Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold502
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: 762056
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 6 of 6
Found at i:750821 original size:16 final size:16
Alignment explanation
Indices: 750756--750823 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
750746 CATAATATCA
750756 AAAAATATAAATAAATAT
1 AAAAATAT--ATAAATAT
* *
750774 -ATAATATTTTAAATAT
1 AAAAATA-TATAAATAT
* *
750790 AATTAATAT-TATATAT
1 AA-AAATATATAAATAT
750806 AAAAATATATAAATAT
1 AAAAATATATAAATAT
750822 AA
1 AA
750824 TATAAATACG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.12
16 23 0.56
17 7 0.17
18 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATATATAAATAT
Found at i:751530 original size:23 final size:22
Alignment explanation
Indices: 751495--751600 Score: 74
Period size: 23 Copynumber: 4.6 Consensus size: 22
751485 AAGATGATTT
*
751495 AATTTAATTTATTGATAATATATA
1 AATTT-ATATATT-ATAATATATA
*
751519 AAATTATATATTATTAATATATTA
1 AATTTATATATTA-TAATATA-TA
* *
751543 AAGTTA-A-ATTCATAAT-TTTA
1 AATTTATATATT-ATAATATATA
* *
751563 TATTTGATGTATTAATAATATATA
1 AATTT-ATATATT-ATAATATATA
751587 AATTTATATATTAT
1 AATTTATATATTAT
751601 TGATAAATTA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
20 5 0.08
21 2 0.03
22 10 0.16
23 29 0.45
24 18 0.28
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (22 bp):
AATTTATATATTATAATATATA
Found at i:751604 original size:34 final size:34
Alignment explanation
Indices: 751504--751611 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 34
751494 TAATTTAATT
* * *
751504 TATTGATAATATATAAAATTATATATTATTAATA
1 TATTAATAATATATAAATTTATATATTATTGATA
*
751538 TATTAAAGTTAA-AT-TCATAATTT-TATA-T-TTGATG
1 TATT-AA--TAATATAT-A-AATTTATATATTATTGATA
751572 TATTAATAATATATAAATTTATATATTATTGATA
1 TATTAATAATATATAAATTTATATATTATTGATA
*
751606 AATTAA
1 TATTAA
751612 ATTATATCGT
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
31 8 0.14
32 7 0.12
33 4 0.07
34 22 0.38
35 3 0.05
36 7 0.12
37 7 0.12
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (34 bp):
TATTAATAATATATAAATTTATATATTATTGATA
Found at i:751985 original size:16 final size:16
Alignment explanation
Indices: 751939--751986 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
751929 AATATAAATT
751939 ATTAAAATTTATAT-A
1 ATTAAAATTTATATAA
*
751954 A-TATAAA-TTATTTAA
1 ATTA-AAATTTATATAA
751969 ATTAAAATTTATATAA
1 ATTAAAATTTATATAA
751985 AT
1 AT
751987 AATAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 7 0.26
15 9 0.33
16 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTAAAATTTATATAA
Found at i:751996 original size:30 final size:31
Alignment explanation
Indices: 751939--752001 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
751929 AATATAAATT
*
751939 ATTAAAATTTATATAATATAAATTA-TTTAA
1 ATTAAAATTTATATAATATAAAATATTTTAA
751969 ATTAAAATTTATATAA-ATAATAATATTTTAA
1 ATTAAAATTTATATAATATAA-AATATTTTAA
752000 AT
1 AT
752002 ATATTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 4 0.13
30 19 0.63
31 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
ATTAAAATTTATATAATATAAAATATTTTAA
Found at i:752043 original size:30 final size:31
Alignment explanation
Indices: 751978--752049 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 31
751968 AATTAAAATT
*
751978 TATATAAATAATAATATTTTAAATATATTTATAA
1 TATATAAA-AATAATA--TTAAATATATATATAA
752012 TATATAAAAATAATA-TAAATATA-ATACTAA
1 TATATAAAAATAATATTAAATATATATA-TAA
752042 TAT-TAAAA
1 TATATAAAA
752050 TTATCAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 7 0.19
30 14 0.39
33 7 0.19
34 8 0.22
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (31 bp):
TATATAAAAATAATATTAAATATATATATAA
Found at i:753750 original size:2 final size:2
Alignment explanation
Indices: 753743--753771 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
753733 TGAGTTATCT
753743 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
753772 CACATTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:754640 original size:28 final size:29
Alignment explanation
Indices: 754604--754674 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
754594 AAGATGATTG
*
754604 TTAAGAATAATTTTTTA-TTTTAAAATTT
1 TTAAAAATAATTTTTTATTTTTAAAATTT
* *
754632 TTATAAATAATTTTTTATTTTTAAAGTTT
1 TTAAAAATAATTTTTTATTTTTAAAATTT
754661 TTAAAAAT-ATTTTT
1 TTAAAAATAATTTTT
754675 AAAAAAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
TTAAAAATAATTTTTTATTTTTAAAATTT
Found at i:754714 original size:17 final size:20
Alignment explanation
Indices: 754680--754720 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
754670 TTTTTAAAAA
754680 AATTATTATTAATCATTTT-T
1 AATTATTATTAA-CATTTTAT
754700 AATTATT-TTAA-ATTTTAT
1 AATTATTATTAACATTTTAT
754718 AAT
1 AAT
754721 CATGCTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.25
18 4 0.20
19 4 0.20
20 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
AATTATTATTAACATTTTAT
Found at i:756812 original size:2 final size:2
Alignment explanation
Indices: 756805--756832 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
756795 CTAGAAATTA
756805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
756833 TTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:756839 original size:2 final size:2
Alignment explanation
Indices: 756834--756858 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
756824 TATATATATT
756834 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
756859 ATGTTCATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:757108 original size:22 final size:22
Alignment explanation
Indices: 757083--757133 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
757073 TCTCTAGCTT
757083 ATTTAATGTTCATTCAATGCTG
1 ATTTAATGTTCATTCAATGCTG
*
757105 ATTTAATGTTCATTTAATGCTG
1 ATTTAATGTTCATTCAATGCTG
757127 ATTTAAT
1 ATTTAAT
757134 TTTGTGCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (22 bp):
ATTTAATGTTCATTCAATGCTG
Found at i:757112 original size:11 final size:11
Alignment explanation
Indices: 757083--757133 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
757073 TCTCTAGCTT
*
757083 ATTTAATGTTC
1 ATTTAATGCTC
* *
757094 ATTCAATGCTG
1 ATTTAATGCTC
*
757105 ATTTAATGTTC
1 ATTTAATGCTC
*
757116 ATTTAATGCTG
1 ATTTAATGCTC
757127 ATTTAAT
1 ATTTAAT
757134 TTTGTGCTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (11 bp):
ATTTAATGCTC
Found at i:757523 original size:14 final size:13
Alignment explanation
Indices: 757484--757569 Score: 50
Period size: 14 Copynumber: 6.3 Consensus size: 13
757474 ATAATGAGTT
757484 TATTATTTTTAT-
1 TATTATTTTTATA
* *
757496 T-TTGATATTAATA
1 TATT-ATTTTTATA
757509 TATATATTTTTATA
1 TAT-TATTTTTATA
* *
757523 TATTATTTTAAATT
1 TATTATTTT-TATA
*
757537 TATTAATATTTTCAAA
1 TATT-AT-TTTT-ATA
*
757553 TATTATTTATATA
1 TATTATTTTTATA
757566 TATT
1 TATT
757570 TAGAATCTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
11 2 0.04
12 7 0.13
13 13 0.24
14 20 0.36
15 5 0.09
16 8 0.15
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (13 bp):
TATTATTTTTATA
Found at i:757548 original size:17 final size:19
Alignment explanation
Indices: 757526--757564 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
757516 TTTTATATAT
757526 TATTTT-AAAT-TTATTAA
1 TATTTTCAAATATTATTAA
*
757543 TATTTTCAAATATTATTTA
1 TATTTTCAAATATTATTAA
757562 TAT
1 TAT
757565 ATATTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTTCAAATATTATTAA
Found at i:757807 original size:15 final size:15
Alignment explanation
Indices: 757787--757817 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
757777 TAAGGAATAT
757787 TTTTTATTTTTTAAA
1 TTTTTATTTTTTAAA
757802 TTTTTATTTTTTAAA
1 TTTTTATTTTTTAAA
757817 T
1 T
757818 AGAAATATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTTTTTAAA
Found at i:760641 original size:37 final size:37
Alignment explanation
Indices: 760600--760680 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
760590 ATTTAATTAA
*
760600 ATTAAAAAAATATTTTTATTTAAAT-TTAATTATAAAT
1 ATTAAAAAAATATTTATATTTAAATATT-ATTATAAAT
* * * *
760637 ATTAAATATATATTTATATTTTAATATTATTTTAAAT
1 ATTAAAAAAATATTTATATTTAAATATTATTATAAAT
*
760674 AATAAAA
1 ATTAAAA
760681 TAAACTTTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
37 34 0.94
38 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTAAAAAAATATTTATATTTAAATATTATTATAAAT
Found at i:761006 original size:23 final size:23
Alignment explanation
Indices: 760960--761004 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
760950 AAAAAATTAT
760960 TTTATTTAAATTTAATTATAAAA
1 TTTATTTAAATTTAATTATAAAA
760983 TTTATATTAAA-TTAA-TATAAAA
1 TTTAT-TTAAATTTAATTATAAAA
761005 ATAAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 9 0.43
24 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATTTAAATTTAATTATAAAA
Found at i:761713 original size:31 final size:32
Alignment explanation
Indices: 761678--761746 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
761668 TTAAAAAGTT
761678 TTAAAA-GAATATTTAT-TTTAATACTATTAAA
1 TTAAAACG-ATATTTATCTTTAATACTATTAAA
* *
761709 TTAAAACGATATTTATCTTTAATATTGTTAAA
1 TTAAAACGATATTTATCTTTAATACTATTAAA
761741 TTAAAA
1 TTAAAA
761747 ATAATATTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 14 0.41
32 20 0.59
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (32 bp):
TTAAAACGATATTTATCTTTAATACTATTAAA
Done.