Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1064
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: 42030
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:10454 original size:18 final size:17
Alignment explanation
Indices: 10414--10457 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
10404 TTAAAATTTT
* *
10414 GTTTATAATTTTTTTAT
1 GTTTTTAATTTTTTTAA
10431 GATTTTTAATATTTTTTAA
1 G-TTTTTAAT-TTTTTTAA
10450 GTTTTTAA
1 GTTTTTAA
10458 AAGGGATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 8 0.35
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (17 bp):
GTTTTTAATTTTTTTAA
Found at i:16613 original size:22 final size:23
Alignment explanation
Indices: 16588--16633 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
16578 CTTTCCTTTC
16588 CTATTTTATAAAAT-AATTTAAA
1 CTATTTTATAAAATAAATTTAAA
16610 CTATTTTATAAAATAGAATTTAAA
1 CTATTTTATAAAATA-AATTTAAA
16634 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 14 0.64
24 8 0.36
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
CTATTTTATAAAATAAATTTAAA
Found at i:18845 original size:1 final size:1
Alignment explanation
Indices: 18839--18897 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
18829 GATTGATTGA
* * * * * * *
18839 TTTTTTTTATTTTTTTTTTATTTTTATTTTTTTTGTTTTTTTGTCTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18898 GAGTCTGAAC
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.05, C:0.02, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Found at i:18871 original size:26 final size:28
Alignment explanation
Indices: 18838--18897 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
18828 TGATTGATTG
18838 ATTTTTTTTATTTTTTT-T-TTATTTTT
1 ATTTTTTTTATTTTTTTGTCTTATTTTT
* *
18864 ATTTTTTTTGTTTTTTTGTCTTGTTTTT
1 ATTTTTTTTATTTTTTTGTCTTATTTTT
18892 -TTTTTT
1 ATTTTTT
18898 GAGTCTGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 16 0.53
27 7 0.23
28 7 0.23
ACGTcount: A:0.07, C:0.02, G:0.05, T:0.87
Consensus pattern (28 bp):
ATTTTTTTTATTTTTTTGTCTTATTTTT
Found at i:18898 original size:17 final size:16
Alignment explanation
Indices: 18839--18897 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 16
18829 GATTGATTGA
18839 TTTTTTTTATTTTTTT
1 TTTTTTTTATTTTTTT
18855 TTTATTTTTATTTTTTT
1 TTT-TTTTTATTTTTTT
*
18872 TGTTTTTTTGTCTTGTTTT
1 T-TTTTTTTAT-TT-TTTT
18891 TTTTTTT
1 TTTTTTT
18898 GAGTCTGAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
16 3 0.08
17 20 0.53
18 10 0.26
19 5 0.13
ACGTcount: A:0.05, C:0.02, G:0.05, T:0.88
Consensus pattern (16 bp):
TTTTTTTTATTTTTTT
Found at i:21187 original size:19 final size:20
Alignment explanation
Indices: 21158--21206 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
21148 CACTTCATGA
* *
21158 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGTATG
*
21177 CAATGTAATGCAAATGTATG
1 AAATGTAATGCAAATGTATG
21197 AAATG-AATGC
1 AAATGTAATGC
21207 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (20 bp):
AAATGTAATGCAAATGTATG
Found at i:22755 original size:108 final size:109
Alignment explanation
Indices: 22597--22886 Score: 456
Period size: 108 Copynumber: 2.6 Consensus size: 109
22587 AATAAATGAG
* * *
22597 AAATCGAAACCCAGCACCTTAGGGCACGTTCCTCAAATTTCCAAACGCAAAACATTGCCTTACTT
1 AAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTAATT
22662 TGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAG-
66 TGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGA
* * *
22705 GAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTT
1 AAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTAATT
22770 TGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAA
66 TGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAG-A
* * * *
22815 AAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCCAAACGCAAAATATTGCCTCAA
1 AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCGAATTT-CCAAACGCAAAATATTGCCTTAA
22880 TTTGAAA
64 TTTGAAA
22887 TATTTTCCTT
Statistics
Matches: 166, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
108 103 0.62
110 24 0.14
111 11 0.07
112 28 0.17
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (109 bp):
AAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTAATT
TGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGA
Found at i:23218 original size:10 final size:11
Alignment explanation
Indices: 23187--23229 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
23177 CGTGAATTAC
*
23187 AAAATATTTAT
1 AAAATATATAT
23198 AAAATATATAT
1 AAAATATATAT
*
23209 AAAAATATATTTT
1 -AAAATATA-TAT
23222 AAAATATA
1 AAAATATA
23230 AAGGATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
12 16 0.57
13 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATATATAT
Found at i:23414 original size:16 final size:16
Alignment explanation
Indices: 23393--23431 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
23383 GAATTATAAA
*
23393 AAAAATAA-AGTAAGAT
1 AAAAATAACA-TAAAAT
23409 AAAAATAACATAAAAT
1 AAAAATAACATAAAAT
23425 AAAAATA
1 AAAAATA
23432 TATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAATAACATAAAAT
Found at i:23611 original size:3 final size:3
Alignment explanation
Indices: 23603--23699 Score: 76
Period size: 3 Copynumber: 32.3 Consensus size: 3
23593 AAGCTATTAT
*
23603 ATA ATA ATA AT- ATA ATA AGTA ATA ATG AT- ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT-A ATA ATA ATA ATA
* * * * *
23648 ATA ATA ATA ATA AAA GATG ATA AT- ATA TTA AAA ATA ATGA AGA A-A
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
23693 ATA ATA A
1 ATA ATA A
23700 AAAAGCTAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
2 8 0.11
3 60 0.79
4 8 0.11
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:23649 original size:42 final size:42
Alignment explanation
Indices: 23603--23704 Score: 113
Period size: 42 Copynumber: 2.4 Consensus size: 42
23593 AAGCTATTAT
23603 ATAATAATAATATAATAAG-TAATAATGATA-TAAATAATAAT-A
1 ATAATAATAATATAA-AAGATAATAAT-ATATTAAA-AATAATGA
*
23645 ATAATAATAATAATAAAAGATGATAATATATTAAAAATAATGA
1 ATAATAATAAT-ATAAAAGATAATAATATATTAAAAATAATGA
* *
23688 AGAA-AATAATAAAAAAG
1 ATAATAATAATATAAAAG
23705 CTAAAAAAGG
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
41 6 0.11
42 29 0.55
43 18 0.34
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (42 bp):
ATAATAATAATATAAAAGATAATAATATATTAAAAATAATGA
Found at i:25290 original size:49 final size:49
Alignment explanation
Indices: 25110--25295 Score: 180
Period size: 49 Copynumber: 3.8 Consensus size: 49
25100 ATATAGTGAT
* * * * * *
25110 TGAAAACCATCATTGTAGGGCCATCTAGGATTGTAGATTAT-ATAAACAA
1 TGAAAACCATCATTGTTGGGCCATCCAAGATGGTAGAATATCA-AAACAG
* * *
25159 T-AAACATCATCATTGTTGGGCCATTCAGGATGGTAGAATATCAAAACAG
1 TGAAA-ACCATCATTGTTGGGCCATCCAAGATGGTAGAATATCAAAACAG
* ** * * *
25208 TGAAAGCCATTGTTCTCGGGCCATCCGAA-ATGGTAGAATATCAAAATAG
1 TGAAAACCATCATTGTTGGGCCATCC-AAGATGGTAGAATATCAAAACAG
*
25257 TGAAAACCATCATTGTTGGGCAATCCAAGATGGTAGAAT
1 TGAAAACCATCATTGTTGGGCCATCCAAGATGGTAGAAT
25296 TTGTAAATTG
Statistics
Matches: 110, Mismatches: 22, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
48 5 0.05
49 100 0.91
50 5 0.05
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (49 bp):
TGAAAACCATCATTGTTGGGCCATCCAAGATGGTAGAATATCAAAACAG
Found at i:35009 original size:597 final size:597
Alignment explanation
Indices: 33857--35128 Score: 2222
Period size: 597 Copynumber: 2.1 Consensus size: 597
33847 TCAATTATCT
* * * * * *
33857 GGTCAGGTTCCATCTTCCATCTTCAAAATTTCTTTTCTGAAGATTATTGATCTCTCCAGCAATAG
1 GGTCAGATTCCAACTTCGATCTTCAACATTTCTTCTCTGAAGACTATTGATCTCTCCAGCAATAG
*
33922 CCTATCAGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGGGCTTTACCTGA
66 CCTATCAGGTAGTTTGCCTAATAATATGTGTCAACATCTTCCCAAGCTTGAAGGGCTTTACCTGA
33987 GTTGGAATGAATTATCTGGTAACATTCCATTTGGCATGGGCAAATGCAACAACCTTAAAAATTTG
131 GTTGGAATGAATTATCTGGTAACATTCCATTTGGCATGGGCAAATGCAACAACCTTAAAAATTTG
* *
34052 TCATTGTCCCGTAATCAATTTATGGGATCATTCCAAGAAGTATTGGAAATCTAACACGACTCCAG
196 TCATTGTCCCGTAATCAATTGAGGGGATCATTCCAAGAAGTATTGGAAATCTAACACGACTCCAG
* *
34117 GAATTATATTTGGGGTTTAATAATCTAGAAGGTAATCAATTTCCTTGATTTCTTGAATTTAAAGT
261 GAATTATATTTGGGGTTTAATAATCTAAAAGGTAATCAATTTCCTTGATTTCTTGAACTTAAAGT
*
34182 ATGTTTTTTTTATAAAAGAGTTTGATTTGTAATAGATAACAAAAGGAAAAACTTTTAATTTTATT
326 A-GTTTTTTTTATAAAAGAGTTTGATTTGTAATAGATAACAAAAGGAAAAACTTTTAATTTCATT
34247 TGATGAAAAACATATGCTGAAATATATTAAAATCTAACATCTCCAAATTACTGTAGAACAGAAAA
390 TGATGAAAAACATATGCTGAAATATATTAAAATCTAACATCTCCAAATTACTGTAGAACAGAAAA
* *
34312 GAAAACCTCTTTGACTTATGCTAACAAAATAGGTAGTTTGACACCTTGATTTTTCGATTATGTGT
455 GAAAACCCCTTTGACTTATGCTAACAAAATAGGTAGTTTGACACCTTGATTTTTCGACTATGTGT
34377 GCAGGTCAAATTCCTGAGGAAATCGGTAATCTTCTTGGTTTGGAAATGCTTAATATTGTAGCAAT
520 GCAGGTCAAATTCCTGAGGAAATCGGTAATCTTCTTGGTTTGGAAATGCTTAATATTGTAGCAAT
34442 TAAAGGCCTTACA
585 TAAAGGCCTTACA
* * *
34455 GGTCAGATTCCAACTTCGATCTTCAACATTTCTTCTCTGAAGGCTATTAATCTCTCCAACAATAG
1 GGTCAGATTCCAACTTCGATCTTCAACATTTCTTCTCTGAAGACTATTGATCTCTCCAGCAATAG
* *
34520 TCTATCAGGTAGTTTGCCTAATAATATGTGTCAACATCTTCCCAAGCTTGAAGGGCTTTACTTGA
66 CCTATCAGGTAGTTTGCCTAATAATATGTGTCAACATCTTCCCAAGCTTGAAGGGCTTTACCTGA
*
34585 GTTTGAATGAATTATCTGGTAACATTCCATTTGGCATGGGCAAATGCAACAACCTTAAAAATTTG
131 GTTGGAATGAATTATCTGGTAACATTCCATTTGGCATGGGCAAATGCAACAACCTTAAAAATTTG
* **
34650 TCATTGTCCTGTAATCAATTGACGGGGATCATTCCAAGAAGTATTGGAAATCTAACACGACTCTG
196 TCATTGTCCCGTAATCAATTGA-GGGGATCATTCCAAGAAGTATTGGAAATCTAACACGACTCCA
*
34715 GGAATTATATTTGGGGTTTAATAATCTAAAAGGTAATCAATTTTCTTGATTTCTTGAACTTAAAG
260 GGAATTATATTTGGGGTTTAATAATCTAAAAGGTAATCAATTTCCTTGATTTCTTGAACTTAAAG
*
34780 TA-TTTTTTTTATAAAAGAGTTTGATTTGTAATAGATAACAAAAGGAAAAACTTTTTATTTCATT
325 TAGTTTTTTTTATAAAAGAGTTTGATTTGTAATAGATAACAAAAGGAAAAACTTTTAATTTCATT
* *
34844 TGATGAAAAACATATGCTGAAATATATTAAAATCTAGCATCTCCAAATTACTGTAGAATAGAAAA
390 TGATGAAAAACATATGCTGAAATATATTAAAATCTAACATCTCCAAATTACTGTAGAACAGAAAA
*
34909 GGAAACCCCTTTGACTTATGCTAACAAAATAGGTAGTTTGACACCTTGATTTTTCGACTATGTGT
455 GAAAACCCCTTTGACTTATGCTAACAAAATAGGTAGTTTGACACCTTGATTTTTCGACTATGTGT
* *
34974 GCAGGTCAAATTCCTGAGGAAATCGGTAATCTTCTTGGTTTGGAACTGCTTAGTATTGTAGCAAT
520 GCAGGTCAAATTCCTGAGGAAATCGGTAATCTTCTTGGTTTGGAAATGCTTAATATTGTAGCAAT
35039 TAAAGGCCTTACA
585 TAAAGGCCTTACA
* * *
35052 GGTCATATTCCAACTTTGATCTTCAACATTTCTTCTCTGAAGACCATTGATCTCTCCAGCAATAG
1 GGTCAGATTCCAACTTCGATCTTCAACATTTCTTCTCTGAAGACTATTGATCTCTCCAGCAATAG
35117 CCTATCAGGTAG
66 CCTATCAGGTAG
35129 ATCTCTCCAA
Statistics
Matches: 636, Mismatches: 37, Indels: 3
0.94 0.05 0.00
Matches are distributed among these distances:
597 331 0.52
598 202 0.32
599 103 0.16
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (597 bp):
GGTCAGATTCCAACTTCGATCTTCAACATTTCTTCTCTGAAGACTATTGATCTCTCCAGCAATAG
CCTATCAGGTAGTTTGCCTAATAATATGTGTCAACATCTTCCCAAGCTTGAAGGGCTTTACCTGA
GTTGGAATGAATTATCTGGTAACATTCCATTTGGCATGGGCAAATGCAACAACCTTAAAAATTTG
TCATTGTCCCGTAATCAATTGAGGGGATCATTCCAAGAAGTATTGGAAATCTAACACGACTCCAG
GAATTATATTTGGGGTTTAATAATCTAAAAGGTAATCAATTTCCTTGATTTCTTGAACTTAAAGT
AGTTTTTTTTATAAAAGAGTTTGATTTGTAATAGATAACAAAAGGAAAAACTTTTAATTTCATTT
GATGAAAAACATATGCTGAAATATATTAAAATCTAACATCTCCAAATTACTGTAGAACAGAAAAG
AAAACCCCTTTGACTTATGCTAACAAAATAGGTAGTTTGACACCTTGATTTTTCGACTATGTGTG
CAGGTCAAATTCCTGAGGAAATCGGTAATCTTCTTGGTTTGGAAATGCTTAATATTGTAGCAATT
AAAGGCCTTACA
Found at i:35134 original size:28 final size:28
Alignment explanation
Indices: 35100--35156 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
35090 GAAGACCATT
*
35100 GATCTCTCCAGCAATAGCCTATCAGGTA
1 GATCTCTCCAACAATAGCCTATCAGGTA
35128 GATCTCTCCAACAATAGCCTATCAGGTA
1 GATCTCTCCAACAATAGCCTATCAGGTA
35156 G
1 G
35157 TTTGCCTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (28 bp):
GATCTCTCCAACAATAGCCTATCAGGTA
Found at i:36736 original size:20 final size:20
Alignment explanation
Indices: 36708--36772 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
36698 TAAATAATAC
*
36708 AATTATTAAAAATTGTTAGA
1 AATTTTTAAAAATTGTTAGA
* *
36728 AATTTTTAAATATTG-TAAA
1 AATTTTTAAAAATTGTTAGA
* *
36747 AATTTATAAAAAATTTATTAGA
1 AATTT-TTAAAAA-TTGTTAGA
36769 AATT
1 AATT
36773 ATAAAAGACG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 8 0.23
20 18 0.51
21 2 0.06
22 7 0.20
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (20 bp):
AATTTTTAAAAATTGTTAGA
Found at i:36751 original size:19 final size:20
Alignment explanation
Indices: 36708--36758 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
36698 TAAATAATAC
* *
36708 AATTATTAAAAATTGTTAGA
1 AATTTTTAAAAATTGTTAAA
*
36728 AATTTTTAAATATTG-TAAA
1 AATTTTTAAAAATTGTTAAA
*
36747 AATTTATAAAAA
1 AATTTTTAAAAA
36759 ATTTATTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (20 bp):
AATTTTTAAAAATTGTTAAA
Done.