Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1063
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: 24986
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4388 original size:46 final size:45
Alignment explanation
Indices: 4246--4410 Score: 170
Period size: 46 Copynumber: 3.6 Consensus size: 45
4236 TACGTATGCC
* * ** *
4246 AGTGGAAGATATGTCTGGGACATGCATCGGCCACATTACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTTCA-GACGAGAGCT
* * * * * *
4292 AGTGTAAGACATATCTGGGACATGAATCGGCTTGAGTA-TACTAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTTCAG-ACGA-GAGCT
*
4338 AGTGTAAGACATGTCTGGGACATGCATCGACTTTCAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-TTCAGACGAGAGCT
*
4384 AGTGTAAGACATGTCTCGGACATGCAT
1 AGTGTAAGACATGTCTGGGACATGCAT
4411 TAGCCTCGAG
Statistics
Matches: 96, Mismatches: 19, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
45 1 0.01
46 90 0.94
47 5 0.05
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTTCAGACGAGAGCT
Found at i:6946 original size:40 final size:40
Alignment explanation
Indices: 6865--6946 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
6855 GTGTTGTACA
* * **
6865 TAGCTAAAGCTATCTCAAACCGCACGCTAAGTGCCAAATT
1 TAGCCAAAGCTATCTCAAACCGCACACTAAGTAACAAATT
* *
6905 TAGCCAAAGCTATAC-CGAACCGCACACTAAGTAACATATT
1 TAGCCAAAGCTAT-CTCAAACCGCACACTAAGTAACAAATT
6945 TA
1 TA
6947 TTCGATATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (40 bp):
TAGCCAAAGCTATCTCAAACCGCACACTAAGTAACAAATT
Found at i:9491 original size:15 final size:16
Alignment explanation
Indices: 9470--9517 Score: 71
Period size: 15 Copynumber: 3.0 Consensus size: 16
9460 TAGACACACA
*
9470 GGTGTGTGTCTAGGTC
1 GGTGTGTGTCTAGGCC
9486 GTGTGTGTGTCTAGGCC
1 G-GTGTGTGTCTAGGCC
9503 -GTGTGTGTCTAGGCC
1 GGTGTGTGTCTAGGCC
9518 ATGTGTGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 15 0.50
16 1 0.03
17 14 0.47
ACGTcount: A:0.06, C:0.17, G:0.42, T:0.35
Consensus pattern (16 bp):
GGTGTGTGTCTAGGCC
Found at i:9493 original size:17 final size:17
Alignment explanation
Indices: 9471--9524 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
9461 AGACACACAG
*
9471 GTGTGTGTCTAGGTCGT
1 GTGTGTGTCTAGGCCGT
9488 GTGTGTGTCTAGGCC--
1 GTGTGTGTCTAGGCCGT
*
9503 GTGTGTGTCTAGGCCAT
1 GTGTGTGTCTAGGCCGT
9520 GTGTG
1 GTGTG
9525 ATTCACGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
15 15 0.44
17 19 0.56
ACGTcount: A:0.07, C:0.15, G:0.41, T:0.37
Consensus pattern (17 bp):
GTGTGTGTCTAGGCCGT
Found at i:9522 original size:15 final size:15
Alignment explanation
Indices: 9489--9524 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
9479 CTAGGTCGTG
*
9489 TGTGTGTCTAGGCCG
1 TGTGTGTCTAGGCCA
9504 TGTGTGTCTAGGCCA
1 TGTGTGTCTAGGCCA
9519 TGTGTG
1 TGTGTG
9525 ATTCACGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.17, G:0.39, T:0.36
Consensus pattern (15 bp):
TGTGTGTCTAGGCCA
Found at i:13681 original size:40 final size:40
Alignment explanation
Indices: 13637--13936 Score: 269
Period size: 40 Copynumber: 7.5 Consensus size: 40
13627 GCTACTCATT
*
13637 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
13677 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * *
13717 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * ** *
13756 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCATTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT-AACTCGCA
*
13797 CAAA-GCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
13836 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * ** *
13875 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCATTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGT-AACTCGCA
13916 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
13937 TGGACATCAT
Statistics
Matches: 210, Mismatches: 33, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
38 4 0.02
39 69 0.33
40 109 0.52
41 28 0.13
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:13751 original size:39 final size:40
Alignment explanation
Indices: 13637--13887 Score: 298
Period size: 40 Copynumber: 6.3 Consensus size: 40
13627 GCTACTCATT
* *
13637 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
13677 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
13717 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * ** *
13756 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCATTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGT-AACTCGCA
* *
13797 CAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
13836 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
13875 CAAATGCCTTCGG
1 CAAATGCCTTCGG
13888 ATCTTAGTCC
Statistics
Matches: 179, Mismatches: 24, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 77 0.43
40 86 0.48
41 14 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:13816 original size:119 final size:119
Alignment explanation
Indices: 13674--13933 Score: 493
Period size: 119 Copynumber: 2.2 Consensus size: 119
13664 ATAGTAACTC
13674 GCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCC
1 GCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCC
* *
13739 GGAATTAGTAACTCGTACAAATGCCTTCGGATCTTAGTCCGGATATGGTCATTTA
65 GGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAGATATGGTCATTTA
13794 GCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCG
1 GCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCG
13859 GAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAGATATGGTCATTTA
66 GAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAGATATGGTCATTTA
13913 GCACAAAGCCTTCGGGACTTA
1 GCACAAAGCCTTCGGGACTTA
13934 GCCTGGACAT
Statistics
Matches: 138, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
119 131 0.95
120 7 0.05
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (119 bp):
GCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCG
GAATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAGATATGGTCATTTA
Found at i:19646 original size:46 final size:46
Alignment explanation
Indices: 19589--19761 Score: 183
Period size: 46 Copynumber: 3.7 Consensus size: 46
19579 TGGTTGAGCA
*
19589 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
19635 TTCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
19680 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
19728 CCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
19762 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 57 0.55
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:19745 original size:93 final size:93
Alignment explanation
Indices: 19586--19756 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
19576 GGATGGTTGA
* * **
19586 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTTCAAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
19651 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
19679 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
*
19744 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
19757 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.