Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold995
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: 34743
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1166 original size:22 final size:21
Alignment explanation
Indices: 1141--1203 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
1131 ATAAAGGTGG
1141 AGAAATAGAGAGAAAAAAAGAA
1 AGAAA-AGAGAGAAAAAAAGAA
* *
1163 AGAAAAAGAAAGAAAAAATAGAG
1 AG-AAAAGAGAGAAAAAA-AGAA
*
1186 AGAAAATAGA-AAAAAAAG
1 AGAAAAGAGAGAAAAAAAG
1204 CTAAACCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 2 0.06
21 6 0.17
22 19 0.54
23 8 0.23
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.05
Consensus pattern (21 bp):
AGAAAAGAGAGAAAAAAAGAA
Found at i:1168 original size:10 final size:10
Alignment explanation
Indices: 1155--1179 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1145 ATAGAGAGAA
1155 AAAAAGAAAG
1 AAAAAGAAAG
1165 AAAAAGAAAG
1 AAAAAGAAAG
1175 AAAAA
1 AAAAA
1180 ATAGAGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:1883 original size:34 final size:34
Alignment explanation
Indices: 1808--1873 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
1798 TATATTTTCC
* *
1808 ATAGGATTTACTGATTTTTTATGTGTTTAACCAT
1 ATAGGATTTAATGATTTTTGATGTGTTTAACCAT
1842 ATAGGATTTAATGATTTTTGATGTGTTTAACC
1 ATAGGATTTAATGATTTTTGATGTGTTTAACC
1874 GAAAGGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (34 bp):
ATAGGATTTAATGATTTTTGATGTGTTTAACCAT
Found at i:4522 original size:18 final size:19
Alignment explanation
Indices: 4490--4540 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 19
4480 AAAATCACAT
4490 TTAATATATGATATAAAAAA
1 TTAATATAT-ATATAAAAAA
4510 TTAATATAT-TAT-AAAAA
1 TTAATATATATATAAAAAA
*
4527 TTATTATATATATA
1 TTAATATATATATA
4541 TTTATATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 13 0.46
18 6 0.21
20 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAATATATATATAAAAAA
Found at i:5493 original size:13 final size:13
Alignment explanation
Indices: 5475--5502 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5465 CATTACAAGC
5475 CAATGTATCGATA
1 CAATGTATCGATA
5488 CAATGTATCGATA
1 CAATGTATCGATA
5501 CA
1 CA
5503 TCTTGTATGT
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:5609 original size:13 final size:13
Alignment explanation
Indices: 5591--5615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5581 TACAATAGTC
5591 ATGTATCGATACA
1 ATGTATCGATACA
5604 ATGTATCGATAC
1 ATGTATCGATAC
5616 TGTGCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:7065 original size:193 final size:193
Alignment explanation
Indices: 6731--7118 Score: 758
Period size: 193 Copynumber: 2.0 Consensus size: 193
6721 GTTCGGTTTC
*
6731 TCACTTCATAGCCAATCTTGGCCATGGATTTGGAACCGATGATGCGAGGTCGAGAGATAGGAATC
1 TCACCTCATAGCCAATCTTGGCCATGGATTTGGAACCGATGATGCGAGGTCGAGAGATAGGAATC
6796 CCGGCATCCCATGACAAATCAATGCCACTAACCTCGAAGAAATGACTAAGGATCATACCATGAAG
66 CCGGCATCCCATGACAAATCAATGCCACTAACCTCGAAGAAATGACTAAGGATCATACCATGAAG
6861 GATTGTCGAATTGCCTTTTAAATCTCGGACAATATCGGTAAAGATGAAGTAGGCAAGGTTAGG
131 GATTGTCGAATTGCCTTTTAAATCTCGGACAATATCGGTAAAGATGAAGTAGGCAAGGTTAGG
6924 TCACCTCATAGCCAATCTTGGCCATGGATTTGGAACCGATGATGCGAGGTCGAGAGATAGGAATC
1 TCACCTCATAGCCAATCTTGGCCATGGATTTGGAACCGATGATGCGAGGTCGAGAGATAGGAATC
6989 CCGGCATCCCATGACAAATCAATGCCACTAACCTCGAAGAAATGACTAAGGATCATACCATGAAG
66 CCGGCATCCCATGACAAATCAATGCCACTAACCTCGAAGAAATGACTAAGGATCATACCATGAAG
*
7054 GATTGTCGAATTGCCTTTTAAATCTCGGACAATATCGGTAAAGATGAAGTAGGCAATGTTAGG
131 GATTGTCGAATTGCCTTTTAAATCTCGGACAATATCGGTAAAGATGAAGTAGGCAAGGTTAGG
7117 TC
1 TC
7119 TTTGGCCGGT
Statistics
Matches: 193, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
193 193 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (193 bp):
TCACCTCATAGCCAATCTTGGCCATGGATTTGGAACCGATGATGCGAGGTCGAGAGATAGGAATC
CCGGCATCCCATGACAAATCAATGCCACTAACCTCGAAGAAATGACTAAGGATCATACCATGAAG
GATTGTCGAATTGCCTTTTAAATCTCGGACAATATCGGTAAAGATGAAGTAGGCAAGGTTAGG
Found at i:12624 original size:24 final size:25
Alignment explanation
Indices: 12592--12638 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
12582 ATGTGGCTAG
*
12592 CATGGCTTTCTTCTTTA-GTTTGCT
1 CATGCCTTTCTTCTTTAGGTTTGCT
12616 CATGCCTTTCTTCTTTAGGTTTG
1 CATGCCTTTCTTCTTTAGGTTTG
12639 GACAATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.09, C:0.21, G:0.17, T:0.53
Consensus pattern (25 bp):
CATGCCTTTCTTCTTTAGGTTTGCT
Found at i:12820 original size:3 final size:3
Alignment explanation
Indices: 12812--12845 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
12802 TCTGAGTCAC
* *
12812 CAT CAT CAT CAT CAT CAT CAT CAT TAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
12846 GTCCTTGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (3 bp):
CAT
Found at i:14377 original size:13 final size:13
Alignment explanation
Indices: 14359--14384 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14349 TACACCAAGT
14359 ATGTATCGATACA
1 ATGTATCGATACA
14372 ATGTATCGATACA
1 ATGTATCGATACA
14385 CAAAAAATTG
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:14382 original size:32 final size:33
Alignment explanation
Indices: 14341--14404 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
14331 TAGCCAAACT
* **
14341 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
14373 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
14405 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:20727 original size:20 final size:20
Alignment explanation
Indices: 20684--20729 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
20674 AAATCTTTTG
20684 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
20705 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
20725 CAAAA
1 CAAAA
20730 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:23131 original size:13 final size:13
Alignment explanation
Indices: 23113--23138 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23103 TACACCAAGT
23113 ATGTATCGATACA
1 ATGTATCGATACA
23126 ATGTATCGATACA
1 ATGTATCGATACA
23139 CAAAAATTTG
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:23136 original size:32 final size:33
Alignment explanation
Indices: 23095--23158 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
23085 TAGCCAAACT
* *
23095 TGTATCGATACAC-CAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
*
23127 TGTATCGATACACAAAAATTTGTATCGATACA
1 TGTATCGATACACAAAAATATGTATCGATACA
23159 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:24483 original size:19 final size:21
Alignment explanation
Indices: 24435--24490 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
24425 CTGCCAATCA
**
24435 CATGTATCGATACAATCTTTG
1 CATGTATCGATACAATCAGTG
*
24456 CAAGTATCGATACAAT-AGT-
1 CATGTATCGATACAATCAGTG
24475 CATGTATCGATACAAT
1 CATGTATCGATACAAT
24491 GTATCGATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
20 1 0.03
21 15 0.48
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (21 bp):
CATGTATCGATACAATCAGTG
Found at i:27119 original size:12 final size:12
Alignment explanation
Indices: 27102--27126 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27092 GCCCATGGTG
27102 TTGGTAGCATAT
1 TTGGTAGCATAT
27114 TTGGTAGCATAT
1 TTGGTAGCATAT
27126 T
1 T
27127 CTTAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (12 bp):
TTGGTAGCATAT
Found at i:29759 original size:2 final size:2
Alignment explanation
Indices: 29752--29790 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29742 AAGCTATTTG
29752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29791 AATGCCCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32450 original size:95 final size:91
Alignment explanation
Indices: 32309--32497 Score: 297
Period size: 93 Copynumber: 2.0 Consensus size: 91
32299 TCAGTTTTTG
*
32309 TTTCTTTCCAGTCAGCTGGCACATAATGAAATACTCTTGAATGGAATTTATTCTGATTAATTGAA
1 TTTCTTCCCAGTCAGCTGGCACATAATGAAATACTCTTGAATGGAATTTATTCTGATTAATTGAA
32374 TCTTAGAAGGTTTTTTTCTTTTTATTCT
66 TCTTAGAA-G-TTTTTTCTTTTTATTCT
* * * *
32402 TTTCTTCCCAGTGAGCTTGCAACCTAATGAAATATTCTTTGAATGGAATTTATTCTGATTAATTG
1 TTTCTTCCCAGTCAGCTGGC-ACATAATGAAATACTC-TTGAATGGAATTTATTCTGATTAATTG
32467 AATCTTAGAAGTTTTTTCTTTTTATTCT
64 AATCTTAGAAGTTTTTTCTTTTTATTCT
32495 TTT
1 TTT
32498 TCTTTCTTAA
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
93 37 0.42
94 15 0.17
95 37 0.42
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (91 bp):
TTTCTTCCCAGTCAGCTGGCACATAATGAAATACTCTTGAATGGAATTTATTCTGATTAATTGAA
TCTTAGAAGTTTTTTCTTTTTATTCT
Done.