Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3880
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: 16807
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Found at i:376 original size:27 final size:27
Alignment explanation
Indices: 346--413 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
336 AAACATAAGA
346 GCATAATC-GTCATTCTACCATACAGGG
1 GCATAA-CGGTCATTCTACCATACAGGG
* * * *
373 GCATTACGGTCATTTTTCCCTACAGGG
1 GCATAACGGTCATTCTACCATACAGGG
*
400 GCATTACGGTCATT
1 GCATAACGGTCATT
414 TTCCAAACTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (27 bp):
GCATAACGGTCATTCTACCATACAGGG
Found at i:427 original size:27 final size:27
Alignment explanation
Indices: 367--426 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
357 ATTCTACCAT
**
367 ACAGGGGCATTACGGTCATTTTTCCCT
1 ACAGGGGCATTACGGTCATTTTTCCAA
394 ACAGGGGCATTACGGTCA-TTTTCCAA
1 ACAGGGGCATTACGGTCATTTTTCCAA
*
420 ACTGGGG
1 ACAGGGG
427 GTATTTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (27 bp):
ACAGGGGCATTACGGTCATTTTTCCAA
Found at i:4095 original size:50 final size:49
Alignment explanation
Indices: 3936--4157 Score: 277
Period size: 49 Copynumber: 4.5 Consensus size: 49
3926 CTGATATGCA
* * * *
3936 TAGTAGCCTGCACATAGCACTACACATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACG
*
3985 TAGTAGCCTGCACCTAGTACTACACACGTGACCAATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACG
* * ** *
4034 TAGTAACCTGCACTTAGTACTGCACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCTGGTACACG
* * * * *
4084 TTGTAGCCTGCACTTAGTACTACACACGTGATCACAGT-TC-GGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCA-ATTATCTGGTACACG
4132 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
4158 TCCGACCTCA
Statistics
Matches: 151, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
48 30 0.20
49 78 0.52
50 43 0.28
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGGTACACG
Found at i:4667 original size:56 final size:55
Alignment explanation
Indices: 4581--4692 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 55
4571 TTTTCCAATA
4581 TATTAAATCATAAAATATATGCAATAATAGTAAGAAATATAATTCAAACATAACAT
1 TATTAAATCATAAAATATATGCAATAATAGTAAG-AATATAATTCAAACATAACAT
4637 TATTAAATCATAAAATATATGCAATAATAGTAAGAATATAATTCAAACATAACAT
1 TATTAAATCATAAAATATATGCAATAATAGTAAGAATATAATTCAAACATAACAT
4692 T
1 T
4693 GCATTATTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 22 0.39
56 34 0.61
ACGTcount: A:0.54, C:0.09, G:0.05, T:0.31
Consensus pattern (55 bp):
TATTAAATCATAAAATATATGCAATAATAGTAAGAATATAATTCAAACATAACAT
Found at i:6593 original size:16 final size:16
Alignment explanation
Indices: 6574--6609 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6564 GAAGTTTTAA
* *
6574 CTTTTTGACTTTTTGG
1 CTTTTCGACTTTTCGG
6590 CTTTTCGACTTTTCGG
1 CTTTTCGACTTTTCGG
6606 CTTT
1 CTTT
6610 CATCGATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.19, G:0.17, T:0.58
Consensus pattern (16 bp):
CTTTTCGACTTTTCGG
Found at i:8537 original size:48 final size:48
Alignment explanation
Indices: 8485--8753 Score: 378
Period size: 48 Copynumber: 5.6 Consensus size: 48
8475 TACCGAGGCT
* * * *
8485 GATGCCATATCCTAGATATGGTCTTACACTGGCACACACATCAATGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAATGTC
* * * * *
8533 GATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATATCAACGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAATGTC
* * * * *
8581 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAACGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAATGTC
* *
8629 GATGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAATGTC
8677 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAATG-C
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAATGTC
8724 TGATGCCATGTCCCAGACATGGTCTTACAC
1 -GATGCCATGTCCCAGACATGGTCTTACAC
8754 AGGATCTCGT
Statistics
Matches: 201, Mismatches: 19, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
47 1 0.00
48 200 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAATGTC
Found at i:8585 original size:96 final size:96
Alignment explanation
Indices: 8440--8753 Score: 389
Period size: 96 Copynumber: 3.3 Consensus size: 96
8430 TCATATCAAC
* * ** * * * * * *
8440 GCCATATCCCAGATATGGTCTTACA-TGAAATCACATACCGAGGCTGATGCCATATCCTAGATAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCA-CACATATCAACGCTGATGCCATGTCCCAGACAT
*
8504 GGTCTTACACTGGCACACACATCAATGTCGAT
65 GGTCTTACACTGGCACACATATCAATGTCGAT
* * * *
8536 GCCATGTCCCAGACATGGTCTTACATTGGCTCTCATATCAACGTTGATGCCATGTCCCAGACATG
1 GCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCTGATGCCATGTCCCAGACATG
* * * * *
8601 GTCTTACACTAGCTCTCATATCAACGTTGAT
66 GTCTTACACTGGCACACATATCAATGTCGAT
* * *
8632 GCCATGTCCCAAACATGGTCTTACACTGGCACACATATCAATGCCGATGCCATGTCCCAGACATG
1 GCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCTGATGCCATGTCCCAGACATG
8697 GTCTTACACTGGCACACATATCAATG-CTGAT
66 GTCTTACACTGGCACACATATCAATGTC-GAT
8728 GCCATGTCCCAGACATGGTCTTACAC
1 GCCATGTCCCAGACATGGTCTTACAC
8754 AGGATCTCGT
Statistics
Matches: 184, Mismatches: 32, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
96 182 0.99
97 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (96 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAACGCTGATGCCATGTCCCAGACATG
GTCTTACACTGGCACACATATCAATGTCGAT
Found at i:8651 original size:144 final size:144
Alignment explanation
Indices: 8484--8753 Score: 441
Period size: 144 Copynumber: 1.9 Consensus size: 144
8474 ATACCGAGGC
* * * *
8484 TGATGCCATATCCTAGATATGGTCTTACACTGGCACACACATCAATGTCGATGCCATGTCCCAGA
1 TGATGCCATATCCCAAACATGGTCTTACACTGGCACACACATCAATGCCGATGCCATGTCCCAGA
* * * *
8549 CATGGTCTTACATTGGCTCTCATATCAACGTTGATGCCATGTCCCAGACATGGTCTTACACTAGC
66 CATGGTCTTACACTGGCACACATATCAACGCTGATGCCATGTCCCAGACATGGTCTTACACTAGC
8614 TCTCATATCAACGT
131 TCTCATATCAACGT
* *
8628 TGATGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCAATGCCGATGCCATGTCCCAGA
1 TGATGCCATATCCCAAACATGGTCTTACACTGGCACACACATCAATGCCGATGCCATGTCCCAGA
*
8693 CATGGTCTTACACTGGCACACATATCAATGCTGATGCCATGTCCCAGACATGGTCTTACAC
66 CATGGTCTTACACTGGCACACATATCAACGCTGATGCCATGTCCCAGACATGGTCTTACAC
8754 AGGATCTCGT
Statistics
Matches: 115, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
144 115 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (144 bp):
TGATGCCATATCCCAAACATGGTCTTACACTGGCACACACATCAATGCCGATGCCATGTCCCAGA
CATGGTCTTACACTGGCACACATATCAACGCTGATGCCATGTCCCAGACATGGTCTTACACTAGC
TCTCATATCAACGT
Found at i:13323 original size:40 final size:39
Alignment explanation
Indices: 13279--13463 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
13269 GCTACTTGTT
*
13279 CAAATGCCTTCGGGTCATAGCCC-GATTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATT-TAGTAACTCGCA
*
13319 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATTTAGTAACTCGCA
* *
13359 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
13398 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGATTTAGTAAC-TCGCA
13439 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
13464 CATCATTCGA
Statistics
Matches: 125, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 35 0.28
40 78 0.62
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCA
Found at i:13381 original size:79 final size:80
Alignment explanation
Indices: 13246--13461 Score: 223
Period size: 79 Copynumber: 2.7 Consensus size: 80
13236 AAATCACGTA
** * * *
13246 CCTTCGGAAT-TTAA-CCGGATATAGCT-ACTT-GTTCAAATGCCTTCGGGTCATAGCCCGATTA
1 CCTTCGG-ATCTTAACCCGGATATAG-TAACTTAGCACAAATGCCTTCGGGACTTAGCCCGAAT-
13307 TAGTAACTCGCACAAATG
63 TAGTAACTCGCACAAATG
* *
13325 CCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATT
1 CCTTC-GGATCTTAACCCGGATATAGTAACTTAGCACAAATGCCTTCGGGACTTAGCCC-GAATT
*
13387 AGTATCTCGCACAAATG
64 AGTAACTCGCACAAATG
** * *
13404 CCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAATGCCTTCGGGACTTAGCCCG
13462 GACATCATTC
Statistics
Matches: 116, Mismatches: 12, Indels: 18
0.79 0.08 0.12
Matches are distributed among these distances:
78 3 0.03
79 66 0.57
80 47 0.41
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (80 bp):
CCTTCGGATCTTAACCCGGATATAGTAACTTAGCACAAATGCCTTCGGGACTTAGCCCGAATTAG
TAACTCGCACAAATG
Found at i:14965 original size:55 final size:55
Alignment explanation
Indices: 14881--15051 Score: 296
Period size: 55 Copynumber: 3.1 Consensus size: 55
14871 TATTAGTTTA
14881 TTGCCCATGCTTCTTA-TTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATT-TTCCATTAACACAACATGTTTCATGACATGTT
14936 TTGCCCATGCTTCTTATTTTATTTTCCATTAACACAACATG-TTCATGACATG-T
1 TTGCCCATGCTTCTTATTTTATTTTCCATTAACACAACATGTTTCATGACATGTT
14989 TTG-CCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTA-TTTTCCATTAACACAACATGTTTCATGACATGTT
15044 TTGCCCAT
1 TTGCCCAT
15052 CATCCCCTTG
Statistics
Matches: 111, Mismatches: 0, Indels: 9
0.93 0.00 0.08
Matches are distributed among these distances:
52 17 0.15
53 24 0.22
54 22 0.20
55 38 0.34
56 10 0.09
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.44
Consensus pattern (55 bp):
TTGCCCATGCTTCTTATTTTATTTTCCATTAACACAACATGTTTCATGACATGTT
Done.