Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold611
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: 19206
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.26
Warning! 4295 characters in sequence are not A, C, G, or T
Found at i:370 original size:54 final size:54
Alignment explanation
Indices: 281--388 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
271 TGGATTTATA
* * * *
281 CACTTAATAATTTTAAATCAAATTTTATTTAAAAAAGGTATTTTAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGGATTTCAATCTTAAAT
*
335 CACTTAATAATCTTAAATCGAATTTGA-TTAGAAAAAGGGATTTCAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTA-AAAAAGGGATTTCAATCTTAAAT
389 TAGTGACGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 3 0.06
54 45 0.94
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (54 bp):
CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGGATTTCAATCTTAAAT
Found at i:8460 original size:6 final size:6
Alignment explanation
Indices: 8449--8501 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
8439 TTGAGCTCTT
*
8449 TTTTTC TTTTTC --TTT- TTTTTC TTTTCCC TTTTTC TTTTTTC TTTTT-
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT-TC TTTTTC -TTTTTC TTTTTC
8495 TTTTTC T
1 TTTTTC T
8502 ACTGTTGGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
4 3 0.08
5 8 0.21
6 17 0.44
7 11 0.28
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:8465 original size:7 final size:7
Alignment explanation
Indices: 8448--8499 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
8438 CTTGAGCTCT
8448 TTTTTTC
1 TTTTTTC
8455 -TTTTTC
1 TTTTTTC
8461 TTTTTT-
1 TTTTTTC
8467 TTCTTTTCC
1 TT-TTTT-C
*
8476 CTTTTTC
1 TTTTTTC
8483 TTTTTTC
1 TTTTTTC
8490 TTTTTT-
1 TTTTTTC
8496 TTTT
1 TTTT
8500 CTACTGTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 12 0.31
7 22 0.56
8 4 0.10
9 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:8467 original size:15 final size:15
Alignment explanation
Indices: 8447--8497 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
8437 ACTTGAGCTC
8447 TTTTTTTCTTTTTCT
1 TTTTTTTCTTTTTCT
* *
8462 TTTTTTTCTTTTCCC
1 TTTTTTTCTTTTTCT
*
8477 TTTTTCT-TTTTTCT
1 TTTTTTTCTTTTTCT
8491 TTTTTTT
1 TTTTTTT
8498 TTCTACTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTTTCT
Found at i:8634 original size:13 final size:13
Alignment explanation
Indices: 8616--8640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8606 GCTGCTGTTG
8616 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
8629 TTTTTTTCTTTT
1 TTTTTTTCTTTT
8641 TTCTGCTGAC
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:8713 original size:19 final size:21
Alignment explanation
Indices: 8674--8713 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
8664 GGATGCCTAC
*
8674 TGCTGGGCTGTCTGGCCTGCT
1 TGCTGGGCTGTCTGGCATGCT
8695 TGCTGGG-TG-CTGGCATGCT
1 TGCTGGGCTGTCTGGCATGCT
8714 GTTAAGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.03, C:0.25, G:0.40, T:0.33
Consensus pattern (21 bp):
TGCTGGGCTGTCTGGCATGCT
Found at i:8884 original size:6 final size:6
Alignment explanation
Indices: 8875--8950 Score: 68
Period size: 6 Copynumber: 12.7 Consensus size: 6
8865 TTGCTCTTCT
* * *
8875 TTTTTC TTTTTA TTTTTC TTTCTT- TTTTTC TTTTAT- TTTCTC TCTTTC
1 TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC TTTT-TC TTTTTC TTTTTC
*
8923 TTCTTCC TTTTTC TTTTTC TTTTT- TTTT
1 TT-TTTC TTTTTC TTTTTC TTTTTC TTTT
8951 CAAACCCTAG
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
5 7 0.12
6 42 0.74
7 8 0.14
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:8891 original size:26 final size:25
Alignment explanation
Indices: 8855--8951 Score: 89
Period size: 26 Copynumber: 4.0 Consensus size: 25
8845 CGACTGTATA
8855 TTTTTATTTTTTGCTCTTCTTTTTTC
1 TTTTTATTTTTT-CTCTTCTTTTTTC
8881 TTTTTA-TTTTTCT-TTCTTTTTT-
1 TTTTTATTTTTTCTCTTCTTTTTTC
* * *
8903 TCTTTTATTTTCTCTCTTTCTTCTTCC
1 T-TTTTATTTTTTCTC-TTCTTTTTTC
*
8930 TTTTT-CTTTTTCT-TT-TTTTTTC
1 TTTTTATTTTTTCTCTTCTTTTTTC
8952 AAACCCTAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
22 6 0.10
23 16 0.27
24 8 0.14
25 11 0.19
26 17 0.29
27 1 0.02
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (25 bp):
TTTTTATTTTTTCTCTTCTTTTTTC
Found at i:8924 original size:49 final size:48
Alignment explanation
Indices: 8856--8950 Score: 129
Period size: 49 Copynumber: 2.0 Consensus size: 48
8846 GACTGTATAT
* * *
8856 TTTTATTTTTTGCTCTTCTTTTTTCTTTTTATTTTTCTTTCTTTTTTTC
1 TTTTATTTTCTGCTCTTCTTCTTCCTTTTTATTTTTCTTT-TTTTTTTC
*
8905 TTTTATTTTCT-CTCTTTCTTCTTCCTTTTTCTTTTTCTTTTTTTTT
1 TTTTATTTTCTGCTC-TTCTTCTTCCTTTTTATTTTTCTTTTTTTTT
8951 CAAACCCTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
48 9 0.22
49 32 0.78
ACGTcount: A:0.03, C:0.17, G:0.01, T:0.79
Consensus pattern (48 bp):
TTTTATTTTCTGCTCTTCTTCTTCCTTTTTATTTTTCTTTTTTTTTTC
Found at i:9053 original size:14 final size:14
Alignment explanation
Indices: 9036--9079 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
9026 CCTCCCCCTT
9036 CTTTTCTTCTTTCC
1 CTTTTCTTCTTTCC
*
9050 CTTTT-TT-TTTCT
1 CTTTTCTTCTTTCC
9062 CTTTTCTTCTTTCC
1 CTTTTCTTCTTTCC
9076 CTTT
1 CTTT
9080 CTCTCCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 9 0.35
13 4 0.15
14 13 0.50
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTTCTTCTTTCC
Found at i:9600 original size:29 final size:30
Alignment explanation
Indices: 9556--9673 Score: 127
Period size: 29 Copynumber: 4.0 Consensus size: 30
9546 TAGAGGACAC
*
9556 AAAACTTTTGAGGTCAAAATGTAATTTTAAG
1 AAAA-TTTAGAGGTCAAAATGTAATTTTAAG
*
9587 AAAATTTAG-GGTCAAAATATAATTTTAA-
1 AAAATTTAGAGGTCAAAATGTAATTTTAAG
* *
9615 AAAGTTGAGAGGTCAAAATGTAATTTT-AG
1 AAAATTTAGAGGTCAAAATGTAATTTTAAG
* *
9644 -AAAGTTAGGTGGTCAAAATGTAAATTTTAA
1 AAAATTTA-GAGGTCAAAATGT-AATTTTAA
9674 ATTTTGTATT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
28 12 0.16
29 46 0.63
30 10 0.14
31 5 0.07
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (30 bp):
AAAATTTAGAGGTCAAAATGTAATTTTAAG
Found at i:11270 original size:227 final size:227
Alignment explanation
Indices: 10873--12451 Score: 3043
Period size: 227 Copynumber: 7.0 Consensus size: 227
10863 CCTGAACAAC
* * ** * *
10873 TAGTGGCGTTTCTAAAAAAATACCGTAAAAGAACATAATTAGTGGCGTTTA-TTGTAAGCGCCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
* *
10937 AAAATACCTTAACCAAAATGCAGCATTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
*
11002 AAAACGCCGCTAAAGAATAGTATTAGCGGCGTTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
131 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
11067 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
196 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
* * *
11099 TAATGGCGTTTTTAAACAAACGTCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCGCCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
11164 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
11229 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
131 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
11294 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
196 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
11326 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
11391 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
11456 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
131 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
11521 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
196 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
11553 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
11618 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
11683 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
131 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
11748 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
196 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
11780 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
11845 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
11910 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
131 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
11975 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
196 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
12007 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
12072 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
12137 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
131 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
12202 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
196 ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
12234 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
1 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
12299 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
66 AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
12364 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
131 AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
12429 ACGCAGCGTTTGGTCTCGAGGTA
196 ACGCAGCGTTTGGTCTCGAGGTA
12452 AAAAACTGAG
Statistics
Matches: 1339, Mismatches: 13, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
226 44 0.03
227 1295 0.97
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (227 bp):
TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCACCGC
AAAATACCTTAACCAAAACGCAGCGTTTGGTTCAATTGTATATTAGAATTAGTGGCGTTTTCGAT
AAAACGCCGCTAAAGAATAGTATTAGCGGCATTTTACAAAAAGCGCCGCAAATATCTTAACGAAA
ACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
Found at i:13220 original size:198 final size:198
Alignment explanation
Indices: 12861--13286 Score: 739
Period size: 198 Copynumber: 2.2 Consensus size: 198
12851 GCCTAATATT
** * * *
12861 TAGTGGCGCTTATGTATAAATGCCGCAATTTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
1 TAGTGGCGCTGGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
*
12926 TATTTAACTTTAGTGGCGCTTTTAGTAAACGCCGCAAAATGGTTTTAATTTTTATGGAGACGATG
66 TATTTAACTTTAGTGGCGCTTTTAGTAAACGCCACAAAATGGTTTTAATTTTTATGGAGACGATG
12991 TCATTTTCTCTAAAACGCAATGACTTTGAGTTAACTGATCGGGAAACGACAGCGTTTGATCATAT
131 TCATTTTCTCTAAAACGCAATGACTTTGAGTTAACTGATCGGGAAACGACAGCGTTTGATCATAT
13056 TAC
196 TAC
* *
13059 TAGTGGTGCTGGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTTCGTTTTCT
1 TAGTGGCGCTGGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
13124 TATTT-ACTTTTAGTGGCGCTTTTAGTAAACGCCACAAAAAT-GTTTTAATTTTTATGGAGACGA
66 TATTTAAC-TTTAGTGGCGCTTTTAGTAAACGCCAC-AAAATGGTTTTAATTTTTATGGAGACGA
13187 TGTCATTTTCTCTAAAACGCAATGACTTTGAGTTAACTGATCGGGAAACGACAGCGTTTGATCAT
129 TGTCATTTTCTCTAAAACGCAATGACTTTGAGTTAACTGATCGGGAAACGACAGCGTTTGATCAT
13252 ATTAC
194 ATTAC
*
13257 TAGTGGCGCTTGTATATAAACGCCGCAAAT
1 TAGTGGCGCTGGTATATAAACGCCGCAAAT
13287 GGGTTAATTA
Statistics
Matches: 216, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
197 2 0.01
198 209 0.97
199 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (198 bp):
TAGTGGCGCTGGTATATAAACGCCGCAAATTACAGAAATTGTTTAGGAAAACGGCTCCGTTTTCT
TATTTAACTTTAGTGGCGCTTTTAGTAAACGCCACAAAATGGTTTTAATTTTTATGGAGACGATG
TCATTTTCTCTAAAACGCAATGACTTTGAGTTAACTGATCGGGAAACGACAGCGTTTGATCATAT
TAC
Done.