Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2753
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: 25164
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:183 original size:35 final size:36
Alignment explanation
Indices: 129--204 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 36
119 TCGAGCTCTA
* * *
129 AAGACCCGATGACTACGTGTGGGGATTTTGTC-GGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCGGGT
*
164 AAGACCCGATAACTTCGTGTGGAGATTATGTCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCGGGT
200 AAGAC
1 AAGAC
205 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 28 0.78
36 8 0.22
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (36 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCGGGT
Found at i:2171 original size:40 final size:40
Alignment explanation
Indices: 2037--2291 Score: 213
Period size: 40 Copynumber: 6.5 Consensus size: 40
2027 TCGAATGATG
* *
2037 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACTATAT
* * *
2077 CCGGACTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
* * *
2115 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
* * *
2155 CCGGGCTAAGTTCCGAAGAGCATTCT-TGCTAGTGA-TGTAT
1 CCGGGCTAAGTCCCGAAG-GCATT-TGTGCGAGTGACTATAT
* * *
2195 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA-TATAT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGTGACTATAT
* ** * *
2235 CCGTGCTAAACCCCGAAGAGCATTCGTGCTG-GTG-TTATAT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGC-GAGTGACTATAT
*
2275 CC-GGCTAGGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
2292 AGCAATCATG
Statistics
Matches: 181, Mismatches: 26, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
38 10 0.06
39 51 0.28
40 107 0.59
41 12 0.07
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATAT
Found at i:5287 original size:47 final size:47
Alignment explanation
Indices: 5177--5585 Score: 714
Period size: 47 Copynumber: 8.7 Consensus size: 47
5167 TTAGGATTCT
5177 ATGT-ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-GCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
5222 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
5269 ATGTGATAAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
5316 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
5363 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
5410 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
5457 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
5504 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
5551 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
5586 TCCCGAAGGG
Statistics
Matches: 348, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
45 4 0.01
46 37 0.11
47 307 0.88
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:5758 original size:36 final size:37
Alignment explanation
Indices: 5703--5780 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
5693 CCGAGCTCTA
* *
5703 AAGACCCGATGACTACGTGTGG-GATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
5739 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
5776 AAGAC
1 AAGAC
5781 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 20 0.53
37 18 0.47
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:7749 original size:56 final size:56
Alignment explanation
Indices: 7685--7795 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
7675 TCCATGGAAA
7685 AACTTTGATACTTTGATATCTTTTCAAATTAATCCCCAAAATAGATAGATTAAGCT
1 AACTTTGATACTTTGATATCTTTTCAAATTAATCCCCAAAATAGATAGATTAAGCT
7741 AACTTTGATACTTTGATATCTTTTCAAATTAATCCCCAAAATAGATAGATTAAGC
1 AACTTTGATACTTTGATATCTTTTCAAATTAATCCCCAAAATAGATAGATTAAGC
7796 AATCCTGATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (56 bp):
AACTTTGATACTTTGATATCTTTTCAAATTAATCCCCAAAATAGATAGATTAAGCT
Found at i:15884 original size:39 final size:40
Alignment explanation
Indices: 15839--16047 Score: 98
Period size: 41 Copynumber: 5.2 Consensus size: 40
15829 CGGGGTTTAG
* * *
15839 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
15878 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
**** * * * **
15918 CCGGATATAGTGGCTAGCACAAATGCCTT-TGGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * * *
15958 CCGGATGTAGTCGCTTAACACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
** * * * *
15999 CCGGATATAGTCACTTAGCACAAAAGCCTTCAGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
16040 CCGGATAT
1 CCGGATAT
16048 CATTCGAGTA
Statistics
Matches: 142, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
39 18 0.13
40 58 0.41
41 63 0.44
42 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:15909 original size:40 final size:41
Alignment explanation
Indices: 15862--16047 Score: 216
Period size: 41 Copynumber: 4.6 Consensus size: 41
15852 CTCGCACAAG
* * * * *
15862 GCCTTCGGGTCTTAACCCGGATATGGTCAC-TAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTTAGCACAAAA
** *
15902 GCCTTCGGGACTTAGCCCGGATATAGTGGC-TAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTTAGCACAAAA
* * * * *
15942 GCCTT-TGGATCTTAGTCCGGATGTAGTCGCTTAACACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCACTTAGCACAAAA
15983 GCCTTCGGGACTTAGCCCGGATATAGTCACTTAGCACAAAA
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTTAGCACAAAA
*
16024 GCCTTCAGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
16048 CATTCGAGTA
Statistics
Matches: 125, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
39 3 0.02
40 56 0.45
41 63 0.50
42 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCACTTAGCACAAAA
Found at i:24058 original size:44 final size:42
Alignment explanation
Indices: 24004--24102 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 42
23994 CGGATCTAGT
*
24004 CGGATGTAGTCGCTTAACAC-AAAAGCCTTTCGGGACTTTTAGCC
1 CGGATATAGTCGCTTAACACAAAAAGCCTTTCGGGAC--TTAG-C
* *
24048 CGGATATAGTCGCTTAGCACAAAAAGCCTTTGGGGACTTAGC
1 CGGATATAGTCGCTTAACACAAAAAGCCTTTCGGGACTTAGC
24090 CGGATATCAGTCG
1 CGGATAT-AGTCG
24103 AGTAACCATT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
42 8 0.16
43 9 0.18
44 18 0.36
45 15 0.30
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.25
Consensus pattern (42 bp):
CGGATATAGTCGCTTAACACAAAAAGCCTTTCGGGACTTAGC
Done.