Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2606
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: 55672
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:1024 original size:15 final size:16
Alignment explanation
Indices: 992--1032 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
982 AATCTGAAAC
*
992 AAGAAAGCCAAGAATA
1 AAGAAATCCAAGAATA
*
1008 AATAAATCCAA-AATA
1 AAGAAATCCAAGAATA
1023 AAGAAATCCA
1 AAGAAATCCA
1033 TGATACCAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.63, C:0.15, G:0.10, T:0.12
Consensus pattern (16 bp):
AAGAAATCCAAGAATA
Found at i:14521 original size:51 final size:49
Alignment explanation
Indices: 14399--14536 Score: 186
Period size: 51 Copynumber: 2.8 Consensus size: 49
14389 AAGCTATCTG
* **
14399 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCA
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGAAAAATTATCCA
* * * *
14448 GTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATAAAAGTTATCGA
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGA-AAAA-TTATCCA
*
14499 GTACGCATAGTAGCCTGTACTTAGTACTACACATGTGA
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGA
14537 CCTCACAATA
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
49 34 0.45
50 2 0.03
51 40 0.53
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (49 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGAAAAATTATCCA
Found at i:25110 original size:46 final size:46
Alignment explanation
Indices: 25059--25186 Score: 147
Period size: 46 Copynumber: 2.8 Consensus size: 46
25049 ATGGTTGAGC
*
25059 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA--AATGT-AACTAG
* * *
25106 -TCCGAACTCGTTGAGCTGAGTCCGAGTTC-GTGAAATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAAATGTAACTA-G
25151 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
25187 GGGGCGGGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.03
43 5 0.07
45 3 0.04
46 28 0.41
47 28 0.41
48 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAAATGTAACTAG
Found at i:27893 original size:19 final size:18
Alignment explanation
Indices: 27869--27905 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
27859 TAGGCCATGT
27869 TGGGCCAAAATGGGCTGTG
1 TGGGCC-AAATGGGCTGTG
*
27888 TGGGCCTAATGGGCTGTG
1 TGGGCCAAATGGGCTGTG
27906 GGCCCCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.16, C:0.16, G:0.43, T:0.24
Consensus pattern (18 bp):
TGGGCCAAATGGGCTGTG
Found at i:36005 original size:40 final size:40
Alignment explanation
Indices: 35894--36096 Score: 252
Period size: 40 Copynumber: 5.1 Consensus size: 40
35884 CGGATGATAA
* * *
35894 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATA-T
* *
35934 CCGGGCTAAG-CCCGAAGGCAATT-GAGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGC-ATTCGTGCGAGTTACTATAT
*
35973 CCGGGCTAAGTCCCGAAGGCATTCGTGAGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
* * *
36013 CCGGGCTAAGTCCCGAAGGCATTTGTCCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
* *
36053 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTA-CTATAT
36093 CCGG
1 CCGG
36097 TTGAATTCCG
Statistics
Matches: 142, Mismatches: 16, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
39 34 0.24
40 108 0.76
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
Found at i:37526 original size:83 final size:88
Alignment explanation
Indices: 37359--37518 Score: 190
Period size: 85 Copynumber: 1.9 Consensus size: 88
37349 GTTGGTATTA
* *
37359 ATCTGAATTATCGTGTAAGACCGTGTCTAGGACAAATGCATCGAATTGAAATTTAATTGTAAGAC
1 ATCTGAATTATCGTATAAGACCGTGTCTAGGACAAATGCATCGAACTGAAATTTAATTGTAAGAC
* *
37424 CATGTCCGGGATATCGGCATCAT
66 CACGTCCGGGACATCGGCATCAT
* *
37447 ATCTG-ATT-TCGTATAGGACC-TGTCTGGGACAAATGCATC-ATACTG-AA-TTACA-TGTAAG
1 ATCTGAATTATCGTATAAGACCGTGTCTAGGACAAATGCATCGA-ACTGAAATTTA-ATTGTAAG
*
37505 ACTACGTCCGGGAC
64 ACCACGTCCGGGAC
37519 GTTGGCATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
83 20 0.32
84 4 0.06
85 21 0.33
86 10 0.16
87 3 0.05
88 5 0.08
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (88 bp):
ATCTGAATTATCGTATAAGACCGTGTCTAGGACAAATGCATCGAACTGAAATTTAATTGTAAGAC
CACGTCCGGGACATCGGCATCAT
Found at i:39168 original size:24 final size:19
Alignment explanation
Indices: 39115--39154 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
39105 AAATATTATT
39115 CATGCTTTAAGCATCCGCA
1 CATGCTTTAAGCATCCGCA
39134 CATGCTTTAAGCATCCGCA
1 CATGCTTTAAGCATCCGCA
39153 CA
1 CA
39155 CTTAGTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (19 bp):
CATGCTTTAAGCATCCGCA
Found at i:46114 original size:15 final size:15
Alignment explanation
Indices: 46094--46122 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46084 AGATTAAGGT
46094 ATGTTTAATGTTGCA
1 ATGTTTAATGTTGCA
46109 ATGTTTAATGTTGC
1 ATGTTTAATGTTGC
46123 TTTGAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
ATGTTTAATGTTGCA
Found at i:47427 original size:40 final size:40
Alignment explanation
Indices: 47340--47557 Score: 228
Period size: 40 Copynumber: 5.4 Consensus size: 40
47330 ATGATATCTA
* *
47340 GGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACTATAACCG
1 GGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACTATATCCG
* * *
47381 GACTAAGATCCGAAGGCATTCGTGCGAGTTG-CTATATCCG
1 GGCTAAGATCCGAAGGCATTTGTGCTAG-TGACTATATCCG
* * *
47421 GGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCG
1 GGCTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCG
* **
47461 GGCTAA-AACCTGAAGGCATTTGTGCTAGCAACTATATCCG
1 GGCTAAGATCC-GAAGGCATTTGTGCTAGTGACTATATCCG
* * *
47501 GGCTAAG-TCCCGAAGGCATTTATGCTAGTGACCACATCCG
1 GGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACTATATCCG
*
47541 GGCTAAGACCCGAAGGC
1 GGCTAAGATCCGAAGGC
47558 CTTGTGCAAG
Statistics
Matches: 149, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
39 4 0.03
40 119 0.80
41 25 0.17
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
GGCTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCG
Found at i:47513 original size:80 final size:79
Alignment explanation
Indices: 47340--47557 Score: 256
Period size: 80 Copynumber: 2.7 Consensus size: 79
47330 ATGATATCTA
* * * *
47340 GGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGCATTCGTG
1 GGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAA-AACCGAAGGCATTCGTG
***
47405 CGAGTTGCTATATCCG
64 CGAGCAACTATATCCG
* * * *
47421 GGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCTGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAAACC-GAAGGCATTCGTGC
*
47486 TAGCAACTATATCCG
65 GAGCAACTATATCCG
* * * *
47501 GGCTAAGTCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGC
1 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAA-AACCGAAGGC
47558 CTTGTGCAAG
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
79 3 0.03
80 85 0.73
81 28 0.24
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (79 bp):
GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAAACCGAAGGCATTCGTGCG
AGCAACTATATCCG
Found at i:55491 original size:38 final size:38
Alignment explanation
Indices: 55444--55535 Score: 134
Period size: 38 Copynumber: 2.4 Consensus size: 38
55434 GCCTTTGGGA
55444 CTTAGCCCGG-TATAGTCGCTAGCACAAATGCCTTCAGGT
1 CTTAGCCCGGATATAGTCGCTAGCAC-AATGCC-TCAGGT
* *
55483 -TTAGCCCGGATATAATCGCTAGCACAATGCCTCGGGT
1 CTTAGCCCGGATATAGTCGCTAGCACAATGCCTCAGGT
55520 CTTAGCCCGGATATAG
1 CTTAGCCCGGATATAG
55536 CAACTCGCCG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
37 5 0.10
38 29 0.60
39 14 0.29
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (38 bp):
CTTAGCCCGGATATAGTCGCTAGCACAATGCCTCAGGT
Done.