Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013689.1 Corchorus capsularis cultivar CVL-1 contig13710, 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: 40784
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:9250 original size:14 final size:14
Alignment explanation
Indices: 9233--9259 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9223 CTTCTTATAT
9233 CTTACTTTAATAAC
1 CTTACTTTAATAAC
9247 CTTACTTTAATAA
1 CTTACTTTAATAA
9260 TGGAATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (14 bp):
CTTACTTTAATAAC
Found at i:10000 original size:22 final size:22
Alignment explanation
Indices: 9975--10158 Score: 120
Period size: 22 Copynumber: 8.4 Consensus size: 22
9965 CAATCAAACT
*
9975 AAAATTACATAGGAAGGTTATC
1 AAAATTTCATAGGAAGGTTATC
* *
9997 AAAATTTCATAGTG-CGGTTACC
1 AAAATTTCATAG-GAAGGTTATC
* **
10019 AAAATTTCATATGAAAATTATC
1 AAAATTTCATAGGAAGGTTATC
* * *
10041 AAAACTTCATAGTGTA-GTTACC
1 AAAATTTCATAG-GAAGGTTATC
** * *
10063 AAAATTTCATAAAAAGATTATT
1 AAAATTTCATAGGAAGGTTATC
* * *
10085 AAAATTTCCTAGGGAGGTTAAC
1 AAAATTTCATAGGAAGGTTATC
* * *
10107 AAAATTTTATACGAAAGTTATC
1 AAAATTTCATAGGAAGGTTATC
* * ***
10129 GAAATTTTATAGTTTGGTTATC
1 AAAATTTCATAGGAAGGTTATC
10151 AAAATTTC
1 AAAATTTC
10159 TTAAAAAGAT
Statistics
Matches: 117, Mismatches: 41, Indels: 8
0.70 0.25 0.05
Matches are distributed among these distances:
21 2 0.02
22 112 0.96
23 3 0.03
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTTATC
Found at i:10041 original size:44 final size:43
Alignment explanation
Indices: 9992--10158 Score: 172
Period size: 44 Copynumber: 3.8 Consensus size: 43
9982 CATAGGAAGG
*
9992 TTATCAAAATTTCATAGTGCGGTTACCAAAATTTCATATGAAAA
1 TTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA-GAAAA
* * *
10036 TTATCAAAACTTCATAGTGTAGTTACCAAAATTTCATAAAAAGA
1 TTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGAAA-A
* * * * * * *
10080 TTATTAAAATTTCCTAGGGAGGTTAACAAAATTTTATACGAAAG
1 TTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA-GAAAA
* * * *
10124 TTATCGAAATTTTATAGTTTGGTTATCAAAATTTC
1 TTATCAAAATTTCATAGTGTGGTTACCAAAATTTC
10159 TTAAAAAGAT
Statistics
Matches: 98, Mismatches: 23, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
43 3 0.03
44 92 0.94
45 3 0.03
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (43 bp):
TTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGAAAA
Found at i:10141 original size:88 final size:88
Alignment explanation
Indices: 9992--10189 Score: 234
Period size: 88 Copynumber: 2.2 Consensus size: 88
9982 CATAGGAAGG
* * * * *
9992 TTATCAAAATTTCATAGTGCGGTTACCAAAATTTCATATGAAAATTATCAAAACTTCATAGTGTA
1 TTATAAAAATTTCATAGGGAGGTTAACAAAATTTCATACGAAAATTATCAAAACTTCATAGTGTA
10057 GTTACCAAAATTTCATAAAAAGA
66 GTTACCAAAATTTCATAAAAAGA
* * * * * * * * *
10080 TTATTAAAATTTCCTAGGGAGGTTAACAAAATTTTATACGAAAGTTATCGAAATTTTATAGTTTG
1 TTATAAAAATTTCATAGGGAGGTTAACAAAATTTCATACGAAAATTATCAAAACTTCATAGTGTA
* *
10145 GTTATCAAAATTTCTTAAAAAGA
66 GTTACCAAAATTTCATAAAAAGA
* *
10168 TTAAAAAAAATTCATAGGGAGG
1 TTATAAAAATTTCATAGGGAGG
10190 GAATTTTTCA
Statistics
Matches: 91, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (88 bp):
TTATAAAAATTTCATAGGGAGGTTAACAAAATTTCATACGAAAATTATCAAAACTTCATAGTGTA
GTTACCAAAATTTCATAAAAAGA
Found at i:10406 original size:22 final size:22
Alignment explanation
Indices: 10326--10424 Score: 71
Period size: 22 Copynumber: 4.5 Consensus size: 22
10316 CATAGGAAGG
* *
10326 TTATCAAATTTTTATGGTGT-A
1 TTATCAAAATTTTATAGTGTGA
* * *
10347 GTTATTAAAATTTTGATAGTGCGG
1 -TTATCAAAATTTT-ATAGTGTGA
* *
10371 TTA-C-CAATTATATAGTGTGA
1 TTATCAAAATTTTATAGTGTGA
*
10391 TTATCAAAATTTTATA-TGGAGA
1 TTATCAAAATTTTATAGT-GTGA
10413 TTATCAAAATTT
1 TTATCAAAATTT
10425 CACATTAAAG
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
20 10 0.17
21 7 0.12
22 34 0.58
23 8 0.14
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.44
Consensus pattern (22 bp):
TTATCAAAATTTTATAGTGTGA
Found at i:10492 original size:21 final size:23
Alignment explanation
Indices: 10457--10513 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
10447 CATAGTGTGA
10457 TAATCAAATTTTCAT-AGGAGGT
1 TAATCAAATTTTCATAAGGAGGT
* *
10479 TAATTAAA-TTTCATAATGAGGT
1 TAATCAAATTTTCATAAGGAGGT
*
10501 T-ATCAAACTTTCA
1 TAATCAAATTTTCA
10514 CAGTGTGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (23 bp):
TAATCAAATTTTCATAAGGAGGT
Found at i:10503 original size:65 final size:66
Alignment explanation
Indices: 10382--10520 Score: 151
Period size: 65 Copynumber: 2.1 Consensus size: 66
10372 TACCAATTAT
* *
10382 ATAGTGTGATTATCAAAATTTTATATGGAGATTATCAAAATTTCACATTAAAGTTATCGAAA-TT
1 ATAGTGTGATAATCAAAATTTTATATGGAGATTATCAAAATTTCACAATAAAGTTATC-AAACTT
10446 TC
65 TC
* * * * *
10448 ATAGTGTGATAATC-AAATTTTCATA-GGAGGTTAAT-TAAATTTCATAATGAGGTTATCAAACT
1 ATAGTGTGATAATCAAAATTTT-ATATGGAGATT-ATCAAAATTTCACAATAAAGTTATCAAACT
10510 TTC
64 TTC
*
10513 ACAGTGTG
1 ATAGTGTG
10521 GTTATCAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
64 3 0.05
65 41 0.66
66 18 0.29
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (66 bp):
ATAGTGTGATAATCAAAATTTTATATGGAGATTATCAAAATTTCACAATAAAGTTATCAAACTTT
C
Found at i:15824 original size:15 final size:15
Alignment explanation
Indices: 15788--15816 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15778 ATTATTTTTA
15788 AATTATAATATATAT
1 AATTATAATATATAT
15803 AATTATAATA-ATAT
1 AATTATAATATATAT
15817 TATTTATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATAATATATAT
Found at i:17306 original size:15 final size:15
Alignment explanation
Indices: 17286--17317 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
17276 AAACGTGTAA
17286 TAATCATCACGGTTT
1 TAATCATCACGGTTT
17301 TAATCATCACGGTTT
1 TAATCATCACGGTTT
17316 TA
1 TA
17318 GGTCAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (15 bp):
TAATCATCACGGTTT
Found at i:19126 original size:2 final size:2
Alignment explanation
Indices: 19119--19145 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19109 CATAATAAAT
19119 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19146 GCCTAATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20904 original size:3 final size:3
Alignment explanation
Indices: 20896--20921 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20886 CCTCAAAAAG
20896 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
20922 CTAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:22777 original size:2 final size:2
Alignment explanation
Indices: 22770--22794 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22760 CGAATCCGTT
22770 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22795 TCGGAGCGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23305 original size:183 final size:183
Alignment explanation
Indices: 22987--23357 Score: 636
Period size: 183 Copynumber: 2.0 Consensus size: 183
22977 TTTTAAATGG
22987 ATATTTTCTCCATAAACGGATTAGGTAGAGCAATTACGGATAATAGTCCATGGTGACGAGGCAAA
1 ATATTTTCTCCATAAACGGATTAGGTAGAGCAATTACGGATAATAGTCCATGGTGACGAGGCAAA
* * *
23052 TTTGGATATTGCTTCTAAGAAATAGGCGGATATATGGCGGATACGAATATCACAAATTTTAAACG
66 TTTGGATATTGCTTCTAAAAAATAGGCGGATATATGACGGATACGAATATCACAAATTTAAAACG
*
23117 GATACGAATTCGGATATTGAGATTTTGGAATATATCTGAACTGCTGTCTCCCT
131 GATACGAATTCGGATATTGAGATTTTGGAATATATCTGAACCGCTGTCTCCCT
* * *
23170 ATATTTTCTCCATAAACGGATTAGGTAGAGCAATTATGGATAATAGTCCATGGTGACGGGGCAGA
1 ATATTTTCTCCATAAACGGATTAGGTAGAGCAATTACGGATAATAGTCCATGGTGACGAGGCAAA
* *
23235 TTTGGATATTGCTTCTAAAAAATAGGCGGATATATGACGGATGC-AGATATCACAAATTTAAAAT
66 TTTGGATATTGCTTCTAAAAAATAGGCGGATATATGACGGATACGA-ATATCACAAATTTAAAAC
*
23299 GGATACGAATTCGGATATTGAGATTTTGGAATATATCTGAACCGTTGTCTCCCT
130 GGATACGAATTCGGATATTGAGATTTTGGAATATATCTGAACCGCTGTCTCCCT
23353 ATATT
1 ATATT
23358 CAATAGGTCT
Statistics
Matches: 177, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
182 1 0.01
183 176 0.99
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (183 bp):
ATATTTTCTCCATAAACGGATTAGGTAGAGCAATTACGGATAATAGTCCATGGTGACGAGGCAAA
TTTGGATATTGCTTCTAAAAAATAGGCGGATATATGACGGATACGAATATCACAAATTTAAAACG
GATACGAATTCGGATATTGAGATTTTGGAATATATCTGAACCGCTGTCTCCCT
Found at i:23840 original size:31 final size:31
Alignment explanation
Indices: 23802--23866 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
23792 AACTGAACTA
23802 ACTCAAACATCCAAGATC-AAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAA-ATCTGGAG
23833 ACTCAAACATCCAAGATCTAAAAATCTGGAG
1 ACTCAAACATCCAAGATCTAAAAATCTGGAG
23864 ACT
1 ACT
23867 GATAACCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAAATCTGGAG
Done.