Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2727
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: 36569
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Found at i:1088 original size:40 final size:40
Alignment explanation
Indices: 964--1171 Score: 210
Period size: 40 Copynumber: 5.2 Consensus size: 40
954 GAATGATACT
* *
964 GGGCTAAGTCCCGAAGGCGCAATTGTGCTAAGTGATTTTATCC
1 GGGCTAAGACCCGAA-G-GCAATTGTGCT-AGTGTTTTTATCC
* * * * * *
1007 GGGCTAAGA-CCGAAGGCATTTGTACGAGT-TGCTATACCC
1 GGGCTAAGACCCGAAGGCAATTGTGCTAGTGT-TTTTATCC
*
1046 GGGTTAAGACCCGAAGGCAATTGTGCTAGTGTTTTTATCC
1 GGGCTAAGACCCGAAGGCAATTGTGCTAGTGTTTTTATCC
* *
1086 GGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATAACC
1 GGGCTAAGACCCGAAGGCAATTGTGCTAGTG-TTTT-TATCC
* *
1128 GGGCTAAGACCCGAAGGC-ATTGTGCTTGTG-TTATATCC
1 GGGCTAAGACCCGAAGGCAATTGTGCTAGTGTTTTTATCC
1166 -GGCTAA
1 GGGCTAA
1172 ATTCCGAAGA
Statistics
Matches: 140, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
37 6 0.04
38 4 0.03
39 18 0.13
40 61 0.44
41 17 0.12
42 26 0.19
43 8 0.06
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
GGGCTAAGACCCGAAGGCAATTGTGCTAGTGTTTTTATCC
Found at i:1101 original size:80 final size:79
Alignment explanation
Indices: 964--1171 Score: 233
Period size: 82 Copynumber: 2.6 Consensus size: 79
954 GAATGATACT
* *
964 GGGCTAAGTCCCGAAGGCGCAATTGTGCTAAGTGATTTTATCCGGGCTAAGACCGAAGGCATTTG
1 GGGCTAAGACCCGAA-G-GCAATTGTGCT-AGTG-TTTTATCCGGGCTAAGACCGAAGGCAATTG
*
1029 TACGAGT-TGCTATACCC
62 TACGAGTATGCTATAACC
* * *
1046 GGGTTAAGACCCGAAGGCAATTGTGCTAGTGTTTTTATCCGGGTTAAGACCCGAAGGCAATTGTG
1 GGGCTAAGACCCGAAGGCAATTGTGCTAGTG-TTTTATCCGGGCTAAGA-CCGAAGGCAATTGTA
* **
1111 CTAGTGATTTTATAACC
64 CGAGT-ATGCTATAACC
* *
1128 GGGCTAAGACCCGAAGGC-ATTGTGCTTGTGTTATATCC-GGCTAA
1 GGGCTAAGACCCGAAGGCAATTGTGCTAGTGTTTTATCCGGGCTAA
1172 ATTCCGAAGA
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
79 25 0.23
80 35 0.32
81 12 0.11
82 37 0.34
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (79 bp):
GGGCTAAGACCCGAAGGCAATTGTGCTAGTGTTTTATCCGGGCTAAGACCGAAGGCAATTGTACG
AGTATGCTATAACC
Found at i:9053 original size:40 final size:40
Alignment explanation
Indices: 8995--9204 Score: 282
Period size: 40 Copynumber: 5.3 Consensus size: 40
8985 ATTTGAATGA
*
8995 TATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
* * * *
9035 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAG-TGATTT
* *
9075 TACCCGGGTTAAGACCCGAAGGC-ATTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
*
9114 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
* * * *
9154 TATACGGGCTAAGACCCGAAGGCATTTGTGCTTGTGATTA
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
9194 TATCC-GGCTAA
1 TATCCGGGCTAA
9205 ATTCCGAAGA
Statistics
Matches: 149, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
38 2 0.01
39 37 0.25
40 108 0.72
41 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTT
Found at i:9118 original size:79 final size:79
Alignment explanation
Indices: 8998--9204 Score: 276
Period size: 79 Copynumber: 2.6 Consensus size: 79
8988 TGAATGATAT
* *
8998 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGC-ATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCAATTG
9063 TGCGAGT-TGCTATA
65 TGCGAGTATGCTATA
* *
9077 CCCGGGTTAAGACCCGAAGGCATTGTGCTAGTGATTTTATCCGGGTTAAGACCCGAAGGCAATTG
1 -CCGGGCTAAGACCCGAAGGCATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCAATTG
* **
9142 TGCTAGTGATTTTATA
65 TGCGAGT-ATGCTATA
* *
9158 -CGGGCTAAGACCCGAAGGCATTTGTGCTTGTGATTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCA-TTGTGCTAGTGATTTTATCCGGGCTAA
9205 ATTCCGAAGA
Statistics
Matches: 113, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
79 72 0.64
80 36 0.32
81 5 0.04
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCAATTGT
GCGAGTATGCTATA
Found at i:17464 original size:27 final size:27
Alignment explanation
Indices: 17434--17507 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
17424 ATCTCATAGG
*
17434 GGCATAACAGTCATTTTATCACACAGA
1 GGCATAATAGTCATTTTATCACACAGA
* *
17461 GGCATAATAGTCATTTTATCATACAGG
1 GGCATAATAGTCATTTTATCACACAGA
*
17488 GGTATAATAGTCATTTTATC
1 GGCATAATAGTCATTTTATC
17508 GACTAGGGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (27 bp):
GGCATAATAGTCATTTTATCACACAGA
Found at i:17517 original size:27 final size:26
Alignment explanation
Indices: 17430--17516 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 26
17420 ATATATCTCA
*
17430 TAGGGGCATAACAGTCATTTTATCAC
1 TAGGGGCATAATAGTCATTTTATCAC
* *
17456 ACAGAGGCATAATAGTCATTTTATCA-
1 -TAGGGGCATAATAGTCATTTTATCAC
*
17482 TACAGGGGTATAATAGTCATTTTATCGAC
1 T--AGGGGCATAATAGTCATTTTATC-AC
17511 TAGGGG
1 TAGGGG
17517 TCCAGGTACA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
27 48 0.96
28 1 0.02
29 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (26 bp):
TAGGGGCATAATAGTCATTTTATCAC
Found at i:21090 original size:29 final size:29
Alignment explanation
Indices: 21057--21130 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
21047 GTTGTGAGAT
* *
21057 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
21086 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
21115 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
21131 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:26958 original size:27 final size:27
Alignment explanation
Indices: 26927--27104 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
26917 TAAATTGTAC
26927 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
26954 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
26980 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
27008 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
27036 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
27063 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
27090 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
27105 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:27041 original size:82 final size:81
Alignment explanation
Indices: 26928--27083 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
26918 AAATTGTACA
* *
26928 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
26992 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
27009 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
27074 TGCGAGTTGA
65 TGCGAATTGA
27084 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:27095 original size:82 final size:81
Alignment explanation
Indices: 26924--27104 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
26914 GATTAAATTG
* *
26924 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
26989 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
27005 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
27069 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
27087 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
27105 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:35112 original size:27 final size:27
Alignment explanation
Indices: 35081--35257 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
35071 TAAATTGTAC
35081 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
35108 TGCACTAAGTGTGCGA-AAGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35133 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
35161 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
35189 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
35216 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
35243 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35258 GACTCAATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
26 21 0.17
27 82 0.65
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:35139 original size:26 final size:26
Alignment explanation
Indices: 35082--35150 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
35072 AAATTGTACA
** * *
35082 GCACTAAGTGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGA-AAGAATATGAT
35109 GCACTAAGTGTGCGAAAGAATATGAT
1 GCACTAAGTGTGCGAAAGAATATGAT
35135 GCACTAAGTGTGCGAA
1 GCACTAAGTGTGCGAA
35151 TTGACCATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
26 23 0.61
27 15 0.39
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGAAAGAATATGAT
Found at i:35221 original size:55 final size:54
Alignment explanation
Indices: 35081--35257 Score: 205
Period size: 55 Copynumber: 3.3 Consensus size: 54
35071 TAAATTGTAC
* **
35081 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGA-AAGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
* * ** *
35133 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAG-TTGAATATGT
* * * *
35189 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
*
35243 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
35258 GACTCAATAT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
52 1 0.01
53 38 0.36
54 22 0.21
55 43 0.41
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATGT
Done.