Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2593
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: 34373
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Found at i:391 original size:13 final size:13
Alignment explanation
Indices: 369--416 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
359 TAAAGCACAG
369 AAAA-GAAAAAAA
1 AAAATGAAAAAAA
*
381 AAAATGAAAAAAT
1 AAAATGAAAAAAA
* *
394 GAATTGAAAAAAA
1 AAAATGAAAAAAA
407 AAAAT-AAAAA
1 AAAATGAAAAA
417 GTATTAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 9 0.31
13 20 0.69
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.10
Consensus pattern (13 bp):
AAAATGAAAAAAA
Found at i:415 original size:24 final size:23
Alignment explanation
Indices: 373--437 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
363 GCACAGAAAA
373 GAAAAAAAAAAATGAAAAAATGAATT
1 GAAAAAAAAAAAT--AAAAA-GAATT
*
399 GAAAAAAAAAAATAAAAAGTATT
1 GAAAAAAAAAAATAAAAAGAATT
422 -AAAAAATTAAAAATAA
1 GAAAAAA--AAAAATAA
438 TCAAATTGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 6 0.17
23 4 0.11
24 13 0.36
26 13 0.36
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (23 bp):
GAAAAAAAAAAATAAAAAGAATT
Found at i:1078 original size:18 final size:19
Alignment explanation
Indices: 1057--1092 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1047 TTTTTAAATT
1057 TAAATA-GTTTTTAAAAAG
1 TAAATATGTTTTTAAAAAG
*
1075 TAAATATTTTTTTAAAAA
1 TAAATATGTTTTTAAAAA
1093 AACTTAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (19 bp):
TAAATATGTTTTTAAAAAG
Found at i:2099 original size:16 final size:15
Alignment explanation
Indices: 2073--2102 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2063 AATGGCAGCG
2073 ATTTTTTTTTCTTTC
1 ATTTTTTTTTCTTTC
2088 ATTTTATTTTTCTTT
1 ATTTT-TTTTTCTTT
2103 TCTTGACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (15 bp):
ATTTTTTTTTCTTTC
Found at i:6206 original size:239 final size:239
Alignment explanation
Indices: 5824--6257 Score: 681
Period size: 239 Copynumber: 1.8 Consensus size: 239
5814 CTAACAAACT
* * *
5824 ACAAGAAGGCAAGCAGAATACATTATACAAAAGAAACCTTTTAAAACTAAAATAAAAAGGAAATC
1 ACAAGAAGGCAAGCAGAATACATTATAAAAAAGAAACCTTTAAAAACTAAAATAAAAAAGAAATC
* * *
5889 CGGAACACCAAGGCCAATCCAGCACCTTGCTTAATTACTCTAAATCAATTGGGTTCATAAAACGA
66 CAGAACACCAAGGCCAATCCAGCACCTTGCCTAATTACCCTAAATCAATTGGGTTCATAAAACGA
* * *
5954 ATACCTCGGAAATGGATAAATCATTCAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGTT
131 ACACCTCGGAAATGGACAAATCATTCAAAAAAACTCTTTCACCAGTATCATTTCTAGAACTGGTT
6019 TGCTTCATTGTCTTCCACCCGGCCTATGTACCAACTACAGGAAG
196 TGCTTCATTGTCTTCCACCCGGCCTATGTACCAACTACAGGAAG
* *
6063 ACAAGAAGGCAAGCAGAATACATTATAAAAAAGAAACCTTTAAAAATTAAAATAAAAAAGAAATT
1 ACAAGAAGGCAAGCAGAATACATTATAAAAAAGAAACCTTTAAAAACTAAAATAAAAAAGAAATC
* *
6128 CAGAACACCAAGGCCAAATCCATCACCTTGCCTAGTTACCCTAAATCAATTGGGTTCATAAAA-G
66 CAGAACACCAAGGCC-AATCCAGCACCTTGCCTAATTACCCTAAATCAATTGGGTTCATAAAACG
* * * * * *
6192 AACAGCTTGGAAATGGACATATCATTCAAAACACCTCTTTCACCAGTTTCATTTCTAGAACTGGT
130 AACACCTCGGAAATGGACAAATCATTCAAAAAAACTCTTTCACCAGTATCATTTCTAGAACTGGT
6257 T
195 T
6258 CTCCGTGCCT
Statistics
Matches: 175, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
239 132 0.75
240 43 0.25
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (239 bp):
ACAAGAAGGCAAGCAGAATACATTATAAAAAAGAAACCTTTAAAAACTAAAATAAAAAAGAAATC
CAGAACACCAAGGCCAATCCAGCACCTTGCCTAATTACCCTAAATCAATTGGGTTCATAAAACGA
ACACCTCGGAAATGGACAAATCATTCAAAAAAACTCTTTCACCAGTATCATTTCTAGAACTGGTT
TGCTTCATTGTCTTCCACCCGGCCTATGTACCAACTACAGGAAG
Found at i:7511 original size:2 final size:2
Alignment explanation
Indices: 7504--7533 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7494 ATGGAGCCTA
7504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7534 TTTAAACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11431 original size:92 final size:92
Alignment explanation
Indices: 11263--11440 Score: 250
Period size: 92 Copynumber: 1.9 Consensus size: 92
11253 GATGAATACG
* ** *
11263 CTGCAACCAGACATATTTGAGACACTAGTCATTATCTTACAGGAAATAGAATAAGCTAAGATACC
1 CTGCAACCAAACATATTCAAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
*
11328 GATAGACTATTTTAACCAAAAAATATC
66 AATAGACTATTTTAACCAAAAAATATC
* * *
11355 CTGCAACCAAACATATTCAAGACACTAGTCATTATTTTACAGGAAATGGAATATA-ATAAGATGC
1 CTGCAACCAAACATATTCAAGACACTAGTCATTATCTTACAGGAAATAGAATA-AGATAAGATAC
* *
11419 CAATATAGTATTTTAACCAAAA
65 CAATAGACTATTTTAACCAAAA
11441 TATACTAACA
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
92 74 0.99
93 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.27
Consensus pattern (92 bp):
CTGCAACCAAACATATTCAAGACACTAGTCATTATCTTACAGGAAATAGAATAAGATAAGATACC
AATAGACTATTTTAACCAAAAAATATC
Found at i:16581 original size:32 final size:32
Alignment explanation
Indices: 16535--16596 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
16525 CAAATTAGCT
*
16535 GAACCATGATAAAACAAAACAGGTCCACAACA
1 GAACCATGACAAAACAAAACAGGTCCACAACA
16567 GAACCATGACAAAACAAAACAGGTCCACAA
1 GAACCATGACAAAACAAAACAGGTCCACAA
16597 ATACCTACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.08
Consensus pattern (32 bp):
GAACCATGACAAAACAAAACAGGTCCACAACA
Found at i:23058 original size:26 final size:26
Alignment explanation
Indices: 22988--23045 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
22978 CTAGGGTTTA
* *
22988 TTAATTATTGCTTTATTATAACAAGT
1 TTAATTATTACTTCATTATAACAAGT
23014 TTAATTATTACTTCATTATAACAAGT
1 TTAATTATTACTTCATTATAACAAGT
23040 TTAATT
1 TTAATT
23046 TTATGTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (26 bp):
TTAATTATTACTTCATTATAACAAGT
Found at i:27509 original size:12 final size:12
Alignment explanation
Indices: 27492--27518 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27482 GGTCACTTAA
27492 AAATCTTTGACC
1 AAATCTTTGACC
27504 AAATCTTTGACC
1 AAATCTTTGACC
27516 AAA
1 AAA
27519 GGTTAAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (12 bp):
AAATCTTTGACC
Done.