Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2424
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: 19990
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Found at i:2450 original size:33 final size:33
Alignment explanation
Indices: 2392--2458 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2382 AAAATTTCCA
*** *
2392 AATGTATCGATACAAAGATCCATGTATTGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2425 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2458 A
1 A
2459 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3163 original size:21 final size:21
Alignment explanation
Indices: 3120--3176 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
3110 GTGTAAAAAA
*
3120 TTACATACAAA-ATTATCATG
1 TTACATACAAACATTATCAAG
3140 TTACATACAAACATTA-CAAAG
1 TTACATACAAACATTATC-AAG
*
3161 TTATATA-AAACATTAT
1 TTACATACAAACATTAT
3177 TGAAACCGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (21 bp):
TTACATACAAACATTATCAAG
Found at i:8642 original size:28 final size:28
Alignment explanation
Indices: 8561--8642 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
8551 TTTTGGAGAT
*
8561 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
8589 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
8617 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
8643 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:8785 original size:51 final size:51
Alignment explanation
Indices: 8625--8795 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 51
8615 GAAATAACGA
* * *
8625 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * * *
8677 AATTGGAGTATCCTCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * * *
8730 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTTGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
8781 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
8796 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 38 0.40
52 17 0.18
53 31 0.32
54 10 0.10
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:8841 original size:27 final size:28
Alignment explanation
Indices: 8779--8853 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
8769 AAATAAAGTT
*
8779 GGGGTTGGAGTATCCCCTCA-GAAATAAC
1 GGGGTTGGAGTATCCCC-GATGAAATAAC
* *
8807 AGGGTTGGAGTATCCCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
*
8834 GGGGTTGGAGTGTCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
8854 TGTGAAGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:11336 original size:13 final size:13
Alignment explanation
Indices: 11318--11343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11308 ATAAAGATCC
11318 ATGTATCGATACA
1 ATGTATCGATACA
11331 ATGTATCGATACA
1 ATGTATCGATACA
11344 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11423 original size:13 final size:13
Alignment explanation
Indices: 11405--11429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11395 ACAATACTTA
11405 TGTATCGATACAT
1 TGTATCGATACAT
11418 TGTATCGATACA
1 TGTATCGATACA
11430 AATTGTTGAA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11511 original size:21 final size:21
Alignment explanation
Indices: 11487--11543 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
11477 CATTTGTAGG
11487 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
11508 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
11529 ATGTATCGATACATT
1 ATGTATCGATACATT
11544 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:11566 original size:13 final size:13
Alignment explanation
Indices: 11548--11572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11538 TACATTTAAA
11548 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
11561 TTTTTTTTTCAA
1 TTTTTTTTTCAA
11573 ACACTTTATC
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:12198 original size:55 final size:54
Alignment explanation
Indices: 12109--12852 Score: 976
Period size: 55 Copynumber: 13.4 Consensus size: 54
12099 ATAAATTGTA
* * * * *
12109 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
12164 TCCTGCTCTTTGAGGACTGAAAGGTGCCATCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
12219 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAATGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
12274 TCCTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
12329 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
12384 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTCGGGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
12439 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
12494 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGATTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* **
12549 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* * *
12610 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
12665 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
12720 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGGGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
12775 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
12830 TCCCGCTCTTTGAGGACTAAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
12853 GCGGAAGGAG
Statistics
Matches: 618, Mismatches: 49, Indels: 45
0.87 0.07 0.06
Matches are distributed among these distances:
54 23 0.04
55 525 0.85
56 22 0.04
60 4 0.01
61 41 0.07
62 3 0.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:12383 original size:29 final size:29
Alignment explanation
Indices: 12298--12383 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
12288 GACTAGAAAA
12298 TGCCACCAACTTGTGTGGGCTTTAAGAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGG
** * *
12327 TGTCCTGC-TCTT-TG-GGGAC-TGAA-AGG
1 TG-CCACCAACTTGTGTGGG-CTTTAAGAGG
12353 TGCCACCAACTTGTGTGGGCTTTAAGAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGG
12382 TG
1 TG
12384 TCCTGCTCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
25 3 0.07
26 8 0.19
27 9 0.21
28 9 0.21
29 10 0.24
30 3 0.07
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.29
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTAAGAGG
Found at i:12461 original size:27 final size:27
Alignment explanation
Indices: 12431--12574 Score: 73
Period size: 27 Copynumber: 5.3 Consensus size: 27
12421 GGTGGGCTTT
12431 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
12458 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
12486 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
12513 GAAA-ATG-CCACCAACTTGTGTGGGATTT
1 GAAAGGTGTCCTGC-TCTT-TG-AGGACTG
12541 GAAAGGTGTCCTGCTCTTTGAGGACT-
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
12567 GAAAGGTG
1 GAAAGGTG
12575 CCACCAACTT
Statistics
Matches: 80, Mismatches: 27, Indels: 21
0.62 0.21 0.16
Matches are distributed among these distances:
25 6 0.08
26 18 0.22
27 20 0.25
28 20 0.25
29 10 0.12
30 6 0.08
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:13843 original size:10 final size:9
Alignment explanation
Indices: 13816--13887 Score: 67
Period size: 9 Copynumber: 7.9 Consensus size: 9
13806 AAGTAGGTTT
13816 TTTTCTTTTC
1 TTTT-TTTTC
*
13826 TCTCTTTTTC
1 T-TTTTTTTC
* *
13836 TTTGTTTTG
1 TTTTTTTTC
*
13845 TTTTTTGT-
1 TTTTTTTTC
13853 TTTTTTTTC
1 TTTTTTTTC
13862 -TTTTTTTC
1 TTTTTTTTC
13870 TTTTTTTTGC
1 TTTTTTTT-C
13880 TTTTTTTT
1 TTTTTTTT
13888 TTGAAGAGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
8 15 0.29
9 18 0.35
10 16 0.31
11 2 0.04
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:13850 original size:17 final size:16
Alignment explanation
Indices: 13830--13890 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
13820 CTTTTCTCTC
*
13830 TTTTTCTTTGTTTTGT
1 TTTTTTTTTGTTTTGT
* *
13846 TTTTTGTTTTTTTTTCT
1 TTTTT-TTTTGTTTTGT
*
13863 TTTTTTCTTTTTTTTGCT
1 TTTTTT-TTTGTTTTG-T
13881 TTTTTTTTTG
1 TTTTTTTTTG
13891 AAGAGAAGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
16 6 0.16
17 24 0.65
18 7 0.19
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTGTTTTGT
Found at i:13853 original size:12 final size:11
Alignment explanation
Indices: 13840--13890 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
13830 TTTTTCTTTG
13840 TTTTGTTTTTT
1 TTTTGTTTTTT
13851 GTTTT-TTTTTCT
1 -TTTTGTTTTT-T
13863 TTTT-TTCTTTT
1 TTTTGTT-TTTT
13874 TTTTGCTTTTTT
1 TTTTG-TTTTTT
13886 TTTTG
1 TTTTG
13891 AAGAGAAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 16 0.46
12 17 0.49
13 2 0.06
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.86
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:13872 original size:40 final size:40
Alignment explanation
Indices: 13813--13890 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 40
13803 CTTAAGTAGG
13813 TTTTTTTCTTTTCTCTCTTTTTCTTTG-TTTTGTTTTTTGTT
1 TTTTTTTCTTTTCTCTCTTTTT-TTTGCTTTT-TTTTTTGTT
*
13854 TTTTTTTCTTTT-TTTCTTTTTTTTGCTTTTTTTTTTG
1 TTTTTTTCTTTTCTCTCTTTTTTTTGCTTTTTTTTTTG
13891 AAGAGAAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
39 11 0.31
40 12 0.34
41 12 0.34
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.83
Consensus pattern (40 bp):
TTTTTTTCTTTTCTCTCTTTTTTTTGCTTTTTTTTTTGTT
Found at i:13878 original size:34 final size:36
Alignment explanation
Indices: 13813--13889 Score: 106
Period size: 34 Copynumber: 2.2 Consensus size: 36
13803 CTTAAGTAGG
13813 TTTTTTTCTTTTCTCTCTTTTTCTTTGTTTTG-TTT
1 TTTTTTTCTTTTCTCTCTTTTTCTTTGTTTTGCTTT
* *
13848 TTTGTTTT-TTTT-TCTTTTTTTCTTTTTTTTGCTTT
1 TTT-TTTTCTTTTCTCTCTTTTTCTTTGTTTTGCTTT
13883 TTTTTTT
1 TTTTTTT
13890 GAAGAGAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
34 21 0.55
35 13 0.34
36 4 0.11
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.84
Consensus pattern (36 bp):
TTTTTTTCTTTTCTCTCTTTTTCTTTGTTTTGCTTT
Done.