Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011660.1 Corchorus capsularis cultivar CVL-1 contig11681, 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: 21251
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:477 original size:37 final size:37
Alignment explanation
Indices: 382--477 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 37
372 AATTTGACTT
* *
382 TTTGTTTCTAACGTCCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCTTATTTAATTTTGCCTTTTGTC
* *
419 TTTGTTTCCAATCAT-TGTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAA-CGTCT-TATTTAATTTTGCCTTTTGTC
457 TTT-TTCTCCAACGTCTTATTT
1 TTTGTT-TCCAACGTCTTATTT
478 GGGCTTAGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
37 19 0.38
38 31 0.62
ACGTcount: A:0.15, C:0.18, G:0.09, T:0.58
Consensus pattern (37 bp):
TTTGTTTCCAACGTCTTATTTAATTTTGCCTTTTGTC
Found at i:643 original size:19 final size:20
Alignment explanation
Indices: 616--653 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
606 TACTATTATT
616 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
636 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
654 ACTGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:875 original size:22 final size:21
Alignment explanation
Indices: 819--1001 Score: 125
Period size: 22 Copynumber: 8.2 Consensus size: 21
809 GTCTCTCTGT
*
819 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
*
840 TGGTTAGT-ATAATTTCATGAGGA
1 -GGTTA-TCAAAATTTCAT-AGGA
* * *
863 GGTTATCAGAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
885 GGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATA-GGA
* *
907 AGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
929 GGTTACCAAAATTTCATAGGATTA
1 GGTTATCAAAATTTCATAGG---A
* ** *
953 GGTTATTAAAATTTTTTAGGTT
1 GGTTATCAAAATTTCATAGG-A
**
975 GGTTATTGAAATTTCATAGGA
1 GGTTATCAAAATTTCATAGGA
996 TGGTTA
1 -GGTTA
1002 ATTATCACAA
Statistics
Matches: 127, Mismatches: 24, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
21 5 0.04
22 101 0.80
23 5 0.04
24 16 0.13
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:933 original size:66 final size:66
Alignment explanation
Indices: 816--947 Score: 144
Period size: 66 Copynumber: 2.0 Consensus size: 66
806 CTTGTCTCTC
* * * * *
816 TGTGGTTATCAAAATTTCATAAGATGGTTAGTATAATTTCATGAGGAGGTTATCAGAATTCCATA
1 TGTGGTTACCAAAATTTCATAAGATAGTTAGTAAAATTTCATGAGGAGGTTACCAAAATTCCATA
881 G
66 G
* * *
882 TGTGGTTACCAAAATTTCATATGGA-AGTTA-TCAAAATTTCAT-AGTGTGGTTACCAAAATTTC
1 TGTGGTTACCAAAATTTCATA-AGATAGTTAGT-AAAATTTCATGAG-GAGGTTACCAAAATTCC
944 ATAG
63 ATAG
948 GATTAGGTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
65 3 0.05
66 50 0.91
67 2 0.04
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (66 bp):
TGTGGTTACCAAAATTTCATAAGATAGTTAGTAAAATTTCATGAGGAGGTTACCAAAATTCCATA
G
Found at i:978 original size:46 final size:44
Alignment explanation
Indices: 820--1001 Score: 156
Period size: 44 Copynumber: 4.1 Consensus size: 44
810 TCTCTCTGTG
* ** * *
820 GTTATCAAAATTTCATAAG-ATGGTTAGTATAATTTCATGAGGA-G
1 GTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT-AGGATA
* *
864 GTTATCAGAATTCCATAGTGTGGTTACCAAAATTTCATATGGA-A
1 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA-GGATA
908 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATTA
1 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGA-TA
* ** *** *
953 GGTTATTAAAATTTTTTAG-GTTGGTTATTGAAATTTCATAGGATG
1 -GTTATCAAAATTTCATAGTG-TGGTTACCAAAATTTCATAGGATA
998 GTTA
1 GTTA
1002 ATTATCACAA
Statistics
Matches: 116, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
43 6 0.05
44 73 0.63
45 3 0.03
46 34 0.29
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATA
Found at i:1062 original size:22 final size:22
Alignment explanation
Indices: 1037--1344 Score: 119
Period size: 22 Copynumber: 13.8 Consensus size: 22
1027 ATCAAAGAGA
* *
1037 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
1059 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
1081 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
1103 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* * *
1125 TTGTCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
1147 TTATCAAAATTTCATA-TGAATG
1 TTATCAAAATTTCATAGTG-AGG
* * *
1169 TTATAAAAGTCTCAATTTCATA-AGAAG
1 TTAT-CAA-----AATTTCATAGTGAGG
** * *
1196 -TGCCAAAATTTGATAG-AAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
1216 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* * * *
1237 TTATCGACATTTCATAGAGATCAGA
1 TTATCAAAATTTCAT--AG-TGAGG
**
1262 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* * * *
1284 TTAGCAAAATTTCAAAGCGAGT
1 TTATCAAAATTTCATAGTGAGG
* * * *
1306 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
1328 TTATCAAAATTTCATAG
1 TTATCAAAATTTCATAG
1345 AGGGGTCAAA
Statistics
Matches: 207, Mismatches: 59, Indels: 40
0.68 0.19 0.13
Matches are distributed among these distances:
20 19 0.09
21 15 0.07
22 131 0.63
23 10 0.05
24 2 0.01
25 17 0.08
26 1 0.00
27 2 0.01
28 10 0.05
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:1397 original size:21 final size:21
Alignment explanation
Indices: 1359--1404 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
1349 GTCAAAAATT
1359 TTTTATAAAGATGTTATCAAAA
1 TTTTATAAAGATGTTATC-AAA
1381 TTTTATAAAGA-GTTATCAAA
1 TTTTATAAAGATGTTATCAAA
1401 TTTT
1 TTTT
1405 CAAAATGCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (21 bp):
TTTTATAAAGATGTTATCAAA
Found at i:1473 original size:22 final size:21
Alignment explanation
Indices: 1444--1981 Score: 219
Period size: 22 Copynumber: 25.0 Consensus size: 21
1434 GTATTTCTGG
1444 GGAGGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
* *
1465 GTATGGTTA-CCAAA--T--TA
1 GGA-GGTTATCAAAATTTCATA
* * *
1482 GGAAGGTTATTAAACTTTTATTA
1 GG-AGGTTATCAAAATTTCA-TA
*
1505 TGGA-GTAATCAAAATTTCA-A
1 -GGAGGTTATCAAAATTTCATA
*
1525 GGAGGATATCAAAATTTCA-A
1 GGAGGTTATCAAAATTTCATA
* *
1545 GGAGGATATCACAATTTCATA
1 GGAGGTTATCAAAATTTCATA
* *
1566 GTTTA-GTTTTCAAAATTTCATA
1 G--GAGGTTATCAAAATTTCATA
*
1588 AGAGGGTTATCAAAATTTCATA
1 GGA-GGTTATCAAAATTTCATA
* * *
1610 GGGAGATTAACAAAATTTCAGAA
1 -GGAGGTTATCAAAATTTCA-TA
** * **
1633 TAAGGTTATTAAAAAATCATA
1 GGAGGTTATCAAAATTTCATA
1654 GGGAGGTTATCAAAA-TT--T-
1 -GGAGGTTATCAAAATTTCATA
* *
1672 GTA-GTTATCAAGATTTCATAA
1 GGAGGTTATCAAAATTTCAT-A
* * *
1693 GAAAGTTATCAAAATTTTATA
1 GGAGGTTATCAAAATTTCATA
*
1714 GGGAGGTTTATCAAAATTTTATA
1 -GGAGG-TTATCAAAATTTCATA
*
1737 GGAAGATTTATCAAAATTTCATA
1 GG-AG-GTTATCAAAATTTCATA
* *
1760 GCAAGGTTATCACAATTTCATA
1 G-GAGGTTATCAAAATTTCATA
* * *
1782 GTGTGATTATCAAAATTTCAGA
1 G-GAGGTTATCAAAATTTCATA
* *
1804 GTGTGATTA-CTAACAA-TTCATA
1 G-GAGGTTATC-AA-AATTTCATA
* * * *
1826 TGGAGGTTTTTAAATTTTCGTAA
1 -GGAGGTTATCAAAATTTCAT-A
* * * *
1849 CGTGGTTATCAATATATCATA
1 GGAGGTTATCAAAATTTCATA
* *
1870 TGGAGGTTATCAACATCTCAATA
1 -GGAGGTTATCAAAATTTC-ATA
* * *
1893 GTGTTGGTTATCAGAATTTCATTG
1 G-G-AGGTTATCAAAATTTCA-TA
*
1917 GGAAGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
* * *
1938 TTGAGGTCT-TCAAAATTCCTTA
1 -GGAGGT-TATCAAAATTTCATA
*
1960 GGGAGGTTAACAAAATTTCATA
1 -GGAGGTTATCAAAATTTCATA
1982 AGAAGTTTAA
Statistics
Matches: 383, Mismatches: 91, Indels: 85
0.69 0.16 0.15
Matches are distributed among these distances:
16 9 0.02
17 12 0.03
18 3 0.01
19 6 0.02
20 35 0.09
21 18 0.05
22 230 0.60
23 54 0.14
24 16 0.04
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
GGAGGTTATCAAAATTTCATA
Found at i:1537 original size:20 final size:20
Alignment explanation
Indices: 1512--1563 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1502 TTATGGAGTA
1512 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
1532 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
1552 ATCACAATTTCA
1 ATCAAAATTTCA
1564 TAGTTTAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:1728 original size:23 final size:23
Alignment explanation
Indices: 1676--1782 Score: 119
Period size: 23 Copynumber: 4.7 Consensus size: 23
1666 AAATTTGTAG
* * *
1676 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTCATAGGAAGGT
* *
1698 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGAAGGT
* *
1721 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGAAGGT
*
1744 TTATCAAAATTTCATAGCAAGG-
1 TTATCAAAATTTCATAGGAAGGT
*
1766 TTATCACAATTTCATAG
1 TTATCAAAATTTCATAG
1783 TGTGATTATC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
22 33 0.45
23 40 0.55
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGAAGGT
Found at i:12873 original size:2 final size:2
Alignment explanation
Indices: 12866--12890 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12856 TAAACAATAA
12866 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12891 CACTAAAGTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13066 original size:31 final size:31
Alignment explanation
Indices: 13014--13097 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
13004 TGCTATAAAT
* *
13014 CTTTTATTTTAG-GAGGATCAATACT-AGAAAA
1 CTTTTACTTTAGTG-GGGTCAATA-TGAGAAAA
*
13045 -TTTTCACTTTAGTGGGGTCAATATGATAAAA
1 CTTTT-ACTTTAGTGGGGTCAATATGAGAAAA
*
13076 CTTTTATTTTAGTGGGGTCAAT
1 CTTTTACTTTAGTGGGGTCAAT
13098 TGATAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 5 0.11
31 35 0.78
32 5 0.11
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (31 bp):
CTTTTACTTTAGTGGGGTCAATATGAGAAAA
Done.