Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold146
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: 441899
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.17
Warning! 204872 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:397627 original size:21 final size:21
Alignment explanation
Indices: 397601--397641 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
397591 ACCAAATACC
397601 ATACCATTTCATACCAATTCT
1 ATACCATTTCATACCAATTCT
*
397622 ATACCATTTCGTACCAATTC
1 ATACCATTTCATACCAATTC
397642 CCAAATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.29, G:0.02, T:0.37
Consensus pattern (21 bp):
ATACCATTTCATACCAATTCT
Found at i:398413 original size:26 final size:27
Alignment explanation
Indices: 398359--398424 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 27
398349 TATTATTTGT
* * *
398359 TTTAAATTG-GTCT-TAGTTTAGACAC
1 TTTAAATTGAGTCTATTGTTTAGAAAA
*
398384 TTT-AATTGTGTCTATTGTTTAGAAAA
1 TTTAAATTGAGTCTATTGTTTAGAAAA
398410 TTTAAATTGAGTCTA
1 TTTAAATTGAGTCTA
398425 AATTAAGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.15
25 7 0.21
26 12 0.35
27 10 0.29
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (27 bp):
TTTAAATTGAGTCTATTGTTTAGAAAA
Found at i:400411 original size:4 final size:4
Alignment explanation
Indices: 400402--400439 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
400392 GTTGTAAAGT
400402 TTTA TTTA -TT- TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
400440 CTTAGTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 4 0.12
4 28 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:400468 original size:12 final size:12
Alignment explanation
Indices: 400447--400491 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
400437 TTACTTAGTT
*
400447 TAAATTTTTATG
1 TAAATATTTATG
*
400459 TAAATATTTAGTT
1 TAAATATTTA-TG
*
400472 TAAATTTTTATG
1 TAAATATTTATG
400484 TAAATATT
1 TAAATATT
400492 CAGTCTAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (12 bp):
TAAATATTTATG
Found at i:400481 original size:13 final size:13
Alignment explanation
Indices: 400441--400481 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
400431 ATTTATTTAC
400441 TTAGTTTAAATTT
1 TTAGTTTAAATTT
* *
400454 TTA-TGTAAATAT
1 TTAGTTTAAATTT
400466 TTAGTTTAAATTT
1 TTAGTTTAAATTT
400479 TTA
1 TTA
400482 TGTAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (13 bp):
TTAGTTTAAATTT
Found at i:400490 original size:25 final size:25
Alignment explanation
Indices: 400441--400491 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
400431 ATTTATTTAC
400441 TTAGTTTAAATTTTTATGTAAATAT
1 TTAGTTTAAATTTTTATGTAAATAT
400466 TTAGTTTAAATTTTTATGTAAATAT
1 TTAGTTTAAATTTTTATGTAAATAT
400491 T
1 T
400492 CAGTCTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (25 bp):
TTAGTTTAAATTTTTATGTAAATAT
Found at i:401243 original size:15 final size:16
Alignment explanation
Indices: 401223--401255 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
401213 AATGGTGAGA
401223 TTTGTTAAT-TTTGTT
1 TTTGTTAATGTTTGTT
*
401238 TTTGTTAGTGTTTGTT
1 TTTGTTAATGTTTGTT
401254 TT
1 TT
401256 GCAGGTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.18, T:0.73
Consensus pattern (16 bp):
TTTGTTAATGTTTGTT
Found at i:406552 original size:24 final size:25
Alignment explanation
Indices: 406499--406552 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
406489 AACAAATTCT
* *
406499 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
406524 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
406547 TTTTTT
1 TTTTTT
406553 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:408793 original size:26 final size:27
Alignment explanation
Indices: 408764--408814 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
408754 CCGTATGCAA
**
408764 TTTTTTTTTTTGAAA-TTTTTTTTTCC
1 TTTTTTTTTTCAAAACTTTTTTTTTCC
408790 TTTTTTTTTTCAAAACTTTTTTTTT
1 TTTTTTTTTTCAAAACTTTTTTTTT
408815 TAACTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTTTTTTTTCAAAACTTTTTTTTTCC
Found at i:408809 original size:15 final size:14
Alignment explanation
Indices: 408766--408828 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 14
408756 GTATGCAATT
*
408766 TTTTTTTTTGAAA-
1 TTTTTTTTTCAAAC
408779 TTTTTTTTTC---C
1 TTTTTTTTTCAAAC
408790 TTTTTTTTTTCAAAAC
1 -TTTTTTTTTC-AAAC
*
408806 TTTTTTTTT-TAAC
1 TTTTTTTTTCAAAC
408819 TTTTTTTTTC
1 TTTTTTTTTC
408829 GAAGCTACGA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
12 10 0.24
13 21 0.51
15 9 0.22
16 1 0.02
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTTTTTTCAAAC
Found at i:417175 original size:12 final size:12
Alignment explanation
Indices: 417113--417191 Score: 58
Period size: 12 Copynumber: 6.7 Consensus size: 12
417103 AAACAAAAAA
417113 GAAAAA-AAATT
1 GAAAAAGAAATT
** **
417124 GAAAAAGTGAGA
1 GAAAAAGAAATT
*
417136 GAAAAAGAAAAT
1 GAAAAAGAAATT
417148 GAAGAAAAGAACATT
1 G-A-AAAAGAA-ATT
417163 GAAAAAGAAATT
1 GAAAAAGAAATT
417175 G--AAAGAAA-T
1 GAAAAAGAAATT
417184 GAAAAAGA
1 GAAAAAGA
417192 TGAAGATGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
9 2 0.04
10 7 0.13
11 11 0.21
12 14 0.26
13 8 0.15
14 8 0.15
15 3 0.06
ACGTcount: A:0.67, C:0.01, G:0.20, T:0.11
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:419777 original size:22 final size:21
Alignment explanation
Indices: 419728--419791 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
419718 GTATTTGGGA
* * *
419728 ATTGGTTCGAAATAGTATGG-
1 ATTGGTACAAAATGGTATGGT
419748 ATTGGTACAAAATGGTATGGT
1 ATTGGTACAAAATGGTATGGT
* *
419769 ATTTGGTACGAATTGGTAATGGT
1 A-TTGGTACAAAATGGT-ATGGT
419792 TCAAAGAGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 17 0.47
21 1 0.03
22 13 0.36
23 5 0.14
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.36
Consensus pattern (21 bp):
ATTGGTACAAAATGGTATGGT
Found at i:424005 original size:17 final size:17
Alignment explanation
Indices: 423980--424034 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
423970 TCTCTTTTCA
*
423980 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
423997 TTCTTTTTTTTTTCATTT
1 TTC-TTTTTTTTTGAATT
* *
424015 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
424032 TTC
1 TTC
424035 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:424008 original size:18 final size:18
Alignment explanation
Indices: 423985--424026 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
423975 TTTCATTCTC
*
423985 TTTTTTTGAATTTTCTTT
1 TTTTTTTCAATTTTCTTT
*
424003 TTTTTTTCATTTTTCTTT
1 TTTTTTTCAATTTTCTTT
424021 TCTTTT
1 T-TTTT
424027 GTATTTTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81
Consensus pattern (18 bp):
TTTTTTTCAATTTTCTTT
Found at i:426161 original size:10 final size:11
Alignment explanation
Indices: 426143--426176 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
426133 AACCGTATGT
426143 AATTTTTTTTC
1 AATTTTTTTTC
426154 AATTTTTTTTC
1 AATTTTTTTTC
*
426165 -TTTTTTTTTC
1 AATTTTTTTTC
426175 AA
1 AA
426177 ACTCTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (11 bp):
AATTTTTTTTC
Found at i:426184 original size:21 final size:20
Alignment explanation
Indices: 426145--426188 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
426135 CCGTATGTAA
** *
426145 TTTTTTTTCAATTTTTTTTCT
1 TTTTTTTTCAAACTCTTTT-T
426166 TTTTTTTTCAAACTCTTTTT
1 TTTTTTTTCAAACTCTTTTT
426186 TTT
1 TTT
426189 ACGTACCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTTTCAAACTCTTTTT
Found at i:426510 original size:22 final size:22
Alignment explanation
Indices: 426480--426523 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
426470 TTTGGTATTT
426480 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
426502 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
426524 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:432631 original size:20 final size:20
Alignment explanation
Indices: 432608--432653 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
432598 GGGTTAAGAT
*
432608 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
432628 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
432648 TGAGCT
1 TGAGCT
432654 AGAAACAAGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:434380 original size:48 final size:48
Alignment explanation
Indices: 434325--434430 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
434315 TTGTCTTTTC
*
434325 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* * *
434373 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTTAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
434421 TTTCTTTTTC
1 TTTCTTTTTC
434431 CATGACACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
48 39 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:435529 original size:27 final size:27
Alignment explanation
Indices: 435473--435531 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
435463 TTTAACTTGA
*
435473 TTTTTTTTGCTCACTTTTTTTCTTTCT
1 TTTTTTTTGCTCACTTTTTTACTTTCT
435500 TTTTTTTTGCTCGA-TTTTTTCACTTT-T
1 TTTTTTTTGCTC-ACTTTTTT-ACTTTCT
435527 TTTTT
1 TTTTT
435532 GAATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (27 bp):
TTTTTTTTGCTCACTTTTTTACTTTCT
Found at i:435538 original size:11 final size:12
Alignment explanation
Indices: 435523--435549 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
435513 ATTTTTTCAC
435523 TTTTTTTTTGAA
1 TTTTTTTTTGAA
435535 TTTTTTTTTGAA
1 TTTTTTTTTGAA
435547 TTT
1 TTT
435550 CGATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Done.