Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1414
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: 31644
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1133 original size:19 final size:20
Alignment explanation
Indices: 1104--1152 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1094 CACTTCGTGA
* *
1104 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
1123 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
1143 AAATG-AATGC
1 AAATGTAATGC
1153 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:2929 original size:8 final size:8
Alignment explanation
Indices: 2916--2958 Score: 50
Period size: 8 Copynumber: 4.9 Consensus size: 8
2906 TAATACTATC
2916 ATAAAAAT
1 ATAAAAAT
2924 ATAAAAAGT
1 ATAAAAA-T
2933 AGTATAAATAT
1 A-TA-AAA-AT
2944 ATAAAAAT
1 ATAAAAAT
2952 ATAAAAA
1 ATAAAAA
2959 AATATACTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 16 0.52
9 5 0.16
10 4 0.13
11 5 0.16
12 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (8 bp):
ATAAAAAT
Found at i:5637 original size:25 final size:25
Alignment explanation
Indices: 5609--5690 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
5599 AAAGGTTAAC
5609 TTTTCCTATGGAGAGTTAAAATAAT
1 TTTTCCTATGGAGAGTTAAAATAAT
* * * * *
5634 TTTTTCTA--CAAAATTAATAAAGGTTAAC
1 TTTTCCTATGGAGAGTT-A-AAA---TAAT
5662 TTTTCCTATGGAGAGTTAAAATAAT
1 TTTTCCTATGGAGAGTTAAAATAAT
5687 TTTT
1 TTTT
5691 TTCTAAAATT
Statistics
Matches: 40, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
23 4 0.10
24 1 0.03
25 17 0.43
28 13 0.32
29 1 0.03
30 4 0.10
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (25 bp):
TTTTCCTATGGAGAGTTAAAATAAT
Found at i:5668 original size:53 final size:53
Alignment explanation
Indices: 5588--5691 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
5578 TGACATATCA
5588 ACAAAATTAATAAAGGTTAACTTTTCCTATGGAGAGTTAAAATAATTTTTTCT
1 ACAAAATTAATAAAGGTTAACTTTTCCTATGGAGAGTTAAAATAATTTTTTCT
5641 ACAAAATTAATAAAGGTTAACTTTTCCTATGGAGAGTTAAAATAATTTTTT
1 ACAAAATTAATAAAGGTTAACTTTTCCTATGGAGAGTTAAAATAATTTTTT
5692 TCTAAAATTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (53 bp):
ACAAAATTAATAAAGGTTAACTTTTCCTATGGAGAGTTAAAATAATTTTTTCT
Found at i:5681 original size:27 final size:27
Alignment explanation
Indices: 5598--5681 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 27
5588 ACAAAATTAA
5598 TAAAGGTTAACTTTTCCTATGGAGAGT
1 TAAAGGTTAACTTTTCCTATGGAGAGT
* * * ** * *
5625 TAAA--ATAATTTTTTCTA-CAAAATT
1 TAAAGGTTAACTTTTCCTATGGAGAGT
5649 AATAAAGGTTAACTTTTCCTATGGAGAGT
1 --TAAAGGTTAACTTTTCCTATGGAGAGT
5678 TAAA
1 TAAA
5682 ATAATTTTTT
Statistics
Matches: 38, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
24 3 0.08
25 10 0.26
26 4 0.11
27 8 0.21
28 10 0.26
29 3 0.08
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (27 bp):
TAAAGGTTAACTTTTCCTATGGAGAGT
Found at i:12714 original size:14 final size:13
Alignment explanation
Indices: 12687--12711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12677 TCAACCAAAA
12687 ACAGTTTTTCTTC
1 ACAGTTTTTCTTC
12700 ACAGTTTTTCTT
1 ACAGTTTTTCTT
12712 TCAAAAGTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (13 bp):
ACAGTTTTTCTTC
Found at i:22597 original size:25 final size:24
Alignment explanation
Indices: 22569--22646 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 24
22559 CTATTCCAAA
22569 ATTAATATTATTTTAATAGTTTAAT
1 ATTAATATTATTTTAATA-TTTAAT
* *
22594 ATTAA-ATTTAATTTAATACTT-AT
1 ATTAATA-TTATTTTAATATTTAAT
* *
22617 ATTAATAGTATTTTAGTAATTTAAT
1 ATTAATATTATTTTAAT-ATTTAAT
22642 ATTAA
1 ATTAA
22647 AGTGATTATC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 14 0.33
24 7 0.16
25 22 0.51
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTAATATTATTTTAATATTTAAT
Found at i:22784 original size:62 final size:62
Alignment explanation
Indices: 22586--22785 Score: 147
Period size: 62 Copynumber: 3.1 Consensus size: 62
22576 TTATTTTAAT
* *
22586 AGTTTAATATTAAATTTAATTTAATACTTATATTAATAGTATTTTAGTAATTTAATATTAAAGTG
1 AGTTTAATATTAAATTTAATTTAATA-TTA-ATCAAT--TA---TATTAATTTAATATTAAAGTG
22651 ATT-
59 ATTA
* * * * * * * * ** * *
22654 A-TCTTAATATAAAATTTAATTTAATATTTATCTATAAGATAAACATT-CTATT-ATTTTAATA
1 AGT-TTAATATTAAATTTAATTTAATATTAATCAATTATATTAA-TTTAATATTAAAGTGATTA
*
22715 AGATTTAATATTAAATTTAATGTAATATTAATCAATTATATTAATTTAATATTAAAGTGATTA
1 AG-TTTAATATTAAATTTAATTTAATATTAATCAATTATATTAATTTAATATTAAAGTGATTA
22778 AGTTTAAT
1 AGTTTAAT
22786 CATAGTTGAA
Statistics
Matches: 98, Mismatches: 27, Indels: 20
0.68 0.19 0.14
Matches are distributed among these distances:
60 4 0.04
61 10 0.10
62 45 0.46
63 8 0.08
64 1 0.01
66 4 0.04
67 3 0.03
68 23 0.23
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (62 bp):
AGTTTAATATTAAATTTAATTTAATATTAATCAATTATATTAATTTAATATTAAAGTGATTA
Found at i:27464 original size:59 final size:59
Alignment explanation
Indices: 27399--27518 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
27389 TCACTAACAA
27399 AATGAAAATTACAACTACATGCAATGCATGAATAGTACAGCTAAAACTTAAAATAAACT
1 AATGAAAATTACAACTACATGCAATGCATGAATAGTACAGCTAAAACTTAAAATAAACT
27458 AATGAAAATTACAACTACATGCAATGCATGAATAGTACAGCTAAAACTTAAAATAAACT
1 AATGAAAATTACAACTACATGCAATGCATGAATAGTACAGCTAAAACTTAAAATAAACT
27517 AA
1 AA
27519 CTCAATTTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.23
Consensus pattern (59 bp):
AATGAAAATTACAACTACATGCAATGCATGAATAGTACAGCTAAAACTTAAAATAAACT
Done.