Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1813
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 124800
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:391 original size:21 final size:23
Alignment explanation
Indices: 330--446 Score: 102
Period size: 22 Copynumber: 5.2 Consensus size: 23
320 GCCTAGCTCT
*
330 TTTAATAACT-AGGCA-AAGCCC
1 TTTAATAACTGGGGCATAAGCCC
351 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
375 TTTAAT-ACT-GTGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
* * **
396 TTATCA-AATTGGGGC-TAAATCC
1 TT-TAATAACTGGGGCATAAGCCC
418 TTTATCATAACTGGGGCATAAGCCC
1 TTTA--ATAACTGGGGCATAAGCCC
443 TTTA
1 TTTA
447 CACTCTCCAT
Statistics
Matches: 75, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
21 14 0.19
22 24 0.32
23 14 0.19
24 14 0.19
25 9 0.12
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:516 original size:20 final size:20
Alignment explanation
Indices: 493--559 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
483 TATGAATACC
493 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
513 TCATGTGCATATCATGCATG
1 TCATGTGCATATCATACATA
533 TCATGTGCATATCATATCATA
1 TCATGTGCATATCATA-CATA
*
554 CCATGT
1 TCATGT
560 TTATAAAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 33 0.80
21 8 0.20
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:523 original size:11 final size:11
Alignment explanation
Indices: 493--547 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
483 TATGAATACC
493 TCATGTGCATA
1 TCATGTGCATA
*
504 TCA--TACATA
1 TCATGTGCATA
513 TCATGTGCATA
1 TCATGTGCATA
*
524 TCA--TGCATG
1 TCATGTGCATA
533 TCATGTGCATA
1 TCATGTGCATA
544 TCAT
1 TCAT
548 ATCATACCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 16 0.44
11 20 0.56
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:20185 original size:49 final size:49
Alignment explanation
Indices: 20100--20233 Score: 178
Period size: 49 Copynumber: 2.7 Consensus size: 49
20090 ATTGATTTGT
* *
20100 AGATAAACTACCACTAATAACACTTTTGTGGACAAGCCACCACTGATATGC
1 AGATATACTACCACTGATAA-A-TTTTGTGGACAAGCCACCACTGATATGC
* * * * *
20151 AGGTATATTGCCACTGATAAATTTTGTAGACAAGCCACCACTGATTTGC
1 AGATATACTACCACTGATAAATTTTGTGGACAAGCCACCACTGATATGC
*
20200 AGATATACTACCATTGATAAATTTTGTGGACAAG
1 AGATATACTACCACTGATAAATTTTGTGGACAAG
20234 TTACCTGTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 55 0.77
50 1 0.01
51 15 0.21
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (49 bp):
AGATATACTACCACTGATAAATTTTGTGGACAAGCCACCACTGATATGC
Found at i:21120 original size:39 final size:39
Alignment explanation
Indices: 21077--21206 Score: 197
Period size: 39 Copynumber: 3.3 Consensus size: 39
21067 TCTTTAACTG
* ** *
21077 GGATATTTTTCCAGCACGTAGCCTGCGAACCTCAAGTCC
1 GGATATATTTCCAGCATATAGCCTGCGAACCTCATGTCC
*
21116 GGATATATTTCCAGCATATAGCCTGTGAACCTCATGTCC
1 GGATATATTTCCAGCATATAGCCTGCGAACCTCATGTCC
*
21155 GGATATATTTCCAGCATATAGCCTGCGGACCTCATGTCC
1 GGATATATTTCCAGCATATAGCCTGCGAACCTCATGTCC
*
21194 GGATATACTTCCA
1 GGATATATTTCCA
21207 ATCTCATATA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 83 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (39 bp):
GGATATATTTCCAGCATATAGCCTGCGAACCTCATGTCC
Found at i:28922 original size:39 final size:39
Alignment explanation
Indices: 28879--29010 Score: 192
Period size: 39 Copynumber: 3.4 Consensus size: 39
28869 AGTCTTTAAC
* * ** * *
28879 CCGGATATTTTTACAGCACGTAGCCTGCAGACCTCAAGT
1 CCGGATATATTTCCAGCATATAGCCTGCGGACCTCATGT
*
28918 CCGGATATATTTCCAGTATATAGCCTGCGGACCTCATGT
1 CCGGATATATTTCCAGCATATAGCCTGCGGACCTCATGT
*
28957 CCAGATATATTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATATTTCCAGCATATAGCCTGCGGACCTCATGT
28996 CCGGATATATTTCCA
1 CCGGATATATTTCCA
29011 ATCTCATATA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 83 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (39 bp):
CCGGATATATTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:33732 original size:5 final size:6
Alignment explanation
Indices: 33716--33740 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
33706 AAATCCAAGT
33716 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
33741 TATTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:33748 original size:5 final size:5
Alignment explanation
Indices: 33740--33768 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
33730 AAAATAAAAA
33740 TTATT TTATT TTATT TTATT TTATT TTAT
1 TTATT TTATT TTATT TTATT TTATT TTAT
33769 GGTTGGCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:34386 original size:20 final size:20
Alignment explanation
Indices: 34361--34405 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
34351 AGGGACCAAA
* *
34361 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
34381 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
34401 ATGAA
1 ATGAA
34406 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:41512 original size:63 final size:64
Alignment explanation
Indices: 41432--41614 Score: 194
Period size: 66 Copynumber: 2.8 Consensus size: 64
41422 AGACATTATG
*
41432 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACG-GATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
41495 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
41560 AA
63 AA
* * * *
41562 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
41615 CGAACTATAT
Statistics
Matches: 98, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 39 0.40
64 5 0.05
65 6 0.06
66 40 0.41
67 5 0.05
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:47658 original size:27 final size:27
Alignment explanation
Indices: 47620--47672 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
47610 TAAAAAGATA
47620 GTTTCACCAAAGCATGAATTATGGATC
1 GTTTCACCAAAGCATGAATTATGGATC
47647 GTTTCACCAAAGCATGAATTATGGAT
1 GTTTCACCAAAGCATGAATTATGGAT
47673 TGATTTGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (27 bp):
GTTTCACCAAAGCATGAATTATGGATC
Found at i:58359 original size:27 final size:27
Alignment explanation
Indices: 58339--58603 Score: 345
Period size: 27 Copynumber: 9.8 Consensus size: 27
58329 GGGTGAAATG
* *
58339 GTAATTTTATAAATCGAGGGTAAAA-T
1 GTAATTTTGTAAATCGAGGGTAAAACA
*
58365 GATAATTTTATAAATCGAGGGTAAAACA
1 G-TAATTTTGTAAATCGAGGGTAAAACA
* *
58393 GTAATTTTGTAAATTGAGGGTAAAATA
1 GTAATTTTGTAAATCGAGGGTAAAACA
*
58420 GTAATTTTGTAAATCAAGGGTAAAACA
1 GTAATTTTGTAAATCGAGGGTAAAACA
58447 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTTTGTAAATCGAGGGTAAAACA
* * *
58474 ATAATTCTGTCAATCGAGGGTAAAAC-
1 GTAATTTTGTAAATCGAGGGTAAAACA
* * *
58500 GATAATTCTATAAATTGAGGGTAAAACA
1 G-TAATTTTGTAAATCGAGGGTAAAACA
*
58528 GTAATTCTGTAAATCGAGGGTAAAACA
1 GTAATTTTGTAAATCGAGGGTAAAACA
* *
58555 GTAATTCTGTAAATTGAGGGTAAAACA
1 GTAATTTTGTAAATCGAGGGTAAAACA
* *
58582 ATAATTTTGTAATTCGAGGGTA
1 GTAATTTTGTAAATCGAGGGTA
58604 CTTTGATAAT
Statistics
Matches: 213, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
26 1 0.00
27 210 0.99
28 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (27 bp):
GTAATTTTGTAAATCGAGGGTAAAACA
Found at i:58612 original size:27 final size:26
Alignment explanation
Indices: 58582--58725 Score: 92
Period size: 27 Copynumber: 5.3 Consensus size: 26
58572 GGGTAAAACA
* *
58582 ATAATTTTGTAATTCGAGGGTACTTTG
1 ATAATTTTATAAATCGAGGGTA-TTTG
* ** *
58609 ATAATTTTACATGTCGAGGGTATTTC
1 ATAATTTTATAAATCGAGGGTATTTG
**
58635 AGTAATTTTGCAAA-CTGAGGGTATTTTG
1 A-TAATTTTATAAATC-GAGGGTA-TTTG
* * *
58663 GTAATTTTACAAATCGAGGATATTTGG
1 ATAATTTTATAAATCGAGGGTATTT-G
* * *
58690 GTAATTTTATAAACCGGGGGTACTTTG
1 ATAATTTTATAAATCGAGGGTA-TTTG
*
58717 GTAATTTTA
1 ATAATTTTA
58726 CAACTGGTGG
Statistics
Matches: 95, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
26 8 0.08
27 80 0.84
28 7 0.07
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.41
Consensus pattern (26 bp):
ATAATTTTATAAATCGAGGGTATTTG
Found at i:58641 original size:54 final size:53
Alignment explanation
Indices: 58583--58756 Score: 181
Period size: 54 Copynumber: 3.2 Consensus size: 53
58573 GGTAAAACAA
* * **
58583 TAATTTTGTAATTCGAGGGTACTTTGATAATTTTACATGTCGAGGGTATTTCAG
1 TAATTTTGTAA-ACGAGGGTACTTTGGTAATTTTACAAATCGAGGGTATTTCAG
* * * **
58637 TAATTTTGCAAACTGAGGGTATTTTGGTAATTTTACAAATCGAGGATATTTGGG
1 TAATTTTGTAAAC-GAGGGTACTTTGGTAATTTTACAAATCGAGGGTATTTCAG
* * *
58691 TAATTTTATAAACCGGGGGTACTTTGGTAATTTTACAACT-G-GTGGTATTTCAG
1 TAATTTTGTAAA-CGAGGGTACTTTGGTAATTTTACAAATCGAG-GGTATTTCAG
*
58744 TAATTTGGTAAAC
1 TAATTTTGTAAAC
58757 TAAAGTATTC
Statistics
Matches: 98, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
52 2 0.02
53 19 0.19
54 76 0.78
55 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.40
Consensus pattern (53 bp):
TAATTTTGTAAACGAGGGTACTTTGGTAATTTTACAAATCGAGGGTATTTCAG
Found at i:58746 original size:26 final size:25
Alignment explanation
Indices: 58626--58749 Score: 88
Period size: 27 Copynumber: 4.7 Consensus size: 25
58616 TACATGTCGA
* *
58626 GGGTATTTCAGTAATTTTGCAAACTG
1 GGGTATTTCGGTAATTTTAC-AACTG
* *
58652 AGGGTATTTTGGTAATTTTACAAATCG
1 -GGGTATTTCGGTAATTTTACAACT-G
* * * *
58679 AGGATATTTGGGTAATTTTATAAACCGG
1 -GGGTATTTCGGTAATTTTA-CAA-CTG
58707 GGGTACTTT-GGTAATTTTACAACTG
1 GGGTA-TTTCGGTAATTTTACAACTG
*
58732 GTGGTATTTCAGTAATTT
1 G-GGTATTTCGGTAATTT
58750 GGTAAACTAA
Statistics
Matches: 78, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
25 6 0.08
26 16 0.21
27 50 0.64
28 6 0.08
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.40
Consensus pattern (25 bp):
GGGTATTTCGGTAATTTTACAACTG
Found at i:60865 original size:27 final size:26
Alignment explanation
Indices: 60817--60876 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
60807 GCGAGGCTGC
*
60817 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
60844 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
60870 CAGATAT
1 CAGATAT
60877 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:60906 original size:21 final size:22
Alignment explanation
Indices: 60877--60920 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
60867 GAACAGATAT
* *
60877 ATATATGTGGCGAAGCCACCAG
1 ATATATGTGACAAAGCCACCAG
*
60899 ATAT-TGTGACAAAGTCACCAG
1 ATATATGTGACAAAGCCACCAG
60920 A
1 A
60921 ATAGATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (22 bp):
ATATATGTGACAAAGCCACCAG
Found at i:61679 original size:27 final size:27
Alignment explanation
Indices: 61649--61950 Score: 361
Period size: 27 Copynumber: 11.2 Consensus size: 27
61639 AACACCCTAG
* *
61649 GGGTAAAATGGTAATTTTATAAATCTA
1 GGGTAAAATGGTAATTTTGTAAATCGA
** * * *
61676 GGGTAAAACAGTAATTCTGTTAATCAA
1 GGGTAAAATGGTAATTTTGTAAATCGA
*
61703 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
* * * *
61730 GGGTGAAATAGTAATTTTATCAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
* *
61757 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
*
61784 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
* *
61811 GGGTAAAATAGTAATTTTTTAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
* * *
61838 GGGTAAAACGGTAATTCTGTAAATCAA
1 GGGTAAAATGGTAATTTTGTAAATCGA
*
61865 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
* * *
61892 GGGTAAAATAGTAATTCTATAAATCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
* * *
61919 GGGTAAAATAGTAGTTTTGTAATTCGA
1 GGGTAAAATGGTAATTTTGTAAATCGA
61946 GGGTA
1 GGGTA
61951 CTTTGATAAT
Statistics
Matches: 235, Mismatches: 40, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 235 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.31
Consensus pattern (27 bp):
GGGTAAAATGGTAATTTTGTAAATCGA
Found at i:61963 original size:81 final size:81
Alignment explanation
Indices: 61649--61950 Score: 451
Period size: 81 Copynumber: 3.7 Consensus size: 81
61639 AACACCCTAG
* * *
61649 GGGTAAAATGGTAATTTTATAAATCTAGGGTAAAACAGTAATTCTGTTAATCAAGGGTAAAACGG
1 GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGG
61714 TAATTTTGTAAATCGA
66 TAATTTTGTAAATCGA
* * * * *
61730 GGGTGAAATAGTAATTTTATCAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATGG
1 GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGG
*
61795 TAATTCTGTAAATCGA
66 TAATTTTGTAAATCGA
* *
61811 GGGTAAAATAGTAATTTTTTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGG
1 GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGG
61876 TAATTTTGTAAATCGA
66 TAATTTTGTAAATCGA
* * * * * *
61892 GGGTAAAATAGTAATTCTATAAATCGAGGGTAAAATAGTAGTTTTGTAATTCGAGGGTA
1 GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTA
61951 CTTTGATAAT
Statistics
Matches: 198, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 198 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.31
Consensus pattern (81 bp):
GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGG
TAATTTTGTAAATCGA
Found at i:62004 original size:27 final size:27
Alignment explanation
Indices: 61974--62096 Score: 110
Period size: 27 Copynumber: 4.6 Consensus size: 27
61964 ACATGTCCAG
*
61974 GGTATTTCAGTAATTTTACAAACTGAA
1 GGTATTTCAGTAATTTTACAAACTGGA
*
62001 GGTATTTC-GTTAATTTTACAAA-TCGA
1 GGTATTTCAG-TAATTTTACAAACTGGA
** * * *
62027 GGATATTTGGGTAATTTTATAAACCGGG
1 GG-TATTTCAGTAATTTTACAAACTGGA
* *
62055 GGTACTTT-GGTAATTTTAC-AACTGGG
1 GGTA-TTTCAGTAATTTTACAAACTGGA
62081 GGTATTTCAGTAATTT
1 GGTATTTCAGTAATTT
62097 GGTAAACTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 13
0.78 0.10 0.13
Matches are distributed among these distances:
25 3 0.04
26 22 0.28
27 48 0.60
28 7 0.09
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (27 bp):
GGTATTTCAGTAATTTTACAAACTGGA
Found at i:62069 original size:54 final size:54
Alignment explanation
Indices: 61943--62075 Score: 142
Period size: 54 Copynumber: 2.5 Consensus size: 54
61933 TTTTGTAATT
** *
61943 CGAGGGTACTTTGATAATTTTACATGTCCAGGGTATTTCAGTAATTTTACAAAC
1 CGAGGGTACTTTGATAATTTTACAAATCCAGGATATTTCAGTAATTTTACAAAC
* * * * ** *
61997 TGAAGGTA-TTTCGTTAATTTTACAAATCGAGGATATTTGGGTAATTTTATAAAC
1 CGAGGGTACTTT-GATAATTTTACAAATCCAGGATATTTCAGTAATTTTACAAAC
* *
62051 CGGGGGTACTTTGGTAATTTTACAA
1 CGAGGGTACTTTGATAATTTTACAA
62076 CTGGGGGTAT
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
53 3 0.05
54 57 0.90
55 3 0.05
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.38
Consensus pattern (54 bp):
CGAGGGTACTTTGATAATTTTACAAATCCAGGATATTTCAGTAATTTTACAAAC
Found at i:67213 original size:44 final size:43
Alignment explanation
Indices: 67165--67321 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 43
67155 TGTGATATCG
*
67165 TGTAAGACCATGTCTGGGACGTTGGCATCGACT-TTTGTTTTACG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGA-TATTTG-TTTACA
* * *
67209 TGTAAGACCATGTTTGGGACATTGGCATCG-TATCTGATTT-CA
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATATTTG-TTTACA
* * * *
67251 TGTAAGACCCTGTCTGGGACAG-TGGCATCAATGTTTGATTACA
1 TGTAAGACCATGTCTGGGAC-GTTGGCATCGATATTTGTTTACA
* * *
67294 TGTAAGACCACGTCTGGAACGCTGGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
67322 TGTATATGCT
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
42 30 0.32
43 35 0.38
44 28 0.30
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGATATTTGTTTACA
Found at i:81891 original size:25 final size:26
Alignment explanation
Indices: 81850--81906 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
81840 CCTTCATATT
*
81850 TTTCTTATGAGAGTTGT-TCTGGGAC
1 TTTCTTATGAGAGTTGTATCTGGGAA
* *
81875 TTTCATTATGATA-TTGTATCTTGGAA
1 TTTC-TTATGAGAGTTGTATCTGGGAA
81901 TTTCTT
1 TTTCTT
81907 TATCTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.51
Consensus pattern (26 bp):
TTTCTTATGAGAGTTGTATCTGGGAA
Found at i:81912 original size:16 final size:15
Alignment explanation
Indices: 81891--81949 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
81881 TATGATATTG
81891 TATCTTGGAATTTCTT
1 TATCTTGG-ATTTCTT
*
81907 TATCTTAGATTTCTT
1 TATCTTGGATTTCTT
* * *
81922 TGTCCTGGACTTCTT
1 TATCTTGGATTTCTT
*
81937 TATCTTGGTTTTC
1 TATCTTGGATTTC
81950 ATGTCATCTT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
15 27 0.79
16 7 0.21
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:83176 original size:28 final size:28
Alignment explanation
Indices: 83145--83204 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
83135 ACTCAAATCT
83145 TTTAGCTCTGCTTTATA-AGAGCTCTCTG
1 TTTAGCTCTGCTTTATACA-AGCTCTCTG
* * *
83173 TTTAGCTTTGCTTTGTACAAGTTCTCTG
1 TTTAGCTCTGCTTTATACAAGCTCTCTG
83201 TTTA
1 TTTA
83205 AATCTCTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.48
Consensus pattern (28 bp):
TTTAGCTCTGCTTTATACAAGCTCTCTG
Found at i:86433 original size:25 final size:25
Alignment explanation
Indices: 86386--86433 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
86376 CAGCATATTG
* * * *
86386 TGGTATTGATATGTTTTGTATTAGT
1 TGGTATTGAAATGGTATGAATTAGT
86411 TGGTATTGAAATGGTATGAATTA
1 TGGTATTGAAATGGTATGAATTA
86434 TGCTTGGTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (25 bp):
TGGTATTGAAATGGTATGAATTAGT
Found at i:88936 original size:13 final size:13
Alignment explanation
Indices: 88914--88952 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
88904 ATCCTGGAAT
*
88914 ATTAAAAACAAGA
1 ATTAAGAACAAGA
*
88927 ATTAAGAACACATA
1 ATTAAGAACA-AGA
88941 ATTAAGAACAAG
1 ATTAAGAACAAG
88953 TCAAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:97199 original size:13 final size:13
Alignment explanation
Indices: 97177--97215 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
97167 ATCCTGGAAT
*
97177 ATTAAAAACAAGA
1 ATTAAGAACAAGA
*
97190 ATTAAGAACACATA
1 ATTAAGAACA-AGA
97204 ATTAAGAACAAG
1 ATTAAGAACAAG
97216 TCAAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:100561 original size:48 final size:48
Alignment explanation
Indices: 100507--100753 Score: 245
Period size: 48 Copynumber: 5.2 Consensus size: 48
100497 TATCTTGAAT
* * * *
100507 ATGGTCTTATATGGGACCACTTATCGATGCCAATTCCATGTCCCAGAC
1 ATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGAC
* * *
100555 ATGGTCTTACATGGGGTCACACAT--AT-CGAA-GCCGATAG-CCCAG-C
1 ATGGTCTTACATGGGATCACATATCGATGCCAATGCC-AT-GTCCCAGAC
* * *
100599 TATGGTCTTACATGATGTTCTCATATCGATGCCAATGCCATGTCCCAGAC
1 -ATGGTCTTACATG-GGATCACATATCGATGCCAATGCCATGTCCCAGAC
* * * *
100649 ATGGTCTTACATGGGATCACATAACGATGCCAATGCCATGTCCTAAAA
1 ATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGAC
* * * * *
100697 ATGGTCTTACATAGGATCAAATATCGATGCCGATGCCATATCCCAGAT
1 ATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGAC
100745 ATGGTCTTA
1 ATGGTCTTA
100754 TACAGGATCT
Statistics
Matches: 162, Mismatches: 27, Indels: 20
0.78 0.13 0.10
Matches are distributed among these distances:
44 3 0.02
45 23 0.14
46 10 0.06
48 99 0.61
49 23 0.14
50 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (48 bp):
ATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGAC
Found at i:102699 original size:30 final size:30
Alignment explanation
Indices: 102665--102855 Score: 108
Period size: 29 Copynumber: 6.4 Consensus size: 30
102655 GAAGCTATCA
102665 CTTTTCATAATTTGATGGTCTTCACCATCC
1 CTTTTCATAATTTGATGGTCTTCACCATCC
*
102695 CTTTTCAT--TGTTGATGGT-TGTTACCATCC
1 CTTTTCATAAT-TTGATGGTCT-TCACCATCC
* * ** * *
102724 CTTTTCATAATTTAATTG-CTGAAGCTACCC
1 CTTTTCATAATTTGATGGTCTTCA-CCATCC
* * *** *
102754 CTTTTCAAAATTTTGATAG-CCAAAGCTATCC
1 CTTTTCATAA-TTTGATGGTCTTCA-CCATCC
* ** * *
102785 CTTTTTATTGTTTGACGGTCGTCACCATCC
1 CTTTTCATAATTTGATGGTCTTCACCATCC
*
102815 CTTTTCAT--TGTTGATGGTCATCACCATCC
1 CTTTTCATAAT-TTGATGGTCTTCACCATCC
102844 CTTTTCATAATT
1 CTTTTCATAATT
102856 CGATAGTCGA
Statistics
Matches: 124, Mismatches: 26, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
28 3 0.02
29 50 0.40
30 46 0.37
31 25 0.20
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (30 bp):
CTTTTCATAATTTGATGGTCTTCACCATCC
Found at i:102868 original size:120 final size:119
Alignment explanation
Indices: 102607--102877 Score: 355
Period size: 120 Copynumber: 2.3 Consensus size: 119
102597 AGCTAACTTG
* * **
102607 TTTCATAATTCGATAGTTGAAGCTATCCCTTTTCATAATTTGATAACTGAAGCTATCACTTTTCA
1 TTTCATAATTCGATAGTCGAAGCTATCCCTTTTCAAAATTTGATAACCAAAGCTATCACTTTTCA
* * ** *
102672 TAATTTGATGGTCTTCACCATCCCTTTTCATTGTTGATGGTTGTTACCATCCCT
66 TAATTTGACGGTCGTCACCATCCCTTTTCATTGTTGATGGTCATCACCATCCCT
** * * * *
102726 TTTCATAATTTAATTG-CTGAAGCTACCCCTTTTCAAAATTTTGATAGCCAAAGCTATCCCTTTT
1 TTTCATAATTCGATAGTC-GAAGCTATCCCTTTTCAAAA-TTTGATAACCAAAGCTATCACTTTT
* **
102790 TATTGTTTGACGGTCGTCACCATCCCTTTTCATTGTTGATGGTCATCACCATCCCT
64 CATAATTTGACGGTCGTCACCATCCCTTTTCATTGTTGATGGTCATCACCATCCCT
102846 TTTCATAATTCGATAGTCGAAGCTATCCCTTT
1 TTTCATAATTCGATAGTCGAAGCTATCCCTTT
102878 CCATTAGTCG
Statistics
Matches: 127, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
119 31 0.24
120 95 0.75
121 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (119 bp):
TTTCATAATTCGATAGTCGAAGCTATCCCTTTTCAAAATTTGATAACCAAAGCTATCACTTTTCA
TAATTTGACGGTCGTCACCATCCCTTTTCATTGTTGATGGTCATCACCATCCCT
Found at i:102876 original size:30 final size:30
Alignment explanation
Indices: 102607--102877 Score: 123
Period size: 30 Copynumber: 9.1 Consensus size: 30
102597 AGCTAACTTG
* *
102607 TTTCATAATTCGATAGTTGAAGCTATCCCT
1 TTTCATAATTTGATAGTCGAAGCTATCCCT
* *
102637 TTTCATAATTTGATA-ACTGAAGCTATCACT
1 TTTCATAATTTGATAGTC-GAAGCTATCCCT
* ** *
102667 TTTCATAATTTGATGGTCTTCA-CCATCCCT
1 TTTCATAATTTGATAGTC-GAAGCTATCCCT
* * * *
102697 TTTCAT--TGTTGATGGTTGTTA-CCATCCCT
1 TTTCATAAT-TTGATAGTCG-AAGCTATCCCT
* * *
102726 TTTCATAATTTAATTG-CTGAAGCTACCCCT
1 TTTCATAATTTGATAGTC-GAAGCTATCCCT
* * *
102756 TTTCAAAATTTTGATAGCCAAAGCTATCCCT
1 TTTCATAA-TTTGATAGTCGAAGCTATCCCT
* ** ** * *
102787 TTTTATTGTTTGACGGTCGTCA-CCATCCCT
1 TTTCATAATTTGATAGTCG-AAGCTATCCCT
* *
102817 TTTCAT--TGTTGATGGTC-ATCA-CCATCCCT
1 TTTCATAAT-TTGATAGTCGA--AGCTATCCCT
*
102846 TTTCATAATTCGATAGTCGAAGCTATCCCT
1 TTTCATAATTTGATAGTCGAAGCTATCCCT
102876 TT
1 TT
102878 CCATTAGTCG
Statistics
Matches: 183, Mismatches: 40, Indels: 36
0.71 0.15 0.14
Matches are distributed among these distances:
28 2 0.01
29 48 0.26
30 105 0.57
31 27 0.15
32 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (30 bp):
TTTCATAATTTGATAGTCGAAGCTATCCCT
Found at i:108651 original size:13 final size:13
Alignment explanation
Indices: 108633--108658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
108623 ATATTATAAT
108633 TATTTTATGTTAA
1 TATTTTATGTTAA
108646 TATTTTATGTTAA
1 TATTTTATGTTAA
108659 AAATAAAAAT
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:110118 original size:40 final size:40
Alignment explanation
Indices: 110029--110229 Score: 329
Period size: 40 Copynumber: 5.1 Consensus size: 40
110019 GGAATAAGAT
110029 CCGAAGGCATTTGTGCTAGTGACTATAT-CGGGCT-AGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
110067 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
110107 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
110147 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
110187 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
110226 CCGA
1 CCGA
110230 GGTACTTGGG
Statistics
Matches: 154, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
38 27 0.18
39 18 0.12
40 107 0.69
41 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:116732 original size:13 final size:13
Alignment explanation
Indices: 116714--116739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
116704 ATATTATAAT
116714 TATTTTATGTTAA
1 TATTTTATGTTAA
116727 TATTTTATGTTAA
1 TATTTTATGTTAA
116740 AAATAAAAAT
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:118130 original size:40 final size:40
Alignment explanation
Indices: 118082--118287 Score: 353
Period size: 40 Copynumber: 5.2 Consensus size: 40
118072 GGACTAAGAT
118082 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
118122 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
118162 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
118202 CCGAAGGCATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
118242 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
118281 CCGAAGG
1 CCGAAGG
118288 TACTTGGGTT
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
39 15 0.09
40 142 0.89
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Done.