Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012789.1 Corchorus olitorius cultivar O-4 contig12822, 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: 2063
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Found at i:1458 original size:26 final size:25
Alignment explanation
Indices: 1419--1625 Score: 94
Period size: 25 Copynumber: 8.3 Consensus size: 25
1409 AAGACTTTTT
*
1419 TTTATTTTTCACTATTTATCTATTTA
1 TTTATTTTTAACTA-TTATCTATTTA
1445 TTTATTTTTAACTATTATCTATTTA
1 TTTATTTTTAACTATTATCTATTTA
* * *
1470 TTT-TTAATTATCATCTATTTATTTA-CTA
1 TTTATT--TT-T-AACTA-TTATCTATTTA
* * *
1498 TTTATTTTT--TTTTTCAACTA-TTA
1 TTTATTTTTAACTATT-ATCTATTTA
* *
1521 TCTACTTATTT-ACTATTTATCTTTTTA
1 TTTA-TT-TTTAACTA-TTATCTATTTA
* *
1548 TTTATTTTTAATTATCATCTATTTA
1 TTTATTTTTAACTATTATCTATTTA
* *
1573 TTTACTATTTATCT-TT-T-TATTTA
1 TTTA-TTTTTAACTATTATCTATTTA
* **
1596 -TTA-ATTTAGTTATTATCTATTTA
1 TTTATTTTTAACTATTATCTATTTA
1619 TTTATTT
1 TTTATTT
1626 ATTATTATTT
Statistics
Matches: 137, Mismatches: 25, Indels: 39
0.68 0.12 0.19
Matches are distributed among these distances:
20 6 0.04
21 2 0.01
22 6 0.04
23 21 0.15
24 8 0.06
25 35 0.26
26 31 0.23
27 11 0.08
28 9 0.07
29 8 0.06
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTATTTTTAACTATTATCTATTTA
Found at i:1548 original size:57 final size:58
Alignment explanation
Indices: 1431--1552 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 58
1421 TATTTTTCAC
* *
1431 TATTTATCTATTTATTTATTTTTAACTATTATCTATTTATTTTTAATTATCATCTATT
1 TATTTATCTATTTATTTATTTTTAACTATTATCTACTTATTTCTAATTATCATCTATT
* *
1489 TATTTA-CTATTTATTTTTTTTTTCAACTATTATCTACTTATTTACT-ATT-T-ATCTTTT
1 TATTTATCTATTTA-TTTATTTTT-AACTATTATCTACTTATTT-CTAATTATCATCTATT
1546 TATTTAT
1 TATTTAT
1553 TTTTAATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
57 19 0.34
58 15 0.27
59 21 0.38
60 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (58 bp):
TATTTATCTATTTATTTATTTTTAACTATTATCTACTTATTTCTAATTATCATCTATT
Found at i:1561 original size:82 final size:84
Alignment explanation
Indices: 1417--1590 Score: 257
Period size: 82 Copynumber: 2.1 Consensus size: 84
1407 AAAAGACTTT
* *
1417 TTTTTATTTTTCACTATTTATCTATTTATTTATTTTTAACTATTATCTATTTATTTTTAATTATC
1 TTTTT-TTTTTCACTATTTATCTACTTATTTATATTTAACTATTATCTATTTATTTTTAATTATC
1482 ATCTATTTATTTACTATTTA
65 ATCTATTTATTTACTATTTA
*
1502 TTTTTTTTTTCAACTA-TTATCTACTTATTTACTATTTATCT-TT-T-TATTTATTTTTAATTAT
1 TTTTTTTTTTC-ACTATTTATCTACTTATTTA-TATTTAACTATTATCTATTTATTTTTAATTAT
1563 CATCTATTTATTTACTATTTA
64 CATCTATTTATTTACTATTTA
*
1584 TCTTTTT
1 TTTTTTT
1591 ATTTATTAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
82 44 0.53
83 1 0.01
84 22 0.27
85 16 0.19
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (84 bp):
TTTTTTTTTTCACTATTTATCTACTTATTTATATTTAACTATTATCTATTTATTTTTAATTATCA
TCTATTTATTTACTATTTA
Found at i:1575 original size:44 final size:44
Alignment explanation
Indices: 1413--1622 Score: 220
Period size: 44 Copynumber: 4.8 Consensus size: 44
1403 ACCAAAAAGA
* * * *
1413 CTTTTT-TTTATTTTTCACTATTTATCTATTTATTTA-TTTTTAA
1 CTTTTTATTTATTTTTAATTA-TTATCTATTTATTTACTATTTAT
*
1456 CTATTATCTATTTATTTTTAATTATCATCTATTTATTTACTATTTA-
1 CT-TT-T-TATTTATTTTTAATTATTATCTATTTATTTACTATTTAT
* * *
1502 ---TTT-TTT-TTTTCAACTATTATCTACTTATTTACTATTTAT
1 CTTTTTATTTATTTTTAATTATTATCTATTTATTTACTATTTAT
*
1541 CTTTTTATTTATTTTTAATTATCATCTATTTATTTACTATTTAT
1 CTTTTTATTTATTTTTAATTATTATCTATTTATTTACTATTTAT
*
1585 CTTTTTATTTATTAATTTAGTTATTATCTATTTATTTA
1 CTTTTTATTTATT--TTTAATTATTATCTATTTATTTA
1623 TTTATTATTA
Statistics
Matches: 140, Mismatches: 14, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
38 28 0.20
39 3 0.02
40 1 0.01
41 1 0.01
42 4 0.03
43 5 0.04
44 44 0.31
45 1 0.01
46 36 0.26
47 17 0.12
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (44 bp):
CTTTTTATTTATTTTTAATTATTATCTATTTATTTACTATTTAT
Found at i:1597 original size:27 final size:27
Alignment explanation
Indices: 1518--1628 Score: 81
Period size: 27 Copynumber: 4.2 Consensus size: 27
1508 TTTTCAACTA
*
1518 TTATCTACTTATT-TACTATTTATCTT-T
1 TTATTTACTTATTAT-CTATTTAT-TTAT
* * *
1545 TTATTTA-TTTTTAAT-TATC-ATCTAT
1 TTATTTACTTATT-ATCTATTTATTTAT
*
1570 TTATTTAC-TATTTATCTTTTTATTTAT
1 TTATTTACTTA-TTATCTATTTATTTAT
* *
1597 TAATTTAGTTATTATCTATTTATTTAT
1 TTATTTACTTATTATCTATTTATTTAT
1624 TTATT
1 TTATT
1629 ATTATTTCTT
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
24 1 0.02
25 13 0.20
26 11 0.17
27 36 0.56
28 3 0.05
ACGTcount: A:0.25, C:0.08, G:0.01, T:0.66
Consensus pattern (27 bp):
TTATTTACTTATTATCTATTTATTTAT
Found at i:1611 original size:19 final size:19
Alignment explanation
Indices: 1589--1631 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1579 ATTTATCTTT
1589 TTATTTATTAATTTAGTTA
1 TTATTTATTAATTTAGTTA
* * *
1608 TTATCTATTTATTTATTTA
1 TTATTTATTAATTTAGTTA
1627 TTATT
1 TTATT
1632 ATTTCTTAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTTATTAATTTAGTTA
Found at i:1655 original size:4 final size:4
Alignment explanation
Indices: 1431--1628 Score: 76
Period size: 4 Copynumber: 50.0 Consensus size: 4
1421 TATTTTTCAC
* * * *
1431 TATT TATC TATT TATT TATT T-TT AACTAT TATC TATT TATT T-TT AATT
1 TATT TATT TATT TATT TATT TATT TA-T-T TATT TATT TATT TATT TATT
* * * ** * *
1479 ATCATC TATT TATT TA-C TATT TATT T-TT TTTT TCAAC TA-T TATC TACT
1 -T-ATT TATT TATT TATT TATT TATT TATT TATT T-ATT TATT TATT TATT
* * *
1527 TATT TA-C TATT TATCT T-TT TATT TATT T-TT AATT ATCATC TATT TATT
1 TATT TATT TATT TAT-T TATT TATT TATT TATT TATT -T-ATT TATT TATT
* * * *
1575 TA-C TATT TATCT T-TT TATT TATT AATT TAGT TA-T TATC TATT TATT
1 TATT TATT TAT-T TATT TATT TATT TATT TATT TATT TATT TATT TATT
1621 TATT TATT
1 TATT TATT
1629 ATTATTTCTT
Statistics
Matches: 141, Mismatches: 33, Indels: 40
0.66 0.15 0.19
Matches are distributed among these distances:
3 24 0.17
4 102 0.72
5 9 0.06
6 6 0.04
ACGTcount: A:0.26, C:0.09, G:0.01, T:0.65
Consensus pattern (4 bp):
TATT
Found at i:1714 original size:13 final size:14
Alignment explanation
Indices: 1698--1732 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1688 TTTATTTTTT
1698 TTATTTTTTTAAA-
1 TTATTTTTTTAAAC
1711 TTATTCTTTTTAAAC
1 TTATT-TTTTTAAAC
1726 TTATTTT
1 TTATTTT
1733 CCTATTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 10 0.50
15 5 0.25
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTTTTTAAAC
Done.