Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1231
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: 49001
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:405 original size:10 final size:9
Alignment explanation
Indices: 389--435 Score: 67
Period size: 9 Copynumber: 4.9 Consensus size: 9
379 CAATCCACGA
389 ATTTTTTTT
1 ATTTTTTTT
398 ACTTTTTTTT
1 A-TTTTTTTT
408 ATTTTTTTT
1 ATTTTTTTT
417 CAATTTTTTTT
1 --ATTTTTTTT
428 ATTTTTTT
1 ATTTTTTT
436 AATCTCTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 17 0.49
10 9 0.26
11 9 0.26
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:415 original size:20 final size:20
Alignment explanation
Indices: 389--435 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
379 CAATCCACGA
*
389 ATTTTTTTT-ACTTTTTTTT
1 ATTTTTTTTCAATTTTTTTT
408 ATTTTTTTTCAATTTTTTTT
1 ATTTTTTTTCAATTTTTTTT
428 ATTTTTTT
1 ATTTTTTT
436 AATCTCTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (20 bp):
ATTTTTTTTCAATTTTTTTT
Found at i:1565 original size:13 final size:13
Alignment explanation
Indices: 1547--1572 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1537 ACCTGAAAGC
1547 AATTTAATTCATA
1 AATTTAATTCATA
1560 AATTTAATTCATA
1 AATTTAATTCATA
1573 TTAGGACACA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:1987 original size:20 final size:21
Alignment explanation
Indices: 1962--2000 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1952 TCAAACAAGC
1962 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
1982 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
2001 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:3338 original size:22 final size:23
Alignment explanation
Indices: 3290--3338 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
3280 TATTGGTATG
3290 ATTAATGTGTCCTAATAAGTCGT
1 ATTAATGTGTCCTAATAAGTCGT
* *
3313 -TTAATGTGTCTTAATAGGT-GT
1 ATTAATGTGTCCTAATAAGTCGT
3334 ATTAA
1 ATTAA
3339 AGAAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (23 bp):
ATTAATGTGTCCTAATAAGTCGT
Found at i:6764 original size:19 final size:21
Alignment explanation
Indices: 6731--6778 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
6721 AGGAAGACAC
6731 AAAAAGA-AATCAAAAA-A-G
1 AAAAAGAGAATCAAAAATAGG
*
6749 AAAAAGAGAATGAAAAATAGG
1 AAAAAGAGAATCAAAAATAGG
6770 AAAAAGAGA
1 AAAAAGAGA
6779 TTGAGAGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 8 0.31
20 1 0.04
21 10 0.38
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (21 bp):
AAAAAGAGAATCAAAAATAGG
Found at i:8326 original size:17 final size:17
Alignment explanation
Indices: 8304--8336 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
8294 TGAAGGCGAG
8304 GCCCAA-TAAGCAAATCA
1 GCCCAATTAAG-AAATCA
8321 GCCCAATTAAGAAATC
1 GCCCAATTAAGAAATC
8337 CATACATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.15
Consensus pattern (17 bp):
GCCCAATTAAGAAATCA
Found at i:17870 original size:23 final size:22
Alignment explanation
Indices: 17819--17870 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
17809 CCTCGTCTTT
*
17819 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
17841 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
17864 TTCTTTT
1 TTCTTTT
17871 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:17879 original size:12 final size:12
Alignment explanation
Indices: 17828--17882 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
17818 TTTCTTTTGT
17828 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
17841 -TCATTTTC-TC
1 TTCTTTTTCAAC
17851 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
17864 TTCTTTTTCAAT
1 TTCTTTTTCAAC
17876 TTCTTTT
1 TTCTTTT
17883 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:17889 original size:17 final size:18
Alignment explanation
Indices: 17864--17901 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
17854 TTTCTTCAAC
* *
17864 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
17881 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
17899 TTC
1 TTC
17902 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:28456 original size:10 final size:9
Alignment explanation
Indices: 28443--28477 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
28433 ACTTTTCACT
28443 TTTTTTATTC
1 TTTTTT-TTC
*
28453 TTTTTTTAC
1 TTTTTTTTC
28462 TTTTTTTTC
1 TTTTTTTTC
28471 TTTTTTT
1 TTTTTTT
28478 GCTCACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:30031 original size:20 final size:20
Alignment explanation
Indices: 30008--30054 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
29998 GGGTTAAAAT
*
30008 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
30028 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
30048 TGAGCTG
1 TGAGCTG
30055 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:32452 original size:23 final size:22
Alignment explanation
Indices: 32401--32452 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
32391 CCTCGTCTTT
*
32401 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
32423 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
32446 TTCTTTT
1 TTCTTTT
32453 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:33788 original size:9 final size:9
Alignment explanation
Indices: 33774--33807 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
33764 GAATTTCGTA
*
33774 TTTTTTGAT
1 TTTTTTGAC
33783 TTTTTTGAC
1 TTTTTTGAC
33792 TTTTTTGAC
1 TTTTTTGAC
33801 TGTTTTT
1 T-TTTTT
33808 TTTGCGGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.09, C:0.06, G:0.12, T:0.74
Consensus pattern (9 bp):
TTTTTTGAC
Found at i:34731 original size:21 final size:22
Alignment explanation
Indices: 34701--34745 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
34691 GAGCAAATTG
*
34701 TTGATTCTATTTTCTTTTTG-AT
1 TTGATTCTATTCT-TTTTTGTAT
34723 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTTTTGTAT
34744 TT
1 TT
34746 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 11 0.52
22 4 0.19
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (22 bp):
TTGATTCTATTCTTTTTTGTAT
Found at i:36872 original size:10 final size:10
Alignment explanation
Indices: 36857--36895 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
36847 CGGTATTGTA
36857 AAAAAAAATG
1 AAAAAAAATG
*
36867 AAAAAAAATT
1 AAAAAAAATG
*
36877 AAAAAAATTCG
1 AAAAAAAAT-G
36888 AAAAAAAA
1 AAAAAAAA
36896 AATCCGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:36896 original size:14 final size:14
Alignment explanation
Indices: 36877--36910 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
36867 AAAAAAAATT
*
36877 AAAAAAATTCGAAA
1 AAAAAAATCCGAAA
36891 AAAAAAATCCGAAA
1 AAAAAAATCCGAAA
36905 AAAAAA
1 AAAAAA
36911 GTTTGTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (14 bp):
AAAAAAATCCGAAA
Found at i:37933 original size:21 final size:20
Alignment explanation
Indices: 37904--37949 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
37894 AATCTTGAAT
*
37904 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
37925 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
37945 GAAAA
1 GAAAA
37950 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:37976 original size:12 final size:12
Alignment explanation
Indices: 37956--37991 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
37946 AAAAAAGAAT
*
37956 TTGAGATTGAGA
1 TTGATATTGAGA
*
37968 TTGATATTGATA
1 TTGATATTGAGA
37980 TTGATATTGAGA
1 TTGATATTGAGA
37992 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (12 bp):
TTGATATTGAGA
Found at i:45543 original size:34 final size:33
Alignment explanation
Indices: 45505--45677 Score: 224
Period size: 32 Copynumber: 5.2 Consensus size: 33
45495 TCACTTGTCT
* *
45505 TTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTCTTGCAGGGAATCTCTCCTGTTCA-GCATTA
* *
45539 TTTCTTGCAGGGAATCTTTCCTGTTCA-CATCA
1 TTTCTTGCAGGGAATCTCTCCTGTTCAGCATTA
45571 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTCTTGCAGGGAATCTCTCCTGTTCA-GCATTA
* *
45605 TTTTGTTGCAGGGAATCTCTCCTGTTCA-CATCA
1 -TTTCTTGCAGGGAATCTCTCCTGTTCAGCATTA
* *
45638 TTTGTTGCAGGGAATCTCTCCTGTTCATGTATTA
1 TTTCTTGCAGGGAATCTCTCCTGTTCA-GCATTA
45672 TTTCTT
1 TTTCTT
45678 TTTGGACCTG
Statistics
Matches: 125, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
32 57 0.46
33 4 0.03
34 38 0.30
35 26 0.21
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (33 bp):
TTTCTTGCAGGGAATCTCTCCTGTTCAGCATTA
Found at i:45646 original size:67 final size:67
Alignment explanation
Indices: 45505--45674 Score: 270
Period size: 67 Copynumber: 2.6 Consensus size: 67
45495 TCACTTGTCT
* * *
45505 TTTCTTGCAGGGAATATTTCCTGTTCACGCATTA-TTTCTTGCAGGGAATCTTTCCTGTTCACAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTCTTGCAGGGAATCTCTCCTGTTCACAT
45569 CA
66 CA
*
45571 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTCTTGCAGGGAATCTCTCCTGTTCACAT
45636 CA
66 CA
* * *
45638 TTTGTTGCAGGGAATCTCTCCTGTTCATGTATTATTT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTT
45675 CTTTTTGGAC
Statistics
Matches: 96, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
66 32 0.33
67 64 0.67
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (67 bp):
TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTCTTGCAGGGAATCTCTCCTGTTCACAT
CA
Found at i:48508 original size:20 final size:22
Alignment explanation
Indices: 48471--48514 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
48461 GAGCAAATTG
48471 TTGATTCTATTTCTTTTTG-AT
1 TTGATTCTATTTCTTTTTGTAT
48492 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTC-TTTTTGTAT
48513 TT
1 TT
48515 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.14
20 10 0.48
21 8 0.38
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (22 bp):
TTGATTCTATTTCTTTTTGTAT
Done.