Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2135
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: 31307
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:2222 original size:26 final size:25
Alignment explanation
Indices: 2192--2243 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
2182 CACCACTGAA
*
2192 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACAT-GCAACCCC
2218 TCGGGGAATCAGCACATGCAACCCC
1 TCGGGGAATCAGCACATGCAACCCC
2243 T
1 T
2244 TTTATTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.27, C:0.35, G:0.23, T:0.15
Consensus pattern (25 bp):
TCGGGGAATCAGCACATGCAACCCC
Found at i:2445 original size:102 final size:100
Alignment explanation
Indices: 2170--2521 Score: 445
Period size: 99 Copynumber: 3.5 Consensus size: 100
2160 TGGTGGATCC
*
2170 CGCACTTAGCACCACCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAATCAGCACAT
1 CGCACTTAGCACCACCAATGAATC-GGGAATCAGCACTTAGCAACCCCTCGGGGAATCAGCACAT
2235 -GCAA-CCCCTTTT-ATTTCAAAGA-ATGGTTGGATAT
65 AGCAACCCCCTTTTCATTTCAAAGATAT-G-TGGATAT
*
2269 CACACTTAGCACCACCAATGAATCGGAGAATCAGCACTTTAGCAACCCCTCGGGGGAATCAGCAC
1 CGCACTTAGCACCACCAATGAATCGG-GAATCAGCAC-TTAGCAACCCCTC-GGGGAATCAGCAC
2334 ATAGCAACCCCCCTTTTCATTTC-AAGATATGTGGATAT
63 ATAGCAA-CCCCCTTTTCATTTCAAAGATATGTGGATAT
2372 CGCACTTAGCACCACCAATGAAATCGGGCGAATCAGCACTTAGCAACCCCTC-GGGAATCAGCAC
1 CGCACTTAGCACCACCAATG-AATC-GG-GAATCAGCACTTAGCAACCCCTCGGGGAATCAGCAC
*
2436 ATAGCAACCCCCTTTCACATTTCAAAGATAT-TGG-TGAT
63 ATAGCAACCCCCTTT-TCATTTCAAAGATATGTGGAT-AT
* * **
2474 CACGCACATAGCACCACC-ATAAATCGGG-ATCAGCACACAGCAACCCCT
1 --CGCACTTAGCACCACCAATGAATCGGGAATCAGCACTTAGCAACCCCT
2522 TTTATATACA
Statistics
Matches: 229, Mismatches: 9, Indels: 30
0.85 0.03 0.11
Matches are distributed among these distances:
98 2 0.01
99 50 0.22
100 14 0.06
101 26 0.11
102 38 0.17
103 35 0.15
104 45 0.20
105 19 0.08
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (100 bp):
CGCACTTAGCACCACCAATGAATCGGGAATCAGCACTTAGCAACCCCTCGGGGAATCAGCACATA
GCAACCCCCTTTTCATTTCAAAGATATGTGGATAT
Found at i:5596 original size:26 final size:26
Alignment explanation
Indices: 5540--5597 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
5530 AATACATAGT
*
5540 TTTAATATGTCTATTTTAGGACATCAA
1 TTTAATATGTCTATCTTAGGACA-CAA
*
5567 -TTAATGTGTCTATCTTAGGGACA-AA
1 TTTAATATGTCTATCTTA-GGACACAA
5592 TTTAAT
1 TTTAAT
5598 CAGCTACTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.07
26 20 0.74
27 5 0.19
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (26 bp):
TTTAATATGTCTATCTTAGGACACAA
Found at i:9370 original size:22 final size:21
Alignment explanation
Indices: 9320--9370 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
9310 TCCACGTCTT
*
9320 TTTCTTTTGTTCTTTTTCTAA
1 TTTCTTTTCTTCTTTTTCTAA
9341 -TTCATTTTCTCTCTTTCTTC-AA
1 TTTC-TTTTCT-TCTTT-TTCTAA
9363 TTTCTTTT
1 TTTCTTTT
9371 TCACTCTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 11 0.44
23 6 0.24
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTCTTTTCTTCTTTTTCTAA
Found at i:12298 original size:18 final size:18
Alignment explanation
Indices: 12277--12324 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
12267 AAACTCTTTT
12277 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
12295 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
12313 TCAATCTCTTTT
1 TCATTCTCTTTT
12325 CTTTTTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:12316 original size:24 final size:23
Alignment explanation
Indices: 12252--12332 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 23
12242 CTTGTTCACA
*
12252 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTC-TT
* * * *
12276 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTC-TT
*
12300 TTCTTTTTCACTCTCAATCTCTT
1 TTCTTTTTCTCTCTCAATCTCTT
12323 TTCTTTTTCT
1 TTCTTTTTCT
12333 TTCATTTCTT
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
23 11 0.24
24 34 0.76
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.60
Consensus pattern (23 bp):
TTCTTTTTCTCTCTCAATCTCTT
Found at i:12385 original size:41 final size:41
Alignment explanation
Indices: 12329--12423 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
12319 TCTTTTCTTT
* * *
12329 TTCTTTCA-TTTCTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTGTTTCTTCTCTCGATTTCATTCAAAA
12369 TTCTCTCATTTTCTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTGTTTCTTCTCTCGATTTCATTCAAAA
*
12410 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
12424 CTCATAATCT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 7 0.14
41 43 0.86
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (41 bp):
TTCTCTCATTTTCTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:12401 original size:20 final size:20
Alignment explanation
Indices: 12336--12401 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
12326 TTTTTCTTTC
*
12336 ATTTCTTGTTTCTTTTCTCG
1 ATTTCTTGTTTCTTCTCTCG
*****
12356 ATTTCATTCAAGATTCTCTC-
1 ATTTC-TTGTTTCTTCTCTCG
12376 ATTTTCTTGTTTCTTCTCTCG
1 A-TTTCTTGTTTCTTCTCTCG
12397 ATTTC
1 ATTTC
12402 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 11, Indels: 6
0.65 0.22 0.12
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.12, C:0.23, G:0.08, T:0.58
Consensus pattern (20 bp):
ATTTCTTGTTTCTTCTCTCG
Found at i:14638 original size:13 final size:13
Alignment explanation
Indices: 14620--14644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14610 GTATTGATCA
14620 TGTGTTCACACCT
1 TGTGTTCACACCT
14633 TGTGTTCACACC
1 TGTGTTCACACC
14645 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:17636 original size:23 final size:22
Alignment explanation
Indices: 17585--17636 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
17575 CCTCGTCTTT
*
17585 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
17607 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
17630 TTCTTTT
1 TTCTTTT
17637 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:23361 original size:20 final size:20
Alignment explanation
Indices: 23338--23384 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
23328 GGGTTAAGAT
*
23338 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
23358 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
23378 TGAGCTG
1 TGAGCTG
23385 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:25229 original size:20 final size:20
Alignment explanation
Indices: 25206--25252 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25196 GGGTTAAGAT
*
25206 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
25226 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
25246 TGAGCTG
1 TGAGCTG
25253 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:29589 original size:20 final size:20
Alignment explanation
Indices: 29566--29612 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
29556 GGGTTAACAT
*
29566 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
29586 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
29606 TGAGCTG
1 TGAGCTG
29613 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:30948 original size:22 final size:22
Alignment explanation
Indices: 30916--30959 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
30906 TTTTGAACCA
*
30916 TTACCATTTCGTACCAAATCCC
1 TTACCAATTCGTACCAAATCCC
*
30938 TTACCAATTCGTACCAATTCCC
1 TTACCAATTCGTACCAAATCCC
30960 AAATACAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.36, G:0.05, T:0.32
Consensus pattern (22 bp):
TTACCAATTCGTACCAAATCCC
Done.