Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2597
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: 36036
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:1211 original size:12 final size:12
Alignment explanation
Indices: 1194--1218 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1184 ACTCACTAGG
1194 CCAACATGTTTC
1 CCAACATGTTTC
1206 CCAACATGTTTC
1 CCAACATGTTTC
1218 C
1 C
1219 ACCCATAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.08, T:0.32
Consensus pattern (12 bp):
CCAACATGTTTC
Found at i:7735 original size:79 final size:80
Alignment explanation
Indices: 7636--7856 Score: 202
Period size: 80 Copynumber: 2.8 Consensus size: 80
7626 CTCGTTCAAG
* * ** * *
7636 TGCCTTCGGGACATAGCCCGGTCA-TAGTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGG-AATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
7699 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
7715 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
7780 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
7795 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
7857 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 37 0.31
80 74 0.63
81 6 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:7787 original size:80 final size:80
Alignment explanation
Indices: 7676--7856 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
7666 CTCATTCAAT
* * *
7676 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
7739 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
7755 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
7819 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
7836 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
7857 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:7816 original size:40 final size:40
Alignment explanation
Indices: 7673--7856 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
7663 TAACTCATTC
* *
7673 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
7713 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
7753 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
7793 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
7834 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
7857 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:10756 original size:21 final size:22
Alignment explanation
Indices: 10717--10757 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
10707 GTTGAAATGT
10717 CACATGGGCGTGTTGCCCCTCC
1 CACATGGGCGTGTTGCCCCTCC
10739 CACATGGGCGTG-TGCCCCT
1 CACATGGGCGTGTTGCCCCT
10758 ATGTTAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.10, C:0.39, G:0.29, T:0.22
Consensus pattern (22 bp):
CACATGGGCGTGTTGCCCCTCC
Found at i:11968 original size:25 final size:23
Alignment explanation
Indices: 11922--11968 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
11912 ATATGTATTA
* *
11922 TTTAATTATAATGGATTTATAAT
1 TTTAATTATAATGAATTAATAAT
11945 TTTAATTTAGTAATGAATTAATAA
1 TTTAA-TTA-TAATGAATTAATAA
11969 AAAGAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 3 0.15
25 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (23 bp):
TTTAATTATAATGAATTAATAAT
Found at i:12539 original size:39 final size:39
Alignment explanation
Indices: 12485--12610 Score: 198
Period size: 39 Copynumber: 3.2 Consensus size: 39
12475 TTCAGTGATG
*
12485 TATATCCGGACTTAGGGTCCGCAGCCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
12524 TATATCCAGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * *
12563 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
12602 TATGTCCGG
1 TATATCCGG
12611 GCTAAAGTCC
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:12624 original size:39 final size:39
Alignment explanation
Indices: 12485--12637 Score: 155
Period size: 39 Copynumber: 3.9 Consensus size: 39
12475 TTCAGTGATG
** * * *
12485 TATATCCGGACTTAGGGTCCGCAGCCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
* ** * *
12524 TATATCCAGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
*
12563 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
* * * *
12602 TATGTCCGGGC-TAAAGTCCCGCAGGCTTCGAGCTGG
1 TATATCCGGACTTAAAGT-CCGCAGGCTACGTGCTGG
12638 TATTATACCG
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
38 5 0.05
39 97 0.95
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (39 bp):
TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
Found at i:12624 original size:78 final size:78
Alignment explanation
Indices: 12485--12628 Score: 191
Period size: 78 Copynumber: 1.8 Consensus size: 78
12475 TTCAGTGATG
* * * **
12485 TATATCCGGACTTAGGGTCCGCAGCCTATGTGCTGGAATTATATCCAGACTTAGGGTCCGCAGGC
1 TATATCCGGACTTAAGGTCCGCAGCCTACGTGCTGGAAATATATCCAGACTTAAAGTCCGCAGGC
12550 TATGTGCTGGAAT
66 TATGTGCTGGAAT
* * * *
12563 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCGGGC-TAAAGTCCCGCAGG
1 TATATCCGGACTTAAGGTCCGCAGCCTACGTGCTGGAAATATATCCAGACTTAAAGT-CCGCAGG
12627 CT
65 CT
12629 TCGAGCTGGT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 4 0.07
78 52 0.93
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (78 bp):
TATATCCGGACTTAAGGTCCGCAGCCTACGTGCTGGAAATATATCCAGACTTAAAGTCCGCAGGC
TATGTGCTGGAAT
Found at i:12637 original size:78 final size:78
Alignment explanation
Indices: 12485--12648 Score: 190
Period size: 78 Copynumber: 2.1 Consensus size: 78
12475 TTCAGTGATG
* * * **
12485 TATATCCGGACTTAGGGTCCGCAGCCTATGTGCTGGAATTATATCCAGACTTAGGGTCCGCAGGC
1 TATATCCGGACTTAAGGTCCGCAGCCTACGTGCTGGAAATATATCCAGACTTAAAGTCCGCAGGC
*
12550 TATGTGCTGGAAT
66 TATGAGCTGGAAT
* * * *
12563 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAATATGTCCGGGC-TAAAGTCCCGCAGG
1 TATATCCGGACTTAAGGTCCGCAGCCTACGTGCTGGAAATATATCCAGACTTAAAGT-CCGCAGG
*
12627 CT-TCGAGCTGGTAT
65 CTAT-GAGCTGGAAT
12641 TATA-CCGG
1 TATATCCGG
12649 GTTTAAATTC
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
77 9 0.12
78 64 0.88
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (78 bp):
TATATCCGGACTTAAGGTCCGCAGCCTACGTGCTGGAAATATATCCAGACTTAAAGTCCGCAGGC
TATGAGCTGGAAT
Found at i:12675 original size:38 final size:38
Alignment explanation
Indices: 12503--12680 Score: 130
Period size: 39 Copynumber: 4.6 Consensus size: 38
12493 GACTTAGGGT
* ** **
12503 CCGCAGCCTATGTGCTGGAATTATATCCAGACTTAGGGT-
1 CCGCAGGCTATGTGCTGGAATTATA-CC-GGGTTAAAGTC
* *
12542 CCGCAGGCTATGTGCTGGAATTATATCCGGACTTAAGGT-
1 CCGCAGGCTATGTGCTGGAATTATA-CCGG-GTTAAAGTC
* * * *
12581 CCGCAGGCTACGTGCTGGAAATATGTCCGGGCTAAAGTC
1 CCGCAGGCTATGTGCTGGAATTAT-ACCGGGTTAAAGTC
* * *
12620 CCGCAGGCT-TCGAGCTGGTATTATACCGGGTTTAAATTC
1 CCGCAGGCTAT-GTGCTGGAATTATACCGGG-TTAAAGTC
12659 CCGCAGGCT-TGTGCTGGTAATT
1 CCGCAGGCTATGTGCTGG-AATT
12681 GGTTTCAAGT
Statistics
Matches: 115, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
38 17 0.15
39 98 0.85
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (38 bp):
CCGCAGGCTATGTGCTGGAATTATACCGGGTTAAAGTC
Found at i:26784 original size:39 final size:39
Alignment explanation
Indices: 26730--26855 Score: 198
Period size: 39 Copynumber: 3.2 Consensus size: 39
26720 TTCAGTGATG
*
26730 TATATCAGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
26769 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
* * * *
26808 TATATCCAGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
*
26847 TATGTCCGG
1 TATATCCGG
26856 GCTAAAGTCC
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
Found at i:26869 original size:39 final size:39
Alignment explanation
Indices: 26730--26893 Score: 188
Period size: 39 Copynumber: 4.2 Consensus size: 39
26720 TTCAGTGATG
* * *
26730 TATATCAGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* *
26769 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* *
26808 TATATCCAGACTTAAGGTCCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
* * * * * *
26847 TATGTCCGGGC-TAAAGTCCCGCAGGCTTCGAGCTGGTAT
1 TATATCCGGACTTAAGGT-CCGCAGGCTACGTGCTGGAAT
26886 TATA-CCGG
1 TATATCCGG
26894 GTTTAAATTC
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
38 9 0.08
39 101 0.92
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTACGTGCTGGAAT
Found at i:33328 original size:48 final size:48
Alignment explanation
Indices: 33268--33490 Score: 275
Period size: 48 Copynumber: 4.6 Consensus size: 48
33258 ATATCGGTGC
* * *
33268 CGATGCCATGTTCCAAAAATGGTCTTACTCTACCTCTCATATAAATGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAACTCTCATATAAATGT
*
33316 CGATGCAATGTTCCAAACATGGTCTTACACTAACTCTCATATAAATGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAACTCTCATATAAATGT
* * * ** * ** * *
33364 CGATGCCATGTTTCAAATAAGGTCTTACACTGGCTCACATATCGAGGC
1 CGATGCCATGTTCCAAACATGGTCTTACACTAACTCTCATATAAATGT
* * *
33412 CGATGCCATGTTCCAGACATGGACTTACTCTAACTCTCATATAAATGT
1 CGATGCCATGTTCCAAACATGGTCTTACACTAACTCTCATATAAATGT
* *
33460 CGATGCCATGTTCCGAACGTGGTCTTACACT
1 CGATGCCATGTTCCAAACATGGTCTTACACT
33491 GGCTCACATA
Statistics
Matches: 142, Mismatches: 33, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 142 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (48 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTAACTCTCATATAAATGT
Done.