Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold638
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: 62167
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8369 original size:10 final size:10
Alignment explanation
Indices: 8354--8429 Score: 75
Period size: 10 Copynumber: 7.6 Consensus size: 10
8344 ACGAGCTCAA
*
8354 TGAGCTAAAT
1 TGAGCTGAAT
8364 TGAGCTTGAA-
1 TGAGC-TGAAT
8374 TGAGCTGAAT
1 TGAGCTGAAT
* *
8384 TGAGCTCAAA
1 TGAGCTGAAT
*
8394 TGAGCTGACT
1 TGAGCTGAAT
8404 TGAGCTCGAA-
1 TGAGCT-GAAT
*
8414 TGAGCTGACT
1 TGAGCTGAAT
8424 TGAGCT
1 TGAGCT
8430 CAAGTGAGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
9 6 0.11
10 43 0.80
11 5 0.09
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (10 bp):
TGAGCTGAAT
Found at i:8375 original size:20 final size:20
Alignment explanation
Indices: 8346--8430 Score: 118
Period size: 20 Copynumber: 4.3 Consensus size: 20
8336 AGCTAAAAAC
*
8346 GAGCTC-AATGAGCTAAATT
1 GAGCTCGAATGAGCTGAATT
*
8365 GAGCTTGAATGAGCTGAATT
1 GAGCTCGAATGAGCTGAATT
* *
8385 GAGCTCAAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
*
8405 GAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATT
8425 GAGCTC
1 GAGCTC
8431 AAGTGAGTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 5 0.08
20 54 0.92
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGAATT
Found at i:8399 original size:40 final size:40
Alignment explanation
Indices: 8346--8437 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
8336 AGCTAAAAAC
*
8346 GAGCTC-AATGAGCTAAATTGAGCTTGAATGAGCTGAATT
1 GAGCTCAAATGAGCTAAATTGAGCTCGAATGAGCTGAATT
* * *
8385 GAGCTCAAATGAGCTGACTTGAGCTCGAATGAGCTGACTT
1 GAGCTCAAATGAGCTAAATTGAGCTCGAATGAGCTGAATT
*
8425 GAGCTCAAGTGAG
1 GAGCTCAAATGAG
8438 TTGAACCACA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 6 0.13
40 41 0.87
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.25
Consensus pattern (40 bp):
GAGCTCAAATGAGCTAAATTGAGCTCGAATGAGCTGAATT
Found at i:8437 original size:10 final size:10
Alignment explanation
Indices: 8346--8437 Score: 64
Period size: 10 Copynumber: 9.3 Consensus size: 10
8336 AGCTAAAAAC
8346 GAGCTCAA-T
1 GAGCTCAATT
*
8355 GAGCTAAATT
1 GAGCTCAATT
*
8365 GAGCTTGAA-T
1 GAGC-TCAATT
*
8375 GAGCTGAATT
1 GAGCTCAATT
*
8385 GAGCTCAAAT
1 GAGCTCAATT
* *
8395 GAGCTGACTT
1 GAGCTCAATT
8405 GAGCTCGAA-T
1 GAGCTC-AATT
* *
8415 GAGCTGACTT
1 GAGCTCAATT
*
8425 GAGCTCAAGT
1 GAGCTCAATT
8435 GAG
1 GAG
8438 TTGAACCACA
Statistics
Matches: 64, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
9 12 0.19
10 48 0.75
11 4 0.06
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.25
Consensus pattern (10 bp):
GAGCTCAATT
Found at i:8437 original size:20 final size:19
Alignment explanation
Indices: 8346--8442 Score: 113
Period size: 20 Copynumber: 4.9 Consensus size: 19
8336 AGCTAAAAAC
*
8346 GAGCTCAATGAGCTAAATT
1 GAGCTCAATGAGCTGAATT
*
8365 GAGCTTGAATGAGCTGAATT
1 GAGC-TCAATGAGCTGAATT
*
8385 GAGCTCAAATGAGCTGACTT
1 GAGCTC-AATGAGCTGAATT
*
8405 GAGCTCGAATGAGCTGACTT
1 GAGCTC-AATGAGCTGAATT
*
8425 GAGCTCAAGTGAGTTGAA
1 GAGCTCAA-TGAGCTGAA
8443 CCACATGAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.10
20 61 0.90
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:11924 original size:17 final size:18
Alignment explanation
Indices: 11902--11943 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
11892 TATCATATCA
*
11902 CTCATTTCTTT-TGCACT
1 CTCATTTCTTTCTGCAAT
*
11919 CTCATTTCTTTCTTCAAT
1 CTCATTTCTTTCTGCAAT
11937 CTCATTT
1 CTCATTT
11944 TCAATTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.14, C:0.29, G:0.02, T:0.55
Consensus pattern (18 bp):
CTCATTTCTTTCTGCAAT
Found at i:13879 original size:22 final size:23
Alignment explanation
Indices: 13835--13879 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
13825 GTACCTATTT
*
13835 CCAAATCTAATTCGTACCAAAAC
1 CCAAATCTAATTCGTAACAAAAC
* *
13858 CCAAATCT-TTTCGTAACTAAAC
1 CCAAATCTAATTCGTAACAAAAC
13880 ATAAATCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.40, C:0.29, G:0.04, T:0.27
Consensus pattern (23 bp):
CCAAATCTAATTCGTAACAAAAC
Found at i:17845 original size:14 final size:13
Alignment explanation
Indices: 17817--17863 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
17807 AATAAGTGAG
**
17817 GAAAAAGAAGGAT
1 GAAAAAGAAAAAT
*
17830 GAGAAGAGAAAAAT
1 GA-AAAAGAAAAAT
17844 GAAAAAGAAAAA-
1 GAAAAAGAAAAAT
17856 GAAAAAGA
1 GAAAAAGA
17864 TGAAATGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 8 0.28
13 11 0.38
14 10 0.34
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (13 bp):
GAAAAAGAAAAAT
Found at i:18019 original size:18 final size:17
Alignment explanation
Indices: 17966--18024 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
17956 AATGATTGTC
*
17966 GAAAAAGAAAGAGCG-A
1 GAAAAAGAAAGAGAGAA
17982 -AAAAAGAAAGAGAGATA
1 GAAAAAGAAAGAGAGA-A
*
17999 GAAAAAGAAACGAGTGAA
1 GAAAAAGAAA-GAGAGAA
*
18017 GAATAAGA
1 GAAAAAGA
18025 GAATGTTCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 13 0.36
17 1 0.03
18 17 0.47
19 5 0.14
ACGTcount: A:0.64, C:0.03, G:0.27, T:0.05
Consensus pattern (17 bp):
GAAAAAGAAAGAGAGAA
Found at i:29006 original size:18 final size:18
Alignment explanation
Indices: 28985--29028 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
28975 AAAGGAAGAC
28985 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
29003 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
29021 AGAGAAAA
1 AGA-AAAA
29029 AAGAGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:30819 original size:33 final size:34
Alignment explanation
Indices: 30782--30853 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
30772 GAGTTAGTTT
30782 ATTAAATTTAATTCAACTCAAATAAGTGTTAG-A
1 ATTAAATTTAATTCAACTCAAATAAGTGTTAGTA
* * * *
30815 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAATTCAACTCAAATAAGTGTTAGTA
30849 ATTAA
1 ATTAA
30854 TTTGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAATTCAACTCAAATAAGTGTTAGTA
Found at i:37429 original size:40 final size:39
Alignment explanation
Indices: 37392--37569 Score: 180
Period size: 40 Copynumber: 4.5 Consensus size: 39
37382 ATATCCGGAC
37392 TAAGATCCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGT
* * *
37432 TAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * *
37472 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
** * * *
37512 TAAGTCCCGAAGGCA-TTGTGAAAGTTACTAAAACCGGGC
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
*
37551 TATGTCCCGAAGGCATTTG
1 TAAGT-CCGAAGGCATTTG
37570 AACGAGGAGC
Statistics
Matches: 119, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
39 32 0.27
40 84 0.71
41 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
Found at i:37482 original size:80 final size:79
Alignment explanation
Indices: 37398--37569 Score: 220
Period size: 80 Copynumber: 2.2 Consensus size: 79
37388 GGACTAAGAT
* **
37398 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGAAAGGTACT
* *
37462 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * *
37478 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGAAAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGAAAGGTACTAA
*
37543 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
37557 CCGAAGGCATTTG
1 CCGAAGGCATTTG
37570 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 37 0.47
80 39 0.49
81 3 0.04
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGAAAGGTACTAA
AACCGGGCTAAGTC
Found at i:37549 original size:39 final size:39
Alignment explanation
Indices: 37345--37571 Score: 172
Period size: 40 Copynumber: 5.7 Consensus size: 39
37335 ATGAATGCTG
* * * * * * *
37345 TCCGGGCTAAGTCCTGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTG-AAAGTTACTAAA
** ** *
37385 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGAAAGTTACTAAA
* * ** *
37424 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGAAAGTTACTAAA
** *
37465 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGAAAGTTACTAAA
37505 TCCGGGTTAAGTCCCGAAGGCATTGTGAAAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGAAAGTTACTAAA
* * *
37544 ACCGGGCTATGTCCCGAAGGCATT-TGAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGAA
37572 CGAGGAGCTA
Statistics
Matches: 156, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
38 4 0.03
39 38 0.24
40 104 0.67
41 10 0.06
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGAAAGTTACTAAA
Found at i:37587 original size:79 final size:80
Alignment explanation
Indices: 37425--37602 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
37415 AGATACAAAT
* * ** * *
37425 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGAAAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
37490 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * *
37505 TCCGGGTTAAGTCCCGAAGG-CATTGTGAAAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGAAAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
37569 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
37584 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
37603 TACGTGATTT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
78 16 0.20
79 47 0.57
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGAAAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:39284 original size:80 final size:80
Alignment explanation
Indices: 39151--39310 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
39141 CCCAAACCCA
39151 ATCTCCGAGTTCAAGGACAACTCGTTTGCACCCCTTATTTGCTTTCTTGGTGTTGATGGCATTTA
1 ATCTCCGAGTTCAAGGACAACTCGTTTGCACCCCTTATTTGCTTTCTTGGTGTTGATGGCATTTA
39216 TTTTGGCTATTCGTT
66 TTTTGGCTATTCGTT
39231 ATCTCCGAGTTCAAGGACAACTCGTTTGCACCCCTTATTTGCTTTCTTGGTGTTGATGGCATTTA
1 ATCTCCGAGTTCAAGGACAACTCGTTTGCACCCCTTATTTGCTTTCTTGGTGTTGATGGCATTTA
39296 TTTTGGCTATTCGTT
66 TTTTGGCTATTCGTT
39311 GCCTAGCCTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.42
Consensus pattern (80 bp):
ATCTCCGAGTTCAAGGACAACTCGTTTGCACCCCTTATTTGCTTTCTTGGTGTTGATGGCATTTA
TTTTGGCTATTCGTT
Found at i:48129 original size:16 final size:16
Alignment explanation
Indices: 48108--48144 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
48098 AAAACTAGCC
48108 TTTTTTTTTCA-AAAT
1 TTTTTTTTTCACAAAT
48123 TTTTTTTTTCACAAAT
1 TTTTTTTTTCACAAAT
48139 TTTTTT
1 TTTTTT
48145 GAGTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTTTTCACAAAT
Found at i:49410 original size:22 final size:24
Alignment explanation
Indices: 49374--49417 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
49364 TAATGATGTG
*
49374 CAAACTATAACATAATTAAAAACA
1 CAAACTATAACATAACTAAAAACA
49398 CAAACTA-AA-ATAACTAAAAA
1 CAAACTATAACATAACTAAAAA
49418 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:51120 original size:26 final size:24
Alignment explanation
Indices: 51091--51138 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
51081 TTTTGTTCAA
*
51091 TCTCAATCTCGTTTTCTTTTTCTCAC
1 TCTCAATCTC-TTTT-TTCTTCTCAC
*
51117 TCTCACTCTCTTTTTTCTTCTC
1 TCTCAATCTCTTTTTTCTTCTC
51139 TCGAGTTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 4 0.20
26 9 0.45
ACGTcount: A:0.08, C:0.33, G:0.02, T:0.56
Consensus pattern (24 bp):
TCTCAATCTCTTTTTTCTTCTCAC
Found at i:53874 original size:19 final size:19
Alignment explanation
Indices: 53830--53874 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
53820 GTTAAAACTC
*
53830 AAAAGAAAAGAAAAATGAGA
1 AAAAG-AAAGAAAAATGAAA
* *
53850 AGAAGAAAGAAAAATTAAA
1 AAAAGAAAGAAAAATGAAA
53869 AAAAGA
1 AAAAGA
53875 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:59356 original size:42 final size:42
Alignment explanation
Indices: 59297--59378 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
59287 AATTCAAAGA
59297 GATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTTG
1 GATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTTG
*
59339 GATAAGAATAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 GATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
59379 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
Done.