Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1927
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: 302399
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 3 of 3
Found at i:294032 original size:27 final size:28
Alignment explanation
Indices: 293969--294044 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
293959 AAAATAAAGT
*
293969 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
293997 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
294024 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
294045 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:296540 original size:13 final size:13
Alignment explanation
Indices: 296522--296547 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
296512 ACAAAGATCC
296522 ATGTATCGATACA
1 ATGTATCGATACA
296535 ATGTATCGATACA
1 ATGTATCGATACA
296548 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:296543 original size:33 final size:33
Alignment explanation
Indices: 296501--296567 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
296491 AAAATTTCCA
***
296501 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
296534 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
296567 A
1 A
296568 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:296611 original size:19 final size:18
Alignment explanation
Indices: 296587--296654 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
296577 CAGTAGCTAA
296587 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
296606 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
296621 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
296638 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
296655 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:296627 original size:13 final size:13
Alignment explanation
Indices: 296609--296633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
296599 ACAATACTTA
296609 TGTATCGATACAT
1 TGTATCGATACAT
296622 TGTATCGATACA
1 TGTATCGATACA
296634 AAACTTATGT
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:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:296631 original size:32 final size:32
Alignment explanation
Indices: 296590--296652 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
296580 TAGCTAATTA
*
296590 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
296622 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
296653 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:296734 original size:21 final size:21
Alignment explanation
Indices: 296710--296765 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
296700 CATTTGTAGG
296710 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
296731 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
296752 ATGTATCGATACAT
1 ATGTATCGATACAT
296766 AAAAATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:296775 original size:1 final size:1
Alignment explanation
Indices: 296771--296821 Score: 75
Period size: 1 Copynumber: 51.0 Consensus size: 1
296761 TACATAAAAA
***
296771 TTTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
296822 CAAACACTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:296809 original size:24 final size:24
Alignment explanation
Indices: 296777--296824 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
296767 AAAATTTTTT
296777 TTTTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTTTCAA
296801 TTTTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTTTCAA
296825 ACACTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (24 bp):
TTTTTTTTTTTTTTTTTTTTTCAA
Found at i:297503 original size:55 final size:55
Alignment explanation
Indices: 297417--298259 Score: 1289
Period size: 55 Copynumber: 15.3 Consensus size: 55
297407 ATAAATTGTA
* * * * * *
297417 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
297472 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
297527 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
297582 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
297637 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGACTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
297692 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
297747 TTCTGCTCTTTGAGGACTGGACAA--TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
297802 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
297857 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
297912 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
297967 TCCTGCTCTTTGAGGACTGGACAA--TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
298022 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
298077 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
298132 TCCTGCTCGTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
298187 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
298242 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
298260 AAAAAGCGGA
Statistics
Matches: 736, Mismatches: 31, Indels: 42
0.91 0.04 0.05
Matches are distributed among these distances:
53 4 0.01
54 22 0.03
55 686 0.93
56 20 0.03
57 4 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:297709 original size:28 final size:28
Alignment explanation
Indices: 297677--297764 Score: 67
Period size: 28 Copynumber: 3.2 Consensus size: 28
297667 CAACTTGTGT
297677 GGACTTTAAGAGGTGTCCTGCTCTTTGG
1 GGACTTTAAGAGGTGTCCTGCTCTTTGG
* ** *
297705 GGAC-TGAA-AGGTG-CCACCAACTTGTGTG
1 GGACTTTAAGAGGTGTCCTGC-TCTT-TG-G
* *
297733 GG-CTTTAAGAGGTGTTCTGCTCTTTGA
1 GGACTTTAAGAGGTGTCCTGCTCTTTGG
297760 GGACT
1 GGACT
297765 GGACAATGCC
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.19
27 8 0.19
28 14 0.33
29 8 0.19
30 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (28 bp):
GGACTTTAAGAGGTGTCCTGCTCTTTGG
Found at i:299245 original size:1 final size:1
Alignment explanation
Indices: 299241--299298 Score: 71
Period size: 1 Copynumber: 58.0 Consensus size: 1
299231 CTTTTCTCTC
* * * * *
299241 TTTTTCTTTGTTTTGTTTTTTTTTGTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
299299 GAAGAGAAGG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.03, G:0.05, T:0.91
Consensus pattern (1 bp):
T
Found at i:299254 original size:10 final size:10
Alignment explanation
Indices: 299226--299298 Score: 71
Period size: 10 Copynumber: 7.5 Consensus size: 10
299216 TTAAGTAGGT
299226 TTTTTCTTTTC
1 TTTTT-TTTTC
* *
299237 TCTCTTTTTC
1 TTTTTTTTTC
* *
299247 -TTTGTTTTG
1 TTTTTTTTTC
*
299256 TTTTTTTTTG
1 TTTTTTTTTC
299266 TTTTTTTTTC
1 TTTTTTTTTC
299276 TTTTTTTTT-
1 TTTTTTTTTC
299285 TTTTTTTTT-
1 TTTTTTTTTC
299294 TTTTT
1 TTTTT
299299 GAAGAGAAGG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
9 19 0.36
10 31 0.58
11 3 0.06
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:299273 original size:29 final size:26
Alignment explanation
Indices: 299241--299298 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 26
299231 CTTTTCTCTC
299241 TTTTTCTTTGTTTTGTTTTTTTTTGTTTT
1 TTTTTCTTT-TTTT-TTTTTTTTT-TTTT
299270 TTTTTCTTTTTTTTTTTTTTTTTTTT
1 TTTTTCTTTTTTTTTTTTTTTTTTTT
299296 TTT
1 TTT
299299 GAAGAGAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 7 0.24
27 9 0.31
28 4 0.14
29 9 0.31
ACGTcount: A:0.00, C:0.03, G:0.05, T:0.91
Consensus pattern (26 bp):
TTTTTCTTTTTTTTTTTTTTTTTTTT
Done.