Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1528
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: 34732
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:4764 original size:40 final size:40
Alignment explanation
Indices: 4670--4814 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
4660 TACTCGAATG
*
4670 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
4711 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
4751 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
4791 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
4815 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:9231 original size:29 final size:29
Alignment explanation
Indices: 9159--9245 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 29
9149 CATAGTATCG
* * *
9159 TATCTTGGGTTTCTTTATCCTGGATCTCTT-
1 TATCTTGGATTTCTTTATTCTGGGT-T-TTC
9189 TAT-TCTGGATTTCTTTATTCTGGGTTTTC
1 TATCT-TGGATTTCTTTATTCTGGGTTTTC
9218 TATCTTGGATTTCTTTATTC--GGTTTTC
1 TATCTTGGATTTCTTTATTCTGGGTTTTC
9245 T
1 T
9246 TGTTATCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
27 8 0.16
28 2 0.04
29 20 0.39
30 21 0.41
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.57
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCTGGGTTTTC
Found at i:9246 original size:14 final size:15
Alignment explanation
Indices: 9168--9246 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
9158 GTATCTTGGG
*
9168 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
9183 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
9198 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
9213 TTT-TCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
9227 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
9241 TTTCTT
1 TTTCTT
9247 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:11687 original size:46 final size:46
Alignment explanation
Indices: 11629--11759 Score: 174
Period size: 46 Copynumber: 2.8 Consensus size: 46
11619 GATGGTTGAG
*
11629 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAA
** * *
11675 TGTCCGAACTCGTTGAGTTGAG-CCTGAGTTCACTCATGGATACGAA
1 CATCCGAACTCGTTGAGTTGAGTCC-GAGTTCACTTATGGATACAAA
* * *
11721 CACCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11760 GCGAGTTACA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
45 2 0.03
46 68 0.94
47 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAA
Found at i:17710 original size:62 final size:63
Alignment explanation
Indices: 17533--17710 Score: 184
Period size: 62 Copynumber: 2.8 Consensus size: 63
17523 TAGTTCGGCT
* * * *
17533 TCTTGTAC-ACATGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGTTTATCTCGTAGCT
1 TCTTGT-CTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACA-TATATCCCGTAGC-
17595 C
63 C
* * * *
17596 TCTTGTCTACATGGTGTCCTTCACTTGGAACCACGCATGCGACCTAGCTACATATATCCCGTAG-
1 TCTTGTCTACATGGTG---TACACTTAGTACCACCCATGCGACCTAGCTACATATATCCCGTAGC
17660 C
63 C
* *
17661 TCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 TCTTGTCTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACAT
17711 CATAATGTCT
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
62 29 0.31
63 14 0.15
65 17 0.18
66 23 0.24
67 10 0.11
68 2 0.02
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (63 bp):
TCTTGTCTACATGGTGTACACTTAGTACCACCCATGCGACCTAGCTACATATATCCCGTAGCC
Found at i:22800 original size:79 final size:78
Alignment explanation
Indices: 22698--22922 Score: 267
Period size: 79 Copynumber: 2.8 Consensus size: 78
22688 GCTCCTCGTT
* *
22698 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
22763 ATTTAGTAACTCGCA
64 ATTTAGTAACTCGCA
* *
22778 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAGCCCG
*
22841 GATTTAGTATCTCGCA
63 GATTTAGTAACTCGCA
* * * * *
22857 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
22921 GA
63 GA
22923 CATCATTCAA
Statistics
Matches: 125, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
78 6 0.05
79 64 0.51
80 42 0.34
81 12 0.10
82 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
TTAGTAACTCGCA
Found at i:22882 original size:119 final size:120
Alignment explanation
Indices: 22698--22922 Score: 291
Period size: 119 Copynumber: 1.9 Consensus size: 120
22688 GCTCCTCGTT
22698 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
22763 ATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * **
22817 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAAC
* *
22878 CCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
62 CCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
22923 CATCATTCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
118 8 0.09
119 63 0.68
120 21 0.23
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:22922 original size:40 final size:39
Alignment explanation
Indices: 22698--22922 Score: 244
Period size: 40 Copynumber: 5.7 Consensus size: 39
22688 GCTCCTCGTT
* *
22698 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ATTCGCA
* * *
22738 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ATTCGCA
22778 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAT-TCGCA
* *
22817 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAT-TCGCA
* * *
22857 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-A-TTCGCA
22898 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
22923 CATCATTCAA
Statistics
Matches: 163, Mismatches: 14, Indels: 16
0.84 0.07 0.08
Matches are distributed among these distances:
38 3 0.02
39 30 0.18
40 117 0.72
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTATTCGCA
Found at i:30705 original size:39 final size:39
Alignment explanation
Indices: 30662--30783 Score: 126
Period size: 39 Copynumber: 3.1 Consensus size: 39
30652 GCTCCTCGTT
*
30662 CAAATGCCTTCGGGACAT-ACCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TA-TAACTCGCA
*
30701 CAAATGCCTTC-GGACTTAACCCGGATTTATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTATAACTCGCA
* * * *
30739 CAAAATGCCTATCGGG-CTTAGCCCGGAATTATATCTCGCA
1 C-AAATGCCT-TCGGGACATAACCCGGATTTATAACTCGCA
30779 CAAAT
1 CAAAT
30784 CTTCGATCTT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
38 14 0.19
39 31 0.42
40 26 0.36
41 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACATAACCCGGATTTATAACTCGCA
Found at i:30771 original size:40 final size:39
Alignment explanation
Indices: 30696--30782 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 39
30686 TTATAGTAAT
*
30696 TCGCAC-AAATGCCTTCGGACTTAACCCGGATTTATAAC
1 TCGCACAAAATGCCTTCGGACTTAACCCGGAATTATAAC
* * *
30734 TCGCACAAAATGCCTATCGGGCTTAGCCCGGAATTATATC
1 TCGCACAAAATGCCT-TCGGACTTAACCCGGAATTATAAC
30774 TCGCACAAA
1 TCGCACAAA
30783 TCTTCGATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 6 0.14
39 8 0.19
40 29 0.67
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (39 bp):
TCGCACAAAATGCCTTCGGACTTAACCCGGAATTATAAC
Done.