Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1517
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: 35560
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Found at i:5011 original size:27 final size:26
Alignment explanation
Indices: 4967--5018 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
4957 CTCGCTGCAA
*
4967 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
4994 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
5019 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:5086 original size:68 final size:67
Alignment explanation
Indices: 4948--5086 Score: 197
Period size: 68 Copynumber: 2.1 Consensus size: 67
4938 GAGGAAGCGT
* * * *
4948 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCACCACATATATCTGTTCTGGTGACCTAGCCACAA
5013 TA
66 TA
* * * *
5015 TCTGGCAGCCTCGCTGCAATCTGGTGGCTTCACATATATATATCTGTTCTGGTGGCCTAGCCACA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCAC-CACATATATCTGTTCTGGTGACCTAGCCACA
5080 ATA
65 ATA
5083 TCTG
1 TCTG
5087 TATCTGGTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 31 0.49
68 32 0.51
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.31
Consensus pattern (67 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCACCACATATATCTGTTCTGGTGACCTAGCCACAA
TA
Found at i:5106 original size:27 final size:26
Alignment explanation
Indices: 5054--5113 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
5044 TCACATATAT
*
5054 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
5080 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
5107 ATATCTG
1 ATATCTG
5114 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:11559 original size:27 final size:26
Alignment explanation
Indices: 11515--11566 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
11505 CTCGCTGCAA
*
11515 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
11542 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
11567 CAGCCTCGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:11633 original size:26 final size:27
Alignment explanation
Indices: 11604--11663 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
11594 CCACATATAT
*
11604 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
11630 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
11657 ATATCTG
1 ATATCTG
11664 GCCGCTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:17208 original size:40 final size:40
Alignment explanation
Indices: 17156--17315 Score: 261
Period size: 40 Copynumber: 4.0 Consensus size: 40
17146 GGATTTAGCT
* *
17156 GGATATAACAACTCGCACAAATGCCTTCGGGTCCTAGCCC
1 GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
*
17196 GGATACAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
1 GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
* *
17236 GGATATAGCAACTCACACAAATGCCTTCGCGTCTTAGCCC
1 GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
17276 GGATATAGCAA-TCGCACAAATGCCTTC-GGTCTTAGCCC
1 GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
17314 GG
1 GG
17316 TTATCATCCG
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
38 12 0.11
39 15 0.13
40 85 0.76
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.21
Consensus pattern (40 bp):
GGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
Found at i:26083 original size:40 final size:40
Alignment explanation
Indices: 26021--26278 Score: 412
Period size: 40 Copynumber: 6.5 Consensus size: 40
26011 AAGCCAAGTA
* * * * *
26021 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
26060 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
26100 CCTTCGAGACTTAGCCCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
26140 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
26180 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
26220 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
26260 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
26279 TTATCATCCA
Statistics
Matches: 205, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
39 12 0.06
40 193 0.94
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:34251 original size:41 final size:40
Alignment explanation
Indices: 34155--34354 Score: 248
Period size: 39 Copynumber: 5.0 Consensus size: 40
34145 CAGCCAAGTA
* * * * * *
34155 CCTTCGGGATTTAACGCGGATATAGCT-ACTTGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
34195 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCA-CAAATG
* *
34236 CCTTCGAGACTTAGCCCGGATATAGCAACTCGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
34275 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA-G
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
34314 CCTTTCGGGACTTAGCCCGG--ATAGTTAACTCGCACAAATG
1 CC-TTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
34354 C
1 C
34355 TGAACACCCC
Statistics
Matches: 142, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
38 4 0.03
39 54 0.38
40 48 0.34
41 36 0.25
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:34290 original size:80 final size:80
Alignment explanation
Indices: 34171--34336 Score: 255
Period size: 80 Copynumber: 2.1 Consensus size: 80
34161 GGATTTAACG
* * *
34171 CGGATATAGCTACTTGCTCGAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAAATG
1 CGGATATAGCAACTCGCACGAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCA-CAAA-G
34236 CC-TTCGAGACTTAGCC
64 CCTTTCGAGACTTAGCC
*
34252 CGGATATAGCAACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAAGCC
1 CGGATATAGCAACTCGCACGAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAAGCC
*
34316 TTTCGGGACTTAGCC
66 TTTCGAGACTTAGCC
34331 CGGATA
1 CGGATA
34337 GTTAACTCGC
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
78 3 0.04
79 23 0.29
80 37 0.47
81 16 0.20
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (80 bp):
CGGATATAGCAACTCGCACGAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAAGCC
TTTCGAGACTTAGCC
Done.