Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: JX402749
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: 104252
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Found at i:22594 original size:20 final size:20
Alignment explanation
Indices: 22569--22628 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
22559 TTTTTCATAA
22569 AGAGAATATCTTGTTTTTTG
1 AGAGAATATCTTGTTTTTTG
22589 AGAGAATATCTTGTTTTTTG
1 AGAGAATATCTTGTTTTTTG
22609 AGAGAATATCTTGTTTTTTG
1 AGAGAATATCTTGTTTTTTG
22629 CTTGATTCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (20 bp):
AGAGAATATCTTGTTTTTTG
Left flanking sequence: Indices 22069 -- 22568
ATAAGTCATATTGTTTTTTGCGTCTGCGGGTATACTATCTAAGCATCATATCTTTTTGACTGCGT
CGAAAGAAAGAGGGCGAAGCGGTTCTTTGCTTTCGCGCAGTGAACCACTAGTGCCGGTAGTCTAT
CTTGTAGGTCATTTGATTGGTATACTGACGATTTTATTATGTCATTTTCTATTGTCGTCTCTGTT
CCATCGTGGTTGAGCGCGTGATGTACAAAAACATGCAAATTTTTGATTCATCCAATACTATACAG
ATTATGACATCTATATATTTCGGTCCAGTGCACTGTGGCGCGTTTTGCGACATGGCTCAGTGTCG
CGCCTCGAGCTAAGCCACGGCACAATACGCGCTGTCCCGCCGAATAAAAATCTCCTCAAGCTTTT
CAGGGTACTGCCCTATTTTTCGGCTGCCAAGCACAGAGCCACCAGCTGAAGATCATTCCTTTTTC
TTGAATGAATCATCATAAATAATGATTATATATTTTTTTTCATAA
Right flanking sequence: Indices 22629 -- 23128
CTTGATTCTGCAAAAGAATTACACAACGTTAAGATCTGTAAAGGTTACATGCTATTTTGTTTTAA
AAAAGGGTAACTAATTACCCTACTTACGGATGGAGAGGGATTCGAACCCCCGGTATTCTCAATAC
TTCGGTTTTCAAGACCGACTCTTTCAACCGCTCAGACATCCATCCTTATCTTAGTAAGATCATCG
GCTCAAAGGAACCAATAATCAACCTACTATTCATTTGCTATGTAAATGGAGATTTGAGAGAAAAA
AGCGGGAAGAAATAAAAAAAAATTTTAGGCGGATATAGATTAAAGGTAAATTATCTGCCTTCCAA
GCAGGAGATATGGGTTCGATTCCCGTTATCCGCAATGGCTAAAAAAACAAATGAAACTTCATATG
CCTGCATCAAGATTCAAAACTTGTCGTCAAATTTCGGAAAATGTTTGGCAGACCAAAAAACTTAC
TCAAAAACAAAAAGCCATTATTTTGAAGCTTCAAAAAAAAACAAA
Found at i:29968 original size:12 final size:12
Alignment explanation
Indices: 29951--29975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29941 ATGCTAAATG
29951 AAATCTATATAT
1 AAATCTATATAT
29963 AAATCTATATAT
1 AAATCTATATAT
29975 A
1 A
29976 GATTTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATCTATATAT
Left flanking sequence: Indices 29451 -- 29950
TGTATCATCATATATAATGTATTAACATCTTGATGTTAATAGGGCGCAACAAAAAATAGATATAT
TTGCCGTTTTCTTTTTTGAGTGTCGGAGAGTAAAACCTGCCGGACTAGGCAGGTGCATAGACCCC
TTCGCCTTTCATCCAATCCGCAAGTTTCCTGTTTACACGGTTCTTTTAGGATCAGGCAGGTACTA
TGGGTCCTCTGACTTCCAACTCAAACCATAGTGTATGGTTGGATCTCGCCGATATCACCTGTGAG
CTATAGCGCTTGAGATGTCGTTTAGTTCTCTGTCCCCGTTACTTTGGGTAATCTGCTTCCATGCG
TAAAAATAGATCTATCTTCTTCTCGTCCTTACCGTTCTTAGCCAACCAGCAGGCTGAAAGCATAA
CAGTGTTCGTTCGTGCGATTCCTCGCGTGCATTTTTTTCGCACTAGTTCGCTGTAGGGTAGGCCG
ACCCGAAAAGAACTGCGATTCTGTTTTATCATCTCATGCTAAATG
Right flanking sequence: Indices 29976 -- 30475
GATTTCATTTGGCAAGCGCCAGCGGACTCGCGGAGGATTATCGAGTAGGCCGAGAAACTAGCCGA
CAGCCGACGAATATCTCCTTTATCGCTGCCTCCGTGGCATGCTCCCCTTTTTCCGCTATTGGGTA
AGCCCCGAGCCCCTCGGGCAGTAGTGCCTTTGTTGTGATCACAAGTAATCTAACGGCCGCCCCTA
AGAAAGCCCCAGAAATTCTATGAAAAATAGAGAAGGTAGAAGTAAGCTGTGGCTTATAAATGGTA
AGATGAGGGGATAAGGGTCGATTGATTTTCATGTTTTTAGTTGACTCTGATTCTGACTCAAGGTG
ACAGGATTTGAACCTATGGCCCTCTGTACCCAAAACAGATGCGCTACCAGACTGCGCTACACCTT
GGCTGATGTTCCCTAATGAATATTTGATAAATGCTTAAATTGTTATTGAGCAACATACAAAAAGA
ACTAAAACTAATAAAAAAAATTCTATTTTTAACGCCACTGAAAAA
Found at i:32233 original size:16 final size:16
Alignment explanation
Indices: 32212--32243 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
32202 ACAGGTGCTG
32212 CATGGCTGTCGTCAGC
1 CATGGCTGTCGTCAGC
32228 CATGGCTGTCGTCAGC
1 CATGGCTGTCGTCAGC
32244 TCGTGTCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.31, G:0.31, T:0.25
Consensus pattern (16 bp):
CATGGCTGTCGTCAGC
Left flanking sequence: Indices 31712 -- 32211
TAGGCGTAAAGGGCACGTAGGCGGTGAATCCGGTTGAAAGTGAAAGTCGCCAGCTCAACTGGCGG
AATGCTTTCAAAACCAATTCACTTGAGTAAGATAGAGGATAGTGGAATTTCGTGTGTAGAGATAA
AATTCACAGATATACGAAGGAACACCAAAAGCGAAGGCAGCTTTCTGGGTCTCTACTGACGCTAA
GGTGCGAAAGCATAGGGAGCAAACAGGATTAGATACCCTGGTAGTCTATGCCGTAAACGATGAGT
GTTCGTCCTTGGTCTGCGCTGTGTGCAAAACGGCTGATCAGGGGCCCAGCTAACGCGTTAAACAC
TCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGG
TGGAGCATGTGGTTTAATTCGATACAACGCGCAAAACCTTACCAGCCCTTGACATATGAATAAGT
TTGCTTGTCCTTAATGGGACGGTACGAAAATTTCTACAGGTGCTG
Right flanking sequence: Indices 32244 -- 32743
TCGTGTCGTGAGATGTTGGGTTAAGTCCTATAACGAGCGCAACCCTCGTTTTGTGTTGCTAAGAC
ATGCGTTTTGGGGTCGATTCTCGATCATTTGAGACTGATAAAGACCACGCGAAGAATGTCACGAC
GCCGTCTGGCTACGATCACACGGTTGATTCGACGAGCACAGCTCTCCTAGCGTGGCACACAAAAC
AATGTGGCACCCAGTCTTTGGAAACAGAATTGACAATCCATGCCATGGACTGCACTCACAAGAAA
CTGCCAGTGATATACTGGAGGAAGGTGGGGATGACGTCAAGTCCGCATGGCCCTTATGGGCTGGG
CTACACACGTGCTACAATGGCAATTACAATAGGAAGCGAGGCTTGAAGGCGGAGCGAATCCAGAA
AGATAGCCTTAGTTCGGATTGTTCTCTGCAACTCGAGAACATGAAGTTGGAATCGCTAGTAATCG
CGGATCAGCATGCCGCGGTGAATATGTACTCAGGCCCTGTACACA
Found at i:33039 original size:14 final size:14
Alignment explanation
Indices: 33020--33047 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33010 TCGGTCCTGT
33020 TTGATAGTAACACA
1 TTGATAGTAACACA
33034 TTGATAGTAACACA
1 TTGATAGTAACACA
33048 AAGAAGCGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
TTGATAGTAACACA
Left flanking sequence: Indices 32520 -- 33019
GGAGGAAGGTGGGGATGACGTCAAGTCCGCATGGCCCTTATGGGCTGGGCTACACACGTGCTACA
ATGGCAATTACAATAGGAAGCGAGGCTTGAAGGCGGAGCGAATCCAGAAAGATAGCCTTAGTTCG
GATTGTTCTCTGCAACTCGAGAACATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCATGCCGC
GGTGAATATGTACTCAGGCCCTGTACACACCGCCCGTCACACCATGGGAATTGGCTTCGCCCGAA
GCATCAAACCAAGGATCACCCATTCTTTCAGTGTTCTACGCCGTTGGTGAGTGTGGTCTACCAGA
GGAATTGGTGGTCTGATGTGGGATACCAAGGTGGGGCCTTTGACTGAGGTGAAGTCGTAACAAGG
TAGCCGTAGGGGAACCTGTGGCTGGATTGACTCCTTTTTTTCGACAAAAGAGAGAAAAAAAAAGA
CTCCAAAAAAGAAACATCTATCTAGTTTCTGTCGTTCGGTCCTGT
Right flanking sequence: Indices 33048 -- 33547
AAGAAGCGGAAAAAAAAGAGTAGATACGCCCTGTGCTCTTCATTCTTTGGACTAGGATTGCATGG
CCCGAAGCAGCATAATGCGATAGTAGCAAAGACTTGAGTGAATTTTTGGTCTATGTCAGTTAGTG
AGAGCCTACCTCGCAGCCTTTCCAATTATGCCTGTGAATGCCCTTACTATTACACAATAACGGCT
TCAGTCGCTATTATGAATATCACGTTGGCGCAGGGCGCTCTAATAATCTACTCCGTTTGAACTTC
ATACATAAACAGTTACTTCTATCGTGTTGCCCCATCGGGGCCAGGTTAAAGGGCGCATGAGGCGA
ATTATCATCCAACAGCCAGGGAAATGAGCGGCAGATTGGTAGAACAGCGGATTAAGAATTCGCAT
GTCGGAATAGTTTAGTCGGTTAGAACAGCGGGATCATAATTCGCACACGGGGGTTCAAATCCCTC
TTCCGATAGGAACTTTCGGATAAGAATTGAACCTACGGGAGGCAA
Found at i:33719 original size:25 final size:25
Alignment explanation
Indices: 33691--33740 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
33681 GATAATTCAT
33691 TAAAATACATAGAGACTCAAATTGC
1 TAAAATACATAGAGACTCAAATTGC
33716 TAAAATACATAGAGACTCAAATTGC
1 TAAAATACATAGAGACTCAAATTGC
33741 ATAGAACGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (25 bp):
TAAAATACATAGAGACTCAAATTGC
Left flanking sequence: Indices 33191 -- 33690
CAGCCTTTCCAATTATGCCTGTGAATGCCCTTACTATTACACAATAACGGCTTCAGTCGCTATTA
TGAATATCACGTTGGCGCAGGGCGCTCTAATAATCTACTCCGTTTGAACTTCATACATAAACAGT
TACTTCTATCGTGTTGCCCCATCGGGGCCAGGTTAAAGGGCGCATGAGGCGAATTATCATCCAAC
AGCCAGGGAAATGAGCGGCAGATTGGTAGAACAGCGGATTAAGAATTCGCATGTCGGAATAGTTT
AGTCGGTTAGAACAGCGGGATCATAATTCGCACACGGGGGTTCAAATCCCTCTTCCGATAGGAAC
TTTCGGATAAGAATTGAACCTACGGGAGGCAAAAAAAAGATATATATATCGTTTTTTTGCTGGTC
ACTAACCTTATCCTAAATCTCCTTCTTCTATCACAGAACACGGTAAAGAAAGATTTACCATGGAT
AACTAGAAATGCAACATAATCAATCAATCATCATAGATAATTCAT
Right flanking sequence: Indices 33741 -- 34240
ATAGAACGGCGGCATCACCTTTAGGTTTCATTCTAGATCTTGTTCACGAACGTTGTGGCTATACT
CTTATGTTCTATCAACAAAGTAGAATTAGCCGTTATGCTAGTAGCTTATGAATCATCATAGATAA
TTCATTGTTGTAGCTCCACAAATGGGAACGCGCGCGAATGGTTCGTTGCTCCGGCTTGCTGCAGG
AGAAATTGAAGTAGGTCTACATGGCTTGCTGAAGAGAAGCGGTATCACCGGCGGCAAGTAGCCGA
CGCGTGGCCTGCGGCATCCATTATTTATGTGGAGCTAGAGGGGCGCTTCTTAGAACAACCATAAC
AACCATAAGGGCGCTTCTTAGAACAACCATGAACAACCATAAGGCCGCAGGGCGCAGCAAATCGA
AATAAAGTCAAGTTGGCGATGGCGGCGATTCTCGCCCTGTGATTGGCGGCGCTGGCGGCGATTCT
CGCCCTGTGATTATTCTCGCCGAAGAGCACCTGTGTATTCGGCGC
Found at i:34083 original size:33 final size:34
Alignment explanation
Indices: 34041--34109 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
34031 GGAGCTAGAG
34041 GGGCGCTTCTTAGAACAACCAT-AACAACCATAA
1 GGGCGCTTCTTAGAACAACCATGAACAACCATAA
34074 GGGCGCTTCTTAGAACAACCATGAACAACCATAA
1 GGGCGCTTCTTAGAACAACCATGAACAACCATAA
34108 GG
1 GG
34110 CCGCAGGGCG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 22 0.63
34 13 0.37
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (34 bp):
GGGCGCTTCTTAGAACAACCATGAACAACCATAA
Left flanking sequence: Indices 33541 -- 34040
GAGGCAAAAAAAAGATATATATATCGTTTTTTTGCTGGTCACTAACCTTATCCTAAATCTCCTTC
TTCTATCACAGAACACGGTAAAGAAAGATTTACCATGGATAACTAGAAATGCAACATAATCAATC
AATCATCATAGATAATTCATTAAAATACATAGAGACTCAAATTGCTAAAATACATAGAGACTCAA
ATTGCATAGAACGGCGGCATCACCTTTAGGTTTCATTCTAGATCTTGTTCACGAACGTTGTGGCT
ATACTCTTATGTTCTATCAACAAAGTAGAATTAGCCGTTATGCTAGTAGCTTATGAATCATCATA
GATAATTCATTGTTGTAGCTCCACAAATGGGAACGCGCGCGAATGGTTCGTTGCTCCGGCTTGCT
GCAGGAGAAATTGAAGTAGGTCTACATGGCTTGCTGAAGAGAAGCGGTATCACCGGCGGCAAGTA
GCCGACGCGTGGCCTGCGGCATCCATTATTTATGTGGAGCTAGAG
Right flanking sequence: Indices 34110 -- 34609
CCGCAGGGCGCAGCAAATCGAAATAAAGTCAAGTTGGCGATGGCGGCGATTCTCGCCCTGTGATT
GGCGGCGCTGGCGGCGATTCTCGCCCTGTGATTATTCTCGCCGAAGAGCACCTGTGTATTCGGCG
CTGGCGGCGCTTTGCGCCCTTGTTGACTCTATTCATCAATTATTCTAAAACGCGTTACAAAGTGA
TGAACAATCAATCGCGGGGCCGAAGGTTCTAGGGGACTAAGCTCGCCAAATAGTACTATGCAACA
CTCGGCGCCTACGGATGGATCATCATAGAGACTCGCAAGAAAAAAATGACATATTTCTAATAAAG
AACTCTACTATAATATAATGAATCATTTTCGATGAATCATCATATATAATAGACTAAAAATCCAC
CGCTACGCGCTTCCGGGCACTACCCTTGTTGACTCTATCCATCAATCGCTACGCGCTTCCGGGCA
CTATGGTAAGACATGAAAACACCCGATCCCATTCCGACCTCGAAA
Found at i:34188 original size:33 final size:33
Alignment explanation
Indices: 34145--34207 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
34135 AAGTCAAGTT
34145 GGCGATGGCGGCGATTCTCGCCCTGTGATTGGC
1 GGCGATGGCGGCGATTCTCGCCCTGTGATTGGC
*
34178 GGCGCTGGCGGCGATTCTCGCCCTGTGATT
1 GGCGATGGCGGCGATTCTCGCCCTGTGATT
34208 ATTCTCGCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.08, C:0.29, G:0.38, T:0.25
Consensus pattern (33 bp):
GGCGATGGCGGCGATTCTCGCCCTGTGATTGGC
Left flanking sequence: Indices 33645 -- 34144
TAACTAGAAATGCAACATAATCAATCAATCATCATAGATAATTCATTAAAATACATAGAGACTCA
AATTGCTAAAATACATAGAGACTCAAATTGCATAGAACGGCGGCATCACCTTTAGGTTTCATTCT
AGATCTTGTTCACGAACGTTGTGGCTATACTCTTATGTTCTATCAACAAAGTAGAATTAGCCGTT
ATGCTAGTAGCTTATGAATCATCATAGATAATTCATTGTTGTAGCTCCACAAATGGGAACGCGCG
CGAATGGTTCGTTGCTCCGGCTTGCTGCAGGAGAAATTGAAGTAGGTCTACATGGCTTGCTGAAG
AGAAGCGGTATCACCGGCGGCAAGTAGCCGACGCGTGGCCTGCGGCATCCATTATTTATGTGGAG
CTAGAGGGGCGCTTCTTAGAACAACCATAACAACCATAAGGGCGCTTCTTAGAACAACCATGAAC
AACCATAAGGCCGCAGGGCGCAGCAAATCGAAATAAAGTCAAGTT
Right flanking sequence: Indices 34208 -- 34707
ATTCTCGCCGAAGAGCACCTGTGTATTCGGCGCTGGCGGCGCTTTGCGCCCTTGTTGACTCTATT
CATCAATTATTCTAAAACGCGTTACAAAGTGATGAACAATCAATCGCGGGGCCGAAGGTTCTAGG
GGACTAAGCTCGCCAAATAGTACTATGCAACACTCGGCGCCTACGGATGGATCATCATAGAGACT
CGCAAGAAAAAAATGACATATTTCTAATAAAGAACTCTACTATAATATAATGAATCATTTTCGAT
GAATCATCATATATAATAGACTAAAAATCCACCGCTACGCGCTTCCGGGCACTACCCTTGTTGAC
TCTATCCATCAATCGCTACGCGCTTCCGGGCACTATGGTAAGACATGAAAACACCCGATCCCATT
CCGACCTCGAAATGTGAAATCGTCTTACGCTATATGTACTGATTTATCAATTTCGGGAGACATGG
TCCAGGCCCGGACAACGTCCAATTTCAATTATAATAAAATAACTA
Found at i:41666 original size:17 final size:17
Alignment explanation
Indices: 41644--41707 Score: 82
Period size: 17 Copynumber: 4.0 Consensus size: 17
41634 AACCACTTAA
41644 TAACTAACACAAATAGT
1 TAACTAACACAAATAGT
41661 TAACTAACACAAATAGT
1 TAACTAACACAAATAGT
**
41678 TAACT---A-TTATAGT
1 TAACTAACACAAATAGT
41691 TAACTAACACAAATAGT
1 TAACTAACACAAATAGT
41708 AATGGATGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
16 1 0.03
17 27 0.69
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (17 bp):
TAACTAACACAAATAGT
Left flanking sequence: Indices 41144 -- 41643
TGAAAAAAAATCTCCATATATTCTTTTATTTCATTGTAGTGGCTTGACAAGTCGACAATGGCGAC
AACTCAAAAATCTATTGTGTGCCTTTCGAGGTAGAACTTTATTTCGACCAAATTACAAAAGAAAA
CTACCACGTAGAAACAAGCAAGGTGGTTTTATTGAGCAGCTTGCTTCTAGCGCAGGTCCCACTTG
TATCTTGTACTTAACTAAAGAAGCACCAGATAATACATGGTCACAGTTATTACCTTTGGCCTCAT
ACAACCAAAATCTAGTTTTATTATACGGACAACTTCAATCTACTTTAATCAATCATATGGATATA
GAAAAAGCGGCTAATTTAGAAATAACATCAGTATTTCAACAACTTTTTGAGCTCATTTTTTACCC
ATATAATTCTTTATGTTCTTGTTTGAACAAGCCAATTTATGCTCTACCCACTATACAAGAAAAGA
CGCAAGGAGGGTTGCTTAGTCACCAGAAGATAACCAACCACTTAA
Right flanking sequence: Indices 41708 -- 42207
AATGGATGATTTGTTTTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTG
ACACTTTCACCTATTAAGTTATACTCGCCCTTTTTTCCAATTCAGACATTAAAATACTCGCTATC
GGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCACCAAGC
GAGTATGCTCACTATCGGACTTGAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTT
ACCATTTTCACCAAGTGAGCTTAGGCAAGCGAAGCGCAGAATCGAAACACAATAACACAATCTTT
TTCTTTAACACAATCCCCATCTTTCGTTTTCCTTTTGCCATTTCATTTTATAGACATCTCCGGCT
TATCCTGGCTCGGCTGAATCTGCGGCATTTTCTCAAATATTTGAAAAATCTATAGTCCTCTGTCT
CAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACTAATCTAT
Found at i:41968 original size:81 final size:81
Alignment explanation
Indices: 41833--41982 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
41823 AAAATACTCG
*
41833 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGCCGTGTTTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
41898 CAAGCGAGTATGCTCA
66 CAAGCGAGTATGCTCA
* *
41914 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCA
41978 CCAAG
65 CCAAG
41983 TGAGCTTAGG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
81 63 0.97
82 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGCCGTGTTTACCATTTTCAC
CAAGCGAGTATGCTCA
Left flanking sequence: Indices 41333 -- 41832
CACTTGTATCTTGTACTTAACTAAAGAAGCACCAGATAATACATGGTCACAGTTATTACCTTTGG
CCTCATACAACCAAAATCTAGTTTTATTATACGGACAACTTCAATCTACTTTAATCAATCATATG
GATATAGAAAAAGCGGCTAATTTAGAAATAACATCAGTATTTCAACAACTTTTTGAGCTCATTTT
TTACCCATATAATTCTTTATGTTCTTGTTTGAACAAGCCAATTTATGCTCTACCCACTATACAAG
AAAAGACGCAAGGAGGGTTGCTTAGTCACCAGAAGATAACCAACCACTTAATAACTAACACAAAT
AGTTAACTAACACAAATAGTTAACTATTATAGTTAACTAACACAAATAGTAATGGATGATTTGTT
TTTTTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATT
AAGTTATACTCGCCCTTTTTTCCAATTCAGACATTAAAATACTCG
Right flanking sequence: Indices 41983 -- 42482
TGAGCTTAGGCAAGCGAAGCGCAGAATCGAAACACAATAACACAATCTTTTTCTTTAACACAATC
CCCATCTTTCGTTTTCCTTTTGCCATTTCATTTTATAGACATCTCCGGCTTATCCTGGCTCGGCT
GAATCTGCGGCATTTTCTCAAATATTTGAAAAATCTATAGTCCTCTGTCTCAAGGTGTGTAGAGA
CTCCTTTTTTATTGATTTATACTAATCTATCTTAGATCCGAGATAGTGCCGAAAAAATGATTCAA
TTTGATCTAACCATGGTTGCCTCGGCAATGGCAATGACTTTTATACAATATGCAGAATACTCCAA
AACCTCTATTTAGAACTGAAAGAAGATAATGCTTTTTTATTTATGAGAAAATCATAAAGTGCAAA
GGTTAAAATTTTGAGCTTTGTTTTACGTAGTTTCGCCATCTATATAATAGAATATGGTAGAAAAG
AATAAGTTGGCGAGGAAGTAAAAATAGATATATATATCTATATAT
Found at i:42482 original size:12 final size:12
Alignment explanation
Indices: 42465--42490 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42455 GTAAAAATAG
42465 ATATATATATCT
1 ATATATATATCT
42477 ATATATATATCT
1 ATATATATATCT
42489 AT
1 AT
42491 TTTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATATATATCT
Left flanking sequence: Indices 41965 -- 42464
TTTACCATTTTCACCAAGTGAGCTTAGGCAAGCGAAGCGCAGAATCGAAACACAATAACACAATC
TTTTTCTTTAACACAATCCCCATCTTTCGTTTTCCTTTTGCCATTTCATTTTATAGACATCTCCG
GCTTATCCTGGCTCGGCTGAATCTGCGGCATTTTCTCAAATATTTGAAAAATCTATAGTCCTCTG
TCTCAAGGTGTGTAGAGACTCCTTTTTTATTGATTTATACTAATCTATCTTAGATCCGAGATAGT
GCCGAAAAAATGATTCAATTTGATCTAACCATGGTTGCCTCGGCAATGGCAATGACTTTTATACA
ATATGCAGAATACTCCAAAACCTCTATTTAGAACTGAAAGAAGATAATGCTTTTTTATTTATGAG
AAAATCATAAAGTGCAAAGGTTAAAATTTTGAGCTTTGTTTTACGTAGTTTCGCCATCTATATAA
TAGAATATGGTAGAAAAGAATAAGTTGGCGAGGAAGTAAAAATAG
Right flanking sequence: Indices 42491 -- 42990
TTTTTTTTTTATTCTGTGGTCTTGCAATTGTGTTTAAAGCTAAGGGCCCAGCCCCCTATTTCCCA
CCGTTTCCGTCAATCAAATAAAGGCTTCGTTTAGCCAGGGGTTATTCTTCTCCCCTGCTGAATTG
CTTCGCGAACGAAGTAGGCTAAAAAAATAAAGATTTTTTTTGTCCGCCTTATTCTCTTCTATCAT
TCAAATGGCCCTATGCGTTTTTGCCAAGCAAAATATTGATTGCATAAGCCATCGGCTTCCACAGA
GACCAATAAAGTGATAACAGCAGCGTAGCCAAGCTTGTTCCGCCCGCTGTGCGCAAAAAAAGAGT
TTTTTCCGGCACTTAGTAAAACAAAATTTTGACACTCCTTGCGTTGCGGATGGTAAGTGGATTAC
TAATAAAATGGAGTGATCCAAGATGACCTCTCTTTCAATTTCAATTATGTCATTATATAGTAATG
GCATGCGGCGAACTCTATTGGATGCGCCAAAAACTTGATTTGTTG
Found at i:49836 original size:22 final size:22
Alignment explanation
Indices: 49805--49848 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
49795 TCTCCTCGAC
49805 CGTGACTGAGACCGTCCAGTCA
1 CGTGACTGAGACCGTCCAGTCA
* *
49827 CGTGATTGAGGCCGTCCAGTCA
1 CGTGACTGAGACCGTCCAGTCA
49849 TAATAGCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (22 bp):
CGTGACTGAGACCGTCCAGTCA
Left flanking sequence: Indices 49305 -- 49804
AATGTTGATCGGCTTAACCATATTTATTACCATAATAGGTCCGTGGGATTTTATTTCTTTCTGGG
TAGATAATCGATTGTATTTTATTTACATAGTGAGTTTTCTATTTATTCATTTTGAAAACGACATT
AGCACGAACTAAAGGGGCATACTTCCTTATATAATACCATGAAACTTTGAGGGACGCAATGATAA
GCCAGTGCTACGCCCTTTTTTTGGCCCCGCCGAGAGGGAGGGCTGAGGCCCGACGAAGCCTAACA
AGCAAAAAAAATAGATTTTTTGGAGCCTAAGCTATGCTCTGCGGTCTAGCTATGATAAACCGTGG
GAAGAAAATGGATCCTCGAATAAAGCACGTTATTGCGGCAGGGTCTATGGGGAATCTGAAGAAGA
AGAAGAAGAAAGTAAAGATTGGAATGATAGAATAATGAATCGAAAGAGAGAAAATCAAAAAAACC
ATAAAACGAAAAAAAAAAATTTCGGCTTTTTTTATTCTCCTCGAC
Right flanking sequence: Indices 49849 -- 50348
TAATAGCAAGCCCTAGAGCATTGAACAAAGCGGTGAAAGGCGAAGCATGCAATTACATAGTATGC
GCGTATAAAAGCTCATCAAGTTATGCAATTATTGCGGGCTTTATGTATATAAGTGCAGGGGGTTA
TGATGATATACCCATAAGGCCTCTATGGCTGGAAAGCCGGGAGGAAATATGGACCCGCGGCCTGC
GAAGAAAGCTGCGTCCCCGGGATCTTCTGGAAAAAGAGTAAACATTTATGTTACAATTTTTAGCT
CCATTTTATTCCAATCTCAGTGGTCTCATTCTGTGTCCTTTATTAGGAAGCATCATTCTTTTCGT
TATCCCCGATCCCAGAATACGACTGATACGAAGTATTGGTTTGTGCACCTCTTTGATTACTTTCT
TATATTCCCTTCTTTTCTGGATACAATTTGATAATTCTACAGCCAAATTTCAATTCGTGGAAACC
ATTCGATGGCTTCCTTACTCAAACATCAATTTTTATATAGGTATA
Found at i:72598 original size:24 final size:24
Alignment explanation
Indices: 72570--72615 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
72560 GCGGCATGGC
72570 TGGCATGTGGCCGCGAATGCGGCA
1 TGGCATGTGGCCGCGAATGCGGCA
72594 TGGCATGTGGCCGCGAATGCGG
1 TGGCATGTGGCCGCGAATGCGG
72616 GGCAGGCGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.24, G:0.43, T:0.17
Consensus pattern (24 bp):
TGGCATGTGGCCGCGAATGCGGCA
Left flanking sequence: Indices 72070 -- 72569
TGGGGCATATCCTGGTGCCCAATCTCCAGTCCGCGTCAATGGAGTCAATCGCCCAGAGGTAGCGT
TGCCGCAATGCGCGTGGAAAAGCATCTGGGAAACCAAGTCATGACCCATAAAAGGACGACTTGGA
AGATACTGTTGGGATTGATGAGGCTGACGAATCCGAATGACGTAGCTGCTGAACGACAGCATTCA
CCAAGCCAGCGGGGAACGACTTGGTCCTGGAATCGGTTCTTTTGGTAGGTATAACGGGGGCCGGA
GACGGAAAACAAGGGCGAAGCAGGGGCATTCTCAGTAAGGGAATAAGACTATGCGGACATCTTAC
CTCGACGAACAGGTAGAAAAAGTCGAAGACGCAATCACGGGATCGACCTACTCTCTAGCGAGAGG
GTCGGCGGAGCCGCTATAGTAAGTCAATAGGGAAATCGACCGAGCCAGGTACTGAAGGGCGGCAG
TCATGATCCGAGGGTAGAGGACCACTTCAGTGGCAGCGGCATGGC
Right flanking sequence: Indices 72616 -- 73115
GGCAGGCGGCGACGCTTCAACTCTTCTGAGAAGACGGGTTGGTCCCAGCAGACATAAGAATGCTG
CTACGATCTCATTCAAGAAGTACCTCGTAAAGCGCGTCAATCTAGATCTAGATTGTTGTTGATGT
GCTTGAAGAAATCAGTGGCGGAGAGCTTTATGACGGGAAACTGTCACGTAAGGTTCGGAGGGCGG
GGAAATCTCCGACCCCTACTTTTGATTATGGTATGGTATTGTCAGATTTAAATGTAGGTATACTT
TATCTATTTGCTATATCTTCTCTAGGCGTGTATGGTATTATTACAGCAGGCTGGTCCAGTAATTC
TAAATATGCTTTTCTAGGAGCATTACGATCTGCAGCTCAAATGGTTTCTTATGAAGTTTCTATTG
GTCTTATTATCATTACCGTACTGATTTGTGTAGGTTCTCGTAACTTTAGTGAGATTGTAATCGCG
CAAAAGCAGATATGGTTTGCTGCGCCCTTGTTTCCTGTATTCATT
Found at i:78009 original size:10 final size:10
Alignment explanation
Indices: 77994--78023 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
77984 TAGCTTCGCC
77994 CTGCTATTGG
1 CTGCTATTGG
78004 CTGCTATTGG
1 CTGCTATTGG
78014 CTGCTATTGG
1 CTGCTATTGG
78024 TCGAGAGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.10, C:0.20, G:0.30, T:0.40
Consensus pattern (10 bp):
CTGCTATTGG
Left flanking sequence: Indices 77494 -- 77993
GAAAGTAGCTAATTGATACGTTCTAGGCATAGACGTTTTTTGCGTTCCGCCAGTCTTATTATAGC
AAGCGCGTAATCATCCGAACAGTTGTCGTCTACTGTTTCAATTAAATTTGATGATTTAGCACATT
GCAAAATTTAATTGACTTCGTTAAGTTTTCTGGAGAAATTATCATTATATATTATGTTATGATTA
TGATGTTGGCACGGCGGCGGCTATTAAAAAAGTTGTTTTTGGTATTAGAACTCCAGTCATTAAGG
CTTTTGTAGCTTCTACAGCAATGACGGCCTATAGCAAAATAAAGTCATAAAGGCGTCTCGAAGCT
TAATAAGTACGGCAATGCCCGGCCCGGGCGACCGGTCCTGCCCAACATCGTGCTCGAGGGCCGGT
GCTGTTTACCGCTCAGCGAAGAAGCTTCTCCCGGCTGAGTAATCGCTCGCTCCTCATGCCAGGTT
TGTTATGGGTTGGCAGTAGCACGGCAGTAGCCTGCTAGCTTCGCC
Right flanking sequence: Indices 78024 -- 78523
TCGAGAGCTTTACTTGATAACGAATCGGTTAGAGCTTTACACAAAGCTCCCAGCTTTTAGACTTT
TGTAATAGTAAAATATGCTTCGCCCTTTAACTTATGTTCTAATGTGTTTACTTCTTAGAAAAAAA
GAGACGATTTGTGGATAACCAATCGTTTTTCAAATCTCTGATAGCTACTTTACCGAAATGGATAC
ATCAATTTCGAAAATCAAAACATGAAAATATATTCTATACCAATCCTGATTACCTATTTCAATTA
TTATGGTTTTTGAAATATCATACCAATACACGTTTTCAGGTCTTAATCGATATTTGTGGAGTTGA
TTATCCCTCTCGAAAACAAAGATTTGAAGTAGTTTATAATTTACTAAGGGCGACCGCGAAGTAAC
CGAATAAAGTGCTCATTCGTACCAAACGAATGAGACGTTGTAGAAGTCTGCAACGAAACGGGCAC
GACTTATTTGACGGATATACCGCTAAAGACACCCAACAGGACGAA
Found at i:86796 original size:21 final size:21
Alignment explanation
Indices: 86770--86812 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
86760 ATAGAACCAA
86770 AAAAGCATGCGATATAATATG
1 AAAAGCATGCGATATAATATG
86791 AAAAGCATGCGATATAATATG
1 AAAAGCATGCGATATAATATG
86812 A
1 A
86813 TTCAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23
Consensus pattern (21 bp):
AAAAGCATGCGATATAATATG
Left flanking sequence: Indices 86270 -- 86769
AATATATAGATTTTTTTTTACTGTGGACATTTAAAAGGTGCCCTGGTTCCATACGGCTCCACTAG
CATAGCGAGTAGAGGCCGAAGCGCTTCGGCCTTATTGGCCATTACTGTGTAATCGGCTTGACGCA
TGCGAGGCCACAGGTCAACTAATCGCGAAAAAGTGCCTTTCGGTGCAAAGCAGAGAGCCGCGCAG
CCATTAGACTCGTGGCTTCGCTTGAACGATACTTCCGGGTTTCTACTAACGTATATAGCCAGTAG
AATGGAAAGATTCCGATGAATCATCTACGATGATTCATTATGTTTGGGAAAATAGCTTAGTTGGT
TAGAGTGCTGGTCTGTCACGCCAGAAGTCGCGGGTTCAAATCCCGTTTTTCCCGGTAATTTTTTG
ATTCAAAAATGAATTATTATAAAATCAGTTCATAAAGAGAGATATATCTCTCTTTATGAACTGGT
AACTAAATCAGTTAAAATCTTTTTTTTTTATTGAAATAGAACCAA
Right flanking sequence: Indices 86813 -- 87312
TTCAATTTTACAGGGCGTAGCCCTTATCCTACCCGCGTCAAAAGTAATCTTGAGGTGTGAAACTT
TAGGGATAATGTAATAATGGTTAAGATTACATACTGAGCTGATGCTAGAGTAAAGAGATTGGAAA
AAAAAATTATGCTATGCGGATGAATAGTGCAAGGAACTAATACAAAGACCTTGTCAAAAAGACTC
TAAGATCTTAATCGGTGTTAGCGGAACCGAAAAATTTTCTATATAGAATTTTATAGAGAGAATAT
CCTAGGTTGCGTAAGTCGTATGTGGGCGCAGAGCGCAGCACGTGTGGTTCTAACCGGGGGAGAAA
AGCATGAGAGGGCCCGCCATCCTGACAAATACAACAATACTGTATCCTGGGTTCAAATCCCATTT
TCTCCGTAGGGGACGTAGTTCAATTGGTAGAGCGCATGTTTTGCAAGCATGAAGCTGTCGGTTCA
ACTCCGATCGTCTCCAAATAAACAAGTGATATATTGTAGAAAAGC
Done.