Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1312
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: 54216
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1717 original size:41 final size:41
Alignment explanation
Indices: 1660--1809 Score: 221
Period size: 41 Copynumber: 3.7 Consensus size: 41
1650 TTGGGGTTTA
1660 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1701 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * * *
1742 AA-CCGAACCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1782 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1810 TGAGTCAGCG
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 32 0.34
41 62 0.66
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:15252 original size:3 final size:3
Alignment explanation
Indices: 15244--15292 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
15234 AAGGAGTATA
15244 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
15292 T
1 T
15293 TTAGCTAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:17835 original size:44 final size:42
Alignment explanation
Indices: 17786--17871 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
17776 TCATCTTTCC
17786 ATGCACCCACGTGAGAAGAGAATAGAAGAAAGAAATTTTCCTTT
1 ATGCACCCACGTGAGAAGAG-A-AGAAGAAAGAAATTTTCCTTT
***
17830 ATGCACCTGTGTGAGAAGAGAAGAAGAAAGAAATTTTCCTTT
1 ATGCACCCACGTGAGAAGAGAAGAAGAAAGAAATTTTCCTTT
17872 CTTTACAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 21 0.54
43 1 0.03
44 17 0.44
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (42 bp):
ATGCACCCACGTGAGAAGAGAAGAAGAAAGAAATTTTCCTTT
Found at i:27199 original size:14 final size:14
Alignment explanation
Indices: 27180--27217 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
27170 TAGTAGTAGT
27180 AGAAGGCTGATGTC
1 AGAAGGCTGATGTC
*
27194 AGAAGGCTGATGTT
1 AGAAGGCTGATGTC
*
27208 AGAAAGCTGA
1 AGAAGGCTGA
27218 GAAGAGGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.21
Consensus pattern (14 bp):
AGAAGGCTGATGTC
Found at i:31413 original size:50 final size:50
Alignment explanation
Indices: 31338--31437 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
31328 ATTCTTGAAA
* *
31338 GTATCTCCATGGAGAAAGATATTGAGATTTGTTCAAAACGGTAAGCTGAG
1 GTATCTCCATGGAGAAAGATATTGAGATTTGTTCAAAAAGGTAAACTGAG
*
31388 GTATCTCCATGGAGAAAGGTATTGAGATTTGTTCAAAAAGGTAAACTGAG
1 GTATCTCCATGGAGAAAGATATTGAGATTTGTTCAAAAAGGTAAACTGAG
31438 TCCACAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (50 bp):
GTATCTCCATGGAGAAAGATATTGAGATTTGTTCAAAAAGGTAAACTGAG
Found at i:41201 original size:23 final size:23
Alignment explanation
Indices: 41171--41217 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
41161 ATACGCGGAT
*
41171 TCCACCCAAACACA-CTAGAATA
1 TCCACCCAAACACACCCAGAATA
41193 TCCATCCCAAACACACCCAGAATA
1 TCCA-CCCAAACACACCCAGAATA
41217 T
1 T
41218 TATAAATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 10 0.45
24 8 0.36
ACGTcount: A:0.43, C:0.38, G:0.04, T:0.15
Consensus pattern (23 bp):
TCCACCCAAACACACCCAGAATA
Found at i:42738 original size:15 final size:14
Alignment explanation
Indices: 42705--42766 Score: 56
Period size: 14 Copynumber: 4.3 Consensus size: 14
42695 ATAATATCAT
*
42705 TATAATTTA-ATTA
1 TATAAATTATATTA
42718 TCATAAATTCATATTA
1 T-ATAAATT-ATATTA
42734 TATAAATTATATTTA
1 TATAAATTATA-TTA
*
42749 TATATCATTA-ATTA
1 TATA-AATTATATTA
42763 TATA
1 TATA
42767 CTTTAAATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
13 1 0.02
14 16 0.38
15 16 0.38
16 9 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAAATTATATTA
Found at i:42905 original size:17 final size:18
Alignment explanation
Indices: 42870--42905 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
42860 TATTGTTCTA
*
42870 TAATTCAACTTTTATCCT
1 TAATTCAACTTTAATCCT
42888 TAATTCAA-TTTAATCCT
1 TAATTCAACTTTAATCCT
42905 T
1 T
42906 TTTTCTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTCAACTTTAATCCT
Found at i:49860 original size:14 final size:14
Alignment explanation
Indices: 49822--49854 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
49812 CGTTTTATTC
*
49822 TATTTACTTTAATT
1 TATTTAATTTAATT
49836 TATTTAATTTAATT
1 TATTTAATTTAATT
49850 TATTT
1 TATTT
49855 GTTTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTAATTTAATT
Found at i:50330 original size:15 final size:14
Alignment explanation
Indices: 50297--50358 Score: 56
Period size: 14 Copynumber: 4.3 Consensus size: 14
50287 ATAATATCAT
*
50297 TATAATTTA-ATTA
1 TATAAATTATATTA
50310 TCATAAATTCATATTA
1 T-ATAAATT-ATATTA
50326 TATAAATTATATTTA
1 TATAAATTATA-TTA
*
50341 TATATCATTA-ATTA
1 TATA-AATTATATTA
50355 TATA
1 TATA
50359 CTTTAAATCA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
13 1 0.02
14 16 0.38
15 16 0.38
16 9 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAAATTATATTA
Found at i:50948 original size:12 final size:13
Alignment explanation
Indices: 50931--50959 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
50921 CTCATACATG
50931 AATAAATAAA-GC
1 AATAAATAAATGC
50943 AATAAATAAATGC
1 AATAAATAAATGC
50956 AATA
1 AATA
50960 GTTATAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:52512 original size:78 final size:76
Alignment explanation
Indices: 52380--52556 Score: 286
Period size: 78 Copynumber: 2.3 Consensus size: 76
52370 TGTATATAAA
* *
52380 GGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 GGGGTTGCTATGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
*
52445 GAAATGTGAAAAG
66 GAAA--TAAAAAG
52458 GGGGTTGCTATGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCTT
1 GGGGTTGCTATGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TGATCCACCATATCTT
52522 TGAAATAAAAAG
65 TGAAATAAAAAG
52534 GGGGTTGC-ATGTGCTGATTCCCC
1 GGGGTTGCTATGTGCTGATTCCCC
52557 CGAGGGGTTG
Statistics
Matches: 95, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
75 15 0.16
76 14 0.15
78 65 0.68
79 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.32
Consensus pattern (76 bp):
GGGGTTGCTATGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
GAAATAAAAAG
Found at i:53518 original size:41 final size:41
Alignment explanation
Indices: 53461--53598 Score: 197
Period size: 41 Copynumber: 3.4 Consensus size: 41
53451 ATTTTTCTCT
53461 GTCTCGAAGGGCTTTTGAGCCAGTGTCATAATCCGAGCTTG
1 GTCTCGAAGGGCTTTTGAGCCAGTGTCATAATCCGAGCTTG
* * *
53502 GTCTCGAAGGGCTTTTGAGCCAGTGTCATAA-CCGAACCTA
1 GTCTCGAAGGGCTTTTGAGCCAGTGTCATAATCCGAGCTTG
* * * * *
53542 GTTTCGAAGGGCCTTCGGGCCAATGTCATAATCCGAGCTTG
1 GTCTCGAAGGGCTTTTGAGCCAGTGTCATAATCCGAGCTTG
53583 GTCTCGAAGGGCTTTT
1 GTCTCGAAGGGCTTTT
53599 TGAGTCAGCG
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 32 0.39
41 50 0.61
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.28
Consensus pattern (41 bp):
GTCTCGAAGGGCTTTTGAGCCAGTGTCATAATCCGAGCTTG
Done.