Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold744
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: 48779
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:6478 original size:40 final size:39
Alignment explanation
Indices: 6399--6615 Score: 258
Period size: 40 Copynumber: 5.5 Consensus size: 39
6389 CGGATGATAA
* * *
6399 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGCTATAT
* * * * * *
6439 CCGGGCTATGTCCCGAAGGCGTTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG-CTATAT
6479 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGGTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGCTATAT
*
6519 CCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGCTATAT
*
6559 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGCTATAT
*
6599 -CTGGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
6616 ATACTTGGGT
Statistics
Matches: 154, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 17 0.11
40 133 0.86
41 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGCTATAT
Found at i:6883 original size:22 final size:22
Alignment explanation
Indices: 6843--6884 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6833 GAATGTGCAT
*
6843 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
6865 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
6885 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:9962 original size:6 final size:6
Alignment explanation
Indices: 9928--10012 Score: 68
Period size: 6 Copynumber: 14.3 Consensus size: 6
9918 AACAAAATTG
* * * *
9928 AAATGA AAATAA AAATCA AAAGAA AAATAA GAAT-A AAATAAA TAAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAAT-AA -AAATAA
* * *
9977 AAATAA AAATAA GAAT-- AAATAA AAAGAA AAAGAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
10013 TAGGAGGATT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.05
5 4 0.06
6 50 0.78
7 3 0.05
8 4 0.06
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:9988 original size:31 final size:30
Alignment explanation
Indices: 9933--10012 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 30
9923 AATTGAAATG
*
9933 AAAAT-AAAAATCAAAAGAAAAATAAGAAT
1 AAAATAAAAAATAAAAAGAAAAATAAGAAT
*
9962 AAAATAAATAAATAAAAATAAAAATAAGAAT
1 AAAATAAA-AAATAAAAAGAAAAATAAGAAT
*
9993 -AAAT-AAAAAGAAAAAGAAAA
1 AAAATAAAAAATAAAAAGAAAA
10013 TAGGAGGATT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 12 0.27
29 7 0.16
30 6 0.13
31 20 0.44
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.14
Consensus pattern (30 bp):
AAAATAAAAAATAAAAAGAAAAATAAGAAT
Found at i:9993 original size:26 final size:25
Alignment explanation
Indices: 9950--9999 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
9940 AAATCAAAAG
*
9950 AAAAATAAGAATAAAATAAATAAAT
1 AAAAATAAAAATAAAATAAATAAAT
9975 AAAAATAAAAATAAGAATAAATAAA
1 AAAAATAAAAATAA-AATAAATAAA
10000 AAGAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (25 bp):
AAAAATAAAAATAAAATAAATAAAT
Found at i:16521 original size:15 final size:14
Alignment explanation
Indices: 16503--16533 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
16493 TTAATTTATT
16503 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
16518 TAATAATAATCTAA
1 TAATAATAATCTAA
16532 TA
1 TA
16534 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:16544 original size:21 final size:20
Alignment explanation
Indices: 16520--16588 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
16510 AATGCTAATA
16520 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
16541 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
16560 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
16581 ATAATAAT
1 ATAATAAT
16589 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:18145 original size:13 final size:13
Alignment explanation
Indices: 18123--18155 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
18113 AAGGGTTTGT
18123 TTAT-TAAACTAA
1 TTATCTAAACTAA
18135 TTATCTAAACTAA
1 TTATCTAAACTAA
*
18148 TTAACTAA
1 TTATCTAA
18156 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:18457 original size:15 final size:14
Alignment explanation
Indices: 18439--18469 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
18429 TTAATTTATT
18439 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
18454 TAATAATAATCTAA
1 TAATAATAATCTAA
18468 TA
1 TA
18470 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:18480 original size:21 final size:20
Alignment explanation
Indices: 18456--18524 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
18446 AATGCTAATA
18456 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
18477 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
18496 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
18517 ATAATAAT
1 ATAATAAT
18525 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:20081 original size:13 final size:13
Alignment explanation
Indices: 20059--20091 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
20049 AAGGGTTTGT
20059 TTAT-TAAACTAA
1 TTATCTAAACTAA
20071 TTATCTAAACTAA
1 TTATCTAAACTAA
*
20084 TTAACTAA
1 TTATCTAA
20092 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:28464 original size:50 final size:49
Alignment explanation
Indices: 28389--28614 Score: 213
Period size: 50 Copynumber: 4.5 Consensus size: 49
28379 TGAATACACG
* * * *
28389 TGTGTAGCACTAAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTGTTAA-TCACA
* * ** *
28439 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACT-TCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TC-A-GACTGTTAATCACA
* * * *
28490 TGTGTAGTACTAAGTGGAGGCTACTACGTGTATCAGA-TGATGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTG-TTA-ATCACA
* * * * * *
28540 TGTGTAGTTCTAAGTGCAGGCTACTACGTGTACCGGATTGTTGATCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTGTTAATCACA
28589 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
28615 TACGTATCAT
Statistics
Matches: 144, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
47 1 0.01
48 2 0.01
49 30 0.21
50 69 0.48
51 36 0.25
52 3 0.02
53 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTGTTAATCACA
Found at i:28619 original size:101 final size:100
Alignment explanation
Indices: 28389--28614 Score: 262
Period size: 101 Copynumber: 2.3 Consensus size: 100
28379 TGAATACACG
* * * * *
28389 TGTGTAGCACTAAGTGTAGGCTACTACGTGTATCATACTGTTAAGTCGCATGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTGTGAAGTCACATGTGTAGTACTAAGT
* *
28454 GCAGGCTACTATGCGTACTCAATGACTTCGATCACG
66 GCAGGCTACTACGCGTACTCAATGA-TTCGATCACA
* * * *
28490 TGTGTAGTACTAAGTGGAGGCTACTACGTGTATCAGA-TGATGAGGTCACGTGTGTAGTTCTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTG-TGAAGTCACATGTGTAGTACTAAG
* * *
28554 TGCAGGCTACTACGTGTAC-CGGATTG-TT-GATCGCA
65 TGCAGGCTACTACGCGTACTC--AATGATTCGATCACA
28589 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
28615 TACGTATCAT
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
99 30 0.28
100 5 0.05
101 70 0.65
102 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (100 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGACTGTGAAGTCACATGTGTAGTACTAAGT
GCAGGCTACTACGCGTACTCAATGATTCGATCACA
Found at i:28744 original size:27 final size:26
Alignment explanation
Indices: 28714--28765 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
28704 GGGAAAACCG
28714 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGT-G-AATATGTGCAAAGTTATT
* *
28741 ATAAGGTGAATATGTGCAAATTTAT
1 ATAAAGTGAATATGTGCAAAGTTAT
28766 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 8 0.36
26 8 0.36
27 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (26 bp):
ATAAAGTGAATATGTGCAAAGTTATT
Found at i:38664 original size:28 final size:28
Alignment explanation
Indices: 38601--38723 Score: 158
Period size: 28 Copynumber: 4.4 Consensus size: 28
38591 ATATTAAGTC
*
38601 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
38628 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
38656 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * * *
38684 TGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
38713 CGCACACTTAG
1 CGCACACTTAG
38724 CGCCAATCTC
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
27 21 0.25
28 47 0.57
29 15 0.18
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:38671 original size:55 final size:57
Alignment explanation
Indices: 38600--38723 Score: 180
Period size: 56 Copynumber: 2.2 Consensus size: 57
38590 TATATTAAGT
* * *
38600 CCGCACACTCAGTGCTATATAATC-AACTTGCACACTTAGTGCTATATAA-TCAAAC
1 CCGCACACTTAGTGCTACATAATCAAACTTGCACACTTAGTGCTATACAATTCAAAC
* * *
38655 TCGCACACTTAGTGCTACATAATCAAACTTGCACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGCTACATAATCAAACTTGCACACTTAGTGCTATACAATTCAAAC
38712 CCGCACACTTAG
1 CCGCACACTTAG
38724 CGCCAATCTC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 21 0.35
56 23 0.38
57 16 0.27
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (57 bp):
CCGCACACTTAGTGCTACATAATCAAACTTGCACACTTAGTGCTATACAATTCAAAC
Found at i:46943 original size:28 final size:28
Alignment explanation
Indices: 46880--47001 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
46870 ATATTAAGTC
*
46880 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
46907 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
46935 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
46963 CGCACACTTAGTGCTGTACAATTTAAAC-
1 CGCACACTTAGTGCTATATAA-TCAAACT
46991 CGCACACTTAG
1 CGCACACTTAG
47002 CGCCAATCTC
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
27 22 0.25
28 60 0.69
29 5 0.06
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.