Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2226
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: 24212
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1592 original size:20 final size:21
Alignment explanation
Indices: 1567--1605 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1557 ACACTCTTCA
1567 TTCTTTTCCTGTT-TTTTTTT
1 TTCTTTTCCTGTTATTTTTTT
*
1587 TTCTTTTTCTGTTATTTTT
1 TTCTTTTCCTGTTATTTTT
1606 CCACCCTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (21 bp):
TTCTTTTCCTGTTATTTTTTT
Found at i:8366 original size:15 final size:16
Alignment explanation
Indices: 8346--8385 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
8336 ATTATATAAA
8346 TTAATTAATATAA-TT
1 TTAATTAATATAACTT
*
8361 TTAATTAATTTAACTT
1 TTAATTAATATAACTT
*
8377 GTAATTAAT
1 TTAATTAAT
8386 TGAATCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
TTAATTAATATAACTT
Found at i:9228 original size:28 final size:27
Alignment explanation
Indices: 9196--9276 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 27
9186 TTTTATTTAT
*
9196 TATTAAAAAATTATTATATTAATATAAA
1 TATTAAAATATT-TTATATTAATATAAA
*
9224 TATTAATAT-TTTTATAATTAAATATAAA
1 TATTAAAATATTTTAT-ATT-AATATAAA
9252 TA--AAAATATTTT-TATTAAT-TAAA
1 TATTAAAATATTTTATATTAATATAAA
9275 TA
1 TA
9277 ATTATTTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
23 6 0.13
24 3 0.06
25 3 0.06
26 9 0.19
27 9 0.19
28 17 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTAAAATATTTTATATTAATATAAA
Found at i:9741 original size:29 final size:29
Alignment explanation
Indices: 9709--9782 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
9699 TATTTTTAAA
*
9709 AAAATAAATTTTTATATTTTTA-TTATAT
1 AAAATAAATTTTTATATTTTGAGTTATAT
* *
9737 CAAAATAAATTTTTTTCTTTTGAGTTATAT
1 -AAAATAAATTTTTATATTTTGAGTTATAT
*
9767 ATAAATTAATTTTTAT
1 A-AAATAAATTTTTAT
9783 TCAAATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 20 0.53
30 18 0.47
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (29 bp):
AAAATAAATTTTTATATTTTGAGTTATAT
Found at i:9820 original size:22 final size:23
Alignment explanation
Indices: 9769--9811 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
9759 AGTTATATAT
*
9769 AAATTAATTTTTATTCAAATAAA
1 AAATTAATTTATATTCAAATAAA
9792 AAATTAATTTATATT-AAATA
1 AAATTAATTTATATTCAAATA
9812 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTAATTTATATTCAAATAAA
Found at i:9821 original size:12 final size:12
Alignment explanation
Indices: 9798--9859 Score: 54
Period size: 13 Copynumber: 5.1 Consensus size: 12
9788 TAAAAAATTA
9798 ATTTATATTAAAT
1 ATTTA-ATTAAAT
9811 ATTTAATTAAAT
1 ATTTAATTAAAT
* *
9823 A-TAAATTAAAA
1 ATTTAATTAAAT
* *
9834 ATTAAAATTAAAA
1 ATT-TAATTAAAT
*
9847 ATTTATTTAAAT
1 ATTTAATTAAAT
9859 A
1 A
9860 CAAAATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
11 9 0.21
12 16 0.38
13 17 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTTAATTAAAT
Found at i:9936 original size:22 final size:23
Alignment explanation
Indices: 9911--9960 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
9901 TTAAAATTTT
9911 ATTTTAA-TATAATAAAA-ATAAA
1 ATTTTAATTA-AATAAAAGATAAA
9933 ATTTTAATTAAATAAAATGATAAA
1 ATTTTAATTAAATAAAA-GATAAA
9957 ATTT
1 ATTT
9961 AACTATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 14 0.56
23 2 0.08
24 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTTTAATTAAATAAAAGATAAA
Found at i:11465 original size:238 final size:229
Alignment explanation
Indices: 11040--11475 Score: 538
Period size: 238 Copynumber: 1.9 Consensus size: 229
11030 TCAACTGCTT
* * * *
11040 ATGAATGGATTAAAACTTTTGAAATTACTCATTGAGATCAGTTGTGAAGTCAGAGAGGGGAGGAA
1 ATGAATGGAGTAAAACTTTTGAAATTACTCATCGAGATCAGTTGCGAAGTCA-AGAGGGAAGGAA
* *
11105 ATGTCTTCATCTTAACTATTTAAGCTGTTGGAATTTTGTTCTTTAAGTTAAGCTTAGTATTAGGA
65 ATGTCTTCATCTTAACTATTTAAGCTGTTGGAATTTTGTTCTTTAAGTAAAACTTAGTATTAGGA
* * *
11170 CTGTATAAACTTCATTTGTTTTAATCATAAGAAATCTGGACTTCTCATAAATTTTTTTTTTTCCA
130 CAGTAAAAACTTCATTTGTTTTAATCATAAGAAATCTGGACTACTCATAAATTTTTTTTTTTCCA
11235 TTTTAGCCATTTGTCATTGATTGATTTTGCTTCTG
195 TTTTAGCCATTTGTCATTGATTGATTTTGCTTCTG
* *
11270 ATGAATGGAGTAAAATTTTTGAAATTACTCATCGAGATCAGTTGCGAAGTC-AGAGGGAAGGAGA
1 ATGAATGGAGTAAAACTTTTGAAATTACTCATCGAGATCAGTTGCGAAGTCAAGAGGGAAGGAAA
* * * ** * *
11334 TGTCTTCTTTTTGACTATTTAAGCTGTTGGGTTTTTTTTTCTTTCGCATGGCTGAGTAAAATTTA
66 TGTCTTCATCTTAACTATTTAAGCTGTT-GGAATTTTGTTCTTT---A------AGTAAAACTTA
* * *
11399 GTATTAGGACAGTAAAAACTTGATTTGTTTTAATCAT-AGTAAATCTGGACTAGTCAT-GATTTT
121 GTATTAGGACAGTAAAAACTTCATTTGTTTTAATCATAAG-AAATCTGGACTACTCATAAATTTT
*
11462 TTTTCTT-CATTTTA
185 TTTTTTTCCATTTTA
11476 ATTATCTGTC
Statistics
Matches: 173, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
228 36 0.21
229 12 0.07
230 47 0.27
232 1 0.01
236 7 0.04
237 13 0.08
238 57 0.33
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (229 bp):
ATGAATGGAGTAAAACTTTTGAAATTACTCATCGAGATCAGTTGCGAAGTCAAGAGGGAAGGAAA
TGTCTTCATCTTAACTATTTAAGCTGTTGGAATTTTGTTCTTTAAGTAAAACTTAGTATTAGGAC
AGTAAAAACTTCATTTGTTTTAATCATAAGAAATCTGGACTACTCATAAATTTTTTTTTTTCCAT
TTTAGCCATTTGTCATTGATTGATTTTGCTTCTG
Found at i:12922 original size:32 final size:30
Alignment explanation
Indices: 12856--12924 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 30
12846 ATATTGATGG
* * **
12856 TAAATTTGATGAATTAAATATAATTATTTT
1 TAAATTTAATGAATTAAATAAAATTATTCA
*
12886 TAAATTTAATGAATATTAAATAAAATTGTTCA
1 TAAATTTAATG-A-ATTAAATAAAATTATTCA
12918 TAAATTT
1 TAAATTT
12925 GATAAATTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 10 0.31
31 1 0.03
32 21 0.66
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (30 bp):
TAAATTTAATGAATTAAATAAAATTATTCA
Found at i:13411 original size:46 final size:46
Alignment explanation
Indices: 13344--13436 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
13334 AGGAGTGAGG
13344 AGGTCAGCAGGGGAGATTGGCTCACATTTCCAATCTTCCTCGCACC
1 AGGTCAGCAGGGGAGATTGGCTCACATTTCCAATCTTCCTCGCACC
*
13390 AGGTCAGCAGGGGAGATTGGCTCACGTTTCCAATCTTCCTCGCACC
1 AGGTCAGCAGGGGAGATTGGCTCACATTTCCAATCTTCCTCGCACC
13436 A
1 A
13437 TATTTGATCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.22, C:0.30, G:0.25, T:0.24
Consensus pattern (46 bp):
AGGTCAGCAGGGGAGATTGGCTCACATTTCCAATCTTCCTCGCACC
Found at i:15422 original size:57 final size:59
Alignment explanation
Indices: 15361--15471 Score: 172
Period size: 57 Copynumber: 1.9 Consensus size: 59
15351 AAAAATTTTC
* * *
15361 TTTAATTTAAATTACTATGATAAATTA-TAAAAAA-ATGTAATGAATTGAGACATGATT
1 TTTAAATTAAATTACTATGACAAATTACGAAAAAATATGTAATGAATTGAGACATGATT
*
15418 TTTAAATTAAATTACTATGACAAATTACGAAAAAATATGTTATGAATTGAGACA
1 TTTAAATTAAATTACTATGACAAATTACGAAAAAATATGTAATGAATTGAGACA
15472 CGACATGTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 25 0.52
58 6 0.12
59 17 0.35
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (59 bp):
TTTAAATTAAATTACTATGACAAATTACGAAAAAATATGTAATGAATTGAGACATGATT
Found at i:16263 original size:19 final size:20
Alignment explanation
Indices: 16230--16271 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
16220 TTTTCTTTTT
*
16230 CTTTTCTTTCTTTCTCTCTC
1 CTTTTCTTTCTTTCTCTCCC
*
16250 CTTTTTTTTC-TTCTCTCCC
1 CTTTTCTTTCTTTCTCTCCC
16269 CTT
1 CTT
16272 ATGAGCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTCTTTCTTTCTCTCCC
Found at i:16770 original size:19 final size:19
Alignment explanation
Indices: 16746--16797 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
16736 AACCCTTGAA
16746 TGTATCGATACATGTTAAT
1 TGTATCGATACATGTTAAT
16765 TGTATCGATACATGTTAAT
1 TGTATCGATACATGTTAAT
*
16784 TTTATCGATACATG
1 TGTATCGATACATG
16798 AGATTGACAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATGTTAAT
Found at i:18447 original size:13 final size:13
Alignment explanation
Indices: 18429--18454 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18419 CAATTTTTTG
18429 TGTATCGATACAT
1 TGTATCGATACAT
18442 TGTATCGATACAT
1 TGTATCGATACAT
18455 ACTTTGGTGT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:18451 original size:33 final size:33
Alignment explanation
Indices: 18409--18473 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
18399 TACAAGCTAA
* *
18409 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
18442 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
18474 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:20724 original size:279 final size:279
Alignment explanation
Indices: 20224--20783 Score: 1120
Period size: 279 Copynumber: 2.0 Consensus size: 279
20214 ACCGGTTCAT
20224 GAAGTTCCAAAAGTGTGAGCCAACTAAACATCTCAAGTGTTGGATAGTAAATAAAGTCGAATGAC
1 GAAGTTCCAAAAGTGTGAGCCAACTAAACATCTCAAGTGTTGGATAGTAAATAAAGTCGAATGAC
20289 CTGAGATACTTCATGTCGACAGCGCGACATGGTCGATAGCCAACCGAGAAAAGGTTCGATTGAAA
66 CTGAGATACTTCATGTCGACAGCGCGACATGGTCGATAGCCAACCGAGAAAAGGTTCGATTGAAA
20354 TGGTTGAGGTTGGCTTGAGTACGAAAACAACCTTCGAAGAAGGTTTGATTTTGTGGATTCGAGGT
131 TGGTTGAGGTTGGCTTGAGTACGAAAACAACCTTCGAAGAAGGTTTGATTTTGTGGATTCGAGGT
20419 GGAGGCACCTCGAGGATGTTTCTGAGCTGTTGATTTCATCCGAGGGGCCATCGGAATGAATCGAA
196 GGAGGCACCTCGAGGATGTTTCTGAGCTGTTGATTTCATCCGAGGGGCCATCGGAATGAATCGAA
20484 GATGTTTTGGTGTTAAACC
261 GATGTTTTGGTGTTAAACC
20503 GAAGTTCCAAAAGTGTGAGCCAACTAAACATCTCAAGTGTTGGATAGTAAATAAAGTCGAATGAC
1 GAAGTTCCAAAAGTGTGAGCCAACTAAACATCTCAAGTGTTGGATAGTAAATAAAGTCGAATGAC
20568 CTGAGATACTTCATGTCGACAGCGCGACATGGTCGATAGCCAACCGAGAAAAGGTTCGATTGAAA
66 CTGAGATACTTCATGTCGACAGCGCGACATGGTCGATAGCCAACCGAGAAAAGGTTCGATTGAAA
20633 TGGTTGAGGTTGGCTTGAGTACGAAAACAACCTTCGAAGAAGGTTTGATTTTGTGGATTCGAGGT
131 TGGTTGAGGTTGGCTTGAGTACGAAAACAACCTTCGAAGAAGGTTTGATTTTGTGGATTCGAGGT
20698 GGAGGCACCTCGAGGATGTTTCTGAGCTGTTGATTTCATCCGAGGGGCCATCGGAATGAATCGAA
196 GGAGGCACCTCGAGGATGTTTCTGAGCTGTTGATTTCATCCGAGGGGCCATCGGAATGAATCGAA
20763 GATGTTTTGGTGTTAAACC
261 GATGTTTTGGTGTTAAACC
20782 GA
1 GA
20784 GGTTTTTCGG
Statistics
Matches: 281, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
279 281 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (279 bp):
GAAGTTCCAAAAGTGTGAGCCAACTAAACATCTCAAGTGTTGGATAGTAAATAAAGTCGAATGAC
CTGAGATACTTCATGTCGACAGCGCGACATGGTCGATAGCCAACCGAGAAAAGGTTCGATTGAAA
TGGTTGAGGTTGGCTTGAGTACGAAAACAACCTTCGAAGAAGGTTTGATTTTGTGGATTCGAGGT
GGAGGCACCTCGAGGATGTTTCTGAGCTGTTGATTTCATCCGAGGGGCCATCGGAATGAATCGAA
GATGTTTTGGTGTTAAACC
Found at i:21307 original size:13 final size:13
Alignment explanation
Indices: 21289--21313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21279 ATAAACCCCC
21289 TGTATCGATACAG
1 TGTATCGATACAG
21302 TGTATCGATACA
1 TGTATCGATACA
21314 TTGAATTTCC
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Done.