Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_024521
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: 141276
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:6380 original size:12 final size:12
Alignment explanation
Indices: 6363--6387 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6353 TGCTTTCTTT
6363 ATATTAAACCTA
1 ATATTAAACCTA
6375 ATATTAAACCTA
1 ATATTAAACCTA
6387 A
1 A
6388 GGAGGTCTTC
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:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATTAAACCTA
Left flanking sequence: Indices 5863 -- 6362
CCAAAGTCTCTGGATATTGAAGACCAGTTATTTTACCCGAGAGTAAGGAAAATCGGCCTTTTCTG
TTCGATTTCCTTCTCAAAGAACCGTACATGACAGTTGCCCGTCATACGGCTCCCCTTATTCTCCA
GCTGGTATATGTTTTTAACTTGAAACCATGGGTGTGGCTCAAAGTAATCTTGTCTGCATAAAGTT
TGTCATGATGATGCCTGCACAAGGATATTTTTTTTCGGTCAAGTACTGAGCCATCCAGTCAGTTT
TTTCCTTCTGTGATTTAAAATGGAAAACCCGTTGATCATAGCTTGGTTGGCAATATGTATGAACT
CAGAATCTTTTTTTTCTTGGCCCCTACTTAAGTCTTCTCCGGACTTTATCGAGCGCCCGATGTTT
AGCGCTGCTCTTAATTGTAGGCGCATTTGGGGGATTTATCGTAAATATTTTCAGACCTAAGAAAA
AGATCGATCCTATTTGAGATTATATAGGTTAAATTTGCTTTCTTT
Right flanking sequence: Indices 6388 -- 6887
GGAGGTCTTCTTTAAGGAATGATGTCACATTTTTATTATATGCTTCGCCAGAAATTGAAGTCCAC
ACAATGATAGAGTCGTCTGCATAGCATATATGGTGAAGGCGTACATAGTTTGGATCCTTCTGGTC
TACAGAGGTTATTCTTTCTTTCACAATCAGCTTAAACTGCCGTCTCTCTTTTCTTTCCAAAGCAA
TCAAGTTACCTCCTAGCTTCCTACGTTTTTGTTTGTTTAATTGGGTCATATTTTGGTATACTTTC
ATTTCCCGTTTCTTTCGACTTGAGCCCTTCTCCGGCTCGAGCTTCAGGCGCAGGATCTCTTCGTT
TTATTTGTGAAGGTAAATGTTGCACAGTAAGAGTGAAAGCGTATTTCCTTGTAAAATGCCTGGGT
CCTTAATATCTACTCCTATTATCTCGGCATTAAACATCTTATGCAATGTGTCGAAGAATCTTTGC
TCATCTATAATCGTCGACATGATATCCACCAACTTTTTACGACAG
Found at i:20930 original size:15 final size:17
Alignment explanation
Indices: 20904--20936 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
20894 GTAAATATGA
20904 TAAAACCTACAA-AACT
1 TAAAACCTACAATAACT
20920 TAAAA-CTACAATAACT
1 TAAAACCTACAATAACT
20936 T
1 T
20937 CTTCATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAACCTACAATAACT
Left flanking sequence: Indices 20404 -- 20903
ATAGAGTGCCTATATCTTTGTGGTTTGTAGAAAACAGCCATCTTTGTGCAAAATTGTTCATTTTA
TAACCCCATCTTTCAATAATATCATGCTTTGTTGAACTAATTTTGACTGATGTTCTCGCAATTTG
GAAAAGCGAAATTCGTCACAAACTGTTTCGCGAAAACAAGTTACTATCTTCTCTTGTAGACTGAT
GCGAGAATGCTCCTGAATAGCTAACAGTGTTTTTAACTTTTGCTCTATTTGTTGGCGCAACACAG
CTTGCACTGTCTGTTTGCACTTAGGTGCACAGCGCGTAATTATATCATTTATACATGATTCTCCG
ATTACTTGCATACTTGAATGCAAACTGGTACTATGTAATTCGTGCTGTTTTTTTAACTCGGACAA
TAGAGCTTCCCGAGAACTCATCAATTGCTGTAACTCTAAAAGAAGAGCTTCGCTTCGCGCATCAA
AAGTAGCTTTTAAAGTTTCACCAAAGGTTTTTTGAGTAAATATGA
Right flanking sequence: Indices 20937 -- 21436
CTTCATTATAAATTAAGATTTGTTTTGAACTCAAAACACTAAAAATTAAAGTAGCAAATATGAGC
AATTCACGCATTCGTATTCCTCTTCTTTCTTGGTCCGTTTTGGATATTTACTAGAGTGTTCCTCT
GTCCGCGTAAAACATATATTTTGTTGAGAGCGGTGCTTTGACGTAAAGCTAGAAAAGTGTGATGA
TAAGTAGAGGGACTCATGGTTGAGAGTGCGTTTTTTTTGATTATTTGTGAGACACTAATTTCTCC
CAAGAAACATACATAAGATTTATTCATTTTTTTCAATTGATTAGCATTTAAGCTTTTTACCATTT
CGTTACACCACTTAGATGCTCCAGATACACTCGAATACAGATAGGATATACTGGTGTCGAAGCAT
TCTTGGAAAAGCACATCCTGTTCAACACTGTAATTGCTCAGCTCTGTGCCTACATTTTGATGTGA
AATCAGCTGCTCTCGTAGTTTGAGAATGCGACTTATTTTGGGTAA
Found at i:29487 original size:24 final size:24
Alignment explanation
Indices: 29460--29509 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
29450 TTTATCATCT
29460 AATTATAGGCATGATAGGTTGGCA
1 AATTATAGGCATGATAGGTTGGCA
29484 AATTATAGGCATGATAGGTTGGCA
1 AATTATAGGCATGATAGGTTGGCA
29508 AA
1 AA
29510 CAAGGAGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (24 bp):
AATTATAGGCATGATAGGTTGGCA
Left flanking sequence: Indices 28960 -- 29459
TCTTTTTTTGCTTTGTCTTTTATCTCGTATTTTATTGTTTGGAGGGGCGAAAATACCAAAAACAA
ATAGAGCAGATGGTCCAACTACAGAACTTTTTATTTTTTCTTATCTTTATGGTTGTGCTTGGTGG
CACGACAGCACCCATACTATTTCAATGGTTGGTAAGTAGAGATGTTCTTATAGGCGCTCCTTTTT
TTCATGGTATTATAATACCTATTTCTACCTCTCTATTATTGGTTTTAGTTTATATACATTTTAGG
GGATTTATATGCTCTATGAACAAAACAGAAAGGATCATTTTGGTAAGAGCAAGACCCATTTTATT
ACCCAACATAATTAGGAAAAGCTCCCCCCAAACTAGAGCTAAAAACGCATTTATTTTATTTTTTA
TTTCCTATTTTCACTTTTTCATTTTCAAATTTATAGGAGACTTATCATATTTAGAATCTTTCTGT
AGTGTGCTTTGTTTTTTATTATCTTGTATATTTCCTTTATCATCT
Right flanking sequence: Indices 29510 -- 30009
CAAGGAGCATAAGCTTAGAATAGAAGGAATTGAACTGTGTAAGCAGGCACAAAGAAGAAAGCGCC
AAGCACTTTGGCCCGACGAGAAAAGAGGCAAAAATGAAAAGAGAGAATTTTTTTCTTTTTTGGAA
AAAGAGAAAAAATCAAAAATATTTTTGATTTTTTTGTTGCGATTTTCAGAAACCTTCGGCCTCAA
CGAAAAAGCCAAATTTTTGGCTCTTTATTTTCTGCTTGCTTTTCTGCAAGCTCTTTTTTTTGTTT
TCGAAAATAATTGGAATATCTTTTTTATTGTTCGCGCCTTACCAAAAAGACTGATAAATGTTGGT
CATGACTTTCAAAAAGTTCCCATGACTATGAAGATTTCACATGGAGGAGTTTGCATTTTTGTTAT
GGGTGTTATTCTGTCGTGCGACCCGGTGGCTTATGTGTGACCATCATTACTTTCAAGCCCACGCC
TACATGGCGTGAACTCTGGTTGAATTCGGGTTTTAAATCTCGCCG
Found at i:39525 original size:11 final size:11
Alignment explanation
Indices: 39509--39533 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39499 CTTTTACTCA
39509 CAGATCGTTTC
1 CAGATCGTTTC
39520 CAGATCGTTTC
1 CAGATCGTTTC
39531 CAG
1 CAG
39534 GCTTCCACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (11 bp):
CAGATCGTTTC
Left flanking sequence: Indices 39009 -- 39508
ACCGTACAAGATGGTCGCCCATCATACGGCTCTCCAATTCAACCTTTCTTTGGATTTGATTTCGT
CACTAGGTTTTGGCTTGTTTTGATAGTGACCGGCCTCCAAGTGGCTTAAGTAACATAAAGGAACT
TGCTTTCTTGCTATAGCGATCACGGGGAATTTTGGCGGGAAATTCTAAAATAACAAAAAAAAGTT
TTTTTTTATTATCTCCCCCCAAGTCCGTCCTTAAGACTCTAAACATGATGCGTTTTCTTTTTTGC
ATATAATGTAGAGAGCACGAAGAGCAGTTATGCCGCATGTTAGTCATCAAGCAAGCCATGCCGTA
GGATCTTTGGTAGTAGAGTTTACTTTACAGTTTACAGCATATCAAATGTCGGATAGTCGAGCTAG
GGCTTTTGACAAGGGCGCCAGTAAGCCGACATTGAAGACAGTATAGGTTTCAATTCTGATAGTGA
AGATCTTTCGGCCTGGTATTTTGTATGAAGTATCTCTTTTACTCA
Right flanking sequence: Indices 39534 -- 40033
GCTTCCACCTGGGTGTCCGTGATACCAGAAAAAAAAAATATATATTTTTTTTGCTTGCTATGCGT
TCTATTCCAGCCTCTAGATGGAAGTAGGCCTTTGAAAGCAGAACGCATAGCGTTCTACACCTTCG
GCCTCTTCTTTTGCTTTGTTTACATAGCAAATGAAAGCGCGCAACGTGTATATTTGTTTTGTGCC
TTTCCAAGTTAACTTTTTCTTGATTATTGCGCTCTGCCTCGCAGGGCTCGCAGTTTATTTTGAGA
GGTCCCATCAATGGTCGTTCTGTCTGGTATCGCTGTCATTAATTTAGGTCTTGTGGTCTTAGTTT
TATGTAAGCCATAATCTATAACAGGTTACCCATGATGTTTTGCAGGTCCAAATAGTTTTCCTCAG
CTTTAAGAAGGCTCAAAATCCAAAAGTCTATTAGCAGCAGCCCCCCTAATTGCTTTTTTCTTCGT
ATTTTTGAACGAATTTCATTTGGGATTTGTGGGAGCCTGGCTAGA
Found at i:41762 original size:21 final size:21
Alignment explanation
Indices: 41736--41777 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
41726 CTAAAAGGTG
41736 CATTATCCATCTATTTATTTT
1 CATTATCCATCTATTTATTTT
41757 CATTATCCATCTATTTATTTT
1 CATTATCCATCTATTTATTTT
41778 GAAGTCGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.00, T:0.57
Consensus pattern (21 bp):
CATTATCCATCTATTTATTTT
Left flanking sequence: Indices 41236 -- 41735
AAATATTTTACTAAATCCATAATAAGAGTCTCTTTTTTGAAAGCCAACTCGATTTCAAGTCAAGC
ACACGCCGATTCCTTAGCCAATCAATATTGCTTCGCTCTTATATGGCAAGGACGATACGGGGCAG
AACAACCACATAAAGGGCAATGAAAAAGCCATCATTAGTAACCATTAATTACTTACTAACTTCAT
CTATGACACCTCTAATAGCAGCAAAAAGAAAATATATATATATATTTTTTTTGCTGCGCTCCGAC
ACCGTCTCAGAGACGATTTATAAATAATAGTCCAATTTCATGACAAAATTAATGAAAAAAAAATA
TATATTTTTTTCATGTCTTCTGGCCTTTTACTAAAGTATGGTGACTCTTTTATATGCTCAAATAG
ATTATTTGCATTGTTGCTCATCTGCCAGTCGATAACGAAATTGTCCACTATACAAACAGTGTAAT
GAAAAACTATGTTAACATCACGACGTCTAACCAAGCTAAAAGGTG
Right flanking sequence: Indices 41778 -- 42277
GAAGTCGTCCTAGGCCCTACGGACCTTTCCTTTGAGCCATTTATAGAATGGAGGGTAAGTATGAA
GAAGTTTGAAAAGAGTAGGACCATTGAAAAATACATACTAGTATATAAAACCAAAGCAGAGGAAC
TTATCTACAATAAACGAGGTTATATAAAACAGCAGTACAAATGTAACTTAACCAAATGTTAACTT
TATTAATATAGAAAAAGGTCTAAAATATGCACATACACCTAGAACATTAATAAGCATATTTTCTC
AAAATTCAATACCGAGGTCAAAGGGCCGAAACAAAATAAAAAGAAAGCCTTACACCTTATTTTCT
AATAATGACAAGTAAGCAAAACTCATATTAAGAAGACCCGTCCTGATATCCGGTAAATTGAACTG
CTTACTATATATTTATCTTATTTAGCGTTCAGGTCTTGCTCATGTTCCTGTGCGAGCGAAAAAAG
AAATCTATATATTTTTGCTGCGCCCTTTGCGCCTTTTTGCTTTAC
Found at i:52197 original size:53 final size:53
Alignment explanation
Indices: 52112--52216 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 53
52102 TACTAGGTTT
52112 TTTCCTTGTCATTTTATCGGAAAAATAGGCACTTTGTGCATAAACCTTCGTCC
1 TTTCCTTGTCATTTTATCGGAAAAATAGGCACTTTGTGCATAAACCTTCGTCC
* * * *
52165 TTTCTTTGTCATTTTATTGGAAGAATATGCACTTTGTGCATAAACCTTCGTC
1 TTTCCTTGTCATTTTATCGGAAAAATAGGCACTTTGTGCATAAACCTTCGTC
52217 TTCAAGCCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (53 bp):
TTTCCTTGTCATTTTATCGGAAAAATAGGCACTTTGTGCATAAACCTTCGTCC
Left flanking sequence: Indices 51612 -- 52111
TGGTGTAAATCAAATGATAAGGTAAATGCTTATTTATTGGGTTTAAGCAAAATGAAACCTAGATT
TTGCTTGTAATGTAAATGATATGATATGTAAATATAAGATACGTATAATGGATTTTTGTTACATT
GATGATCTTGAATAGTCATTTATGGGATAATAAGGAGGTTGATTGGTTAAGTTTTTTCAGTGGCC
TGGTTTTTTGCATGCTTTTCCATTTGGTTATATTAACGTTAGTTTAGTATTTTTGGGGATCAATA
ATTAGCGCGCAAATTGAAAATGAATAATTCTCCAGCTAATACGACTGCTTTTATGTTAATTATAG
CTAGATCTATGAAATTGCCCACAGCCAAACTATGTGTAGTTTGTTTGGGTGGTGTAATAGTGGTA
AATTATGGAAACAAACGTTTGTTTCCCAAATTGCGCCCACCAATGGCCAGGTTTGCTAATGTAAT
AGAGAGAACTACCAGTTAGCCCGAAACTTAGTAAGTACTAGGTTT
Right flanking sequence: Indices 52217 -- 52716
TTCAAGCCCCAGTACACCCTCAAAGGCGCTATAGTAAAGGACCTGACCAGAAGGCATGTCCGTCA
TTTTGAAGTATAAATGAAAGCCTTATTGGCGAATATTTTGGTAGTGAGTAGTAACATAGGTGCAA
TTCCTACTGTATCCAAAAAAATGCATTGGATGGATGCCTAGGCATTGGGAAGGAAGGACGCTTTT
AAGGGCGAAACGCCATGGAAAGATAACATCTGTGATCCATGGATCTCCAATCGGGAAACCGTATC
TGAGCAGAGCGGCGCATTAGTGTGCTGCGCTCTGCTTTGGATTTTCAAAACTTAGCAAACTGAAA
CATCTAAGTAGCTAAAGGAAAGGAAATCAACCGAGACTCCGTTAGTAGCGGCGAGCGAAAGCGGA
TTAGGCTTTGTGAGAAGGCTGAGAAAGCGCAAAGCGCTTTCTCGGCCTTCTCTCTTCATTTAATT
TGTTCGAAATTGAATGATGGAAAAACCATTTAAGGAATTGTGAAA
Found at i:61511 original size:81 final size:81
Alignment explanation
Indices: 61373--61522 Score: 257
Period size: 81 Copynumber: 1.9 Consensus size: 81
61363 AGGATACTCG
*
61373 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTGAGACTGTCGTGTCTACCATTTTCAC
1 CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGTCGTGTCTACCATTTTCAC
61438 CAAGCAAGTATGCTCA
66 CAAGCAAGTATGCTCA
* *
61454 CTATCGGACTT-GAACCGATAACCCATAGGAACAGATTTTAAGTCTGTCGTGTTTACCATTTTCA
1 CTATCGGA-TTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGTCGTGTCTACCATTTTCA
61518 CCAAG
65 CCAAG
61523 TAAGCTTAAG
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:0.18, T:0.29
Consensus pattern (81 bp):
CTATCGGATTCGAACCGATAACCCATAGGAACAGATTTTAAGACTGTCGTGTCTACCATTTTCAC
CAAGCAAGTATGCTCA
Left flanking sequence: Indices 60873 -- 61372
TTATCTTTTATCCGTATAATTCTTTATGTTTTTGTTTAAATCAGCCAATACAAGCAGAGTAATCT
ATCGGCAAAAATGGCTGATGATGTCCGAGCATGGGCGCAATGTGGCCTTATCCTTTTATGTTTGA
TTTGCTATAGGACAAGAGACGGAAGGATCTAATAGGGTGACTTAGTCACCAAAGGATAACCACCC
AATAACTAAGGGGCCCGCTTTGCTAATTAAGGCCACAAGCTTGATCGACAGAGCTGGGGCACTTT
ATAGCAAAGCTTTTTTTCCCATTTGGAAAATCACAGCAAAAATTGGAAAATTCCTACAAAATCTT
TTTTGCTGCGAAAAGCAGCGCTCCCGAAGATTGTCAAGATTTAAGCTAATAGATGATTTGTTCTT
CTGGCGAATAACGGGATTTGAACCCGTGTTTTCAAATTCACAATCTGACACTTTCACCTATTAAG
TTATACTCGCCCTTTTATTTTCCAATTTAGACATTAGGATACTCG
Right flanking sequence: Indices 61523 -- 62022
TAAGCTTAAGGAAGCAAAGCGCAGAGCGGAGACACAATCTTTCTGTTCTGTTTGATTTTTGCCAT
TTTCTTTTTTAGACACTCCCGGCTTGCAATGCGAGGCTTACCCTGGCTTGGCTGGACTTGCGGCA
TTTTTCTAAATATTTGAAAAAATATATATTTTGCTGCGCTCTCTGCCCTAAAGCGTGGAAAGCCC
TCTCTTTATTGATTTATATCAATCTATCTCAGATCCGAGATAGTGCCGAAAAAATGACTTAATTT
AATCTGACCATGGTCGCAAAAGCCTTGGCAATGGCAATGACTTTTGCACGACATGGAAAATACTT
CAATAAAAGGGTCCTCTCCTTACTCTATCTAAAAAAAGAAAATGCTTTTCCTTGCTGAAGGCTGA
AGAAAAGCAATAAAGTTTCAAAATGAAAATAAAAAATGCATAGCAAAAAAAATTTTGAGCTTTGT
TTTACGTTTCGCTCTCTATATAATATGATATAGTAAGAGAAAATA
Found at i:96501 original size:17 final size:17
Alignment explanation
Indices: 96479--96512 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
96469 ATATTTCATT
96479 TTTGTGGAAAGCGAGTA
1 TTTGTGGAAAGCGAGTA
96496 TTTGTGGAAAGCGAGTA
1 TTTGTGGAAAGCGAGTA
96513 AAAAATATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.29
Consensus pattern (17 bp):
TTTGTGGAAAGCGAGTA
Left flanking sequence: Indices 95979 -- 96478
GCTACTTTGATCAAAGCAGTTATACTTATAGTAATCATGATCGTTGCCTACGCAGCATTGGAAGC
AGGCCAGACAAAATCAAATTGTTATGCATATCACAAGTATACTCAGTCATGTCACAAGGCAAATA
TTCTGGTAGACTCAAAGGTTATAGCCTAATTACTCTAAAAAAAAGTCGACCTATGGCACAGGACA
TTATGGCGTCGATCCAAAAAACATACAAGGCGGAAAGAAAATCTTATCGCTGAAAAAAAAATATG
TTTGCTACGCCCCGCCTGTTCCTTAAAATATGCAGTCTGCTTTCCTTCCAACAGCAATAAAATGA
GTAAAACCGTAGCTGCTTAAGAGCAACCGTGAAAATTGTATAAGAAGAGCAAGAAAGTTAACCAA
CGCCGCGCAGCACGCGCGTGCTTGCCTTATGCCGGCCCGCTCAGGCTGGTGTCTACGTCGTGTTC
TAGAAAGGCGGCCTCATGCTGATGGTATAGCAGTAATATTTCATT
Right flanking sequence: Indices 96513 -- 97012
AAAAATATAGACCTGCGGCCTTCTTCGTCTATTATGCGAGGGTGCGCGGCTCACCCGCGCACCCC
CCTTTTTTTATTTCTTTTGGTTTAGATTGTTCGTAAAAAGCGCCATTATGTAAAGCGTACATACA
TATTAGAGTGGGTGGGCTACATGTACTAAACGATAAAACTACTTTATAAAGGAAAATGCTTATAT
GTATGGATCTCGAAAAGGTGCATAGCCTTTCGTTGGCTTTGCAGACGAAGGACGCAGCAAATATA
TATATTTTTTTTTGTTTCATAAATTAGTAGAAAAAGATGCTGCGCCCCGCGGCCTGATTTGTTTT
ACAAGCTCAAATCAGTCCCGATTTAAATTAAACTTTTTAAAGGCTTATTAGCCCGTTTTCTGATT
GCACTAATCGAAAAAAAAAGCAATGCATTCTTCTTGCGCAAGCGTTTTGTCGATGCTTAGCTCAA
AGGCAAGAAGTCTTTTTTAAGGCAAGAAGTCTTTTTTCGCCGTAA
Found at i:96991 original size:19 final size:19
Alignment explanation
Indices: 96967--97004 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
96957 GCTTAGCTCA
96967 AAGGCAAGAAGTCTTTTTT
1 AAGGCAAGAAGTCTTTTTT
96986 AAGGCAAGAAGTCTTTTTT
1 AAGGCAAGAAGTCTTTTTT
97005 CGCCGTAAAC
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:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (19 bp):
AAGGCAAGAAGTCTTTTTT
Left flanking sequence: Indices 96467 -- 96966
TAATATTTCATTTTTGTGGAAAGCGAGTATTTGTGGAAAGCGAGTAAAAAATATAGACCTGCGGC
CTTCTTCGTCTATTATGCGAGGGTGCGCGGCTCACCCGCGCACCCCCCTTTTTTTATTTCTTTTG
GTTTAGATTGTTCGTAAAAAGCGCCATTATGTAAAGCGTACATACATATTAGAGTGGGTGGGCTA
CATGTACTAAACGATAAAACTACTTTATAAAGGAAAATGCTTATATGTATGGATCTCGAAAAGGT
GCATAGCCTTTCGTTGGCTTTGCAGACGAAGGACGCAGCAAATATATATATTTTTTTTTGTTTCA
TAAATTAGTAGAAAAAGATGCTGCGCCCCGCGGCCTGATTTGTTTTACAAGCTCAAATCAGTCCC
GATTTAAATTAAACTTTTTAAAGGCTTATTAGCCCGTTTTCTGATTGCACTAATCGAAAAAAAAA
GCAATGCATTCTTCTTGCGCAAGCGTTTTGTCGATGCTTAGCTCA
Right flanking sequence: Indices 97005 -- 97504
CGCCGTAAACCTGCGGCCAAAAAAATATATATATATTTTTTTTTTTGCTGCAGGTGGGTGTCTGT
TTTCTGACTATAGCCAATAACGTGTCACGTTCAAAATTATTATAACATTTTACAACTTTCTTTGA
GGAAGGCCATTACTTATTTAGGCTACCTCCAAGGGTTTACCTTCTAATCACCCGTAAGGTAGCCT
CACCTTGTTAGTCTGTGGTCCACAACCCATGTTTTTCTAAAGCTAGCAGAAAGAAATATATATTT
CTTTTTTTTTCGTAGCTTTTAACATGGAACAAGATAAAAAAAAAGCCAACAAAATGAGACTGTAT
ATCATTGGTATTTTAGCAAGAATACTTGGAATAATAATACCCCTTTTACTAGGAGTAGCCTTTTT
AGTTTTAGCTGAACGTAAAGTAATGGCTTCCATGCAACGTAGAAAGGGTCCTAATGTAGTGGGAT
TGTTTGGATTGTTACAACCTTTAGCAGATGGTTTTAAATTAATGA
Found at i:104667 original size:20 final size:20
Alignment explanation
Indices: 104638--104685 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
104628 CATAATCTTA
* * *
104638 AAATACAATATACTATGTGT
1 AAATAAAATATACCACGTGT
104658 AAAT-AAA-ATACCACGTGT
1 AAATAAAATATACCACGTGT
104676 AAATAAAATA
1 AAATAAAATA
104686 AATAAATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 13 0.57
19 5 0.22
20 5 0.22
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.27
Consensus pattern (20 bp):
AAATAAAATATACCACGTGT
Left flanking sequence: Indices 104138 -- 104637
GCTATCAAAAGAGTCATTTTTGTTTTTCTGGCCTAGTCACCAAGGCCGGAGGAACTTTTACAGTA
ATGACAGCCTTAATTATAGCAAAATCAAGTCGTAGGAGCGTTTCGAAGCTTAATAAGGACGGCGA
TGTTCAGGCGACCAGTCTTTTTTCCATTGCCCAACATCGTGCCTTCGGCACTAAATGTGCCGTGC
CGTGTACCATTGCGTAGCAAAACTTCTTTCGGCCAAGTATCCTTACAAAGCCAGGCCGAAGGCAG
CAGTAGCACCTTTATCTTTTTACAAGGGACCTGCAGCCTCCGGCCTCACTTTCACACAAGTCGGT
CAGAGCTTTACTCGAGGACACGATGACTTTAATCTATTCTAATTCCACGGATCTCGCAATTGTTC
TTTCAGTCTATGGTAACATTTCAGTTTTTCGTATATTTTATCGTATTTTCATTTTAGTTAACCGA
TGGTTCATAAGATATGCTATGAAAAAGTTTAATACCATAATCTTA
Right flanking sequence: Indices 104686 -- 105185
AATAAATTAGTATATTCGTTCCTACCAAAAAATATCTTTTATACTTCGATTTAGGATTTGGCTGG
TTATGTATTTCGATCTTTTCCTTTTATGGTATATTTTAGATGCTCTATCATGGGCAAGTAAATAG
TCTACTGCGGCTATATGGAAAAGCATCCATAAAAAAATATAGATTTGGATGCTTTACGTTTTCTG
CTTTTCTTAAGTTTACTAGGTTGACAAGCTCAAATCGGTCCAATTTGTAGCAGAGCACTCTGTAA
CATTTTGACATTTGCACTGAAGACTAAATGGCCACACAGCATATTTATTACTGTGGGGGTCCTTA
TCTCGAATCTTTGCAGCCCTCATTTATACATCCAGCCTTTATTCATAGAAGAATTTCCATAGAAT
AAAGAAGGGTCTCCTCTATTTAAGAAAGACGAAAGCCCGTACAAGGACCTTCGGCCTTTTGATGT
AAGCTATACATAAATTCTGACTTCGGGCCCCATACTTTTTATTTC
Found at i:108336 original size:13 final size:13
Alignment explanation
Indices: 108318--108343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
108308 GACCTTTTGT
108318 GAAGACGCTGCGC
1 GAAGACGCTGCGC
108331 GAAGACGCTGCGC
1 GAAGACGCTGCGC
108344 TCGGGTGATG
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:0.23, C:0.31, G:0.38, T:0.08
Consensus pattern (13 bp):
GAAGACGCTGCGC
Left flanking sequence: Indices 107818 -- 108317
CTCACGTATTCGTGTACAAAGCAGTGTAGACGAAATAACTCCAATTTGTTCGATAGTCAGTATAT
TTCCATCAGCCAGCTGGTGGGAGCGAGAAGTGTGGGATATGTTTGGTGTTTATTTTTCCAACCAC
CCCGATTTACGCCGTATATTAACAGATTACGGTTTTGAGGGTCATCCATTACGAAAAGACTTTCC
TTTAAGTGGATATGTGGAAGTACGTTATGATGATTCAGAGAAACGTGTGGTTTCTGAACCTATAG
AGATGACTCAAGAATTTCGCTATTTTGATTTTGCTAGTCCTTGGGAACAAATGTCGCGTAGTGAC
AAATCAAATAAAAAGTAAGCAAAAATTGCTTACAGCCATCTTGAAAATATGCAATTTCGTAGTAT
AGTAATTGCATGCTTAGCTCAGTTTTACGGCATGCCAAATAATTTGCTTTGCTTGTTCAAACCAA
ACTCAGTCTTTTCAAGCCGAAACAGCAGGAGTGTTGACCTTTTGT
Right flanking sequence: Indices 108344 -- 108843
TCGGGTGATGGGAGTGAGAATAAGGCTTTTGCTACTTTATTGGCTTGACGAAGAGGGAAAAAGTA
AGGAAAATAAAATAAAGAAAATGTGCCGATCCCCCCAAATATTTTGGCTACGCCCTAAAAAATTA
TTTATTTTTCGTATCTTTTCTTCCCTCTTTGCTTTATTGGCTCTAAGAAACTTGGTCAAATCCCC
TCCCCCCTCCCCGTCCCAATTTATCATCTTCAATGATAAATTGGGCACAATTTGAAGGTTCAGAT
TGTGGAATTATTTAATTTATTGGTAGAAGGTTTGATTACTTTACGAACAAATTGACTGGAAATAA
ATTGGCTGGAGCGGAACTATCTACATTATTAGAACAAAAAATTACCAATTACTACACTAAATTGC
AAGTAGATGAGATCGGTCGAGTGGTCTCAGTTGGAGATGGAATTGCACGTGTTTATGGATTAAAC
AAGATTCAAGCTGGGGAAATGGTTGAATTTGCTAGCGGTGTGAAA
Found at i:129003 original size:25 final size:25
Alignment explanation
Indices: 128966--129015 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
128956 CCAAGAGAGC
**
128966 GCAGCAAAAAAAAAATCTTTTTTTT
1 GCAGCAAAAAAAAAAGATTTTTTTT
**
128991 GCAGCAAGCAAAAAAGATTTTTTTT
1 GCAGCAAAAAAAAAAGATTTTTTTT
129016 TGCTGCATAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (25 bp):
GCAGCAAAAAAAAAAGATTTTTTTT
Left flanking sequence: Indices 128466 -- 128965
ATGGCAATGTCGTTGTTACGATTATTTCCGGAAATACAAAATCATTTCGAGATTTTTGAGCATAT
CCGAGGGTTTGATATAACTATTGTTACTTCAGCCAACACACAAGATGAGACTTTCATTTTGTGGA
GTGGCTTTTTGCAAAAAGAGGTTTAGTCGTATGTCAAATCAAATTGTACGAGATCACACACGTAG
ATTGCTTGTGGCTAGATATGAATTAGAGCGAATGCAATGTAAAGCCATTTCTCGACATCAAAACC
TTCCTAATCAGATACGTTATGAATATTTTTTAAAGTCGTCTAAGTTGCCAAGAAATAGTTCCAAA
ACACGAATAAGAAACCGATGTATTTTCACGGGTCGCCCTCGCTCCGTATATAAGTTATTTCGCGT
TTCTCGCATAGTTTTTCGTGAATTAGCATCTAAAGGTTCTTTAATAGGCATAAACAAATCATGTT
GGTAGTCAATAGAATAAAGGTTAGCTTTGCGAGTACCAAGAGAGC
Right flanking sequence: Indices 129016 -- 129515
TGCTGCATACATTGTTTTTGCCTGACTTTGCCTAAGTATTCCTTTATTGAAAAGACTTAGTATGG
AGTCTTGGGAACAACGTACTTCAAGGCTAAAGACTAGCTCAAGTGAAAAGGGGACAGCGTAAGCA
AATGTATAAAAGCCTTGTCAAAGATGACCGGGATGAGCTTTTGGGCTCAATTGGATTTTGACGGA
CTGCGAACTATGGACGAAATTGCCCCTGTATATTGGGCATGTTGAAATTACATGAGTTCCTTAAA
GTGTAGTACAGTCCTCAAAATCGGCATAGGTTAAGTGCTATTAATGGGGTATGGTAAAACAATAT
TTCTCTATATGAAGGTGCGCCCGTAAGGGCGTATAATGAGATGTTAGTAGGGGAAAAGCAAAAAA
GCGAAGGCCGAGCTGTAATGGCTCAGATAGGGTCGACCTACATGAAAGGGTAGCTTACTTAAGTA
AAATTACATTTACTACAATTGAATTAAAGCCAATATGAGGACAAC
Done.