Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1386
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: 31986
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:2515 original size:10 final size:10
Alignment explanation
Indices: 2476--2516 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
2466 CATATTTTCA
2476 CTTTTTCCTTT
1 CTTTTT-CTTT
*
2487 CTTTTTCTCT
1 CTTTTTCTTT
*
2497 ATTTTTCTTT
1 CTTTTTCTTT
2507 CTTTTTCTTT
1 CTTTTTCTTT
2517 TTCAATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:2515 original size:26 final size:28
Alignment explanation
Indices: 2484--2544 Score: 81
Period size: 26 Copynumber: 2.2 Consensus size: 28
2474 CACTTTTTCC
**
2484 TTTCTTTTTCTCTATTTTTC-T-TTCTT
1 TTTCTTTTTCAATATTTTTCTTGTTCTT
*
2510 TTTCTTTTTCAATTTTTTTCTTGTTCTT
1 TTTCTTTTTCAATATTTTTCTTGTTCTT
2538 TTTCTTT
1 TTTCTTT
2545 CATCTTTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 17 0.57
27 1 0.03
28 12 0.40
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (28 bp):
TTTCTTTTTCAATATTTTTCTTGTTCTT
Found at i:2517 original size:16 final size:15
Alignment explanation
Indices: 2484--2545 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
2474 CACTTTTTCC
* *
2484 TTTCTTTTTCTCTATT
1 TTTCTTTTT-TTTCTT
2500 TTTCTTTCTTTTTCTT
1 TTTCTTT-TTTTTCTT
*
2516 TTTCAATTTTTTTCTT
1 TTTC-TTTTTTTTCTT
*
2532 GTTCTTTTTCTTTC
1 TTTCTTTTT-TTTC
2546 ATCTTTTCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 4 0.11
16 30 0.79
17 4 0.11
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTCTTTTTTTTCTT
Found at i:2536 original size:22 final size:23
Alignment explanation
Indices: 2499--2541 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2489 TTTTCTCTAT
*
2499 TTTTCTTTCTTTTTCTTTTTCAA
1 TTTTCTTTCTTGTTCTTTTTCAA
2522 TTTT-TTTCTTGTTCTTTTTC
1 TTTTCTTTCTTGTTCTTTTTC
2542 TTTCATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTCTTTCTTGTTCTTTTTCAA
Found at i:2552 original size:26 final size:25
Alignment explanation
Indices: 2484--2552 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 25
2474 CACTTTTTCC
2484 TTTCTTTTTC-TCTATTTTTCTTTCTT
1 TTTC-TTTTCATCT-TTTTTCTTTCTT
2510 TTTCTTTTTCAAT-TTTTTTCTTGTTCTT
1 TTTC-TTTTC-ATCTTTTTTC-T-TTCTT
2538 TTTC-TTTCATCTTTT
1 TTTCTTTTCATCTTTT
2553 CCAAAGACTC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
25 2 0.05
26 24 0.63
27 2 0.05
28 10 0.26
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.75
Consensus pattern (25 bp):
TTTCTTTTCATCTTTTTTCTTTCTT
Found at i:7723 original size:14 final size:15
Alignment explanation
Indices: 7693--7723 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7683 CGATTTTTTT
7693 TCACTTTTTTTTGAA
1 TCACTTTTTTTTGAA
7708 TCACTTTTTTTT-AA
1 TCACTTTTTTTTGAA
7722 TC
1 TC
7724 CAATACAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.16, G:0.03, T:0.61
Consensus pattern (15 bp):
TCACTTTTTTTTGAA
Found at i:11004 original size:46 final size:46
Alignment explanation
Indices: 10935--11032 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 46
10925 AGTTGTCTTG
10935 GCTTAAGACACTTTAAATGGCTGTAG-AACAAAGACAAATTAAATTA
1 GCTTAAGACACTTTAAATGGCTGTAGTAACAAAGACAAATT-AATTA
* ***
10981 GCTTAAGACAAC-TTAAATTGCTGTAGTAATTTAGACAAATTAATTA
1 GCTTAAGAC-ACTTTAAATGGCTGTAGTAACAAAGACAAATTAATTA
*
11027 ACTTAA
1 GCTTAA
11033 CTTATTAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
46 32 0.71
47 13 0.29
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (46 bp):
GCTTAAGACACTTTAAATGGCTGTAGTAACAAAGACAAATTAATTA
Found at i:12421 original size:6 final size:6
Alignment explanation
Indices: 12412--12441 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
12402 CTCATTTTCA
12412 TCATTT TCATTT TCATTT TCATTT TCATTT
1 TCATTT TCATTT TCATTT TCATTT TCATTT
12442 ATTTCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (6 bp):
TCATTT
Found at i:12446 original size:27 final size:27
Alignment explanation
Indices: 12403--12459 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
12393 TTTTGAAATC
*
12403 TCATTTTCATCATTTTCATTTTCATTT
1 TCATTTTCATCATTTTCAATTTCATTT
* *
12430 TCATTTTCAT-TTATTTCAATTTCTTTT
1 TCATTTTCATCAT-TTTCAATTTCATTT
12457 TCA
1 TCA
12460 ATGTTCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.19, C:0.18, G:0.00, T:0.63
Consensus pattern (27 bp):
TCATTTTCATCATTTTCAATTTCATTT
Found at i:14626 original size:12 final size:12
Alignment explanation
Indices: 14604--14640 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
14594 TATTGTGCAC
14604 GAATATTTTTTTA
1 GAAT-TTTTTTTA
*
14617 GAATTTTTTTTT
1 GAATTTTTTTTA
14629 GAATTTTTTTTA
1 GAATTTTTTTTA
14641 CAAACCTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
GAATTTTTTTTA
Found at i:21756 original size:23 final size:24
Alignment explanation
Indices: 21721--21765 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
21711 TTTCTTTTGT
21721 TTCTTTTTCTAAC-TCATTTTCTC
1 TTCTTTTTCTAACGTCATTTTCTC
*
21744 TTCTTTCTT-TAACGTCTTTTTC
1 TTCTTT-TTCTAACGTCATTTTC
21766 AATTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.11, C:0.24, G:0.02, T:0.62
Consensus pattern (24 bp):
TTCTTTTTCTAACGTCATTTTCTC
Found at i:24126 original size:25 final size:23
Alignment explanation
Indices: 24092--24137 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
24082 AAACAACTTC
24092 TAGAGAAAACTCAAGAGAGAAATCT
1 TAGAGAAAACTCAA-AGA-AAATCT
24117 TAGAGAAAACTCAAAGAAAAT
1 TAGAGAAAACTCAAAGAAAAT
24138 TCTGCTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 3 0.14
25 14 0.67
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (23 bp):
TAGAGAAAACTCAAAGAAAATCT
Found at i:27705 original size:29 final size:29
Alignment explanation
Indices: 27672--27744 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
27662 ATGTATTAGT
* *
27672 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
27701 TTAGGACATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
27730 TTAGGACATATTTAA
1 TTAGGACATATTTAA
27745 TAATATCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:29027 original size:55 final size:56
Alignment explanation
Indices: 28923--29028 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 56
28913 ATTAATGCCG
* * *
28923 TCCATGCATGGGAACATCTCATTAAATCCATGTCTTTGCTTCCCTTTAAATGCCAT
1 TCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTTCACATTAAATGCCAT
* * *
28979 TCCATGCATGGGAACATCTCCTT-AATTCGTGGCTTTGCTGT-ACATTAAAT
1 TCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCT-TCACATTAAAT
29029 CAGCAAGCAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
55 20 0.47
56 23 0.53
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (56 bp):
TCCATGCATGGGAACATCTCATTAAATCCATGGCTTTGCTTCACATTAAATGCCAT
Found at i:29324 original size:23 final size:22
Alignment explanation
Indices: 29290--29354 Score: 103
Period size: 23 Copynumber: 2.9 Consensus size: 22
29280 GAACACCTTT
*
29290 AAAACATGCATTAAATTCGGCC
1 AAAACATACATTAAATTCGGCC
29312 AGAAACATACATTAAATTCGGCC
1 A-AAACATACATTAAATTCGGCC
29335 AAAGACATACATTAAATTCG
1 AAA-ACATACATTAAATTCG
29355 TCTGGAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 3 0.08
23 37 0.93
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (22 bp):
AAAACATACATTAAATTCGGCC
Found at i:29592 original size:13 final size:13
Alignment explanation
Indices: 29576--29610 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
29566 TTTAAACAAA
*
29576 TTAATTAACTTAT
1 TTAATTAACTAAT
29589 TTAATTAACTAAT
1 TTAATTAACTAAT
*
29602 TTAACTAAC
1 TTAATTAAC
29611 AACAACTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAATTAACTAAT
Done.