Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3260
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: 34775
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:15726 original size:19 final size:19
Alignment explanation
Indices: 15651--15728 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 19
15641 AATATTTTTC
*
15651 ATTTATGCAATTTTAATTA
1 ATTTATGTAATTTTAATTA
*
15670 A-TT-T-TAATTTT--TAA
1 ATTTATGTAATTTTAATTA
* ** *
15684 ATATTATTTAATTTTTTTTC
1 AT-TTATGTAATTTTAATTA
15704 ATTTATGTAATTTTAATTA
1 ATTTATGTAATTTTAATTA
15723 ATTTAT
1 ATTTAT
15729 TTTATACTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
14 3 0.07
16 8 0.18
17 2 0.04
18 9 0.20
19 20 0.44
20 3 0.07
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTATGTAATTTTAATTA
Found at i:16673 original size:7 final size:7
Alignment explanation
Indices: 16658--16687 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
16648 AAAATAGTCG
*
16658 TTTAATA
1 TTTAGTA
16665 TTTAGTA
1 TTTAGTA
16672 TTTAGTA
1 TTTAGTA
16679 TTTAGTA
1 TTTAGTA
16686 TT
1 TT
16688 ATGTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (7 bp):
TTTAGTA
Found at i:17337 original size:18 final size:18
Alignment explanation
Indices: 17314--17348 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17304 GCCAGGTGCG
* *
17314 TATCCTAGCCCTTATATA
1 TATCCTAACCATTATATA
17332 TATCCTAACCATTATAT
1 TATCCTAACCATTATAT
17349 GTTTCCTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (18 bp):
TATCCTAACCATTATATA
Found at i:20926 original size:96 final size:97
Alignment explanation
Indices: 20820--21016 Score: 297
Period size: 96 Copynumber: 2.0 Consensus size: 97
20810 CTACTGTAGA
* * * *
20820 AAAAGAGCGTCCACATGGGAGCTTTTTTCAAAAATTTTGCTGACATTTCATCCTGCTTGAAGCGT
1 AAAAGAGCGTCCACATAGGAGCTTTTATCAAAAATTTTGCTGACAGTGCATCCTGCTTGAAGCGT
20885 CTTTGATACTATTTGTTCAGAAACATCTTCTC
66 CTTTGATACTATTTGTTCAGAAACATCTTCTC
* ***
20917 AAAA-AGCGTCCACGTAGGAGCTTTTATCTGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCGT
1 AAAAGAGCGTCCACATAGGAGCTTTTATCAAAAATTTTGCTGACAGTGCATCCTGCTTGAAGCGT
**
20981 CTTTGATACTATTTGTTCAGAAATGTCTTCTC
66 CTTTGATACTATTTGTTCAGAAACATCTTCTC
21013 AAAA
1 AAAA
21017 TTATTTTTTC
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
96 86 0.96
97 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (97 bp):
AAAAGAGCGTCCACATAGGAGCTTTTATCAAAAATTTTGCTGACAGTGCATCCTGCTTGAAGCGT
CTTTGATACTATTTGTTCAGAAACATCTTCTC
Found at i:21146 original size:126 final size:125
Alignment explanation
Indices: 20917--21153 Score: 402
Period size: 126 Copynumber: 1.9 Consensus size: 125
20907 ACATCTTCTC
20917 AAAAAGCGTCCACGTAGGAGCTTTTATCTGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTC
1 AAAAAGCGTCCACGTAGGAGCTTTTATCTGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTC
* *
20982 TTTGATACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAGGAACTACTGTAGA
66 TTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAGGAACTACTGTAGA
* * * *
21042 AAAAGAGCGTCCACGTGGGAGCTTTTTTCTGTATTTTTGCTGACAGTGCATCTTGCTTGAAGCGT
1 AAAA-AGCGTCCACGTAGGAGCTTTTATCTGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCGT
*
21107 TTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCA
65 CTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCA
21154 AGGTAAAAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
125 4 0.04
126 100 0.96
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (125 bp):
AAAAAGCGTCCACGTAGGAGCTTTTATCTGTAATTTTGCTGACAGTGCATCCTGCTTGAAGCGTC
TTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAGGAACTACTGTAGA
Found at i:21285 original size:30 final size:30
Alignment explanation
Indices: 21212--21405 Score: 120
Period size: 34 Copynumber: 6.3 Consensus size: 30
21202 TTAAAAAAAC
* *
21212 TAAACCCTAATTTAATTAAATTTAACCATAAACCC
1 TAAACCCTAATTTAATT-TATTT-A--A-AAACCA
* *
21247 TAAGCCCTAATTTAATTTATTTAAAATCC-
1 TAAACCCTAATTTAATTTATTTAAAAACCA
21276 TAGAACCCTAATTTACTTAATTTATTTAAAAACCA
1 TA-AACCCTAA--T--TTAATTTATTTAAAAACCA
21311 TAAACCCTAATTTAATTTATTT-AAAACC-
1 TAAACCCTAATTTAATTTATTTAAAAACCA
* *
21339 T------TATTTTAATTTATTT-AAAACCC
1 TAAACCCTAATTTAATTTATTTAAAAACCA
* *
21362 CAAACCCTAATTTACTTAGTTTATTTAAAAATCA
1 TAAACCCTAATTTA---A-TTTATTTAAAAACCA
21396 TAAACCCTAA
1 TAAACCCTAA
21406 ACCCTAATTT
Statistics
Matches: 130, Mismatches: 11, Indels: 37
0.73 0.06 0.21
Matches are distributed among these distances:
22 20 0.15
28 1 0.01
29 14 0.11
30 22 0.17
31 1 0.01
32 3 0.02
33 8 0.06
34 43 0.33
35 18 0.14
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.38
Consensus pattern (30 bp):
TAAACCCTAATTTAATTTATTTAAAAACCA
Found at i:21322 original size:64 final size:65
Alignment explanation
Indices: 21214--21336 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 65
21204 AAAAAAACTA
* * *
21214 AACCCTAATTTAATTAAATTTAACCATAAACCCTAAGCCCTAATTTAATTTATTTAAAATCCTAG
1 AACCCTAATTTAATTAAATTTAACCAAAAACCATAAACCCTAATTTAATTTATTTAAAATCCTAG
* ***
21279 AACCCTAATTTACTT-AATTTATTTAAAAACCATAAACCCTAATTTAATTTATTTAAAA
1 AACCCTAATTTAATTAAATTTAACCAAAAACCATAAACCCTAATTTAATTTATTTAAAA
21337 CCTTATTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 37 0.73
65 14 0.27
ACGTcount: A:0.43, C:0.18, G:0.02, T:0.37
Consensus pattern (65 bp):
AACCCTAATTTAATTAAATTTAACCAAAAACCATAAACCCTAATTTAATTTATTTAAAATCCTAG
Found at i:21346 original size:22 final size:22
Alignment explanation
Indices: 21312--21361 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
21302 TAAAAACCAT
21312 AAACCCTAATTTAATTTATTTA
1 AAACCCTAATTTAATTTATTTA
* *
21334 AAACCTTATTTTAATTTATTTA
1 AAACCCTAATTTAATTTATTTA
21356 AAACCC
1 AAACCC
21362 CAAACCCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (22 bp):
AAACCCTAATTTAATTTATTTA
Found at i:21379 original size:85 final size:85
Alignment explanation
Indices: 21253--21499 Score: 316
Period size: 85 Copynumber: 2.8 Consensus size: 85
21243 ACCCTAAGCC
* *
21253 CTAATTTAATTTATTTAAAATCCTAGAACCCTAATTTACTTAATTTATTTAAAAACCATAAACCC
1 CTAATTTAATTTATTTAAAA-CCCAAAACCCTAATTTACTTAATTTATTTAAAAACCATAAACCC
21318 TAATTTAATTTATTTAAAACCT
65 TAATTTAATTTATTT-AAACCT
* * * *
21340 -TATTTTAATTTATTTAAAACCCCAAACCCTAATTTACTTAGTTTATTTAAAAATCATAAACCCT
1 CTAATTTAATTTATTTAAAACCCAAAACCCTAATTTACTTAATTTATTTAAAAACCATAAACCCT
** *
21404 AAACCCTAATTTATTTAAAGCT
66 -AA-TTTAATTTATTTAAACCT
* * *
21426 CTAACTTAGTTTATTTAAAACCCTAAAAACCCTAATTTACTTAATTTATTTAAAAACCATAAACT
1 CTAATTTAATTTATTTAAAACCC--AAAACCCTAATTTACTTAATTTATTTAAAAACCATAAACC
*
21491 CTTATTTAA
64 CTAATTTAA
21500 ATAATTTTTA
Statistics
Matches: 136, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
85 40 0.29
86 25 0.18
87 32 0.24
88 1 0.01
89 38 0.28
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.40
Consensus pattern (85 bp):
CTAATTTAATTTATTTAAAACCCAAAACCCTAATTTACTTAATTTATTTAAAAACCATAAACCCT
AATTTAATTTATTTAAACCT
Found at i:21505 original size:34 final size:35
Alignment explanation
Indices: 21435--21514 Score: 83
Period size: 34 Copynumber: 2.3 Consensus size: 35
21425 TCTAACTTAG
* **
21435 TTTATTTAAAACCCTAAAAACCCTAATTTACTTAA
1 TTTATTTAAAAACCTAAAAACCCTAATTTAAATAA
* * *
21470 TTTATTTAAAAACC-ATAAACTCTTATTTAAATAA
1 TTTATTTAAAAACCTAAAAACCCTAATTTAAATAA
21504 TTT-TTATAAAA
1 TTTATT-TAAAA
21515 TAACACTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 2 0.05
34 23 0.61
35 13 0.34
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (35 bp):
TTTATTTAAAAACCTAAAAACCCTAATTTAAATAA
Found at i:23141 original size:27 final size:27
Alignment explanation
Indices: 23111--23288 Score: 106
Period size: 27 Copynumber: 6.6 Consensus size: 27
23101 ATATTGAGCC
* * *
23111 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
23138 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
23165 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
23193 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
*** **
23220 CGCACACTTAGTGC-ATCATGTTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
23247 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
23274 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
23289 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:23204 original size:55 final size:55
Alignment explanation
Indices: 23111--23288 Score: 195
Period size: 54 Copynumber: 3.3 Consensus size: 55
23101 ATATTGAGCC
* * * *
23111 CGCACACTCAGTGCTATACA--ATCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATGTTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
23165 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCAT-GTTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
23220 CGCACACTTAGTGC-ATCATGTTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATGTTCAACTCGCACACTTAGTGCCACATAGTCAAAT
23274 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
23289 GTACAATTTA
Statistics
Matches: 103, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
52 2 0.02
54 57 0.55
55 44 0.43
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATGTTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:31032 original size:27 final size:27
Alignment explanation
Indices: 31002--31177 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
30992 ATATTGAGCC
* * *
31002 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
31029 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
31056 CGCACACTTAGTGCTACATAGT-AACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
31082 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
31109 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
31136 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
31163 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31178 GTACAATTTA
Statistics
Matches: 124, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
26 22 0.18
27 100 0.81
28 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:31139 original size:80 final size:80
Alignment explanation
Indices: 31023--31176 Score: 213
Period size: 80 Copynumber: 1.9 Consensus size: 80
31013 TGCTATACAA
* *
31023 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGT-AACTCGCAC
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAA-TCGCAC
31087 ACTTAGTGCCGCATGG
65 ACTTAGTGCCGCATGG
* * **
31103 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTC-AATCGCA
31167 CACTTAGTGC
64 CACTTAGTGC
31177 TGTACAATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
79 2 0.03
80 46 0.71
81 15 0.23
82 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAATCGCACA
CTTAGTGCCGCATGG
Found at i:34051 original size:41 final size:41
Alignment explanation
Indices: 33896--34225 Score: 450
Period size: 41 Copynumber: 8.0 Consensus size: 41
33886 AAAAATGTAT
* * *
33896 AAACACAGAGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAA
1 AAAC-CAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAA
* * ****
33938 AAA-CAGAGCAATAGCGGCGTTTTAACAAAAACGCCGCTAA
1 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAA
* *
33978 AAA-CAG-GTCAATAGCTGCGCTTTCGGTAAAACGCCGCTAA
1 AAACCAGAG-CATTAGCGGCGCTTTCGGTAAAACGCCGCTAA
*
34018 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGTTAA
1 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAA
34059 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAAACGCCGCTAA
1 AAACCAGAGCATTAGCGGCGCTTTCGGT-AAAACGCCGCTAA
*
34101 AAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAA
1 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAA
* * ** *
34142 AAACCAGAGAATTAACGGCGCTTTCTATAAAATGCCGCTAA
1 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAA
34183 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAA
1 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAA
34224 AA
1 AA
34226 GTCATATAAC
Statistics
Matches: 258, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.00
40 68 0.26
41 146 0.57
42 43 0.17
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18
Consensus pattern (41 bp):
AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAA
Found at i:34149 original size:124 final size:123
Alignment explanation
Indices: 33896--34225 Score: 452
Period size: 124 Copynumber: 2.7 Consensus size: 123
33886 AAAAATGTAT
* * * *
33896 AAACACAGAGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAAA-CAGAGCAATAGCGGCG-TT
1 AAAC-CAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTT
**** *
33959 TTAACAAAAACGCCGCTAAAAACAGGTCAATAGCTGCGCTTTCGGTAAAACGCCGCTAA
65 TCGGTAAAAACGCCGCTAAAAACAGGTCAATAGCGGCGCTTTCGGTAAAACGCCGCTAA
*
34018 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGTTAAAAACCAGAGCATTAGCGGCGCTTT
1 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTT
* *
34083 CGGTAAAAACGCCGCTAAAAACCAGAG-CATTAGCGGCGCTTTTGGTAAAACGCCGCTAA
66 CGGTAAAAACGCCGCTAAAAA-CAG-GTCAATAGCGGCGCTTTCGGTAAAACGCCGCTAA
* * ** *
34142 AAACCAGAGAATTAACGGCGCTTTCTATAAAATGCCGCTAAAAACCAGAGCATTAGCGGCGCTTT
1 AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTT
34207 CGGT-AAAACGCCGCTAAAA
66 CGGTAAAAACGCCGCTAAAA
34226 GTCATATAAC
Statistics
Matches: 186, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
121 36 0.19
122 19 0.10
123 35 0.19
124 95 0.51
125 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18
Consensus pattern (123 bp):
AAACCAGAGCATTAGCGGCGCTTTCGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTT
CGGTAAAAACGCCGCTAAAAACAGGTCAATAGCGGCGCTTTCGGTAAAACGCCGCTAA
Done.