Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3178
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: 24515
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1385 original size:40 final size:40
Alignment explanation
Indices: 1269--1444 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
1259 ACCCAAGTAT
*
1269 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
1308 CTTCGGGTCTTAGCCC-GATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
1347 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
1387 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
1427 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
1445 TTATCATCCG
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
38 1 0.01
39 51 0.43
40 64 0.54
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:4829 original size:40 final size:40
Alignment explanation
Indices: 4774--4951 Score: 236
Period size: 40 Copynumber: 4.5 Consensus size: 40
4764 TGGATGATAA
* * *
4774 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
4814 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
4854 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
4894 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
4934 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
4952 TACTTGGCTT
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 16 0.13
40 110 0.87
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:12613 original size:40 final size:40
Alignment explanation
Indices: 12546--12708 Score: 213
Period size: 40 Copynumber: 4.1 Consensus size: 40
12536 ACCCAAGTAT
* *
12546 CTTCGGGATTTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGC
*
12585 CTTCGGGCCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * * *
12625 CTTCGGGTCTTAGCCCGAATATAATC-ACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* *
12665 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGC
12705 CTTC
1 CTTC
12709 AGATCTTAGT
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
39 13 0.12
40 91 0.86
41 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:16032 original size:47 final size:45
Alignment explanation
Indices: 15979--16099 Score: 136
Period size: 47 Copynumber: 2.6 Consensus size: 45
15969 TGGCCATGAT
15979 ATGTGATAAGGCCGAATGGCCAATGTGATGA-ATGTGGAAGTGCATAC
1 ATGTGATAAGGCCGAATGGCCAATGTGAT-ATATGTGGAAGTG-A-AC
* ** * * *
16026 ATGTGATAAGGCCGGATGGTTAATGTGATATATGTGTACGTGAAT
1 ATGTGATAAGGCCGAATGGCCAATGTGATATATGTGGAAGTGAAC
*
16071 ATGTGATAAGGCCGAATGACCAATTGTGA
1 ATGTGATAAGGCCGAATGGCCAA-TGTGA
16100 AAAGTGTGCA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
45 20 0.32
46 7 0.11
47 35 0.56
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (45 bp):
ATGTGATAAGGCCGAATGGCCAATGTGATATATGTGGAAGTGAAC
Found at i:16232 original size:39 final size:40
Alignment explanation
Indices: 16173--16257 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
16163 AAATGAATTG
* * * * *
16173 TGCTGAGATTGTATCTGGG-TTAGAGACCCGCTGGCTTCA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
*
16212 TGCTGGGATTGTATCCGGGTTTAAAGTCCCGCAGGCTTAA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
16252 TGCTGG
1 TGCTGG
16258 TGAATTAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 17 0.44
40 22 0.56
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.31
Consensus pattern (40 bp):
TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
Found at i:17606 original size:45 final size:45
Alignment explanation
Indices: 17555--17728 Score: 208
Period size: 45 Copynumber: 3.8 Consensus size: 45
17545 GATTTTGGCA
*
17555 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACG
*** * * * *
17600 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-A-ACG
17647 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACG
* *
17692 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17729 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
45 64 0.60
46 14 0.13
47 29 0.27
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACG
Found at i:17708 original size:92 final size:92
Alignment explanation
Indices: 17551--17720 Score: 297
Period size: 92 Copynumber: 1.8 Consensus size: 92
17541 CTAGGATTTT
* *
17551 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGTCCGAACTCGTTGAGT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGCCCGAACTCGTTGAGT
17616 TGAGTCCGAGTTCGAGAGATGTAACTA
66 TGAGTCCGAGTTCGAGAGATGTAACTA
*
17643 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGCCCGAACTCGTTGAG
17707 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
17721 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 9 0.12
92 65 0.88
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (92 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:20682 original size:28 final size:28
Alignment explanation
Indices: 20651--20711 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
20641 TCGTATCTTG
* *
20651 GGTTTCTTTATCCTGGATCTCTTTATTT
1 GGTTTCTCTATCCTGGATCTCTTTATTC
* *
20679 GGTTTCTCTATCTTGGATTTCTTTATTC
1 GGTTTCTCTATCCTGGATCTCTTTATTC
20707 GGTTT
1 GGTTT
20712 TCTTGTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.57
Consensus pattern (28 bp):
GGTTTCTCTATCCTGGATCTCTTTATTC
Found at i:23129 original size:46 final size:45
Alignment explanation
Indices: 23076--23251 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
23066 GGATTTGGCA
23076 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
23122 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
23169 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
23215 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
23252 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:23231 original size:93 final size:93
Alignment explanation
Indices: 23072--23243 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
23062 ACTAGGATTT
* *
23072 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
23137 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
23165 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
23230 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
23244 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Done.