Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020216.1 Corchorus olitorius cultivar O-4 contig20249, whole genome shotgun sequence
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: 2254
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Found at i:1481 original size:23 final size:22
Alignment explanation
Indices: 1444--1561 Score: 81
Period size: 23 Copynumber: 5.3 Consensus size: 22
1434 AGCTAAAAAA
1444 ATAATAATAAATTAATAAATAG
1 ATAATAATAAATTAATAAATAG
1466 ATAATAACTAAATTAATAAATA-
1 ATAATAA-TAAATTAATAAATAG
1488 A-AA-AGATAAATAGTAAATAAATAG
1 ATAATA-ATAAAT--T-AATAAATAG
*
1512 GTAATAATTAAA--AATAAATA-
1 ATAATAA-TAAATTAATAAATAG
1532 A-AA-ACATAAATAGTAAATAAATAG
1 ATAATA-ATAAAT--T-AATAAATAG
1556 ATAATA
1 ATAATA
1562 GTTAAAGATA
Statistics
Matches: 76, Mismatches: 2, Indels: 32
0.69 0.02 0.29
Matches are distributed among these distances:
18 5 0.07
19 3 0.04
20 6 0.08
21 11 0.14
22 9 0.12
23 30 0.39
24 1 0.01
25 5 0.07
26 6 0.08
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (22 bp):
ATAATAATAAATTAATAAATAG
Found at i:1483 original size:19 final size:18
Alignment explanation
Indices: 1437--1736 Score: 97
Period size: 19 Copynumber: 16.3 Consensus size: 18
1427 AATAGGTAGC
*
1437 TAAAAAAATAATAATAAA
1 TAAATAAATAATAATAAA
* *
1455 TTAATAAATAGATAATAAC
1 TAAATAAATA-ATAATAAA
*
1474 TAAATTAAT-A-AATAAA
1 TAAATAAATAATAATAAA
*
1490 -AAGATAAATAGTAAATAAA
1 TAA-ATAAATAAT-AATAAA
* *
1509 TAGGTAATAATTAAAAATAAA
1 TA---AATAAATAATAATAAA
*
1530 TAAA-AACATAAATAGTAAA
1 TAAATAA-AT-AATAATAAA
* * *
1549 TAAATAGATAATAGTTAA
1 TAAATAAATAATAATAAA
* * *
1567 -AGATAATTAAATAGTAAA
1 TAAATAAAT-AATAATAAA
* * *
1585 TAAATAGATAATAGTTAA
1 TAAATAAATAATAATAAA
1603 -AAATAAATAAATAGATAAA
1 TAAATAAAT-AATA-ATAAA
*
1622 TGGTAAATAAGTAGATAATAAA
1 ---TAAATAAATA-ATAATAAA
* *
1644 AAAAGTAAATAGTAAATAAA
1 TAAA-TAAATAAT-AATAAA
* *
1664 TAGATAAATAGTGAATAAA
1 TAAATAAATAAT-AATAAA
* *
1683 TAGAT-AATAGTTAA-AAA
1 TAAATAAATA-ATAATAAA
*
1700 TGTAA-AAATAA-AA-AAA
1 T-AAATAAATAATAATAAA
1716 TAAA-AAA-AATAA-AAA
1 TAAATAAATAATAATAAA
1731 TAAATA
1 TAAATA
1737 GTAAATAAAT
Statistics
Matches: 215, Mismatches: 39, Indels: 58
0.69 0.12 0.19
Matches are distributed among these distances:
14 2 0.01
15 16 0.07
16 17 0.08
17 19 0.09
18 50 0.23
19 65 0.30
20 15 0.07
21 8 0.04
22 12 0.06
23 11 0.05
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (18 bp):
TAAATAAATAATAATAAA
Found at i:1489 original size:4 final size:4
Alignment explanation
Indices: 1437--1759 Score: 78
Period size: 4 Copynumber: 83.2 Consensus size: 4
1427 AATAGGTAGC
* * * * *
1437 TAAA AAAA T-AA T-AA TAAA TTAA TAAA TAGA T-AA TAAC TAAA TTAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* ** *
1482 TAAA TAAA -AAGA TAAA T-AG TAAA TAAA TAGG T-AA T-AA TTAA -AAA
1 TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * *
1526 TAAA TAAA -AACA TAAA T-AG TAAA TAAA TAGA TAATA GTTAA -AGA TAAT
1 TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA
* * * *
1574 TAAA T-AG TAAA TAAA TAGA TAATA GTTAA -AAA TAAA TAAA TAGA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA TAAA TAAA
** * * * * *
1622 T-GG TAAA TAAG TAGA T-AA TAAA AAAA GTAAA T-AG TAAA TAAA TAGA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA -TAAA TAAA TAAA TAAA TAAA
* * * * * *
1668 TAAA T-AG TGAA TAAA TAGA TAATA GTTAA -AAA TGTAA -AAA TAAA AAAA
1 TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA T-AAA TAAA TAAA TAAA
* * *
1716 TAAA -AAA -AATA AAAA TAAA T-AG TAAA TAAA TATAA TAAA AAAA T
1 TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TA-AA TAAA TAAA T
1760 CTTTTTGGTC
Statistics
Matches: 223, Mismatches: 65, Indels: 62
0.64 0.19 0.18
Matches are distributed among these distances:
3 45 0.20
4 151 0.68
5 21 0.09
6 6 0.03
ACGTcount: A:0.66, C:0.01, G:0.08, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:1504 original size:27 final size:27
Alignment explanation
Indices: 1449--1510 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
1439 AAAAAATAAT
* *
1449 AATAAATTAATAAATAGATAATAACTA
1 AATAAATAAATAAAAAGATAATAACTA
* *
1476 AATTAATAAATAAAAAGATAA-ATAGTA
1 AATAAATAAATAAAAAGATAATA-ACTA
1503 AATAAATA
1 AATAAATA
1511 GGTAATAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (27 bp):
AATAAATAAATAAAAAGATAATAACTA
Found at i:1541 original size:44 final size:43
Alignment explanation
Indices: 1457--1673 Score: 218
Period size: 44 Copynumber: 5.1 Consensus size: 43
1447 ATAATAAATT
*
1457 AATAAATAGATAATAACTAAATTAATAAATAAAAAGATAAATAGTA
1 AATAAATAGATAATAATTAAA--AATAAATAAAAA-ATAAATAGTA
*
1503 AATAAATAGGTAATAATTAAAAATAAATAAAAACATAAATAGTA
1 AATAAATAGATAATAATTAAAAATAAATAAAAA-ATAAATAGTA
* *
1547 AATAAATAGATAATAGTTAAAGAT-AAT------TAAATAGTA
1 AATAAATAGATAATAATTAAAAATAAATAAAAAATAAATAGTA
* * *
1583 AATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATGGTA
1 AATAAATAGATAATAATTAAAAATAAATAAA-AAATAAATAGTA
* **
1627 AATAAGTAGATAATAA--AAAAAGTAAATAGTAAATAAATAGATA
1 AATAAATAGATAATAATTAAAAA-TAAATAAAAAATAAATAG-TA
1670 AATA
1 AATA
1674 GTGAATAAAT
Statistics
Matches: 147, Mismatches: 14, Indels: 23
0.80 0.08 0.12
Matches are distributed among these distances:
36 32 0.22
37 3 0.02
42 13 0.09
43 15 0.10
44 65 0.44
46 19 0.13
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (43 bp):
AATAAATAGATAATAATTAAAAATAAATAAAAAATAAATAGTA
Found at i:1579 original size:36 final size:35
Alignment explanation
Indices: 1537--1675 Score: 149
Period size: 36 Copynumber: 3.8 Consensus size: 35
1527 AAATAAAAAC
1537 ATAAATAGTAAATAAATAGATAATAGTTAAAGATAA
1 ATAAATAGTAAATAAATAGATAATAGTTAAA-ATAA
*
1573 TTAAATAGTAAATAAATAGATAATAGTTAAAAATAA
1 ATAAATAGTAAATAAATAGATAATAGTT-AAAATAA
*
1609 ATAAATAGATAAATGGTAAATA-AGTAGATA-ATAAAA-AA
1 ATAAATAG-TAAA---TAAATAGA-TA-ATAGTTAAAATAA
1647 AGTAAATAGTAAATAAATAGATAAATAGT
1 A-TAAATAGTAAATAAATAGAT-AATAGT
1676 GAATAAATAG
Statistics
Matches: 88, Mismatches: 4, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
35 10 0.11
36 40 0.45
37 7 0.08
38 7 0.08
39 12 0.14
40 9 0.10
41 3 0.03
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (35 bp):
ATAAATAGTAAATAAATAGATAATAGTTAAAATAA
Found at i:1581 original size:80 final size:75
Alignment explanation
Indices: 1487--1670 Score: 251
Period size: 80 Copynumber: 2.4 Consensus size: 75
1477 ATTAATAAAT
*
1487 AAAAAGATAAATAGTAAATAAATAGGTAATAATTAAAAATAAATAAAAACATAAATAGTAAATAA
1 AAAAAG-TAAATAGTAAATAAATAGATAATAATTAAAAATAAATAAAAACATAAATAGTAAATAA
1552 ATAGATAATAGTTA
65 ATAGATAATA---A
* * * * *
1566 AAGATAATTAAATAGTAAATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATGGTAAATA
1 AA-A-AAGTAAATAGTAAATAAATAGATAATAATTAAAAATAAATAAAAACATAAATAGTAAATA
*
1631 AGTAGATAATAA
64 AATAGATAATAA
1643 AAAAAGTAAATAGTAAATAAATAGATAA
1 AAAAAGTAAATAGTAAATAAATAGATAA
1671 ATAGTGAATA
Statistics
Matches: 95, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
75 24 0.25
76 1 0.01
77 3 0.03
79 2 0.02
80 63 0.66
81 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.10, T:0.26
Consensus pattern (75 bp):
AAAAAGTAAATAGTAAATAAATAGATAATAATTAAAAATAAATAAAAACATAAATAGTAAATAAA
TAGATAATAA
Found at i:1715 original size:9 final size:9
Alignment explanation
Indices: 1703--1736 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1693 TTAAAAATGT
1703 AAAAAT-AA
1 AAAAATAAA
1711 AAAAATAAA
1 AAAAATAAA
1720 AAAAATAAA
1 AAAAATAAA
1729 AATAAATA
1 AA-AAATA
1737 GTAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 6 0.25
9 13 0.54
10 5 0.21
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAATAAA
Found at i:1750 original size:23 final size:22
Alignment explanation
Indices: 1688--1759 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
1678 ATAAATAGAT
* *
1688 AATAGTTAAAAATGTAAAAATAA
1 AATAGTAAAAAATATAAAAAT-A
* * *
1711 AAAAATAAAAAAAATAAAAATA
1 AATAGTAAAAAATATAAAAATA
*
1733 AATAGTAAATAAATATAATAAAAA
1 AATAGTAAA-AAATATAA-AAATA
1757 AAT
1 AAT
1760 CTTTTTGGTC
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
22 8 0.21
23 23 0.61
24 7 0.18
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (22 bp):
AATAGTAAAAAATATAAAAATA
Done.