTCCATTCGAAGTAAGGTAACAAGATTCGATGTTGCACCA
CCTTCAACTCGATCCGGAGTTTTTCGAGAAAAGGTCCTATCCTTC
Right flanking sequence: Indices 168274 -- 168773
TAGAAAATCGAAAACGTACATAGCTGTTCCAGCCGAAATACTTGGAATAATTCTACCACTTCTAC
TAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAGGGT
CCTGATGTAGTGGGAGCTTTCGGATTGTTACAACCTCTAGCGGATGGTTTGAAATTGATTCTAAA
AGAACCTATTTCGCCAAGTAGTGCTAATTTCTCCCTTTTTAGAATGGCTCCAGTGACTACATTTA
TGTTAAGTCTGGTTGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATTCGAAC
ATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGGTTG
GTCTAGTAATTAGGGGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTCAAAAATGGG
TTTGTGCCGCAGGTGTTGAACGATCTACTCTACACAGGTGTGGGC
Found at i:207549 original size:12 final size:12
Alignment explanation
Indices: 207532--207558 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
207522 GAAGGGAATA
207532 AAATAAAAAAAG
1 AAATAAAAAAAG
207544 AAATAAAAAAAG
1 AAATAAAAAAAG
207556 AAA
1 AAA
207559 AGAGAGGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAATAAAAAAAG
Left flanking sequence: Indices 207032 -- 207531
AACTGTCTTTTCTGTATACTTTCCCCGGTTCCGTTGCTACCGCGGGCTTTACGCAATCGATCGGA
TCATATAGATATCCCTTCAACACAACATAGGTCATTGAAAGGATCTCGGAGACCCACCAAAGCAC
GAAAGCCAGGATCTTTCATAAAATGGATTCCTATTCGAAGAGTTCATAACCGCATGGATAAGCTC
ACACTAACCCGTCAATTTGAGATACAATTCGGGATTTTCCTTGGGAGGTATCGGGAAGGAATTGG
AATGTAATAATATCGATTTATATAGATACATTTATACAGATACAGAAAAAAAGGTTCTCTATTGA
TTCAAACGTGTACCTACGGGATAGGGATAGAGAAAGAGGAAAAACCGAAGATTTCACACAGTATT
TTTGATCGAAAAATAAATCTGATTTATTTCGTACCTTTCGCTTAATGAGAAAATGGGTCAGATTA
TACAGGATCAAATCTATGGGACTTAAGGAATGATGGAAGGGAATA
Right flanking sequence: Indices 207559 -- 208058
AGAGAGGGAAAAATAAGTAAATAAAAATGAAATAGAAGAGCCCAGATTCAAAATGAATGAAAACG
TGACTGAATTGGTCCTGGTTACTCTTCGGAAGGGAGTGGAAGAAGGGAAGAGATTCTCGAACAAG
GAAAAGGATCCAATGACTTCAAAAGAATTGAACGAGGAGCCGTATGAGGTGAAAATCTCATGTAC
GGTTCTGTAGAGTGGCAGTAAGGGTGACTTATCTGTCAACTTTTCCACTATCACCCCCAAAAAAC
CAAACTCTGCCTTACGTAAAGTTGCCAGAGTACGCTTAACCTCTGGATTTGAAATCACTGCTTAT
ATACCTGGTATTGGCCATAATTTACAAGAACATTCTGTAGTCTTAGTAAGAGGGGGGAGGGTTAA
AGATTTACCCGGTGTGAGATATCACATTGTTCGAGGAACCCTAGATGCTGTCGGAGTAAAGGATC
GTCAACAAGGGCGTTCTAGTGCGTTGTAGATTCTTATCCAAGACT
Found at i:207550 original size:17 final size:17
Alignment explanation
Indices: 207528--207561 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
207518 GATGGAAGGG
207528 AATAAAATAAA-AAAAGA
1 AATAAAA-AAAGAAAAGA
207545 AATAAAAAAAGAAAAGA
1 AATAAAAAAAGAAAAGA
207562 GAGGGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AATAAAAAAAGAAAAGA
Left flanking sequence: Indices 207028 -- 207527
AAAGAACTGTCTTTTCTGTATACTTTCCCCGGTTCCGTTGCTACCGCGGGCTTTACGCAATCGAT
CGGATCATATAGATATCCCTTCAACACAACATAGGTCATTGAAAGGATCTCGGAGACCCACCAAA
GCACGAAAGCCAGGATCTTTCATAAAATGGATTCCTATTCGAAGAGTTCATAACCGCATGGATAA
GCTCACACTAACCCGTCAATTTGAGATACAATTCGGGATTTTCCTTGGGAGGTATCGGGAAGGAA
TTGGAATGTAATAATATCGATTTATATAGATACATTTATACAGATACAGAAAAAAAGGTTCTCTA
TTGATTCAAACGTGTACCTACGGGATAGGGATAGAGAAAGAGGAAAAACCGAAGATTTCACACAG
TATTTTTGATCGAAAAATAAATCTGATTTATTTCGTACCTTTCGCTTAATGAGAAAATGGGTCAG
ATTATACAGGATCAAATCTATGGGACTTAAGGAATGATGGAAGGG
Right flanking sequence: Indices 207562 -- 208061
GAGGGAAAAATAAGTAAATAAAAATGAAATAGAAGAGCCCAGATTCAAAATGAATGAAAACGTGA
CTGAATTGGTCCTGGTTACTCTTCGGAAGGGAGTGGAAGAAGGGAAGAGATTCTCGAACAAGGAA
AAGGATCCAATGACTTCAAAAGAATTGAACGAGGAGCCGTATGAGGTGAAAATCTCATGTACGGT
TCTGTAGAGTGGCAGTAAGGGTGACTTATCTGTCAACTTTTCCACTATCACCCCCAAAAAACCAA
ACTCTGCCTTACGTAAAGTTGCCAGAGTACGCTTAACCTCTGGATTTGAAATCACTGCTTATATA
CCTGGTATTGGCCATAATTTACAAGAACATTCTGTAGTCTTAGTAAGAGGGGGGAGGGTTAAAGA
TTTACCCGGTGTGAGATATCACATTGTTCGAGGAACCCTAGATGCTGTCGGAGTAAAGGATCGTC
AACAAGGGCGTTCTAGTGCGTTGTAGATTCTTATCCAAGACTTGT
Found at i:217398 original size:14 final size:14
Alignment explanation
Indices: 217381--217410 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
217371 AGCTATCCTT
217381 AATATAAAGATAAA
1 AATATAAAGATAAA
217395 AATATAAAGATAAA
1 AATATAAAGATAAA
217409 AA
1 AA
217411 CTAAAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AATATAAAGATAAA
Left flanking sequence: Indices 216881 -- 217380
AGCTACTCAGAATCAATTGGCAAGAGGTCAACGATTACGTGAGTTGCTCAAACAATCTCAATCAG
CCCCCCTTGCGGTGGAAGAACAGATATTGACTCTTTATACCGGAACGAACGGTTATCTTGATTCA
TTAGAAATTGGACAGGTAAGGAAATTTCTTGTTGAGTTACGTACTTACTTAAAAACGAATAAACC
GCAGTTCCAAGAAATCATATCTTCTACCAAGACATTTACCGAGGAAGCGGAAACCCTTTTGAAAG
AAGCGACCAGATGGAACGTTTTCTACTTGTATAAAGAAAGTTATTACTTTGAATCTTCATCAATC
TTTCTATTAATTAGTAATTATAATCTTTCTATATAATCTTTAGTTTAGAATATACTTTTCTATTA
TGATCTTATGACTTTATATTATAGTTTCTAATAAACTTTATTATTTATTATAAATTAAAAATTAA
ATAAATAACTTAAAATAACTTATTAATTTATAATAAGCTATCCTT
Right flanking sequence: Indices 217411 -- 217910
CTAAAATCTTTAAACTCGATATCTATTATATAGATATAGAATTATCTATCTATATTTTATTCTAT
ATATATTCTATAATAATAATAATAAAAGTATATATTTTAGTAGTACTTTAGTTTTCGGCTTTTTA
GTATTCACTCCTAGTCTCGTATCGCACACAAAGACAAGATAGTCCTTCCCTCACTCCGAAAACAC
TTCGTTCACTGGCTCAGGAAAGGTTCGATTATACCCCTAGCCACCTACCAATCTGTTCATACGAA
GAAATGAGGGATATACGAGACCCATCTCACATATTATGTACGCTATTCGTTTCGGAGGTGAGCTA
TCTCTTTTTTGTGGAATTTAAGTGGAATTACTAAACAACAAACCATTCTCGAAAGAAGCAATAAG
TGAGTGTGCAGATTCGAATGTCGCAAAGCAAGAGCAAGCCATCCATTCTCTGCTTGTCCGCTCTC
ACCGGAGATAGACTTTGTCTGTGGCGTTAAGCAGGTGTGCTCCTG
Found at i:257651 original size:18 final size:18
Alignment explanation
Indices: 257628--257665 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
257618 TTCACGGGGA
257628 AGCAGAGGAAGCTATTCT
1 AGCAGAGGAAGCTATTCT
257646 AGCAGAGGAAGCTATTCT
1 AGCAGAGGAAGCTATTCT
257664 AG
1 AG
257666 TATATCACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (18 bp):
AGCAGAGGAAGCTATTCT
Left flanking sequence: Indices 257128 -- 257627
CTTGCGTCCTTTATTAGATGGTAAAGTCCTACACTTTCTTGCGCATCAGCCCGTATTTGTTAAAG
AAATATAAAATGAATAGGTATATCGATTTGTGAATCTACTTTCCGCTGAGGATTTTATGTTGTGT
GAGAAGGCCATTTTGTTGCTGCGGCTCAATTTACATGTCTTTAATAGATTTTGATCTTTTCTTCA
CTATAAATGAATTTACTACCAATATGTGCGTAGCTAACTTTGAGACTTTATTGTGTATTGCTCTT
TTTGGTTATAATAAGACTATGGGTATTACTACTACTACTATGCCAACAGTTTTTCTTGAACCTTT
AGCAACGACAGTCACATATTTGGATATACAACTGTATTTGATACCAAAAGAGGAAACTTTCGCGT
CTATACCACTAATTTATCCGGGTAGAGTTCTTCTTTCGTCTTCTTGTTGTGACTTTCATCACCAC
GGTACAACCTATTCCCGCTTTCCTCTGATGTTTACTTCACGGGGA
Right flanking sequence: Indices 257666 -- 258165
TATATCACGTCTTCAGTCTAATTCATGTCATCGACGAAGGGGGAGTGATATAACATTTTATAGTA
ATATGGCAGTAAATAAGAGAGAGATGACACAGTATAAAATCATAGAGAAACGTTTGTGGTATTCT
AAACACTTCAGTCACTCTCCTGGATATCCACCTAGCTTTCTGCGTAGTATCGATAAGTAGGCGGC
AACTCGTCATGAGGAGGCCACTACCGGAATAATAGTTGCTAGTCAATATACTACGGTGCAGATAA
AAATAGAATATCTCAAGTAATAGAAAGATGTCTGTAAATAAGAGTGATATGATCAAGTAATAGAT
AGACTTTCACATATACAAGTCTTGTCAATCCCTGTCATTATAACCCCACTTAATCAAATCTTTAC
ATTGATATTGTTGTTATACGGTACAACCTTTAGAATTAGTCTCTTATGCTTTCATTAGAAAGAGA
AAGTAAAGGCAAGAAGTGGCTGTTTCCAGTCACCTGTTGTCCACA
Found at i:278424 original size:20 final size:20
Alignment explanation
Indices: 278399--278436 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
278389 GTACTACTTC
278399 CCTTCTCTTATTCTTTTTTT
1 CCTTCTCTTATTCTTTTTTT
278419 CCTTCTCTTATTCTTTTT
1 CCTTCTCTTATTCTTTTT
278437 CATACTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.68
Consensus pattern (20 bp):
CCTTCTCTTATTCTTTTTTT
Left flanking sequence: Indices 277899 -- 278398
GCCGGGGCTTCTTCCTCGAGTCCTGTCATGATCGCGCACTCGACGAAAGAGCTTTACAAGCGGCA
TTGCCCTTCTTCACTCACGCGATATTGCTGGATCGGGCTTTCGCCCATTGTCCAAGATTCCCCAC
TGCTGCCCCCCGTGGGAGTCCGGGCCGTGTCTCAGTCCCAGTGTGGCTGATCATCCGAAAAGACC
AGCTAAGCATCATTGGCTTGGTCAGCCTTTACCTAACCAACTACCGTAATACTACGCAGGCTCAT
CAAACAGCGCTTTTTAGCTTTCTTCAGGATTTGGGCCCGAACTGTTCGGCAGATTCCCACGCGTT
ACGCACCCGTTCGCCACTTTGTTCTCAAGGCGAGACAAGCGCGCCCGAAAACAACGTTCGACTTG
CATGTGTTAAGCATATAGCTAGCGTTCCTTCTGAGCCAGGATCAAACTCTTTTTTTAACTATGAT
TGGGCCCTGCAGTGGTAGAACCTGGTGAACCGGGCGTACTACTTC
Right flanking sequence: Indices 278437 -- 278936
CATACTCTCAAAGAAAGTCTAAGTGGATTGTTCTACTTATCTTATAGAGTGAGCGTTTACACACG
GATGGACCGGGCGAACGAGACTACAACGCGGCCATTGATCATCTCTTATGACATTTTCTTGAGCG
CGGGAAGAAGAAGGAATAGGAATGGACCGAATGATGGATAGCGACTGGTTCGGATGCAAGAGAGC
CGTGAAAAAACTTTGCCTAATAAACAAAAACAAATAGGATTGATTATGTATCACAATTTCATCAC
TACATCGAAGGCTTTTTTGTAAATAAATATATTGAGAAGATAGCTTGGTACCCAAACAGTATCAA
TGATTGTGATCCTCATTGTGTACATAATTCGTGTTAGGATCTACCAAAGAAATTTTTTGGGTCTA
GGGCATATAACAAAAGAGTTTCCATTTCTATCGGTCATAAAATAAAAATAAAAAAAGTCCTTTCG
AAACTTCACGGGGCTAGCAACTACTACGATGACTTTGCTGCCTCA
Found at i:278444 original size:18 final size:19
Alignment explanation
Indices: 278403--278444 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
278393 TACTTCCCTT
* *
278403 CTCTTATTCTTTTTTTCCTT
1 CTCTTATTC-TTTTTTCATA
278423 CTCTTATTC-TTTTTCATA
1 CTCTTATTCTTTTTTCATA
278441 CTCT
1 CTCT
278445 CAAAGAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
20 9 0.45
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (19 bp):
CTCTTATTCTTTTTTCATA
Left flanking sequence: Indices 277903 -- 278402
GGGCTTCTTCCTCGAGTCCTGTCATGATCGCGCACTCGACGAAAGAGCTTTACAAGCGGCATTGC
CCTTCTTCACTCACGCGATATTGCTGGATCGGGCTTTCGCCCATTGTCCAAGATTCCCCACTGCT
GCCCCCCGTGGGAGTCCGGGCCGTGTCTCAGTCCCAGTGTGGCTGATCATCCGAAAAGACCAGCT
AAGCATCATTGGCTTGGTCAGCCTTTACCTAACCAACTACCGTAATACTACGCAGGCTCATCAAA
CAGCGCTTTTTAGCTTTCTTCAGGATTTGGGCCCGAACTGTTCGGCAGATTCCCACGCGTTACGC
ACCCGTTCGCCACTTTGTTCTCAAGGCGAGACAAGCGCGCCCGAAAACAACGTTCGACTTGCATG
TGTTAAGCATATAGCTAGCGTTCCTTCTGAGCCAGGATCAAACTCTTTTTTTAACTATGATTGGG
CCCTGCAGTGGTAGAACCTGGTGAACCGGGCGTACTACTTCCCTT
Right flanking sequence: Indices 278445 -- 278944
CAAAGAAAGTCTAAGTGGATTGTTCTACTTATCTTATAGAGTGAGCGTTTACACACGGATGGACC
GGGCGAACGAGACTACAACGCGGCCATTGATCATCTCTTATGACATTTTCTTGAGCGCGGGAAGA
AGAAGGAATAGGAATGGACCGAATGATGGATAGCGACTGGTTCGGATGCAAGAGAGCCGTGAAAA
AACTTTGCCTAATAAACAAAAACAAATAGGATTGATTATGTATCACAATTTCATCACTACATCGA
AGGCTTTTTTGTAAATAAATATATTGAGAAGATAGCTTGGTACCCAAACAGTATCAATGATTGTG
ATCCTCATTGTGTACATAATTCGTGTTAGGATCTACCAAAGAAATTTTTTGGGTCTAGGGCATAT
AACAAAAGAGTTTCCATTTCTATCGGTCATAAAATAAAAATAAAAAAAGTCCTTTCGAAACTTCA
CGGGGCTAGCAACTACTACGATGACTTTGCTGCCTCACCCAAACC
Found at i:278445 original size:20 final size:20
Alignment explanation
Indices: 278400--278442 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
278390 TACTACTTCC
* *
278400 CTTCTCTTATTCTTTTTTTC
1 CTTCTCTTATTCTTTTTATA
278420 CTTCTCTTATTCTTTTTCATA
1 CTTCTCTTATTCTTTTT-ATA
278441 CT
1 CT
278443 CTCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (20 bp):
CTTCTCTTATTCTTTTTATA
Left flanking sequence: Indices 277900 -- 278399
CCGGGGCTTCTTCCTCGAGTCCTGTCATGATCGCGCACTCGACGAAAGAGCTTTACAAGCGGCAT
TGCCCTTCTTCACTCACGCGATATTGCTGGATCGGGCTTTCGCCCATTGTCCAAGATTCCCCACT
GCTGCCCCCCGTGGGAGTCCGGGCCGTGTCTCAGTCCCAGTGTGGCTGATCATCCGAAAAGACCA
GCTAAGCATCATTGGCTTGGTCAGCCTTTACCTAACCAACTACCGTAATACTACGCAGGCTCATC
AAACAGCGCTTTTTAGCTTTCTTCAGGATTTGGGCCCGAACTGTTCGGCAGATTCCCACGCGTTA
CGCACCCGTTCGCCACTTTGTTCTCAAGGCGAGACAAGCGCGCCCGAAAACAACGTTCGACTTGC
ATGTGTTAAGCATATAGCTAGCGTTCCTTCTGAGCCAGGATCAAACTCTTTTTTTAACTATGATT
GGGCCCTGCAGTGGTAGAACCTGGTGAACCGGGCGTACTACTTCC
Right flanking sequence: Indices 278443 -- 278942
CTCAAAGAAAGTCTAAGTGGATTGTTCTACTTATCTTATAGAGTGAGCGTTTACACACGGATGGA
CCGGGCGAACGAGACTACAACGCGGCCATTGATCATCTCTTATGACATTTTCTTGAGCGCGGGAA
GAAGAAGGAATAGGAATGGACCGAATGATGGATAGCGACTGGTTCGGATGCAAGAGAGCCGTGAA
AAAACTTTGCCTAATAAACAAAAACAAATAGGATTGATTATGTATCACAATTTCATCACTACATC
GAAGGCTTTTTTGTAAATAAATATATTGAGAAGATAGCTTGGTACCCAAACAGTATCAATGATTG
TGATCCTCATTGTGTACATAATTCGTGTTAGGATCTACCAAAGAAATTTTTTGGGTCTAGGGCAT
ATAACAAAAGAGTTTCCATTTCTATCGGTCATAAAATAAAAATAAAAAAAGTCCTTTCGAAACTT
CACGGGGCTAGCAACTACTACGATGACTTTGCTGCCTCACCCAAA
Found at i:333707 original size:20 final size:21
Alignment explanation
Indices: 333682--333721 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
333672 AACGTAGTTG
333682 TTGCTTGGTGAG-TCCTTCGT
1 TTGCTTGGTGAGCTCCTTCGT
* *
333702 TTGCTTTGTGTGCTCCTTCG
1 TTGCTTGGTGAGCTCCTTCG
333722 GTTTTCTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.03, C:0.23, G:0.28, T:0.47
Consensus pattern (21 bp):
TTGCTTGGTGAGCTCCTTCGT
Left flanking sequence: Indices 333182 -- 333681
AGGTTGGGTTGGACGACATACATCTTGGAAGGAAGGTTCATTCTTTGAATCTGATAGTGACTTTT
GTTCCACTGCTATCGTCAAGCTTGGACATGGTGCAACAAGAAGAGAATTAGCAGAATAGGATAAA
GAATTTAATATATATCATCGACCTTCCTACCCCACCCACCGCCCTGATCCTGAATCTGCTTTAGA
CTAGCTTTACATTACGAAATACCAGTTCGAGGGAAGAACCCAGAACCCGATCTACGGCCGAATAG
CAACTCGTACGTAAGCATACACACTTCAAGCAGAACTCAACTCAAAGCGATCATTCTTTCAGAAC
CTTACCTACATAGCCATTCTTGCAGATCCGGGCGTTGCGTCGTTGTTTTGCAAGATCTCGCTTTC
GGTTCGTAGAGTGGATCAAACAAACATGTGTTCAGCTTGATTCGTTGGTGCAGTCACTTCGTCAT
CTTATGATTTGAAACTAGATTCCGCCTACGCAAACAACGTAGTTG
Right flanking sequence: Indices 333722 -- 334221
GTTTTCTAGTAGTAAGATCGGTTTCAAGATTGAATCAGTGGTCAGCCTGTGCTTGAACGACGGCA
TTCCAAGAAGCAACTTCCTGGATGGTCCCCTATTGATGAATCAAATCACTTGGAAAATATATATA
TATTTTTAGTTTAGCTCGGTTAACAACTGAACAATCACGGTAAGGCACCACCCTCCTCAGTCATT
CTCCCGCTTAAAGGAACACAGTCAATAGCACCATTTGAAATCATCTCTTGAATAGGCCAACATCC
ATCTATAAGCTCACTAACGGGAGGATCACATGAGAGTCTAAAATCAGGAAGACTAGGCTTCCAAA
TGCTTATTATATCACGCCTGCCATAGCGCACCACATCTACCCCCTCTAGTAAGCTTGACCAAGCG
TCTGGACGCACTGAAGAAATAATAATCTGAAAAGGAAAGTAAAAACTTTTTAGAACTCTTGCCAC
TCAGGAAGTCTCCACCAGCCTCTTTAAAATTGATACCTTGATTAA
Found at i:378619 original size:29 final size:29
Alignment explanation
Indices: 378539--378620 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 29
378529 AAGAGGGGCT
* *
378539 AAGGAGAGGCACGAAGTAGCTCGAGTGAT
1 AAGGAGAGGCACGAAGTAGCTCGACTGAC
* * * *
378568 AACGAGTGGGGA-GAACG-AACTCGACTGAC
1 AAGGAG-AGGCACGAA-GTAGCTCGACTGAC
*
378597 AAGGAGAGGTACGAAGTAGCTCGA
1 AAGGAGAGGCACGAAGTAGCTCGA
378621 GTGATAACGA
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
28 4 0.10
29 31 0.79
30 4 0.10
ACGTcount: A:0.35, C:0.16, G:0.37, T:0.12
Consensus pattern (29 bp):
AAGGAGAGGCACGAAGTAGCTCGACTGAC
Left flanking sequence: Indices 378039 -- 378538
GGGGTCCGGGTAAGGGTGATTTCACTATATTTCTGACAGACCTATCACAAGTGTCTTTTTTCTTT
AGTCATTTTGAAAGGCATCCGAGAGGTAATCCCACCGGGGTTAAAGCACTTCTGTGCCTCGTGAT
AGAGCCAGAACTGCTGCCGATCAAGATGTGGAATCCGTTTACCCATATTGAGATTTTCGCTTCGT
CTTAAGATACGAGCACAAAACAAGGTAGCACAGTTGATTCGAAGTCTGATAGAAAAGAGCTGAAA
TCCTAAAGCTGATAGTCACTAAGCTGGAATTCAATCCAGTTGAAGGCGCCAACGGCGGGTAGCCC
CTCTAAAATATAGAGTTATTTAAATCACCGATCGAAAGGTAATCATCGCGTGTCGAATTCGAAGA
AGGAGATTCAAGAGCGGGAATTACCTTTGCTTCGCAACCTTCTTTGCCCGGTTTTCAACGGGAAG
CACGTGGCTAGGGGACTGATTCCAATGTGAAAGAAAAGAGGGGCT
Right flanking sequence: Indices 378621 -- 379120
GTGATAACGAGTGGGGAACTTAAGCAACCTTAATTTATCGTGATAGGTCCTCTGAAGGAGGTGCA
TTGGAAGTGGAACAACTGGTTGTACCAGGGCCTGGAGACTCGCTCATTCTACGGCTGCCAGAAAT
GGTGGCCAGAGAACGAATAAAGAAGGTCACTCGACCAAGGATGGCACCTGTTCAAGGGGGTTCGT
TGCTACGTTTAATCCTGGAAAGCCCCGATTAGCTCCCCTATGTATGTCACTGCGTAAGTCTTTGA
CTCTCCGATCAAATAAAGGATACAAACAACCTCGATGAAATCACTTCCCCTGATTCTTATTCTTC
ATCTGGGTGTCCAGGTGCCGGAAAGGCAAGATACGTGTGAGAAATAGAGGATTTCGAGTCAAAAG
GAAGTCCATCGTGGTTGGGGCAACCCTAATGGATTTATAGGCGCCGCTACGCTTCTTCTTAAGTT
GGTGCCTTGGAGTAAGTCGACTTTGTTTTGCTTTTACACGTACTA
Found at i:380503 original size:16 final size:16
Alignment explanation
Indices: 380477--380546 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
380467 TACTATACAG
380477 ACTATATCATATATTAT
1 ACTATA-CATATATTAT
380494 ACTATACATATATTAT
1 ACTATACATATATTAT
380510 ACTATACATATATTAT
1 ACTATACATATATTAT
*
380526 ACTATATATATA-TAT
1 ACTATACATATATTAT
380541 ACTATA
1 ACTATA
380547 TTACAAACCT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
15 9 0.17
16 37 0.71
17 6 0.12
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (16 bp):
ACTATACATATATTAT
Left flanking sequence: Indices 379977 -- 380476
TCGTCCCAGCTTAGCTCACCTTTCCTGCGGAACCTTAAGTCGCTCTCTTTTGTCACTTGCTGTGC
CTCCTTTGCTTCGCAACCTTTAAAGTCGAGTTCTTTGGAACTAAAGTACCGTAGCTTCGCTTCCT
TAGCAACTATTGACAGAGAGGATATGGAATAAGATTCTTTCTTAAAGCCACAGGCGCCAGAGGTT
CTGAAAGAAAGCTCGACTAAAGGGAGAGGCGAGCGTATAACAACCTGTTGAAGACTACGTTCATG
CGTATCCCCTGGAACCCCTGAACTCCCTATCGGATAGTTCTTCAATAACGCTTGACCTAGCTGGA
AGAAGTAATTTTACCCCAGCCACTGGTTAGAGCGTATAGCAACAGAACCATGTAATCATTGAAGA
CTACGTTCATGCCCCGCACCCGCGAGTCATTCTCTATCTTTCAGCTTCTTATTCAATTGACATGT
AAGACTATATATTAGGGTATACTATACTTACTACTTACTATACAG
Right flanking sequence: Indices 380547 -- 381046
TTACAAACCTGCCAATACCCCCGGAGGGCACCCCGCTTCAGCGGGCCATTGGACCGAGCTGGCGG
CGAGAGGGAAACTATAACAACATCTATACAATGGAAGTATTAACCGAAGGAGGAGTGAAGGTCCC
CGTCAGGGACCGGAACGGTGGCTTCAATAAGAATCGATAACAGCAATCAATGTAATGAAGACTAC
GTTCAATTGCATTACATTTTTTCAAGGAAATAACGTATTAGACTTTACGTTTTCATTAGATTCAT
GAAACCCCGTGTTTTTGGCATAAACCTACTTTCTGCCTATAAACTCGTTGCAAATCGATCGATTT
CGAGTTGTTTTGCATGTAGGGGGATCCTCACTAAAAAAAAAAAGAAAGCCGTTCATAAGTAAAAA
TGGGTTTGTAAGCTTTTCCATGTAGGGGCCGACTCAATCGATTGAATCCAATGCCACGGCATCCC
CTTCAATTACTTCTTCTGCTTCTCTTTCAGAGCCTTTCTTTCAGC
Found at i:380504 original size:21 final size:22
Alignment explanation
Indices: 380486--380549 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 22
380476 GACTATATCA
*
380486 TATATTATAC-TATACATATAT
1 TATACTATACATATACATATAT
* *
380507 TATACTATACATATA-TTATAC
1 TATACTATACATATACATATAT
*
380528 TATA-TATATATATAC-TATAT
1 TATACTATACATATACATATAT
380548 TA
1 TA
380550 CAAACCTGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 15 0.42
21 17 0.47
22 4 0.11
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
TATACTATACATATACATATAT
Left flanking sequence: Indices 379986 -- 380485
CTTAGCTCACCTTTCCTGCGGAACCTTAAGTCGCTCTCTTTTGTCACTTGCTGTGCCTCCTTTGC
TTCGCAACCTTTAAAGTCGAGTTCTTTGGAACTAAAGTACCGTAGCTTCGCTTCCTTAGCAACTA
TTGACAGAGAGGATATGGAATAAGATTCTTTCTTAAAGCCACAGGCGCCAGAGGTTCTGAAAGAA
AGCTCGACTAAAGGGAGAGGCGAGCGTATAACAACCTGTTGAAGACTACGTTCATGCGTATCCCC
TGGAACCCCTGAACTCCCTATCGGATAGTTCTTCAATAACGCTTGACCTAGCTGGAAGAAGTAAT
TTTACCCCAGCCACTGGTTAGAGCGTATAGCAACAGAACCATGTAATCATTGAAGACTACGTTCA
TGCCCCGCACCCGCGAGTCATTCTCTATCTTTCAGCTTCTTATTCAATTGACATGTAAGACTATA
TATTAGGGTATACTATACTTACTACTTACTATACAGACTATATCA
Right flanking sequence: Indices 380550 -- 381049
CAAACCTGCCAATACCCCCGGAGGGCACCCCGCTTCAGCGGGCCATTGGACCGAGCTGGCGGCGA
GAGGGAAACTATAACAACATCTATACAATGGAAGTATTAACCGAAGGAGGAGTGAAGGTCCCCGT
CAGGGACCGGAACGGTGGCTTCAATAAGAATCGATAACAGCAATCAATGTAATGAAGACTACGTT
CAATTGCATTACATTTTTTCAAGGAAATAACGTATTAGACTTTACGTTTTCATTAGATTCATGAA
ACCCCGTGTTTTTGGCATAAACCTACTTTCTGCCTATAAACTCGTTGCAAATCGATCGATTTCGA
GTTGTTTTGCATGTAGGGGGATCCTCACTAAAAAAAAAAAGAAAGCCGTTCATAAGTAAAAATGG
GTTTGTAAGCTTTTCCATGTAGGGGCCGACTCAATCGATTGAATCCAATGCCACGGCATCCCCTT
CAATTACTTCTTCTGCTTCTCTTTCAGAGCCTTTCTTTCAGCTCC
Found at i:380506 original size:2 final size:2
Alignment explanation
Indices: 380479--380547 Score: 54
Period size: 2 Copynumber: 33.5 Consensus size: 2
380469 CTATACAGAC
* *
380479 TA TA TCA TA TA T- TA TA CTA TA CA TA TA T- TA TA CTA TA CA TA
1 TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
380520 TA T- TA TA CTA TA TA TA TA TA TA CTA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA -TA TA T
380548 TACAAACCTG
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
1 3 0.05
2 42 0.76
3 10 0.18
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 379979 -- 380478
GTCCCAGCTTAGCTCACCTTTCCTGCGGAACCTTAAGTCGCTCTCTTTTGTCACTTGCTGTGCCT
CCTTTGCTTCGCAACCTTTAAAGTCGAGTTCTTTGGAACTAAAGTACCGTAGCTTCGCTTCCTTA
GCAACTATTGACAGAGAGGATATGGAATAAGATTCTTTCTTAAAGCCACAGGCGCCAGAGGTTCT
GAAAGAAAGCTCGACTAAAGGGAGAGGCGAGCGTATAACAACCTGTTGAAGACTACGTTCATGCG
TATCCCCTGGAACCCCTGAACTCCCTATCGGATAGTTCTTCAATAACGCTTGACCTAGCTGGAAG
AAGTAATTTTACCCCAGCCACTGGTTAGAGCGTATAGCAACAGAACCATGTAATCATTGAAGACT
ACGTTCATGCCCCGCACCCGCGAGTCATTCTCTATCTTTCAGCTTCTTATTCAATTGACATGTAA
GACTATATATTAGGGTATACTATACTTACTACTTACTATACAGAC
Right flanking sequence: Indices 380548 -- 381047
TACAAACCTGCCAATACCCCCGGAGGGCACCCCGCTTCAGCGGGCCATTGGACCGAGCTGGCGGC
GAGAGGGAAACTATAACAACATCTATACAATGGAAGTATTAACCGAAGGAGGAGTGAAGGTCCCC
GTCAGGGACCGGAACGGTGGCTTCAATAAGAATCGATAACAGCAATCAATGTAATGAAGACTACG
TTCAATTGCATTACATTTTTTCAAGGAAATAACGTATTAGACTTTACGTTTTCATTAGATTCATG
AAACCCCGTGTTTTTGGCATAAACCTACTTTCTGCCTATAAACTCGTTGCAAATCGATCGATTTC
GAGTTGTTTTGCATGTAGGGGGATCCTCACTAAAAAAAAAAAGAAAGCCGTTCATAAGTAAAAAT
GGGTTTGTAAGCTTTTCCATGTAGGGGCCGACTCAATCGATTGAATCCAATGCCACGGCATCCCC
TTCAATTACTTCTTCTGCTTCTCTTTCAGAGCCTTTCTTTCAGCT
Done.