Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold350
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: 32143
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:6390 original size:29 final size:29
Alignment explanation
Indices: 6327--6394 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
6317 TAATCAACCA
6327 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
6356 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
6385 CGCACACTTA
1 CGCACACTTA
6395 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:6506 original size:173 final size:173
Alignment explanation
Indices: 6217--6542 Score: 537
Period size: 173 Copynumber: 1.9 Consensus size: 173
6207 AACTCAAGGT
* * *
6217 ACTTACCTTTTCCACTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCACTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
* *
6282 GAAAATATATATTGGGTTGCACACATAACGTTTAGTAATCAACCACGCACACTTAGTGCCATGCA
66 GAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGCA
6347 CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
6390 ACTTACCTTTTCCGCTGTCC-AAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCACTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
** * *
6454 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTT-GCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
6519 ACTTTAAACTCGCACACTTAGTGC
130 ACTTTAAACTCACACACTTAGTGC
6543 TGTACAATTT
Statistics
Matches: 141, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
172 59 0.42
173 82 0.58
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (173 bp):
ACTTACCTTTTCCACTGTCCAAAATCGACTCGGTAAAGTCACACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTGCACACATAACGCTTAATAATCAACCACGCACACTTAGTGCCATGCA
CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:6534 original size:29 final size:28
Alignment explanation
Indices: 6495--6570 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 28
6485 CTTAATAATC
6495 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTG-C-TGTACATTTA
*
6525 AACTCGCACACTTAGTGCTGTACAATTTA
1 AACCCGCACACTTAGTGCTGTAC-ATTTA
6554 AACCCGCACACTTAGTG
1 AACCCGCACACTTAGTG
6571 TCAATCTCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.79
30 3 0.07
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (28 bp):
AACCCGCACACTTAGTGCTGTACATTTA
Found at i:15283 original size:21 final size:21
Alignment explanation
Indices: 15257--15297 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
15247 CAGACGAGCA
* *
15257 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
15278 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
15298 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:23317 original size:30 final size:30
Alignment explanation
Indices: 23281--23343 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
23271 GTTACGAGAG
*
23281 TATCTAGATATATTTAACCCATACTTTATT
1 TATCTAGACATATTTAACCCATACTTTATT
* *
23311 TATCTAGACCTATTTGACCCATACTTTATT
1 TATCTAGACATATTTAACCCATACTTTATT
23341 TAT
1 TAT
23344 TAACTGAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (30 bp):
TATCTAGACATATTTAACCCATACTTTATT
Found at i:26214 original size:36 final size:37
Alignment explanation
Indices: 26086--26236 Score: 252
Period size: 37 Copynumber: 4.1 Consensus size: 37
26076 TTATTACGAA
* * * *
26086 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
26123 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
26160 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
26197 GTCTTA-CCGGACAAAATCCCCACACGTAGTCATC-G
1 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
26232 GTCTT
1 GTCTT
26237 TAGAGCTCGG
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
35 6 0.05
36 28 0.25
37 76 0.69
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
Found at i:26442 original size:47 final size:47
Alignment explanation
Indices: 26355--26814 Score: 669
Period size: 47 Copynumber: 9.7 Consensus size: 47
26345 CCCTTCGGGA
* * ** * * *
26355 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
26402 CCTGTTACATATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
26449 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
26496 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26543 CTTATCACATATATACAC-TTCA-ATTCACATCACACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATT--CAT--CACATCGGCCATTAGGC
26591 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
26638 CTTATCACATATATACACTTTCACATTCATTACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26685 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
26731 CTTATCACATGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
26780 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
26815 AGAATCCTAA
Statistics
Matches: 381, Mismatches: 21, Indels: 22
0.90 0.05 0.05
Matches are distributed among these distances:
45 3 0.01
46 22 0.06
47 268 0.70
48 65 0.17
49 20 0.05
50 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:26639 original size:142 final size:141
Alignment explanation
Indices: 26355--26814 Score: 669
Period size: 142 Copynumber: 3.2 Consensus size: 141
26345 CCCTTCGGGA
* ** * * * * * *
26355 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCGGCCCTGTTACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
26420 TTTCACATTCATCACATCGGCCATTGGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
26485 GGCCATTGGGC
131 GGCCATTAGGC
* *
26496 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACAC
26561 -TTCA-ATTCACATCACACATCGG-CATTAGGCCTTATCACATATATACACTTTCACATTCATCA
66 TTTCACATT--CAT--CACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
26623 CATCGGCCATTAGGC
127 CATCGGCCATTAGGC
* *
26638 CTTATCACATATATACACTTTCACATTCATTACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACAC
26703 TTTCACATTCATCACATCGGCCATTAGG-CTTATCACATGTATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACA--TATATACACTTTCACATTCATCACA
26767 TCGGCCATTAGGC
129 TCGGCCATTAGGC
* *
26780 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATCCATCACAT
26815 AGAATCCTAA
Statistics
Matches: 290, Mismatches: 19, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
139 3 0.01
140 21 0.07
141 65 0.22
142 186 0.64
143 12 0.04
144 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:26675 original size:189 final size:188
Alignment explanation
Indices: 26355--26814 Score: 662
Period size: 189 Copynumber: 2.4 Consensus size: 188
26345 CCCTTCGGGA
* * ** * * * * * *
26355 CTTATCACA-TTTATACACTTTCACATCCATCATGTTGGCCACTCGGCCCTGTTACATATATACA
1 CTTATCACAGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
*
26419 CTTTCACATTCATCACATCGGCCATTGGGCCTTATCACATATATACACTTTCACATTCATCACAT
66 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
* *
26484 CGGCCATTGGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGG
131 CGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG
26542 CCTTATCACA-TATATACAC-TTCA-ATTCACATCACACATCGG-CATTAGGCCTTATCACATAT
1 -CTTATCACAGTATATACACTTTCACATT--CAT--CACATCGGCCATTAGGCCTTATCACATAT
26603 ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCAT
61 ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCAT
*
26668 TACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG
126 CACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG
* *
26731 CTTATCACATGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATGC
1 CTTATCACA-GTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
26796 A-TGTTCACATCCATCACAT
65 ACT-TTCACATTCATCACAT
26815 AGAATCCTAA
Statistics
Matches: 245, Mismatches: 17, Indels: 19
0.87 0.06 0.07
Matches are distributed among these distances:
186 2 0.01
187 4 0.02
188 38 0.16
189 177 0.72
190 17 0.07
191 4 0.02
192 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (188 bp):
CTTATCACAGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG
Found at i:31566 original size:39 final size:43
Alignment explanation
Indices: 31518--31613 Score: 146
Period size: 39 Copynumber: 2.3 Consensus size: 43
31508 TTGGTTTTCA
31518 GCACTAAGTGTGCAGGCAATAAGTGTTC-ACGGTT-T-GATTG
1 GCACTAAGTGTGCAGGCAATAAGTGTTCAACGGTTGTAGATTG
*
31558 GCAC-AAGTGTGCGGGCAATAAGTGTTCAACGGTTGTGAGATTG
1 GCACTAAGTGTGCAGGCAATAAGTGTTCAACGGTTGT-AGATTG
31601 GCACTAAGTGTGC
1 GCACTAAGTGTGC
31614 GGACTTGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
39 22 0.44
40 10 0.20
41 1 0.02
43 9 0.18
44 8 0.16
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCAGGCAATAAGTGTTCAACGGTTGTAGATTG
Found at i:31631 original size:29 final size:30
Alignment explanation
Indices: 31599--31672 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
31589 GTTGTGAGAT
*
31599 TGGCACTAAGTGTGCGGA-CTTGAAATGCA
1 TGGCACTAAGTGTGCGGAGCTTGAAATACA
* * *
31628 TGGCACTAAGTGTGC-GAGTTTTAAGTACA
1 TGGCACTAAGTGTGCGGAGCTTGAAATACA
31657 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31673 TGGTTGATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 2 0.05
29 37 0.95
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (30 bp):
TGGCACTAAGTGTGCGGAGCTTGAAATACA
Found at i:32060 original size:39 final size:37
Alignment explanation
Indices: 32017--32090 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 37
32007 AATGACCATA
32017 TCCGGACCT-AGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 TCCGGA-CTAAGTTCCGAAGAGC-TTCGTGC-AGTGATGT
32056 TCCGGACTAAGTTCCGAAGAGCTTCGTGCAGTGAT
1 TCCGGACTAAGTTCCGAAGAGCTTCGTGCAGTGAT
32091 ATATCCGTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
37 6 0.18
38 9 0.26
39 19 0.56
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.27
Consensus pattern (37 bp):
TCCGGACTAAGTTCCGAAGAGCTTCGTGCAGTGATGT
Found at i:32111 original size:38 final size:39
Alignment explanation
Indices: 32030--32122 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 39
32020 GGACCTAGTT
* ***
32030 CCGAAGAGCATTCGTGCTAGTGATGTTCCGGACTAAGTT
1 CCGAAGAGCATTCGTGCTAGTGATATTCCGGACTAAACC
32069 CCGAAGAGC-TTCGTGC-AGTGATATATCCGTG-CTAAACC
1 CCGAAGAGCATTCGTGCTAGTGATAT-TCCG-GACTAAACC
32107 CCGAAGAGCATTCGTG
1 CCGAAGAGCATTCGTG
32123 GGTGGTGTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 7 0.15
38 24 0.51
39 16 0.34
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGAAGAGCATTCGTGCTAGTGATATTCCGGACTAAACC
Done.