Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_291
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: 101210
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:806 original size:13 final size:13
Alignment explanation
Indices: 788--812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
778 CCGAAACTAG
788 AAAGAAAAAAAAC
1 AAAGAAAAAAAAC
801 AAAGAAAAAAAA
1 AAAGAAAAAAAA
813 TGCTCATCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAC
Found at i:1979 original size:40 final size:40
Alignment explanation
Indices: 1890--2153 Score: 351
Period size: 40 Copynumber: 6.7 Consensus size: 40
1880 TTGAATGCTG
* *
1890 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
1929 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
1969 TCCGGGCTAAG-CCCGAAGGTATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2008 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
2048 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
2088 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
2129 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2154 AACGAGGAGC
Statistics
Matches: 204, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
39 52 0.25
40 142 0.70
41 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:2171 original size:120 final size:118
Alignment explanation
Indices: 1890--2186 Score: 329
Period size: 119 Copynumber: 2.5 Consensus size: 118
1880 TTGAATGCTG
* *
1890 TCCGGGCTAAGTCCCGAAGGC-TTGTG--CTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
1 TCCGGGCTAAGTCCCGAAGGCATT-TGAAC-GAGTGACTAA-ATCCGG-TTAA-ATCCCGAAGGC
* * *
1950 ATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGTATTTGTGCGAGTTACTAAA
61 ATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
* ** * *
2008 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTT
* *
2073 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
65 GTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTGTGCGAATTACTA-AA
* * *
2129 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
2187 TACGTGATTT
Statistics
Matches: 152, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
118 23 0.15
119 64 0.42
120 63 0.41
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (118 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTG
TGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTGCGAATTACTAAA
Found at i:8761 original size:13 final size:13
Alignment explanation
Indices: 8743--8767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8733 CCGAAACTAG
8743 AAAGAAAAAAAAC
1 AAAGAAAAAAAAC
8756 AAAGAAAAAAAA
1 AAAGAAAAAAAA
8768 TGCTCATCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAC
Found at i:9980 original size:79 final size:80
Alignment explanation
Indices: 9845--10068 Score: 289
Period size: 79 Copynumber: 2.8 Consensus size: 80
9835 TTGAATGCTG
* * *
9845 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGCTAAG-TCCCGAAGGCA
*
9906 TTTGTGCGAGATACTAAT
63 TTTGTGCGAGATACTAAA
*
9924 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
*
9988 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAA
* * *
10003 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
10067 TG
65 TG
10069 AACGAGGAGC
Statistics
Matches: 129, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
78 10 0.08
79 61 0.47
80 56 0.43
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:10082 original size:40 final size:40
Alignment explanation
Indices: 9845--10068 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
9835 TTGAATGCTG
* *
9845 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
9884 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
9924 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
9963 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
10003 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
10044 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10069 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 53 0.32
40 103 0.62
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:10086 original size:80 final size:80
Alignment explanation
Indices: 9845--10101 Score: 244
Period size: 79 Copynumber: 3.2 Consensus size: 80
9835 TTGAATGCTG
* * * *
9845 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAA-TTACTAA-ATCCGGGCTAAG-TCCCGAAGGCA
** *
9906 TTTGTGCGAGAT-ACTAAT
63 TTTGAACGAG-TGACTAAA
* * *
9924 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
** *
9988 GTGCGAGTTACTAAA
66 GAACGAGTGACTAAA
*
10003 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
*
10067 TGAACGAG-GAGCTATA
65 TGAACGAGTGA-CTAAA
* *
10083 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
10102 TACGTGATTT
Statistics
Matches: 154, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
78 11 0.07
79 73 0.47
80 68 0.44
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GAACGAGTGACTAAA
Found at i:12874 original size:19 final size:19
Alignment explanation
Indices: 12830--12874 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12820 GTTAAAACAC
*
12830 AAAAGAAAAGAAAAATGAGA
1 AAAAG-AAAGAAAAATGAAA
* *
12850 AGAAGAAAGAAAAATTAAA
1 AAAAGAAAGAAAAATGAAA
12869 AAAAGA
1 AAAAGA
12875 GAGTGAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAAGAAAGAAAAATGAAA
Found at i:18368 original size:42 final size:42
Alignment explanation
Indices: 18309--18390 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
18299 AATTCAAAGA
*
18309 GATAAGAACAAGAGTTCAAATGTTTGAATTTCAAATGTTTTG
1 GATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTTG
18351 GATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 GATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
18391 CACACATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (42 bp):
GATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTTG
Found at i:29555 original size:40 final size:40
Alignment explanation
Indices: 29511--29814 Score: 459
Period size: 40 Copynumber: 7.6 Consensus size: 40
29501 AAGTGAACAT
* * * * *
29511 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAA
29551 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
29591 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
*
29631 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
*
29671 ATCTGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
*
29711 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
* * *
29751 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
* * *
29790 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
29815 TGAACGAGGA
Statistics
Matches: 247, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
39 35 0.14
40 212 0.86
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
Found at i:37968 original size:13 final size:13
Alignment explanation
Indices: 37950--37974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37940 TTCGAGAGAT
37950 TTGTGAGGTTTTG
1 TTGTGAGGTTTTG
37963 TTGTGAGGTTTT
1 TTGTGAGGTTTT
37975 ATTTTCATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.36, T:0.56
Consensus pattern (13 bp):
TTGTGAGGTTTTG
Found at i:39748 original size:19 final size:19
Alignment explanation
Indices: 39726--39766 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
39716 ATACAAAAGA
*
39726 AAAGAAAAATGAAAAAAAT
1 AAAGAAAAATCAAAAAAAT
*
39745 AAAGAAAATTCAAAAAAAT
1 AAAGAAAAATCAAAAAAAT
39764 AAA
1 AAA
39767 ATGAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAGAAAAATCAAAAAAAT
Found at i:46492 original size:19 final size:21
Alignment explanation
Indices: 46459--46506 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
46449 AGGAAGACAA
46459 AAAAAGA-AATCAAAAA-A-G
1 AAAAAGAGAATCAAAAAGAGG
*
46477 AAAAAGAGAATGAAAAAGAGG
1 AAAAAGAGAATCAAAAAGAGG
46498 AAAAAGAGA
1 AAAAAGAGA
46507 TTGAGAGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 8 0.31
20 1 0.04
21 10 0.38
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.04
Consensus pattern (21 bp):
AAAAAGAGAATCAAAAAGAGG
Found at i:52452 original size:45 final size:45
Alignment explanation
Indices: 52388--52607 Score: 332
Period size: 45 Copynumber: 4.9 Consensus size: 45
52378 ATTTCCTGGC
*
52388 TAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAAATCGAAGA
1 TAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
52433 TAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
1 TAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
* * * *
52478 TAGCTGATCTTATCTTCCTGTATTGGCAGAGAAGTAGATTGAAGA
1 TAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
* * *
52523 TAGTAGATCTTGTCTTCCTGCATTGGCAGTGAAGTAGATCGAAGA
1 TAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
* ** *
52568 TAGCAGATCTTGTCTTCCTGTACTAACAGTGAAGTAGATC
1 TAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
52608 AAAGGCATCA
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 159 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (45 bp):
TAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
Found at i:54721 original size:31 final size:29
Alignment explanation
Indices: 54643--54723 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 29
54633 AATCATTATT
*
54643 TCTATTTTTATAACTTATATATGTAATCA
1 TCTATTTTTATAACTTATATATATAATCA
* *
54672 -CTATTTTCATAATCTATATATACATACAT-A
1 TCTATTTTTATAA-CT-TATATATATA-ATCA
54702 TCTATTTTTATAACTTATATAT
1 TCTATTTTTATAACTTATATAT
54724 GTACATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 11 0.26
29 8 0.19
30 11 0.26
31 13 0.30
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.51
Consensus pattern (29 bp):
TCTATTTTTATAACTTATATATATAATCA
Found at i:54751 original size:19 final size:18
Alignment explanation
Indices: 54729--54788 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
54719 TATATGTACA
54729 TATATATACTTATATTTTT
1 TATATATA-TTATATTTTT
* *
54748 TATACATATTTTATAATTTTA
1 TAT--ATATATTAT-ATTTTT
54769 TATATATATCTATATTTTT
1 TATATATAT-TATATTTTT
54788 T
1 T
54789 TCATTTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 14 0.42
20 7 0.21
21 12 0.36
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATATATTATATTTTT
Found at i:54766 original size:21 final size:20
Alignment explanation
Indices: 54738--54786 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
54728 ATATATATAC
*
54738 TTATATTTTTTATACATATT
1 TTATATTTTATATACATATT
*
54758 TTATAATTTTATATATATA-T
1 TTAT-ATTTTATATACATATT
*
54778 CTATATTTT
1 TTATATTTT
54787 TTTCATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 8 0.32
21 12 0.48
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATATTTTATATACATATT
Found at i:69465 original size:47 final size:47
Alignment explanation
Indices: 69243--69886 Score: 901
Period size: 47 Copynumber: 13.4 Consensus size: 47
69233 CAGCCAAGAG
* * *
69243 AGTGTATATGTGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
69290 AGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTA--TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
69339 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
69390 AGTATATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AG----TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
69441 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
69488 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
69535 AGTGTATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
69586 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
69633 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
69680 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
69727 AGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
69774 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * * * * * * * *
69821 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
69868 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
69887 TCCCGAAAGG
Statistics
Matches: 553, Mismatches: 32, Indels: 24
0.91 0.05 0.04
Matches are distributed among these distances:
47 372 0.67
49 43 0.08
51 134 0.24
53 4 0.01
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:69553 original size:145 final size:145
Alignment explanation
Indices: 69245--69827 Score: 949
Period size: 145 Copynumber: 4.0 Consensus size: 145
69235 GCCAAGAGAG
* *
69245 TGTATATGTGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATGTGATAA
1 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTA--TATATGTGATAA
* * *
69310 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTGATAAGGCCTAATGGCCGA
64 GGCCTAATAGCCGACGTGATGAATGTGAAA--G--TGTATATATGTGATAAGGCCTAATAGCCGA
*
69375 TGTGATGAATGTGAAAGTATA
125 TGTGATGAATGTGAAAGTGTA
*
69396 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGG
1 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
*
69461 CCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGAT
66 CCTAATAGCCGACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
69526 GAATGTGAAAGTGTA
131 GAATGTGAAAGTGTA
*
69541 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGG
1 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
*
69606 CCTAATAGCCGACGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGAT
66 CCTAATAGCCGACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
69671 GAATGTGAAA--G--
131 GAATGTGAAAGTGTA
*
69682 TGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
1 TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
* * * *
69747 CCTAATGGCCGATGCGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAT
66 CCTAATAGCCGACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
69812 GAATGTGAAAGTGTA
131 GAATGTGAAAGTGTA
69827 T
1 T
69828 ATATGTGACA
Statistics
Matches: 413, Mismatches: 15, Indels: 14
0.93 0.03 0.03
Matches are distributed among these distances:
141 133 0.32
143 2 0.00
145 189 0.46
147 1 0.00
149 39 0.09
151 49 0.12
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.30
Consensus pattern (145 bp):
TGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCTAATAGCCGACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGAT
GAATGTGAAAGTGTA
Found at i:70061 original size:37 final size:37
Alignment explanation
Indices: 70005--70083 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
69995 CCGAGCTCTA
* * * *
70005 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
* *
70042 AAGACCCGATAACTTCGTGTGGAGATTATGTCTAGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
70079 AAGAC
1 AAGAC
70084 TTCATAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
Found at i:76828 original size:18 final size:18
Alignment explanation
Indices: 76807--76848 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
76797 AGGAAGACAT
76807 AAAAAGA-AATCGAAAAAG
1 AAAAAGAGAAT-GAAAAAG
76825 AAAAAGAGAATGAAAAAG
1 AAAAAGAGAATGAAAAAG
76843 AGAAAA
1 A-AAAA
76849 AAGAGATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (18 bp):
AAAAAGAGAATGAAAAAG
Found at i:78651 original size:33 final size:34
Alignment explanation
Indices: 78614--78685 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
78604 GAGTTAGTTT
78614 ATTAAATTTAATTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAATTCAGCTCAAATAAGTGTTAGTA
* * *
78647 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAATTCAGCTCAAATAAGTGTTAGTA
78681 ATTAA
1 ATTAA
78686 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAATTCAGCTCAAATAAGTGTTAGTA
Found at i:82144 original size:16 final size:17
Alignment explanation
Indices: 82125--82163 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
82115 GTCCTATATC
82125 TTTCTTT-AACTTT-TT
1 TTTCTTTAAACTTTATT
82140 GTTTCTTTAAACTTTATT
1 -TTTCTTTAAACTTTATT
82158 TTTCTT
1 TTTCTT
82164 CTTTTCCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 12 0.57
18 2 0.10
ACGTcount: A:0.15, C:0.13, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTCTTTAAACTTTATT
Found at i:86231 original size:20 final size:20
Alignment explanation
Indices: 86206--86250 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
86196 AATGTGTCTT
86206 GTCTTAACCGAATTAATTGG
1 GTCTTAACCGAATTAATTGG
** *
86226 GTCTTAACTTAATTAATTGT
1 GTCTTAACCGAATTAATTGG
86246 GTCTT
1 GTCTT
86251 GTTCTATTTA
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:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (20 bp):
GTCTTAACCGAATTAATTGG
Found at i:98444 original size:22 final size:24
Alignment explanation
Indices: 98408--98451 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
98398 TAATGATGTG
*
98408 CAAACTATAACATAATTAAAAACA
1 CAAACTATAACATAACTAAAAACA
98432 CAAACTA-AA-ATAACTAAAAA
1 CAAACTATAACATAACTAAAAA
98452 TTAATGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 2 0.11
24 7 0.37
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (24 bp):
CAAACTATAACATAACTAAAAACA
Found at i:100212 original size:27 final size:27
Alignment explanation
Indices: 100161--100212 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
100151 TTTTGTTCAA
* *
100161 TCTCAATCTCGTTTTTCTTTTTCTCAC
1 TCTCAATCTCGTTTTTCCTTCTCTCAC
* *
100188 TCTCACTCTCTTTTTTCCTTCTCTC
1 TCTCAATCTCGTTTTTCCTTCTCTC
100213 GAGTTCGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.08, C:0.35, G:0.02, T:0.56
Consensus pattern (27 bp):
TCTCAATCTCGTTTTTCCTTCTCTCAC
Done.