Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1865
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: 10346
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Found at i:294 original size:37 final size:37
Alignment explanation
Indices: 244--322 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
234 TTATTACGAA
* * *
244 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
281 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
318 GTCTT
1 GTCTT
323 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:562 original size:47 final size:47
Alignment explanation
Indices: 441--758 Score: 521
Period size: 47 Copynumber: 6.7 Consensus size: 47
431 CCCTTCGGGA
* * * * * *
441 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCAACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCC-ATTAGGC
* *
489 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
536 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
583 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
630 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
677 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
724 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
759 AGAATCCTAA
Statistics
Matches: 257, Mismatches: 12, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
46 1 0.00
47 222 0.86
48 34 0.13
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:4147 original size:40 final size:40
Alignment explanation
Indices: 4115--4337 Score: 272
Period size: 40 Copynumber: 5.6 Consensus size: 40
4105 CCAGCATGAT
* * * * *
4115 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAA
***
4155 TGCTCTTCGGGGTTTAG-CACGGATATATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTC-CGGATATATCACTAGCACGAA
*
4195 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAA
*
4235 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAA
*
4275 TGCTCTTCGGAACTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGAACTTAGTCCGGATAT-ATCAC-TAGCACGAA
* * *
4316 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGAACTTAGTCCGGA
4338 CATCATTCAA
Statistics
Matches: 165, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 149 0.90
41 9 0.05
42 6 0.04
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATATATCACTAGCACGAA
Found at i:4682 original size:29 final size:29
Alignment explanation
Indices: 4643--4721 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
4633 CTTAATAATC
*
4643 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
4673 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
4702 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
4722 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:4764 original size:43 final size:43
Alignment explanation
Indices: 4703--4805 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
4693 TGCATTTCAA
4703 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
4746 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
4789 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
4806 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:6743 original size:36 final size:37
Alignment explanation
Indices: 6671--6759 Score: 130
Period size: 36 Copynumber: 2.5 Consensus size: 37
6661 TTATTACGAA
* *
6671 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
*
6708 GTCTTACCCGGACAAAATC-CCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
6744 GTCTTA--CGGACAAAAT
1 GTCTTACCCGGACAAAAT
6760 ACTAGTCATC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
34 10 0.20
36 21 0.43
37 18 0.37
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
Found at i:6970 original size:47 final size:47
Alignment explanation
Indices: 6892--7253 Score: 611
Period size: 47 Copynumber: 7.7 Consensus size: 47
6882 CCCTTCGGGA
* * * * * *
6892 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
6939 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
6986 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7033 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7080 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7127 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
7174 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
7221 CTTATCTCATATATGCA--TTCACATCCATCACAT
1 CTTATCACATATATACACTTTCACATTCATCACAT
7254 AGAATCCTAA
Statistics
Matches: 302, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
45 15 0.05
47 287 0.95
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Done.