Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_580
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: 57552
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:819 original size:40 final size:40
Alignment explanation
Indices: 755--938 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
745 CCGAGCTTGG
*
755 GTTCGAAGGGCTTTTGAGCCAGTGCTAATAACTGAACTTA
1 GTTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTA
* *
795 ATTACGAAGGGC-TTTGAGCAAGTGCTAATAACCGAACTTA
1 GTT-CGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTA
* *
835 GTTTGAAGGGCTTTTGAGCCAGTG-TCATAACCGAACTTA
1 GTTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTA
* * * *
874 GTTCCGAAGGGCCTTCGAGCCAGTGGCCTAAT--CCGAGCTTG
1 GTT-CGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTA
915 GTCTCGAAGGGC-TTTGAGCCAGTG
1 GT-TCGAAGGGCTTTTGAGCCAGTG
939 TTAAGAATCG
Statistics
Matches: 123, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
39 25 0.20
40 68 0.55
41 26 0.21
42 1 0.01
43 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
GTTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTA
Found at i:931 original size:80 final size:77
Alignment explanation
Indices: 742--939 Score: 236
Period size: 80 Copynumber: 2.5 Consensus size: 77
732 TCGGGGTGTA
*
742 AATCCGAGCTTGGGTTCGAAGGGCTTTTGAGCCAGTGCTAATAACTGAACTTAATTACGAAGGGC
1 AATCCGAGCTT-GGTTCGAAGGGCTTTTGAGCCAGTG-TAATAACCGAACTTAATTACGAAGGGC
*
807 TTTGAGCAAGTGCT
64 TTCGAGCAAGTGCT
* * * * * *
821 AATAACCGAACTTAGTTTGAAGGGCTTTTGAGCCAGTGTCATAACCGAACTTAGTTCCGAAGGGC
1 AAT--CCGAGCTTGGTTCGAAGGGCTTTTGAGCCAGTGTAATAACCGAACTTAATTACGAAGGG-
*
886 CTTCGAGCCAGTGGCCT
63 CTTCGAGCAAGT-G-CT
903 AATCCGAGCTTGGTCTCGAAGGGC-TTTGAGCCAGTGT
1 AATCCGAGCTTGGT-TCGAAGGGCTTTTGAGCCAGTGT
940 TAAGAATCGT
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
79 25 0.25
80 55 0.54
81 16 0.16
82 5 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (77 bp):
AATCCGAGCTTGGTTCGAAGGGCTTTTGAGCCAGTGTAATAACCGAACTTAATTACGAAGGGCTT
CGAGCAAGTGCT
Found at i:7933 original size:40 final size:41
Alignment explanation
Indices: 7813--7997 Score: 216
Period size: 41 Copynumber: 4.6 Consensus size: 41
7803 TGAGCTTGGG
*
7813 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAAT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
*
7854 TACGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* * * *
7895 TTCGAAGGGCTTTTGTGCCAATG-TCATAACCGGACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* * * * *
7935 TCCGAAGGGCCTTCGAGCCAGTGGCCTAAT--CCGAGCTTGGT
1 TTCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGT
*
7976 CTCGAAGGGC-TTTGAGCCAGTG
1 TTCGAAGGGCTTTTGAGCCAGTG
7998 TTAAGAATCG
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 42 0.34
41 76 0.62
43 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
Found at i:7953 original size:81 final size:82
Alignment explanation
Indices: 7813--7994 Score: 219
Period size: 81 Copynumber: 2.2 Consensus size: 82
7803 TGAGCTTGGG
* * *
7813 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAATTACGAAGGGCTTTTGAGCCAGT-G
1 TTCGAAGGGCTTTTGAGCCAATGCTAATAACCGAACTTAATTACGAAGGGCCTTCGAGCCAGTGG
7877 -CTAATAACCGAACTTAGT
66 CCTAAT--CCGAACTTAGT
* * * * *
7895 TTCGAAGGGCTTTTGTGCCAATG-TCATAACCGGACTTAGTTCCGAAGGGCCTTCGAGCCAGTGG
1 TTCGAAGGGCTTTTGAGCCAATGCTAATAACCGAACTTAATTACGAAGGGCCTTCGAGCCAGTGG
* *
7959 CCTAATCCGAGCTTGGT
66 CCTAATCCGAACTTAGT
*
7976 CTCGAAGGGC-TTTGAGCCA
1 TTCGAAGGGCTTTTGAGCCA
7995 GTGTTAAGAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
80 8 0.09
81 51 0.59
82 22 0.26
83 5 0.06
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (82 bp):
TTCGAAGGGCTTTTGAGCCAATGCTAATAACCGAACTTAATTACGAAGGGCCTTCGAGCCAGTGG
CCTAATCCGAACTTAGT
Found at i:8019 original size:81 final size:76
Alignment explanation
Indices: 7799--8024 Score: 202
Period size: 81 Copynumber: 2.8 Consensus size: 76
7789 TCGGGGTGTA
* * *
7799 AATCTGAGCTTGGGTTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAATTACGAAGGGC
1 AATCCGAGCTT-GGTTCGAAGGGCTTTTGAGCCAGTG-TAATAACCG-GCTT-ATTCCGAAGGGC
* *
7864 TTTTGAGCCAGTGCT
62 CTTCGAGCCAGTGCT
* * * * *
7879 AATAACCGAACTTAGTTTCGAAGGGCTTTTGTGCCAATGTCATAACCGGACTTAGTTCCGAAGGG
1 AAT--CCGAGCTT-GGTTCGAAGGGCTTTTGAGCCAGTGTAATAACCGG-CTTA-TTCCGAAGGG
7944 CCTTCGAGCCAGTGGCCT
61 CCTTCGAGCCAGT-G-CT
* *
7962 AATCCGAGCTTGGTCTCGAAGGGC-TTTGAGCCAGTGTTAAGAATCGTGCTTGATTCCGAAGGG
1 AATCCGAGCTTGGT-TCGAAGGGCTTTTGAGCCAGTG-TAATAACCG-GCTT-ATTCCGAAGGG
8025 TGGTTGTGCC
Statistics
Matches: 118, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
80 16 0.14
81 66 0.56
82 31 0.26
83 5 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (76 bp):
AATCCGAGCTTGGTTCGAAGGGCTTTTGAGCCAGTGTAATAACCGGCTTATTCCGAAGGGCCTTC
GAGCCAGTGCT
Found at i:10142 original size:13 final size:13
Alignment explanation
Indices: 10124--10148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10114 GAATTGATAT
10124 GTGTGAAAATTTC
1 GTGTGAAAATTTC
10137 GTGTGAAAATTT
1 GTGTGAAAATTT
10149 TATTATTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:12355 original size:124 final size:124
Alignment explanation
Indices: 12135--12385 Score: 502
Period size: 124 Copynumber: 2.0 Consensus size: 124
12125 AAATGATGAT
12135 ACATGAAAAGTGATATATGAAATATGTGACATATGTTATGTAAATTCTTAAAAGCTTATTTGCTA
1 ACATGAAAAGTGATATATGAAATATGTGACATATGTTATGTAAATTCTTAAAAGCTTATTTGCTA
12200 TTTGAGTTATGCCTTATTATGCTATGAATGGGAAATTAGTACTATAGATAGTGAGATAG
66 TTTGAGTTATGCCTTATTATGCTATGAATGGGAAATTAGTACTATAGATAGTGAGATAG
12259 ACATGAAAAGTGATATATGAAATATGTGACATATGTTATGTAAATTCTTAAAAGCTTATTTGCTA
1 ACATGAAAAGTGATATATGAAATATGTGACATATGTTATGTAAATTCTTAAAAGCTTATTTGCTA
12324 TTTGAGTTATGCCTTATTATGCTATGAATGGGAAATTAGTACTATAGATAGTGAGATAG
66 TTTGAGTTATGCCTTATTATGCTATGAATGGGAAATTAGTACTATAGATAGTGAGATAG
12383 ACA
1 ACA
12386 CTTCAAGTAA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 127 1.00
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (124 bp):
ACATGAAAAGTGATATATGAAATATGTGACATATGTTATGTAAATTCTTAAAAGCTTATTTGCTA
TTTGAGTTATGCCTTATTATGCTATGAATGGGAAATTAGTACTATAGATAGTGAGATAG
Found at i:13598 original size:27 final size:27
Alignment explanation
Indices: 13568--13622 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
13558 CTATGACTCG
13568 AGAAAATAACTTGACCAAAACATAAGT
1 AGAAAATAACTTGACCAAAACATAAGT
13595 AGAAAATAACTTGACCAAAACATAAGT
1 AGAAAATAACTTGACCAAAACATAAGT
13622 A
1 A
13623 AATGTGTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.56, C:0.15, G:0.11, T:0.18
Consensus pattern (27 bp):
AGAAAATAACTTGACCAAAACATAAGT
Found at i:27407 original size:40 final size:40
Alignment explanation
Indices: 27352--27609 Score: 369
Period size: 40 Copynumber: 6.5 Consensus size: 40
27342 TGGATGATAA
* * *
27352 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
27392 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
27432 CCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
27472 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
27512 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
27552 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
27592 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
27610 TACCTGGCTT
Statistics
Matches: 201, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
39 16 0.08
40 185 0.92
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:35553 original size:40 final size:40
Alignment explanation
Indices: 35498--35755 Score: 360
Period size: 40 Copynumber: 6.5 Consensus size: 40
35488 CGGATGATAA
* * *
35498 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
35538 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35578 CCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
35618 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35658 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
35698 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
35738 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
35756 TACCTGCCTT
Statistics
Matches: 199, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 16 0.08
40 183 0.92
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:42403 original size:23 final size:22
Alignment explanation
Indices: 42377--42429 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42367 TTGAGAGTGA
*
42377 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
42400 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
42422 AAAAGAAA
1 AAAAGAAA
42430 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:45554 original size:10 final size:10
Alignment explanation
Indices: 45539--45576 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
45529 ATTTGGGAAT
45539 TGGTATGAAA
1 TGGTATGAAA
*
45549 TGGTATGGAAT
1 TGGTAT-GAAA
45560 TGGTATGAAA
1 TGGTATGAAA
45570 TGGTATG
1 TGGTATG
45577 GTATTTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (10 bp):
TGGTATGAAA
Found at i:45560 original size:21 final size:21
Alignment explanation
Indices: 45534--45596 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
45524 TTGGTATTTG
45534 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
45555 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTATGAAATGGTAT
* * *
45576 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTATGAAATGGTA
45597 ATGGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 23 0.61
22 15 0.39
ACGTcount: A:0.30, C:0.02, G:0.33, T:0.35
Consensus pattern (21 bp):
GGAATTGGTATGAAATGGTAT
Found at i:49606 original size:40 final size:40
Alignment explanation
Indices: 49403--49606 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
49393 CGGAATTTAA
** *
49403 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
49443 CCGGTTATAGTAACTCGCACAATTGCCTTTGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
49483 CCGAATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
49522 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
49562 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
49602 CCGGA
1 CCGGA
49607 CATCATTCAA
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.24
40 89 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54235 original size:40 final size:40
Alignment explanation
Indices: 54191--54452 Score: 319
Period size: 39 Copynumber: 6.7 Consensus size: 40
54181 GCTCCTCGTT
* *
54191 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
54231 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
54271 CAAATACCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54310 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
54349 CAAATGCCTTCGGG-CTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
54388 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
54429 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54453 CATCATTAAA
Statistics
Matches: 201, Mismatches: 13, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 126 0.63
40 62 0.31
41 11 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Done.