Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011738.1 Corchorus capsularis cultivar CVL-1 contig11759, 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: 10762
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9000 original size:19 final size:19
Alignment explanation
Indices: 8978--9015 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
8968 CTAAATAATA
8978 TTTT-AATTATTCCATTATT
1 TTTTAAATTATTCC-TTATT
8997 TTTTAAATTATTCCTTATT
1 TTTTAAATTATTCCTTATT
9016 AAATTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTAAATTATTCCTTATT
Found at i:9148 original size:22 final size:21
Alignment explanation
Indices: 9092--9207 Score: 79
Period size: 22 Copynumber: 5.2 Consensus size: 21
9082 GTCTCTATGT
*
9092 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
** * *
9113 TAATTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* *
9136 GGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
9158 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* * *
9182 GGTTATTAAAATTTCTTAGGT
1 GGTTATCAAAATTTCATAGGA
9203 GGTTA
1 GGTTA
9208 ATTATCACAA
Statistics
Matches: 71, Mismatches: 18, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
21 8 0.11
22 43 0.61
23 3 0.04
24 17 0.24
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:9267 original size:22 final size:21
Alignment explanation
Indices: 9239--9612 Score: 129
Period size: 22 Copynumber: 16.9 Consensus size: 21
9229 TGTTATCAAA
*
9239 GAGGTTATCAAAATGTCATAG
1 GAGGTTATCAAAATTTCATAG
*
9260 CGAGGTTAT-AAGAATTACATAG
1 -GAGGTTATCAA-AATTTCATAG
* * *
9282 TGTGGTTAACAAAATTTTATTAG
1 -GAGGTTATCAAAATTTCA-TAG
* *
9305 GAGGTTA-CTAATATTTCATGGG
1 GAGGTTATC-AAAATTTCAT-AG
9327 GAGGTTATCAAAATTTCATATG
1 GAGGTTATCAAAATTTCATA-G
* *
9349 AAGGTTATAAAAGTCTCAATTTCATA-
1 GAGGTTAT-CAA-----AATTTCATAG
* * * *
9375 -AGGAGTACCAAAATTTGATAT
1 GAGG-TTATCAAAATTTCATAG
*
9396 AAGGTTATC-AAATCTT-ATA-
1 GAGGTTATCAAAAT-TTCATAG
* *
9415 AAGTGATTATCGAAATTTCATAG
1 GAG-G-TTATCAAAATTTCATAG
9438 AGATCGGATTATCAAAATTT-ATAG
1 -GA--GG-TTATCAAAATTTCATAG
* *
9462 GAAGATTATCAAAATTACATAG
1 G-AGGTTATCAAAATTTCATAG
* * *
9484 CATTGTTATCAAAATTTCAAAG
1 GA-GGTTATCAAAATTTCATAG
* *
9506 CGAGGTTATCAAAATTACATAAT
1 -GAGGTTATCAAAATTTCAT-AG
* *
9529 GTGATTAT-AAGAATTTCATAAAG
1 GAGGTTATCAA-AATTTCAT--AG
* * * *
9552 G-GGTCAACAAAATTTTATAAA
1 GAGGTTATCAAAATTTCAT-AG
*
9573 GAGGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCAT-AG
*
9595 GAGGTTATCAAATTTTCA
1 GAGGTTATCAAAATTTCA
9613 AAATGCGATT
Statistics
Matches: 270, Mismatches: 48, Indels: 68
0.70 0.12 0.18
Matches are distributed among these distances:
19 3 0.01
20 16 0.06
21 33 0.12
22 166 0.61
23 16 0.06
24 6 0.02
25 18 0.07
26 3 0.01
28 9 0.03
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (21 bp):
GAGGTTATCAAAATTTCATAG
Found at i:9563 original size:44 final size:43
Alignment explanation
Indices: 9489--9637 Score: 111
Period size: 44 Copynumber: 3.4 Consensus size: 43
9479 CATAGCATTG
* * * * *
9489 TTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGA
1 TTAT-AAAATTTCATAA-AGAGGTCAACAAAATTTCATAATGAGA
* * * *
9533 TTATAAGAATTTCATAAAGGGGTCAACAAAATTTTATAAAGAGG
1 TTATAA-AATTTCATAAAGAGGTCAACAAAATTTCATAATGAGA
* * * * *
9577 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGCGA
1 TTAT-AAAATTTCATAAAGAGGTCAACAAAATTTCATAATGAGA
*
9621 TTACAAAAATTTCATAA
1 TTA-TAAAATTTCATAA
9638 TGGTATTTCT
Statistics
Matches: 82, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
43 2 0.02
44 76 0.93
45 4 0.05
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (43 bp):
TTATAAAATTTCATAAAGAGGTCAACAAAATTTCATAATGAGA
Found at i:9679 original size:22 final size:22
Alignment explanation
Indices: 9653--9968 Score: 69
Period size: 22 Copynumber: 14.7 Consensus size: 22
9643 TTTCTGGGAA
9653 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* * *
9675 GGTTA-CCAAA--T--TAGGAA
1 GGTTATCAAAATTTCATAGTAT
* * *
9692 GGTTATTAAACTTT--TATTAT
1 GGTTATCAAAATTTCATAGTAT
* * *
9712 GGAGTAATCAAAATTTCATAATTT
1 GG-TTA-TCAAAATTTCATAGTAT
* * *
9736 AGTTTTCAAAATTTCATAAG-AG
1 GGTTATCAAAATTTCAT-AGTAT
9758 GGTTATCAAAAATTTCATAGTAT
1 GGTTATC-AAAATTTCATAGTAT
* *
9781 -GTAGATCAAAATTTCATAATGA-
1 GGT-TATCAAAATTTCATAGT-AT
* * *
9803 GGTTATCAAGAA-ATCATTGGGA-
1 GGTTATCAA-AATTTCA-TAGTAT
9825 GGTTATCAAAA-TT--T-GTA-
1 GGTTATCAAAATTTCATAGTAT
* * *
9842 -GTTATCAACATTTTATAAG-AA
1 GGTTATCAAAATTTCAT-AGTAT
* * * *
9863 AGTTATCAAAATTTTATAGGAA
1 GGTTATCAAAATTTCATAGTAT
* * * *
9885 GATTTATCAAAATTTTATAGGAA
1 G-GTTATCAAAATTTCATAGTAT
* *
9908 GATTTATCAAAATTTCATAGCGAT
1 G-GTTATCAAAATTTCATAG-TAT
* * *
9932 -GTTATCACAATTTCGTAGTGT
1 GGTTATCAAAATTTCATAGTAT
* *
9953 GATTGTCAAAATTTCA
1 GGTTATCAAAATTTCA
9969 AAATGTATTA
Statistics
Matches: 221, Mismatches: 47, Indels: 52
0.69 0.15 0.16
Matches are distributed among these distances:
16 9 0.04
17 13 0.06
18 3 0.01
19 2 0.01
20 7 0.03
21 13 0.06
22 106 0.48
23 61 0.28
24 7 0.03
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:9891 original size:23 final size:23
Alignment explanation
Indices: 9843--9927 Score: 127
Period size: 23 Copynumber: 3.7 Consensus size: 23
9833 AAATTTGTAG
* * *
9843 TTATCAACATTTTATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
9865 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
9888 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
*
9911 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
9928 CGATGTTATC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 18 0.31
23 40 0.69
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:9937 original size:45 final size:43
Alignment explanation
Indices: 9841--9944 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 43
9831 CAAAATTTGT
* *
9841 AGTTATCAACATTTTATAAGAAAGTTATCAAAATTTTATAGGA
1 AGTTATCAAAATTTTATAAGAAAGTTATCAAAATTTCATAGGA
* *
9884 AGATTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGA
1 AG--TTATCAAAATTTTATAAGAA-AGTTATCAAAATTTCATAG-GA
* *
9931 TGTTATCACAATTT
1 AGTTATCAAAATTT
9945 CGTAGTGTGA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
43 2 0.04
45 29 0.57
46 17 0.33
47 3 0.06
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (43 bp):
AGTTATCAAAATTTTATAAGAAAGTTATCAAAATTTCATAGGA
Found at i:10153 original size:22 final size:22
Alignment explanation
Indices: 10128--10234 Score: 74
Period size: 22 Copynumber: 4.9 Consensus size: 22
10118 TTCCTTAGGG
*
10128 AGGTTAACAAAATTTCATAAAA
1 AGGTTATCAAAATTTCATAAAA
** *
10150 AGGTTAAAAAAAATT-ATAAAA
1 AGGTTATCAAAATTTCATAAAA
* * * **
10171 AGATTCTCGAAATTTCAT-AGT
1 AGGTTATCAAAATTTCATAAAA
* * **
10192 AGCGTTGTTAAAATTTCATAGGA
1 AG-GTTATCAAAATTTCATAAAA
10215 AGGTTATCAAAATTTCATAA
1 AGGTTATCAAAATTTCATAA
10235 TGTGATCATA
Statistics
Matches: 63, Mismatches: 19, Indels: 6
0.72 0.22 0.07
Matches are distributed among these distances:
21 18 0.29
22 42 0.67
23 3 0.05
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAAAA
Done.