Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold697
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: 26651
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1147 original size:3 final size:3
Alignment explanation
Indices: 1139--1173 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1129 ACTAAAGCTT
1139 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1174 TTCTTCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5622 original size:27 final size:27
Alignment explanation
Indices: 5582--5642 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
5572 AACTATCACA
*
5582 GGAGAGGGCCCGCTTCGAAACGAAAGT
1 GGAGAGGGCCCGCTTCAAAACGAAAGT
* *
5609 GGAGAGGGCTCGCTTCAAAACGGAAGT
1 GGAGAGGGCCCGCTTCAAAACGAAAGT
5636 GGAGAGG
1 GGAGAGG
5643 CATGAGGAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.41, T:0.11
Consensus pattern (27 bp):
GGAGAGGGCCCGCTTCAAAACGAAAGT
Found at i:5932 original size:18 final size:18
Alignment explanation
Indices: 5911--5945 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5901 TGACTGGTGG
* *
5911 GGTCGAGGCAATCGAGGA
1 GGTCGAGACAACCGAGGA
5929 GGTCGAGACAACCGAGG
1 GGTCGAGACAACCGAGG
5946 GAGTTGGTCG
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:0.29, C:0.20, G:0.43, T:0.09
Consensus pattern (18 bp):
GGTCGAGACAACCGAGGA
Found at i:6634 original size:26 final size:25
Alignment explanation
Indices: 6590--6642 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
6580 ATAGTATTGA
*
6590 TGCCATGAGGCGATTAGGATCGAAG
1 TGCCATGAGGCGATCAGGATCGAAG
6615 TGCCATGATGGCGATCAGGATCGAAG
1 TGCCATGA-GGCGATCAGGATCGAAG
6641 TG
1 TG
6643 ACTCGGCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (25 bp):
TGCCATGAGGCGATCAGGATCGAAG
Found at i:6750 original size:59 final size:59
Alignment explanation
Indices: 6671--6797 Score: 191
Period size: 59 Copynumber: 2.2 Consensus size: 59
6661 TCTGGGATTG
*
6671 CCTTGGTGGCGATCTGAGTTTGAGTGACGAGGCATCACTTAGTGTTTGAATTTAGGTCA
1 CCTTGGTGGCGATCTAAGTTTGAGTGACGAGGCATCACTTAGTGTTTGAATTTAGGTCA
* ** * *
6730 CCTTGGTGGCGATCTAAGTTTGAGTGACTAGGTGTCACTTAGTGTTTGAATTTGGGTCG
1 CCTTGGTGGCGATCTAAGTTTGAGTGACGAGGCATCACTTAGTGTTTGAATTTAGGTCA
*
6789 CCTCGGTGG
1 CCTTGGTGG
6798 TGATTACAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.17, C:0.16, G:0.32, T:0.35
Consensus pattern (59 bp):
CCTTGGTGGCGATCTAAGTTTGAGTGACGAGGCATCACTTAGTGTTTGAATTTAGGTCA
Found at i:13687 original size:28 final size:28
Alignment explanation
Indices: 13647--13718 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
13637 AAAAAAAAAT
* ** *
13647 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
* *
13675 CGGGGTTGGAGTATCTCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
13703 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
13719 TAGATTGTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:13785 original size:52 final size:51
Alignment explanation
Indices: 13729--13827 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
13719 TAGATTGTGA
* * *
13729 AAAATTGGTATTTTTAGAAATAAAATCGGAGTTAGAGTATCCCCGATTATAG
1 AAAATTAGTATTTTGA-AAATAAAATCGGAGTTAGAATATCCCCGATTATAG
* * *
13781 AAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATT
1 AAAATTAGTATTTTGAAAATAAAATCGGAGTTAGAATATCCCCGATT
13828 GTGGAGAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
51 28 0.68
52 13 0.32
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (51 bp):
AAAATTAGTATTTTGAAAATAAAATCGGAGTTAGAATATCCCCGATTATAG
Found at i:16206 original size:13 final size:13
Alignment explanation
Indices: 16188--16215 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16178 ATACAAAGAT
16188 CAATGTATCGATA
1 CAATGTATCGATA
16201 CAATGTATCGATA
1 CAATGTATCGATA
16214 CA
1 CA
16216 CAGAAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:16211 original size:33 final size:33
Alignment explanation
Indices: 16169--16235 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
16159 AAAATTTCCA
**
16169 AATGTATCGATACAAAGATCAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
16202 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
16235 A
1 A
16236 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:16276 original size:13 final size:13
Alignment explanation
Indices: 16258--16282 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16248 TAGCTAATTA
16258 TGTATCGATACAT
1 TGTATCGATACAT
16271 TGTATCGATACA
1 TGTATCGATACA
16283 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:16480 original size:7 final size:7
Alignment explanation
Indices: 16468--16502 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
16458 AATCCTCCAC
16468 CTACTAA
1 CTACTAA
16475 CTACTAA
1 CTACTAA
16482 CTACTAA
1 CTACTAA
*
16489 CTAC-AC
1 CTACTAA
16495 CTACTAA
1 CTACTAA
16502 C
1 C
16503 AAAAATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (7 bp):
CTACTAA
Found at i:18315 original size:20 final size:20
Alignment explanation
Indices: 18273--18311 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
18263 AATGAATAAT
*
18273 TTTTTAAGAATAAATATGTA
1 TTTTTAAGAATAAATATGAA
*
18293 TTTTTAA-AATATATATGAA
1 TTTTTAAGAATAAATATGAA
18312 ATTTGAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
TTTTTAAGAATAAATATGAA
Found at i:20925 original size:2 final size:2
Alignment explanation
Indices: 20913--20955 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
20903 GAAGACGAAG
*
20913 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20955 A
1 A
20956 GCTTCAAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20982 original size:29 final size:29
Alignment explanation
Indices: 20946--21004 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
20936 TATATATATA
20946 TATATATATAGCTTCAAATCATGGTTAAG
1 TATATATATAGCTTCAAATCATGGTTAAG
20975 TATATATATAGCTTCAAATCATGGTTAAG
1 TATATATATAGCTTCAAATCATGGTTAAG
21004 T
1 T
21005 TTCAAAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (29 bp):
TATATATATAGCTTCAAATCATGGTTAAG
Found at i:22021 original size:2 final size:2
Alignment explanation
Indices: 22005--22039 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
21995 TCACATCCAA
*
22005 AT AT A- AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22040 TGCAATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:23339 original size:2 final size:2
Alignment explanation
Indices: 23332--23367 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
23322 TTCCAAACAT
23332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23368 ATTGTAGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26465 original size:2 final size:2
Alignment explanation
Indices: 26458--26501 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
26448 GGAATGCTGA
26458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26499 AT A
1 AT A
26502 CATTTGGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.