Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: KC784954
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: 100725
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:1407 original size:2 final size:2
Alignment explanation
Indices: 1395--1444 Score: 73
Period size: 2 Copynumber: 24.0 Consensus size: 2
1385 ATAGATAAGA
*
1395 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT TT AT CAT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
1439 AT AT AT
1 AT AT AT
1445 TACTCGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 40 0.91
3 4 0.09
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 895 -- 1394
GTGTCACTAAGTTTATCATATCATATAAAGAGAAGGCGTAGCCTTCGGGCACCTCTTTAATTATC
TTATATTATACAGTCTGCAGTAATCCTACAGTGAAGGCTATGTAAATCCATGGTTCTCGTTATTC
AAGTATTTTGACACTTCTTTTCCTCCAGCTTGTTTAAGGTCGGTGTGAGTGACTTTCACACTTAT
TTCTGTGCTCCTGGAGAAGTGCACCTTTCTTTGGCACCCGCCTTGCGCAATATATCTATATCAGG
CCGAAGGCGCAGATTTTGTTTTTTAATTGCTTTCCAAGTTCTGTGTTGTTCTGTCCTTGCTATTT
TGTCTTGCAAGTTATACTCTGTTCTGTATAGAATGGAGGCTGCAAGGTAAGAGCGTATACGAGCA
AAACCAGGCTAAATTTGGGAGCTGTTAACTTGATGTAAGGGGATTATCGAGAAAAGAGTAAAAAG
AAAAAAGTAAATTCATCTTTTGTACTAGTGATACCATAGATAAGA
Right flanking sequence: Indices 1445 -- 1944
TACTCGAAAATATTCCTTTACTCCAGTTCATCAGGAGTCCACTCTGATCCTCGATCCGAGGCGAA
TTTCCATTATTTTCAAGTTCCTAAGTCATATTAAATATACGCCACCATCTTAATACATGAGATAC
CCGTCTCTTGAATTGATAATTATTGCGAATATCAACAAGACTCTTGGAGTAGAAAAGTTCGCAAA
AAGCGAATACGAAAGTCTTATTAGTATCTTCTACCAATCGATAAAGAATCATGACTATTGCGGCT
AATAATGTTGTACTAGGGAAATAAAGATTTAGACCGGTATTGGTAAAAAAAAATATGACGAAATT
GAAAAATAATGATCATAAATCTAAATGGCTATATATTTGACCTAAATTTGACAATAAATAGATTT
ATTTTATGAATCAAGATCTTAGGTTTTATTTAATGTAGTAATAAAAATGAAACATAAATTTATTA
ATATGAGGGCACAGTGGGGTGTTACTCGCCACATTAGGAAATTAG
Found at i:1457 original size:21 final size:21
Alignment explanation
Indices: 1395--1445 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1385 ATAGATAAGA
* *
1395 ATATCATATATAT-ATATATAT
1 ATAT-ATATTTATCATAAATAT
*
1416 ATATATATTTATCATATATAT
1 ATATATATTTATCATAAATAT
1437 ATATATATT
1 ATATATATT
1446 ACTCGAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATATATTTATCATAAATAT
Left flanking sequence: Indices 895 -- 1394
GTGTCACTAAGTTTATCATATCATATAAAGAGAAGGCGTAGCCTTCGGGCACCTCTTTAATTATC
TTATATTATACAGTCTGCAGTAATCCTACAGTGAAGGCTATGTAAATCCATGGTTCTCGTTATTC
AAGTATTTTGACACTTCTTTTCCTCCAGCTTGTTTAAGGTCGGTGTGAGTGACTTTCACACTTAT
TTCTGTGCTCCTGGAGAAGTGCACCTTTCTTTGGCACCCGCCTTGCGCAATATATCTATATCAGG
CCGAAGGCGCAGATTTTGTTTTTTAATTGCTTTCCAAGTTCTGTGTTGTTCTGTCCTTGCTATTT
TGTCTTGCAAGTTATACTCTGTTCTGTATAGAATGGAGGCTGCAAGGTAAGAGCGTATACGAGCA
AAACCAGGCTAAATTTGGGAGCTGTTAACTTGATGTAAGGGGATTATCGAGAAAAGAGTAAAAAG
AAAAAAGTAAATTCATCTTTTGTACTAGTGATACCATAGATAAGA
Right flanking sequence: Indices 1446 -- 1945
ACTCGAAAATATTCCTTTACTCCAGTTCATCAGGAGTCCACTCTGATCCTCGATCCGAGGCGAAT
TTCCATTATTTTCAAGTTCCTAAGTCATATTAAATATACGCCACCATCTTAATACATGAGATACC
CGTCTCTTGAATTGATAATTATTGCGAATATCAACAAGACTCTTGGAGTAGAAAAGTTCGCAAAA
AGCGAATACGAAAGTCTTATTAGTATCTTCTACCAATCGATAAAGAATCATGACTATTGCGGCTA
ATAATGTTGTACTAGGGAAATAAAGATTTAGACCGGTATTGGTAAAAAAAAATATGACGAAATTG
AAAAATAATGATCATAAATCTAAATGGCTATATATTTGACCTAAATTTGACAATAAATAGATTTA
TTTTATGAATCAAGATCTTAGGTTTTATTTAATGTAGTAATAAAAATGAAACATAAATTTATTAA
TATGAGGGCACAGTGGGGTGTTACTCGCCACATTAGGAAATTAGA
Found at i:11831 original size:21 final size:17
Alignment explanation
Indices: 11778--11830 Score: 106
Period size: 17 Copynumber: 3.1 Consensus size: 17
11768 TTTAAGATTA
11778 TAGATAGATAGGCTAAC
1 TAGATAGATAGGCTAAC
11795 TAGATAGATAGGCTAAC
1 TAGATAGATAGGCTAAC
11812 TAGATAGATAGGCTAAC
1 TAGATAGATAGGCTAAC
11829 TA
1 TA
11831 AAAGCTACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.25
Consensus pattern (17 bp):
TAGATAGATAGGCTAAC
Left flanking sequence: Indices 11278 -- 11777
TAGGATATACTGGTATCAGAGCATTCTTTGAAAACAACATCTTGTTCAACACTGTAATCGCTCAG
CTGCTCTATGCCTACATTTTGATTTTGATGCGAAATCAGCTGTTTCCGTAATTTGAGAATGCGAC
TTATTTTGGGTAATCCATCATTATATAATAATACATAAAAGGCCATATAAAACACACATAACCAA
ACAAATTGCGTCAAATACGTAAATTGATCTAGTTGAGGCATTTTCTTTCACTTTTTCTTTGCCGA
TTCAAATACTTATTGAATCACGAGAGAAGAAAAAAATTTTTCTTCTTGAGCCTTTAATATTAAAG
CTCTTTAAGCAAAACCTGGCAAACGGGCTGCAGATTTTTATGGAAAATTGAAGACAGAAAAGTTC
ATAGAAAAACTAGAGTCATGACTAAAATATATATATATATTTTTTATTATTGGCATTCTACATAA
CGCAGAGCGAACATCACGATTGTTTTAAAATATTTTTTAAGATTA
Right flanking sequence: Indices 11831 -- 12330
AAAGCTACTAGTATTTCCACTACTCTTCACTCCATCATCAAGGTATCGAATTTACACGTGGGTAT
ATCCCCCACATAGAGGTATGGAGCGATGCTTGTAGCCACCAGCATTAATCGGTCAGTCATTTTCA
TGATGACATCCTTTTTTTAAAACCTAGTTCTTTCGTTGCTCTGCGTTAACACAACAACAAAATTT
AATTACTTGCCCGGCCTTGGTCTCTGAGTCTAGAATTGTTTGTGACGGATCGTTCCGTATTTTCA
CGTGTTTTCCCAGTGTAGACTTGAGGCTTTGGGCCTAAGCGCTTTAGGCTTTGTTTGGTCTTTCG
GGTCGTAAGAACCATGGGAATAAGGTTGGAATTTTTATTTTTTCCCTTTTCGATCTTTTCATATT
TATGAAAAAATGTGTTTTTTTTCGTGTTTCGCAAGTGTTTCCGCTTTGCGTTTAAACGCTCTATG
TGTTCTCGATGTGCTCTTGCCGGCGAAGAATAATCTAGTTTGCCA
Found at i:14501 original size:2 final size:2
Alignment explanation
Indices: 14496--14531 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14486 AGCTCAAAAA
14496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14532 TTTTCGGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 13996 -- 14495
AAAATAATTCAACAAATGGCGAAGAAGACCAATCAGAGCTATATCAATCATAAATGGATTGGAGG
GTTTTTAACCAATCGAAAACATATGAAAAATGTACAAAAACACTTTCAGAATTTTTATGCGCATT
CCAAATTTAAAGATGCCTCTACATCGTCGCCCTTCGATCTTTTTCCACATTTCAGAAAAATGCAA
AAATGTTTTGAAGGAATCATGACACACGATATTCCAGATTGTTTGGTAATAATGAATGCGCATAA
AAATTCTATGGCTATACTTGAAGCTAATCAATTACAGATACCTATCGTATCTTTGGTGGATTCTA
ATATTTCAAACAGATTACAGAAATTAATAACTTATCCCATTCCAGTGAATGATGATTCTATACAG
TTTGTATATCTATTTTGCAATTTGATCACGAAAACAGTCATTTTTTCACAAAGTGCTTGGCCACT
CTCGCGAAAGCCCTCAAATCGAGACGGCAGGCTGTAGCTCAAAAA
Right flanking sequence: Indices 14532 -- 15031
TTTTCGGATTGAAAAATTAAGAGAAAAAACCTTGAAACTCTTTCTGAAATTGTTTTATCAACAGA
TTGTACTTAATTTATCTACACTAATTACGACTTTTTCTGTATTTCTGTCATATATCGTAGTCACG
CCCTTAATGATAGGCTTTTCTAAAGACTTCTTATGTCATTTTCATCTAGGTCTAATTTGGATTCG
TTTATTGTTCTCCTTTCTTCCCGAACGTTTTCTTCAGAATGATTTTGAAGATGGTACACTTGAAT
TGTATTGTTCAAGCGGCTATTGTTTGCAAAAAATATTACTTTCTAAATTGCTAGGTCATTGGGTC
CTTCAAATAAGTGCTGTTTCCTGTACTTTTCCAGTGGTACAACTTCCATACCAATTTGATCAGCT
CAAAATGAATTGGTTCACCCTTATTATAGGAAGCCTGGTATTTACCCTTATGTGTGCTATTCATT
CTTGTTTGGCTCTCGGAATAATATCTCATAGTGGTAGTAGTTTGC
Found at i:22367 original size:17 final size:17
Alignment explanation
Indices: 22345--22379 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
22335 AGTGAATCAG
22345 CAGTGCAGGTAGTTTAT
1 CAGTGCAGGTAGTTTAT
22362 CAGTGCAGGTAGTTTAT
1 CAGTGCAGGTAGTTTAT
22379 C
1 C
22380 TTGTAGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (17 bp):
CAGTGCAGGTAGTTTAT
Left flanking sequence: Indices 21845 -- 22344
TTCAAGTTCCGACTTGTACGGATAGAGGGACTCGAACCCCCACAAACATTATGGTCACCAGAGCC
TAAATCTGGCATGTCTACCAATTCCATCATATCCGCCAAAAGTTAATTCAAATTTAATCCGTGGA
AACTCTTTTTCCTTCTTCCCCAATTCAATTATCAGAACCTTTTCATGGCCTCAATACTATCTCAG
ATAATGCCTCAACATCCCATCCCATGGATTGCCAGATTGTTTATCGTCGATCGATAATCACAGTC
ACATAGACAAAGGCCCTTGTTGTTGAACTATAGAGGTTACACATATTTGGACTCTGTAAGTTATT
TGTGTTTCAAAGTTATTTCTTCCGATTTCTCACCGTGAAAATAACTAGATTAGAGTTGCTCATTA
ATAATCGGTCTATAAGTCATATCTTCTGCGTTGGCGGGTGTGCCTGCGCCAAGATCGGAAAAAAA
AATAGGTCAAAGTGGGTCCTTGCTTTCGCGTAGTGAGTGAATCAG
Right flanking sequence: Indices 22380 -- 22879
TTGTAGTCATTCGACTGGCATACTGACGATTTTATTATGTTATTTTTTCTTTTATTATGTTATTT
TTTCATTGTTGTCCCTATCATATTGTGGTTGGGCGCGTTCGGCTGCATGGTTCAGCGTCGCGTTT
CAAGCTAATAGATAATAAACCACGCCACTAGGCAATCACTAATGCGTTGTCTTGCTGAATAAAAC
TCTCCTCAAGCTCTTTCAGGCTATTGCCTCATTTCTCGGCTATCGGGCACAGAGCCAACAGCCAA
AACCATTACTTTTCCGCGAATGAATCATCATAAATAATGACTATGTATTTTCTTTTCATAAAGCG
AATATCTTGTTTTTTTCTACACTTTTTATATTCTGCAAAATAATTACACAACGTTAAAATCTATA
AGAGTTATATGCTTCGGCGAACAAAATAGAAATTTTGTCCCAAAAATGGTTAACTAATTACCCTA
TTAACGGATGGAGAGGGATTCGAACCCCCGGTATTCTCAATACTT
Found at i:22434 original size:20 final size:20
Alignment explanation
Indices: 22409--22448 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
22399 ATACTGACGA
22409 TTTTATTATGTTATTTTTTC
1 TTTTATTATGTTATTTTTTC
22429 TTTTATTATGTTATTTTTTC
1 TTTTATTATGTTATTTTTTC
22449 ATTGTTGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTATTATGTTATTTTTTC
Left flanking sequence: Indices 21909 -- 22408
CTAAATCTGGCATGTCTACCAATTCCATCATATCCGCCAAAAGTTAATTCAAATTTAATCCGTGG
AAACTCTTTTTCCTTCTTCCCCAATTCAATTATCAGAACCTTTTCATGGCCTCAATACTATCTCA
GATAATGCCTCAACATCCCATCCCATGGATTGCCAGATTGTTTATCGTCGATCGATAATCACAGT
CACATAGACAAAGGCCCTTGTTGTTGAACTATAGAGGTTACACATATTTGGACTCTGTAAGTTAT
TTGTGTTTCAAAGTTATTTCTTCCGATTTCTCACCGTGAAAATAACTAGATTAGAGTTGCTCATT
AATAATCGGTCTATAAGTCATATCTTCTGCGTTGGCGGGTGTGCCTGCGCCAAGATCGGAAAAAA
AAATAGGTCAAAGTGGGTCCTTGCTTTCGCGTAGTGAGTGAATCAGCAGTGCAGGTAGTTTATCA
GTGCAGGTAGTTTATCTTGTAGTCATTCGACTGGCATACTGACGA
Right flanking sequence: Indices 22449 -- 22948
ATTGTTGTCCCTATCATATTGTGGTTGGGCGCGTTCGGCTGCATGGTTCAGCGTCGCGTTTCAAG
CTAATAGATAATAAACCACGCCACTAGGCAATCACTAATGCGTTGTCTTGCTGAATAAAACTCTC
CTCAAGCTCTTTCAGGCTATTGCCTCATTTCTCGGCTATCGGGCACAGAGCCAACAGCCAAAACC
ATTACTTTTCCGCGAATGAATCATCATAAATAATGACTATGTATTTTCTTTTCATAAAGCGAATA
TCTTGTTTTTTTCTACACTTTTTATATTCTGCAAAATAATTACACAACGTTAAAATCTATAAGAG
TTATATGCTTCGGCGAACAAAATAGAAATTTTGTCCCAAAAATGGTTAACTAATTACCCTATTAA
CGGATGGAGAGGGATTCGAACCCCCGGTATTCTCAATACTTCGATTTTCAAGACCGACTCTTTCA
ACCGCTCAGACATCCATCCTTACCTTGATAAGATTATCAGCTCAA
Found at i:43572 original size:81 final size:81
Alignment explanation
Indices: 43437--43586 Score: 282
Period size: 81 Copynumber: 1.9 Consensus size: 81
43427 AAGATACTCG
*
43437 CTATCGGATTTGAACCGATAACCCATAGGAACAGATTTTGAGACTGTCGTGTTTACCATTTTCAC
1 CTATCGGATTTGAACCGATAACCCATAGGAACAGATTTTAAGACTGTCGTGTTTACCATTTTCAC
43502 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
*
43518 CTATCGGATTTGAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCAC
1 CTATCGGATTTGAACCGATAACCCATAGGAACAGATTTTAAGACTGTCGTGTTTACCATTTTCAC
43583 CAAG
66 CAAG
43587 TGAGCTTGGG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (81 bp):
CTATCGGATTTGAACCGATAACCCATAGGAACAGATTTTAAGACTGTCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 42937 -- 43436
AGTATTTCAACAACTTTTTGAGCTCATCTTTTACCCATATAATTCTCTATGTTCTTGTCTGAACA
AGCCAATACGAGTGGAGTAACCCATCAGAGAAAATGGCTGAGAATATCCGCAATGTTCAACGTCC
CATCCTTTTTCTATGCCTCATACATAATACGAGAAGAGACGAAAGGATCCAATGAGGTGACTTAG
TCACCGGAGGATAACCACCGAGTAAGCCCACTTCGGCAATCCAGGCCGCAGGCTTGATTGACAGA
GCTGGGGCACGTAGTTTATAACGAAGCTTTTTTTTAAATATTTTCGGGAAATCCCCAGAAATTAT
TCTTTGCTGCAATGCAAAAAGAGCGCCCTCGAATATTGTAAAGATTTAAGCTAATGGATTTATTT
GTTTTTATGGCGAATAACGGGATTCGAACCCGTTTTTTCAAATTCACAATCTGACACTTTCACCT
AGTAAGTTATACTCGCCCTTCTTTACTCGGACATTAAGATACTCG
Right flanking sequence: Indices 43587 -- 44086
TGAGCTTGGGAAAGCAGAGTACAAAGTGGAAACACAATCTTTTTGTTTCGTTTTCTTTCTACTAT
CTCATTTTCCAGACACCCCCAGCTTATTTCAGCCGGACCTGCGGCATTTTTTCAAATATTTGAAA
AAATCTATAGTCCTCTGCCTTAAGGTATGTAGAGATTTCCTAATTATTGATTTATACTAATCTAT
CTCGGATCCGAGATAGTGCCGAAAAAATGACTCAATTTGATCTAACCATGGTTAACCCTGGCAAT
GACAATAATTTTTCTACAATATGCAGAATACTCCAATAAAAAGGTAAGCCTCTCTTGATTTTATT
TATGACTGAAAGGAGGGAAAAACAATAAAATGCAAAGGTTAGAATAGAAAATTTTTGAGCTTTGT
TCTACGTAATTTTGCTATTTATATAATATAATATAGTAAGAGATAATAAGTTGACGAAGAAGTAA
AAATATATGTCTATAAAAATATATATATATTTTTATATACATATG
Found at i:46440 original size:15 final size:15
Alignment explanation
Indices: 46417--46451 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
46407 GAAAAAAACA
*
46417 ATATATATAAATAAT
1 ATATTTATAAATAAT
46432 ATATTTATAAATAAT
1 ATATTTATAAATAAT
46447 ATATT
1 ATATT
46452 GTTTTTCCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATTTATAAATAAT
Left flanking sequence: Indices 45917 -- 46416
GAAAATCTGCACAAATAGGATTGCATACTCGGTTACCTGATGCAATGGAGGGTTTTTGAATATTT
GAGGGCTCTCATGTGCCATTAAGTACATTCTACCAATCTCACTGTATGCTGGGATCGTCAACCGA
ATGAGAGTCTCTCACCGGAAAAATATCTCATTTTGACCAATCAGCAGGAAACCTATGAGAAGGCC
AAGCCCACCCGACGAAGTAAAGGCTAAGAGAGTTCTATAGGATCCTCAGAGACTGTACGTGAGAC
CTCTTGTTTGAAATATAATTTATCCCTTGAAAGAAGAGCTGGCCAGATTTACCTAAGATACGAAA
CACTATATTTTGTCGTGAAGGTTCGATCATTTTTTTTTTTCCAAATTATAGTCCAGATGCGCATT
ATGGAATAGAAAGATTCATTTAGGGTTTGGGCGTATAGAGAGAGTTTGTATTGAATTAAATACTC
ATCATTTTGGTTATGAGCTTCATTCGAAATAATAGGAAAAAAACA
Right flanking sequence: Indices 46452 -- 46951
GTTTTTCCAGCGCAACCTGGTGTTGCATCACAATTTTCGGCCCGAGCCCAGTCTTATCGTCATCG
TTATCAAAGCGCTGCGCGCCGGATCTACCCAAATATTTTCCTTTGCAAAATATATTATCAAAATA
TATTATATATTTGTGATGAGCATTAGAATGGGGCTGAGATGGTGTCTCATGTATTATATAAGAGA
GGAAAAACATCTTGGTTGTAGAGGCACAGCAGCAGCCATACGTAAGATTCTTGGGAGAATCTCTA
TTTCATAAGTGGAAGATCCAGTCCCTACTCTCGCTAGGCTATCGGCTTATTACCTAATGCTTTAA
AATATATTATTTATTTGTTTTATGGAAGCGTAAGAGGTTTAAGAGTGGCCCACTCCAGTATCTGC
TTTGATTCACGCAGCTACTATGGTAACAGCAGGCGTTTTTATGATAGCAAGGTGCTCCCCTTTAT
TCGAATATTCACCCACTGCTTTGATCGTTATCACTTCCGTAGGAG
Found at i:46580 original size:13 final size:13
Alignment explanation
Indices: 46562--46587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46552 TTTTCCTTTG
46562 CAAAATATATTAT
1 CAAAATATATTAT
46575 CAAAATATATTAT
1 CAAAATATATTAT
46588 ATATTTGTGA
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:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
CAAAATATATTAT
Left flanking sequence: Indices 46062 -- 46561
CGGAAAAATATCTCATTTTGACCAATCAGCAGGAAACCTATGAGAAGGCCAAGCCCACCCGACGA
AGTAAAGGCTAAGAGAGTTCTATAGGATCCTCAGAGACTGTACGTGAGACCTCTTGTTTGAAATA
TAATTTATCCCTTGAAAGAAGAGCTGGCCAGATTTACCTAAGATACGAAACACTATATTTTGTCG
TGAAGGTTCGATCATTTTTTTTTTTCCAAATTATAGTCCAGATGCGCATTATGGAATAGAAAGAT
TCATTTAGGGTTTGGGCGTATAGAGAGAGTTTGTATTGAATTAAATACTCATCATTTTGGTTATG
AGCTTCATTCGAAATAATAGGAAAAAAACAATATATATAAATAATATATTTATAAATAATATATT
GTTTTTCCAGCGCAACCTGGTGTTGCATCACAATTTTCGGCCCGAGCCCAGTCTTATCGTCATCG
TTATCAAAGCGCTGCGCGCCGGATCTACCCAAATATTTTCCTTTG
Right flanking sequence: Indices 46588 -- 47087
ATATTTGTGATGAGCATTAGAATGGGGCTGAGATGGTGTCTCATGTATTATATAAGAGAGGAAAA
ACATCTTGGTTGTAGAGGCACAGCAGCAGCCATACGTAAGATTCTTGGGAGAATCTCTATTTCAT
AAGTGGAAGATCCAGTCCCTACTCTCGCTAGGCTATCGGCTTATTACCTAATGCTTTAAAATATA
TTATTTATTTGTTTTATGGAAGCGTAAGAGGTTTAAGAGTGGCCCACTCCAGTATCTGCTTTGAT
TCACGCAGCTACTATGGTAACAGCAGGCGTTTTTATGATAGCAAGGTGCTCCCCTTTATTCGAAT
ATTCACCCACTGCTTTGATCGTTATCACTTCCGTAGGAGCTATGACGTCATTTTTTGCGGCAACT
ACTGGAATATTACAGAACGATTTAAAGAGGGTCATAGCCTATTCAACTTGTAGTCAATTAGGCTA
TATGATATTTGCTTGCGGTATTTCCAACTATTCCGTTAGCATATT
Found at i:60693 original size:2 final size:2
Alignment explanation
Indices: 60688--60713 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60678 GTATTTTTTC
60688 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
60714 GAGAAAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 60188 -- 60687
TCATTTACCCGCGCGTTCTGTCCAGGATTCTCTAGGCTCGACCGGCGTGTGCCGGCATGAACATG
GTTTGTATCCTGACCCAGGGGCTTCCTTTCACCGTTTACCATCGGCTATTTGAGTAGATCAGTCC
TCATATTCGTCTCCCTTCCAAAAGAGTGGCCATCGTCGAGATTCGTAGACCTATCCCATACAGAA
CACTTTCCTGACTCCACGGCATCGAGGTAAACGGAAGTTGGATTATCGTCTAAAACCCCGACGAA
GTTTTTATACCATCGGGTAGTGGGCGCGAGCTCCGCACGTAAATGAAAGATACAAATTTCCTATA
GGAATAGGAATTAATGGAATAATTGCAAATTGTTCTAGTGGACTGCAAGCCATCATGATAAATTC
TCTTTTTCCTATTTCAGCGCAGGGCGAAACCAAGAAGCCGCCTTGTTGCTCGCCGCTTCCCAAGG
CAAAGAAAATAAAAAAAATATTTTTATTTCTTTCGGTATTTTTTC
Right flanking sequence: Indices 60714 -- 61213
GAGAAAATACCTCGAAGCCAAGCCTGAGTTGCCCTACATTCGCGCAGTGAATATAGTGTTAATTT
CTATCTATGTTTTTTCTCAATAATGAATGGTAACTTTCTAAAAGAAAGGAAAGGCGAAATCATGA
TCAAACAGATTCGGAGAGCTCCTCAAATTTTCTTACTTTTCTGCATTTTATTAAAATCTATATTA
TATATTTCGCGCGCCTAGATTTTTTGTCGGTCTGCTGCACGCTTTTGTTCTACGAGTTAATGAAC
AAAGTACGCGTGATTTTATGCCATCCATGCGCGTCCTATCAGAATAAAATAAAATTTAAAGTCTC
TGAGCCTCCCTTTCCTTGCCCCGATTACATGAACTAACCAAGTGGGGGGTCGAAGATCCCGACCG
ACTATATGCCTTCCAAAATTTGGTCAAAAAGCAAAAGTGAAAAGCATTCATTTACATAGCTAATT
AATGAACCCTTTCGTACGGAAACAACCCAAAGCGGTTGGGAGCCG
Found at i:75276 original size:2 final size:2
Alignment explanation
Indices: 75271--75306 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
75261 CGAATAAAAA
* *
75271 AT AT AT AT AG AT AT AT AT AT AT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75307 TTCTTTTACC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Left flanking sequence: Indices 74771 -- 75270
AAGGGGTCACGAAGCTACACCCTTACTCTCCTAGTTTATGTACATTGCTTTTTTTAGGAGGTTGG
TTACCTATCCTAAATATTCCTATTCTCAATGTAATTCCGGGTTCTATCTGGTTCAGTATTAAAGT
TCTCTCCTTTCTATTTGTATATATATGGGTACGTGCAGCATTTCCACGATATCGTTATGACCAAT
TAATGAGACTTGGCTGGAAAGTATTTTTGCCTCTATCATTGGCTTGGGTAGTTTTTGTATCCGGG
GTTCTAGTAGCCTTCGATTGGCTCCCTTAAAACTCATTGAGCAATTTTACCGCAGTGCAACTAAA
AATATATATATATATATATTTTTTAATTAAAAAAAACTTCTGGTGGGACCTTAAGAGAGTTGAAT
AGCAGCTCGAAGACCAAATTATTTGATTGAAAGAAATATAAAATAATATTTTTTATTCGTTCTAT
TAACTCCGTAAATACAGGCTTTGAGCGGTATAGAACGAATAAAAA
Right flanking sequence: Indices 75307 -- 75806
TTCTTTTACCTAAGGCCTTGTAATGATGGGTAAATCCTGCCCATGGTGGATTGCGTCAATCATGA
AGAACACAGAGTTTCCATGATCCGCGAAAACAAGAAAGCACAAAATAATTAATATGGCAAGACGA
CTATCGATTCTCAAACAACCTATATTTTCTACATTTAACAATCATTTGATAGATTATCCAACGCC
AAGCAATATAAGTTATTGGTGGAGTTTTGGTTCGTTGGCTGGTCTTTGCTTATTTATTCAGATAA
TTACAGGCGTTTTTTTAGCTATGCATTATACGCCTCATGTGGATCTAGCTTTCTCAAGCGTAGAA
CACATCATGAGAGATGTGAAAGGCGGCTGGTTGCTTCGTTATATGCATGCTAATGGGGCAAGTAT
GTTTTTCATTGTGGTTTATCTTCATATCTTTCGTGGTTTATATTATGGAAGTTATTCCAGTCCTA
GGGAATTAGTTTGGTGTCTTGGAGTTGTCATTTTATTGTTAATGA
Found at i:75954 original size:18 final size:18
Alignment explanation
Indices: 75931--75970 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
75921 CTTCTCTCCC
75931 ATGGAGAGCGCAAAGTGT
1 ATGGAGAGCGCAAAGTGT
75949 ATGGAGAGCGCAAAGTGT
1 ATGGAGAGCGCAAAGTGT
75967 ATGG
1 ATGG
75971 GGCAACCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.40, T:0.17
Consensus pattern (18 bp):
ATGGAGAGCGCAAAGTGT
Left flanking sequence: Indices 75431 -- 75930
AGACGACTATCGATTCTCAAACAACCTATATTTTCTACATTTAACAATCATTTGATAGATTATCC
AACGCCAAGCAATATAAGTTATTGGTGGAGTTTTGGTTCGTTGGCTGGTCTTTGCTTATTTATTC
AGATAATTACAGGCGTTTTTTTAGCTATGCATTATACGCCTCATGTGGATCTAGCTTTCTCAAGC
GTAGAACACATCATGAGAGATGTGAAAGGCGGCTGGTTGCTTCGTTATATGCATGCTAATGGGGC
AAGTATGTTTTTCATTGTGGTTTATCTTCATATCTTTCGTGGTTTATATTATGGAAGTTATTCCA
GTCCTAGGGAATTAGTTTGGTGTCTTGGAGTTGTCATTTTATTGTTAATGATCGTAACAGCTTTT
ATAGGATACGTACTGCCATGGGGTCAATTTGGCCCTTCCTTCTACTGATAGAAGGATAAGAAACC
CTACTAAATGCGGGAAACTCTTTATTACTAAGGTACTTCTCTCCC
Right flanking sequence: Indices 75971 -- 76470
GGCAACCTTTGGTGGCAGTTGTTAACGCTGCTGTCTTGCGTGGGTGTAAAATCATGAGTAAAAAT
CCTTAGCATGTCCTCATAGACTAGACAATCCGCAGGAAAATTCTCGCTACACTAAAATAGGCATC
TTCGGCCTTGTAAAAGAATGGCATAGAGAGTTCCTCAGAGACTACACGTGGGGTGTCTAGCCTGT
CATTGATCTTTGGCTAGGTAAATATATAGTCCCATTTCCCATACATAATGTCTATTCCACTCTAG
TGAATGAATAAATAGAGGCCAAAGGCCCACCAGTATTTAAGATTTCAGATTAAATAGAACCTCGG
CTAGTTTGAGTTGGCTCCTTATTCCAGGGCAGTTAAGAGAGTTTCTAAAAAAATTGTTGAGACTA
TTCGACTGTTGAAGTATCAGCCTATTCTTTATTGGCCTATGTATGATGGGGCCGGAGAGCGCGCG
GGCTAAAACGTCCAAATAGTTCTACAAAATACTGATAAAAAAAAT
Found at i:80757 original size:17 final size:17
Alignment explanation
Indices: 80735--80769 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
80725 TCCACATACG
80735 TAGAGAATATATTATTA
1 TAGAGAATATATTATTA
80752 TAGAGAATATATTATTA
1 TAGAGAATATATTATTA
80769 T
1 T
80770 TCTTTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (17 bp):
TAGAGAATATATTATTA
Left flanking sequence: Indices 80235 -- 80734
AAAATATATATATTTTTTTCTAGCTGATTTGATATATTCTGATCGCCTTCATGCCTTTAGGAACA
TTGTTAGAAAGAGCAGTTCCAGGCAGAGAGCCTTTTTTGGCTCATAAATAGAGGGTTATCAATCT
GTGGGTTACCACCTCTATAAGATAATAAGCTTTCACCTAATTCTCCAGGTGCGAATAATCGGTAA
ACACGGGCCAAGACCTACCTTGTTTGTACGGTATAGAAGGGGCCAGGGTTGAACTGAGCGGGCCA
GCCACTTTCCAGCCATTTCCATCTCCTATATGCGCAATATGATCAAATAAAGCTACCTGATAGAT
AACAAGGTGCTGGTCAAGAACTGGCAACCATAAAGAGCAAAGTCCGCTCGAAGCCCATAATTCGT
TTACTTACAAGAATTATCGTGATAAGCAAATACGGGGGCGCAGCAGTTCTGAAAGCCATATGTGC
TGCTAGTTTTGGCCATAATGCAAGGTCACGGGTGCTCCACATACG
Right flanking sequence: Indices 80770 -- 81269
TCTTTTTTGCCGCCGAAAAGAGCCAACGCTTAGAGCCAGATGATCGCGAATAACCTTAGCTGAAC
TTGAGTTGGAGAGCCGTGTGATAGGTAACTATCTCGCACGGTTCGGAGAGCACTTTATTATATCG
TGGAAATGCACAGGGAAACTGCGGCTCCGTGATGGAATTCTCGACTCTATGTATTCAATATAATT
CACGCATTCGCGTACAAACTAGTGTGGACGAAATAACTTCAATTTGTTCGGCAGTCCGTATATTT
CCGTCGGCCGGCTGGTGGGAGCGAGAAGTTTGGGATATGTTTGGTGTTCATTTTTCTAATCATCC
TGATTTACGCCGTATATTAACAGATTATGGTTTTGAGGGTCATCCATTACGAAAAGACTTTCCTT
TAAGTGGATATGTGGAGGTACGTTATGATGATTCAGAGAAACGCGTGGTTTCTGAACCTATTGAG
ATGACTCAAGAATTTCGCTATTTCAATTTCGCTAGTCCTTGGGAA
Found at i:87530 original size:18 final size:18
Alignment explanation
Indices: 87507--87545 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
87497 CATGGAACAT
87507 TTATTTTATAGTAGCCAA
1 TTATTTTATAGTAGCCAA
87525 TTATTTTATAGTAGCCAA
1 TTATTTTATAGTAGCCAA
87543 TTA
1 TTA
87546 ATCAAACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (18 bp):
TTATTTTATAGTAGCCAA
Left flanking sequence: Indices 87007 -- 87506
GGGAAATAGCTTAGTTGGTTAGAGTGCTGGTCTGTCACGCCAGAAGTCGCGGGTTCAAATCCCGT
TTTTCCCGGTAAAATTTGATCCAAAAATAAATTATTATAAAACTAGTCTATAAAGATATATATAT
ATCTTTATAGACTGGGAACTGGATCAGTTAAAATTTTTTCTTCATCAACAAGGAAGTATGGCTGA
AAAGCTATGCAATATAATAGAATTAAATTTCACAGGGCATAGTGTTCCTATCTTACCCGTGGCGA
AAGTAATAAAGTAATCCCGAGGTGTGAAGCTCTAGTAACAATGTAATGATGGTTGGGATTCCATA
CTAAGCTAATGCTGGGATAAAGAGATTGGAAAAAAGATTATGCTATGCTTTTTTCATTAGAAGCG
GATTTTTATACTGGCAAAGCAGAGAAGCCTAAGCTTATAAAAGTGTTTCGTGGACCGCGGATCGA
ATTGGTACACTTAACTTGCCACATATAGTGTCATACATGGAACAT
Right flanking sequence: Indices 87546 -- 88045
ATCAAACCATTATTGACATATTGAACAGTTGCTCAATAAATCGTATGTGGAAAAACTCGTACGTA
TGGTTCTGACTGATGGAAGAAAAGGAAGGCGTAAGAGGCCTGTCTATCCCGACAAATACAACAAT
ACTGTATCATGGGTTCAAATCCCATTTCTTCCGTAGGGGACGTAGTTCAATTGGTAGAGCGCATG
TTTTGCAAGCATGAAGCTGTCGGTTCAAGTCCGATCGTCTCCAGATAGACAGGTGAGTGATGTAC
TCTGGAAAAAAACAGCATAAGTGCTTTATTTATAATAGCCGCAGGAGATATCGTTATGCTTTGTC
TGAACTTGGCTTTGGTAAAGACAATCTGAAGATCAAACTGAATAATTTGTTGAGTGAGAGAGAGT
AAAACGTGTTAGGACTAGAGATGGAAAGCGCGTAGAGAGTTGGCGCCCTGAGTCTAATAAAGGCC
GTAGGCAGCTGTGTCCCCATTCTTGATTTATCATTCCAATGTCCC
Found at i:94157 original size:15 final size:15
Alignment explanation
Indices: 94137--94166 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
94127 CAAGTACCCA
*
94137 GCAAAAAATAATATT
1 GCAAAAAAGAATATT
94152 GCAAAAAAGAATATT
1 GCAAAAAAGAATATT
94167 CTCTTTTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (15 bp):
GCAAAAAAGAATATT
Left flanking sequence: Indices 93637 -- 94136
AATTATCAATGGCAACATCGTTGTTACGATTATTTCCGGAAATACAAAATCATTTCGAGATTTTT
GAGCATATTCAAGGGTTTGATGTAACTATTGTCACTTCAGCCAAAACACAAGATGAAGCTTTCAT
TTTGTGGAGTGGCTTTTTGCAAAAAGAGGTTTAGTCATATGTCAAATCAAATTATACGAGATCAC
ACACGTAGATTGCTTGTGGCCAAATATGAATCAGAGCGAATGCAATATAAAGCCATTTCTCGATA
TAAAAATCTTACTAATCAAATACGTTATGAATATTTTTTAAAGTTGTCTAAGTTGTCAAGAAATA
GTTCTAGAACGAGAGTAAGAAATCGATGTATTTTTACGGGTCGCCCTCGTTCCGTATATAAGTTA
TTTCGCGTTTCTCGTATAGTTTCTCGTGAATTAGCATCTAAAGGTTATTTAATAGGCATAAACAA
ATCGTGTTGGTAGTCTGATAAAGGGGTTAGCTTTGCAAGTACCCA
Right flanking sequence: Indices 94167 -- 94666
CTCTTTTTTCTTGCCCTACGTTCTCAGGCGTTAATTTTTCACAGTGCTGTGCGGCCTTCGGCCTC
TGAATATCGAACGAATTCAACCTGTGCGACGCGCTATGTATGCGCCGAGACGAATGATGAGTGCT
CACTGGGCTCAGAGCAATGCCAGCCGGCAGTCAATCTGATCGTGGAATGTCAGTCAAACACCTCA
CCCATTGGTCCACGCAATATTCGGCTACTCCGCAAGATTGCAAAATACTCCGCTCGATCAGGGGA
GTGAATAGACAGTAGATTCCCTTGGAATTAAGGATATTGAAACCCTTTCAATAAAATATCGCCGA
GCGTAGACCATTTCATAATCTTACCTAACCCACAAAGTGTGGTTACTATCTTTGTGTACGCGAGT
TGATACAACTCAATTGCTATAATTATAGAGATTTTAATCTTCGAAAATTTAATAAAAAGAATGAA
AACAATCTCTGAATCAGAGTCTCTAATTTCTTCATCAGCAACTCA
Done.