Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1122
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: 28111
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Found at i:2739 original size:42 final size:44
Alignment explanation
Indices: 2674--2758 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
2664 GCAGGCCACC
2674 TAAAATATACTATCTAAAGAAGTAA-TTTATT-ATTTAATTTAAT
1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTT-ATTTAAT
* *
2717 TAAAATATAGT-TCTAAATAAGTAATTTTATTAATTTATTTAA
1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAA
2759 ACATAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 12 0.32
43 22 0.58
44 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (44 bp):
TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAAT
Found at i:3381 original size:8 final size:8
Alignment explanation
Indices: 3370--3414 Score: 54
Period size: 8 Copynumber: 5.1 Consensus size: 8
3360 TATATTTAAA
3370 TATATTTT
1 TATATTTT
3378 TATATTTT
1 TATATTTT
3386 TATATTTTT
1 TATA-TTTT
3395 TATAAATTTT
1 TAT--ATTTT
3405 TATATATTT
1 TATAT-TTT
3414 T
1 T
3415 TTTTCAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 14 0.42
9 11 0.33
10 7 0.21
11 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TATATTTT
Found at i:3382 original size:10 final size:10
Alignment explanation
Indices: 3355--3415 Score: 74
Period size: 10 Copynumber: 6.4 Consensus size: 10
3345 GTTTTAGTGA
3355 TTTTATATAT
1 TTTTATATAT
**
3365 TTAAATATA-
1 TTTTATATAT
3374 TTTT-TATAT
1 TTTTATATAT
3383 TTTTATAT-T
1 TTTTATATAT
*
3392 TTTTATAAAT
1 TTTTATATAT
3402 TTTTATATAT
1 TTTTATATAT
3412 TTTT
1 TTTT
3416 TTTCAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 4 0.10
9 14 0.33
10 24 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATATAT
Found at i:3487 original size:25 final size:26
Alignment explanation
Indices: 3433--3489 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
3423 ATACTATAAG
* *
3433 ATTTTTATATATTTGTAATTGTATGC
1 ATTTTTATATATTTATAATTGTATAC
*
3459 ATTTTTATA-ATTTTATAATT-TATAT
1 ATTTTTATATA-TTTATAATTGTATAC
3484 ATTTTT
1 ATTTTT
3490 TAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (26 bp):
ATTTTTATATATTTATAATTGTATAC
Found at i:4411 original size:31 final size:31
Alignment explanation
Indices: 4352--4441 Score: 114
Period size: 31 Copynumber: 2.9 Consensus size: 31
4342 TATGTGATAG
* * *
4352 TACAGGGTTTGAATATG-AAATATTAATGA-
1 TACATGGTATGAATATGAAAATATGAATGAT
4381 TA-ATAGGATATGAATATGAAAATATGAATGAT
1 TACAT-GG-TATGAATATGAAAATATGAATGAT
4413 TACATGGTATGAATATGAAAATATGAATG
1 TACATGGTATGAATATGAAAATATGAATG
4442 GTTGATACCA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.02
29 4 0.08
30 9 0.17
31 33 0.62
32 4 0.08
33 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (31 bp):
TACATGGTATGAATATGAAAATATGAATGAT
Found at i:8213 original size:23 final size:23
Alignment explanation
Indices: 8183--8232 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
8173 TACATACGTA
*
8183 ATCAGGAAGCTCACAAAGAGCCT
1 ATCAGGAAGCTCACAAAAAGCCT
*
8206 ATCAGGAAGCTCACAAAAAGCTT
1 ATCAGGAAGCTCACAAAAAGCCT
8229 ATCA
1 ATCA
8233 TCCATTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (23 bp):
ATCAGGAAGCTCACAAAAAGCCT
Found at i:8383 original size:26 final size:26
Alignment explanation
Indices: 8351--8415 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
8341 ATGAGAGCAA
* *
8351 TAATCAGGAAGTTCAC-AATGAACTTT
1 TAATCAGGAAGCTCACGAA-GAACCTT
*
8377 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAGCTCACGAAGAACCTT
8403 TAATCAGG-AGCTC
1 TAATCAGGAAGCTC
8416 CGGATAGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.14
26 28 0.80
27 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (26 bp):
TAATCAGGAAGCTCACGAAGAACCTT
Found at i:10881 original size:64 final size:65
Alignment explanation
Indices: 10756--10929 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 65
10746 GCAAACAAAC
* *
10756 ATTCGAACCACATATGTAT---AATTTACA-ACATTAAATTTCAGCTCAAAGAATTTGTAACCTA
1 ATTCGAACCACATATGTATAGAAAATT-CATACATTAAATTCCAGCTCAAAGAATTTGTAACCTA
10817 T
65 T
* *
10818 ATTCGAACCTCATATGTATGGAAAATTCATACATTAAATTCCA-CTCAAA-AATTTTGTAACCTA
1 ATTCGAACCACATATGTATAGAAAATTCATACATTAAATTCCAGCTCAAAGAA-TTTGTAACCTA
10881 T
65 T
* * * * *
10882 ATTTGAACCACATATGTATATATAATTCATACATTGAA-TACAGCTCAA
1 ATTCGAACCACATATGTATAGAAAATTCATACATTAAATTCCAGCTCAA
10930 GAACTTTAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
62 18 0.19
63 5 0.05
64 57 0.59
65 16 0.17
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (65 bp):
ATTCGAACCACATATGTATAGAAAATTCATACATTAAATTCCAGCTCAAAGAATTTGTAACCTAT
Found at i:11048 original size:21 final size:22
Alignment explanation
Indices: 11007--11049 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
10997 TCAAAGAACT
11007 TATATCATACATTCAAACTTTA
1 TATATCATACATTCAAACTTTA
11029 TATAT-ATA-ATTCACAACTTTA
1 TATATCATACATTCA-AACTTTA
11050 AATTCAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATCATACATTCAAACTTTA
Found at i:18785 original size:64 final size:65
Alignment explanation
Indices: 18605--18785 Score: 216
Period size: 64 Copynumber: 2.9 Consensus size: 65
18595 GCAAACAAAC
*
18605 ATTTGAACCACATATGTATA-AT--TTACA-ACATTAAATTTCAGCTCAAAGAA-TTTGTAACCT
1 ATTTGAACCACATATGTATATATAATT-CATACATTAAATTACAGCTC-AAGAACTTTGTAACCT
18665 AT
64 AT
* * * * *
18667 ATTCGAACCTCATATGTATGTAAAATTCATACATTAAATTCCA-CTCAA-ACACTTTGTAACCTA
1 ATTTGAACCACATATGTATATATAATTCATACATTAAATTACAGCTCAAGA-ACTTTGTAACCTA
18730 T
65 T
*
18731 ATTTGAAACACATATGTATATATAATTCATACATTAAA-TACAGCTCAAGAACTTT
1 ATTTGAACCACATATGTATATATAATTCATACATTAAATTACAGCTCAAGAACTTT
18786 AAATATATAT
Statistics
Matches: 100, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
62 18 0.18
63 7 0.07
64 60 0.60
65 15 0.15
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (65 bp):
ATTTGAACCACATATGTATATATAATTCATACATTAAATTACAGCTCAAGAACTTTGTAACCTAT
Found at i:18900 original size:21 final size:22
Alignment explanation
Indices: 18859--18901 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
18849 TCAAAGAACT
18859 TATATCATACATTCAAACTTTA
1 TATATCATACATTCAAACTTTA
18881 TATAT-ATA-ATTCACAACTTTA
1 TATATCATACATTCA-AACTTTA
18902 AATTCAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATCATACATTCAAACTTTA
Found at i:19511 original size:28 final size:28
Alignment explanation
Indices: 19480--19533 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
19470 CATGCATTTC
* *
19480 ATTTA-TTTCATATTTTAGTCCCTAAAAA
1 ATTTATTTTCACAATTTAG-CCCTAAAAA
19508 ATTTATTTTCACAATTTAGCCCTAAA
1 ATTTATTTTCACAATTTAGCCCTAAA
19534 TACTCAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (28 bp):
ATTTATTTTCACAATTTAGCCCTAAAAA
Found at i:24380 original size:42 final size:44
Alignment explanation
Indices: 24315--24399 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
24305 GCAGGCCACC
24315 TAAAATATACTATCTAAAGAAGTAA-TTTATT-ATTTAATTTAAT
1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTT-ATTTAAT
* *
24358 TAAAATATAGT-TCTAAATAAGTAATTTTATTAATTTATTTAA
1 TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAA
24400 ACATAAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 12 0.32
43 22 0.58
44 4 0.11
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (44 bp):
TAAAATATACTATCTAAAGAAGTAATTTTATTAATTTATTTAAT
Found at i:24603 original size:16 final size:15
Alignment explanation
Indices: 24586--24631 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 15
24576 AATTGCATAT
24586 TTTAAAAAATAAATA
1 TTTAAAAAATAAATA
*
24601 TTTATAATAATAAATA
1 TTTA-AAAAATAAATA
24617 --TAAAAAATAAATA
1 TTTAAAAAATAAATA
24630 TT
1 TT
24632 GATAGTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 10 0.38
14 2 0.08
15 4 0.15
16 10 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAAAAAATAAATA
Found at i:25020 original size:8 final size:8
Alignment explanation
Indices: 25009--25053 Score: 54
Period size: 8 Copynumber: 5.1 Consensus size: 8
24999 TATATTTAAA
25009 TATATTTT
1 TATATTTT
25017 TATATTTT
1 TATATTTT
25025 TATATTTTT
1 TATA-TTTT
25034 TATAAATTTT
1 TAT--ATTTT
25044 TATATATTT
1 TATAT-TTT
25053 T
1 T
25054 TTTTCAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 14 0.42
9 11 0.33
10 7 0.21
11 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TATATTTT
Found at i:25021 original size:10 final size:10
Alignment explanation
Indices: 24994--25054 Score: 74
Period size: 10 Copynumber: 6.4 Consensus size: 10
24984 GTTTTAGTGA
24994 TTTTATATAT
1 TTTTATATAT
**
25004 TTAAATATA-
1 TTTTATATAT
25013 TTTT-TATAT
1 TTTTATATAT
25022 TTTTATAT-T
1 TTTTATATAT
*
25031 TTTTATAAAT
1 TTTTATATAT
25041 TTTTATATAT
1 TTTTATATAT
25051 TTTT
1 TTTT
25055 TTTCAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 4 0.10
9 14 0.33
10 24 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATATAT
Found at i:25126 original size:25 final size:26
Alignment explanation
Indices: 25072--25128 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
25062 ATACTATAAG
* *
25072 ATTTTTATATATTTGTAATTGTATGC
1 ATTTTTATATATTTATAATTGTATAC
*
25098 ATTTTTATA-ATTTTATAATT-TATAT
1 ATTTTTATATA-TTTATAATTGTATAC
25123 ATTTTT
1 ATTTTT
25129 TAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (26 bp):
ATTTTTATATATTTATAATTGTATAC
Found at i:26056 original size:31 final size:31
Alignment explanation
Indices: 26006--26086 Score: 114
Period size: 31 Copynumber: 2.6 Consensus size: 31
25996 GTATAGGGTT
*
26006 TGAATATG-AAATATTAATGA-TA-ATAGGATA
1 TGAATATGAAAATATGAATGATTACAT-GG-TA
26036 TGAATATGAAAATATGAATGATTACATGGTA
1 TGAATATGAAAATATGAATGATTACATGGTA
26067 TGAATATGAAAATATGAATG
1 TGAATATGAAAATATGAATG
26087 GTTGATACCA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
30 8 0.17
31 33 0.70
32 4 0.09
33 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.19, T:0.32
Consensus pattern (31 bp):
TGAATATGAAAATATGAATGATTACATGGTA
Done.