Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3476
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: 51725
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:7136 original size:27 final size:27
Alignment explanation
Indices: 7105--7281 Score: 203
Period size: 27 Copynumber: 6.6 Consensus size: 27
7095 TATATTAGTC
* * * *
7105 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
7132 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
7159 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
** * *
7186 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
7213 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
7240 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
7267 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
7282 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
27 128 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:7243 original size:81 final size:81
Alignment explanation
Indices: 7126--7280 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 81
7116 TGCTATATAA
* * *
7126 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAACTCGCAC
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
7191 ACTTAGTGCCGCATGG
66 ACTTAGTGCCGCATGG
* * **
7207 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
7271 CACTTAGTGC
65 CACTTAGTGC
7281 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.02
81 65 0.98
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:9458 original size:46 final size:46
Alignment explanation
Indices: 9402--9561 Score: 191
Period size: 46 Copynumber: 3.5 Consensus size: 46
9392 TGGTTGAGCA
9402 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
9448 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
9493 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
9541 CCCGAGCTCGTTGAGTTGAGT
1 TCCGAACTCGTTGAGTTGAGT
9562 TGAGTCCGAG
Statistics
Matches: 96, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 48 0.50
47 29 0.30
48 4 0.04
50 5 0.05
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:13592 original size:20 final size:20
Alignment explanation
Indices: 13555--13598 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
13545 ATATATCTGA
* *
13555 AAATTTAAGTTCTCTTTTTT
1 AAATTTAAATACTCTTTTTT
13575 AAATTTAAATA--CTTTTTT
1 AAATTTAAATACTCTTTTTT
13593 AAATTT
1 AAATTT
13599 TTATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.59
20 9 0.41
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (20 bp):
AAATTTAAATACTCTTTTTT
Found at i:22752 original size:30 final size:30
Alignment explanation
Indices: 22718--22778 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
22708 TTCCCGAGCC
*
22718 TAGGGGTAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
22748 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
22778 T
1 T
22779 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:23360 original size:68 final size:68
Alignment explanation
Indices: 23277--23439 Score: 174
Period size: 67 Copynumber: 2.4 Consensus size: 68
23267 TGCTGAGTGC
* * *
23277 ACATCATGT-GTACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTTGCATGGGTGATACTA-
1 ACATCATGTAG-ACAAGAGAGCTACGAGACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAG
* *
23340 TG-TGT
63 TGAAGG
* * *
23345 ACATCATGTAGACAAGAGAGCTAC-A-AGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTG
1 ACATCATGTAGACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTG
23408 AAGG
65 AAGG
*
23412 ACACCATGTAGACAAGAGAGCTACGAGA
1 ACATCATGTAGACAAGAGAGCTACGAGA
23440 TAAACTGGCT
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
64 23 0.29
65 3 0.04
66 4 0.05
67 25 0.31
68 23 0.29
69 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (68 bp):
ACATCATGTAGACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGA
AGG
Found at i:25351 original size:18 final size:17
Alignment explanation
Indices: 25320--25354 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
25310 GATTTTGGGT
25320 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
25337 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
25355 AAATCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:25598 original size:31 final size:31
Alignment explanation
Indices: 25563--25621 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
25553 AAAAGACTTA
25563 AAATTT-ATAAAATTCTAAAAT-ATATAAATAT
1 AAATTTCA-AAAATTC-AAAATAATATAAATAT
25594 AAATTTCAAAAATTCAAAATAATATAAA
1 AAATTTCAAAAATTCAAAATAATATAAA
25622 AAATTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 5 0.19
31 20 0.77
32 1 0.04
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (31 bp):
AAATTTCAAAAATTCAAAATAATATAAATAT
Found at i:25886 original size:20 final size:20
Alignment explanation
Indices: 25863--25900 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25853 ACTTTTAGAG
*
25863 TTTTATAATTATTTTGAAAA
1 TTTTAAAATTATTTTGAAAA
*
25883 TTTTAAAATTTTTTTGAA
1 TTTTAAAATTATTTTGAA
25901 TTGTTATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTAAAATTATTTTGAAAA
Found at i:26250 original size:12 final size:12
Alignment explanation
Indices: 26228--26261 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
26218 AGTTGAACCC
26228 AATAA-TTAAAT
1 AATAATTTAAAT
26239 AATAATTTAAAT
1 AATAATTTAAAT
*
26251 ATTAATTTAAA
1 AATAATTTAAA
26262 ATAAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATAATTTAAAT
Found at i:26272 original size:22 final size:23
Alignment explanation
Indices: 26247--26295 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
26237 ATAATAATTT
*
26247 AAATATTA-AT-TTAAAATAAAA
1 AAATATTAGATATCAAAATAAAA
26268 GAAAT-TTAGATATCAAAATAAAA
1 -AAATATTAGATATCAAAATAAAA
26291 AAATA
1 AAATA
26296 AACCTAGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 3 0.13
22 10 0.43
23 10 0.43
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (23 bp):
AAATATTAGATATCAAAATAAAA
Found at i:33115 original size:42 final size:42
Alignment explanation
Indices: 33018--33122 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
33008 AGGGTTACCG
* * *
33018 AGATTATGTGTAAGACCATATTTGGGATATGGAATCATTATG
1 AGATTTTGTGTAAGACCATATCTGGGATATGGAATCATTATA
* * * **
33060 AGACTTCGGGTAAGACCATATCTGGGATATGGCTTCGA-TATA
1 AGATTTTGTGTAAGACCATATCTGGGATATGGAATC-ATTATA
33102 AGATTTTGTGTAAGACCATAT
1 AGATTTTGTGTAAGACCATAT
33123 GTAACGCCCC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 50 0.98
43 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (42 bp):
AGATTTTGTGTAAGACCATATCTGGGATATGGAATCATTATA
Found at i:35289 original size:33 final size:33
Alignment explanation
Indices: 35203--35295 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 33
35193 ATGCATTTTG
* * * *
35203 GATACTAT-ACTGAAATGGGCTAAGACCCACATT
1 GATACTGTCACTGATATGGGCTAAG-GCCACACT
35236 GATACTGTCACTG-TATTGGGCTAAGGCCACACT
1 GATACTGTCACTGATA-TGGGCTAAGGCCACACT
* *
35269 GATATTG-CAACTGATATGGGCTTAGGC
1 GATACTGTC-ACTGATATGGGCTAAGGC
35296 TCAGACCGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
32 1 0.02
33 34 0.68
34 15 0.30
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (33 bp):
GATACTGTCACTGATATGGGCTAAGGCCACACT
Found at i:46150 original size:104 final size:103
Alignment explanation
Indices: 46028--46250 Score: 376
Period size: 104 Copynumber: 2.2 Consensus size: 103
46018 AATGGATATC
46028 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
46093 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACC-ATAAACCGGGGAATCA
46132 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
*
46197 GGATCACGCACATAGCACCACCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCATAAACCGGGGAATCA
**
46235 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
46251 TTTATATACA
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
103 28 0.25
104 84 0.74
105 1 0.01
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCATAAACCGGGGAATCA
Found at i:46612 original size:29 final size:29
Alignment explanation
Indices: 46579--46642 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
46569 TAATCCACCA
46579 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
46608 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
46638 CCCAA
1 CCCAA
46643 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:46616 original size:30 final size:30
Alignment explanation
Indices: 46586--46642 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
46576 CCACCCAACT
46586 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
46615 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
46643 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Done.