Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009755.1 Corchorus capsularis cultivar CVL-1 contig09776, 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: 32710
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1546 original size:109 final size:109
Alignment explanation
Indices: 1355--1577 Score: 401
Period size: 109 Copynumber: 2.0 Consensus size: 109
1345 CACTTACGCA
* * *
1355 ATTAAGGTGCATTGCATACTCGTAATTTTGGTTCGTTACTGACACGAAGGTTGATATTTGTGATA
1 ATTAAGATGCATTGCATACTCATAATTTTGGTTCGTGACTGACACGAAGGTTGATATTTGTGATA
1420 CCGAACCCCGTGTGCTCCACTCCCCAAAAACAGCGGAGTAATTT
66 CCGAACCCCGTGTGCTCCACTCCCCAAAAACAGCGGAGTAATTT
*
1464 ATTAAGATGCTTTGCATACTCATAATTTTGGTTCGTGACTGACACGAAGGTTGATATTTGTGATA
1 ATTAAGATGCATTGCATACTCATAATTTTGGTTCGTGACTGACACGAAGGTTGATATTTGTGATA
*
1529 CCGAACCCCGTGTGCTCCACTCCCCAAAAACAGCGGAGTAGTTT
66 CCGAACCCCGTGTGCTCCACTCCCCAAAAACAGCGGAGTAATTT
1573 ATTAA
1 ATTAA
1578 ATTCCTCTTT
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (109 bp):
ATTAAGATGCATTGCATACTCATAATTTTGGTTCGTGACTGACACGAAGGTTGATATTTGTGATA
CCGAACCCCGTGTGCTCCACTCCCCAAAAACAGCGGAGTAATTT
Found at i:4859 original size:22 final size:22
Alignment explanation
Indices: 4834--4896 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
4824 GGTTACCAAA
*
4834 GAGGTTATCAAAATATCATAGC
1 GAGGTTATCAAAATTTCATAGC
*
4856 GAGGTTAT-AAGAATTTCATAGT
1 GAGGTTATCAA-AATTTCATAGC
* *
4878 GTGGTTAACAAAATTTCAT
1 GAGGTTATCAAAATTTCAT
4897 TAAATATTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGC
Found at i:4938 original size:22 final size:21
Alignment explanation
Indices: 4913--5175 Score: 122
Period size: 22 Copynumber: 11.8 Consensus size: 21
4903 TTTCATGGGG
4913 AGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* * *
4935 AGGTTATAAAAATCTCAATTTCATA
1 AGGTTATCAAAATTTC-A--T-AGA
* * *
4960 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
4982 AGGTTATC-AAATCTCATAGA
1 AGGTTATCAAAATTTCATAGA
* *
5002 ATGATTATCGAAATTTCATAGA
1 A-GGTTATCAAAATTTCATAGA
5024 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
* *
5049 AGATTATCAAAATTCCATAG-
1 AGGTTATCAAAATTTCATAGA
* *
5069 TGTTGTTATCAAAATTACATA-A
1 AG--GTTATCAAAATTTCATAGA
* *
5091 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * *
5114 GGGGTCAACAAAATTTTATA-A
1 -AGGTTATCAAAATTTCATAGA
*
5135 AGAGTTTATCAAAATTTCATAAA
1 AG-G-TTATCAAAATTTCATAGA
*
5158 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
5176 AAATGTGATT
Statistics
Matches: 184, Mismatches: 35, Indels: 44
0.70 0.13 0.17
Matches are distributed among these distances:
20 13 0.07
21 24 0.13
22 104 0.57
23 7 0.04
24 9 0.05
25 18 0.10
26 9 0.05
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:5502 original size:38 final size:38
Alignment explanation
Indices: 5451--5559 Score: 146
Period size: 38 Copynumber: 2.9 Consensus size: 38
5441 ATAATGAGGT
*
5451 TATCAAAAAATCATAGGGAGGTTATCAAAATTTGTAGC
1 TATCAAGAAATCATAGGGAGGTTATCAAAATTTGTAGC
* *
5489 TATCAAGAAATCATAGGGAGTTTATCAAAATTTGTAGT
1 TATCAAGAAATCATAGGGAGGTTATCAAAATTTGTAGC
** * * *
5527 TATCAAGATTTCATAAGAAAGTTATCAAAATTT
1 TATCAAGAAATCATAGGGAGGTTATCAAAATTT
5560 CATAGGGAGG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (38 bp):
TATCAAGAAATCATAGGGAGGTTATCAAAATTTGTAGC
Found at i:5578 original size:23 final size:22
Alignment explanation
Indices: 5295--5651 Score: 185
Period size: 22 Copynumber: 16.8 Consensus size: 22
5285 AGATTTCAAT
*
5295 GAGGATATCAAAA-TTC--AGG
1 GAGGTTATCAAAATTTCATAGG
* **
5314 GAGGATATCAAAATTTCATACA
1 GAGGTTATCAAAATTTCATAGG
* * *
5336 AAGGTTATCATAATTTCATAGTT
1 GAGGTTATCAAAATTTCATAG-G
* * * *
5359 TA-GTTTTCAAAATTTCACA-A
1 GAGGTTATCAAAATTTCATAGG
*
5379 GAGGGCTATCAAAATTTCATA-G
1 GA-GGTTATCAAAATTTCATAGG
* * *
5401 TATGTAGATCAAAATTTCATAGG
1 GAGGT-TATCAAAATTTCATAGG
* * **
5424 GAGATTAACAAAATTTCATAAT
1 GAGGTTATCAAAATTTCATAGG
**
5446 GAGGTTATCAAAAAATCATAGG
1 GAGGTTATCAAAATTTCATAGG
5468 GAGGTTATCAAAA-TT--T--G
1 GAGGTTATCAAAATTTCATAGG
* * *
5485 TA-GCTATCAAGAA-ATCATAGG
1 GAGGTTATCAA-AATTTCATAGG
*
5506 GAGTTTATCAAAA-TT--T--G
1 GAGGTTATCAAAATTTCATAGG
* * *
5523 TA-GTTATCAAGATTTCATAAG
1 GAGGTTATCAAAATTTCATAGG
* *
5544 AAAGTTATCAAAATTTCATAGG
1 GAGGTTATCAAAATTTCATAGG
*
5566 GAGGTTTATCAAAATTTTATAGG
1 GAGG-TTATCAAAATTTCATAGG
* * *
5589 AAGATTTATCAAAATTTCATAGC
1 GAG-GTTATCAAAATTTCATAGG
* *
5612 GAGGTTATCACAATTTCATAGT
1 GAGGTTATCAAAATTTCATAGG
* *
5634 GTGATTATCAAAATTTCA
1 GAGGTTATCAAAATTTCA
5652 AAGTGTGATT
Statistics
Matches: 254, Mismatches: 62, Indels: 41
0.71 0.17 0.11
Matches are distributed among these distances:
16 15 0.06
17 9 0.04
19 17 0.07
20 4 0.02
21 9 0.04
22 159 0.63
23 41 0.16
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.33
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAGG
Found at i:5673 original size:22 final size:23
Alignment explanation
Indices: 5594--5671 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 23
5584 ATAGGAAGAT
* * * *
5594 TTATCAA-AATTTCATAGCGAGG
1 TTATCAACAATTTCAAAGTGTGA
*
5616 TTATC-ACAATTTCATAGTGTGA
1 TTATCAACAATTTCAAAGTGTGA
5638 TTATCAA-AATTTCAAAGTGTGA
1 TTATCAACAATTTCAAAGTGTGA
5660 TTA-CTAACAATT
1 TTATC-AACAATT
5672 CATATGGAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.04
22 41 0.85
23 5 0.10
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (23 bp):
TTATCAACAATTTCAAAGTGTGA
Found at i:7192 original size:21 final size:22
Alignment explanation
Indices: 7157--7204 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
7147 TTCCTTAGGG
* *
7157 AGGTTAACCAAATTTCATAAGA
1 AGGTTAACAAAATTTCATAAAA
*
7179 AGGTTAA-AAAATTTTATAAAA
1 AGGTTAACAAAATTTCATAAAA
7200 AGGTT
1 AGGTT
7205 CTCGAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (22 bp):
AGGTTAACAAAATTTCATAAAA
Found at i:7249 original size:22 final size:22
Alignment explanation
Indices: 7068--7259 Score: 113
Period size: 22 Copynumber: 8.7 Consensus size: 22
7058 CTATGTATGG
* * *
7068 AGGTTATCAACATCTCATAGTGT
1 AGGTTATCAAAATTTCATAG-GA
* *
7091 TGGTTATCAAAATTTCATTGGGA
1 AGGTTATCAAAATTTCA-TAGGA
*
7114 A-GTTATCAAAATTTCATACTG-
1 AGGTTATCAAAATTTCATA-GGA
* * *
7135 AGGTCT-TCAAAATTCCTTAGGG
1 AGGT-TATCAAAATTTCATAGGA
* * *
7157 AGGTTAACCAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
* * **
7179 AGGTTA-AAAAATTTTATAAAA
1 AGGTTATCAAAATTTCATAGGA
* * * *
7200 AGGTTCTCGAAATTCCATAGTA
1 AGGTTATCAAAATTTCATAGGA
** *
7222 TCGTTATTAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
7244 AGGTTATCAAAATTTC
1 AGGTTATCAAAATTTC
7260 CTAATGGGAT
Statistics
Matches: 124, Mismatches: 38, Indels: 15
0.70 0.21 0.08
Matches are distributed among these distances:
21 20 0.16
22 86 0.69
23 16 0.13
24 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:11313 original size:2 final size:2
Alignment explanation
Indices: 11306--11386 Score: 78
Period size: 2 Copynumber: 41.0 Consensus size: 2
11296 TTTTGATAAC
* **
11306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT GC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
**
11348 ACT AGT -T CC A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11387 GTTTTATGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
1 3 0.05
2 60 0.91
3 3 0.05
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:12529 original size:2 final size:2
Alignment explanation
Indices: 12522--12552 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12512 TAGTATCGTG
12522 TA TA 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 TA TA T
12553 TGGTGTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27810 original size:18 final size:18
Alignment explanation
Indices: 27787--27824 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
27777 TTCTTTTCGA
*
27787 AAACTCTTAAGGAGCAAG
1 AAACTCTTAAGGAACAAG
27805 AAACTCTTAAGGAACAAG
1 AAACTCTTAAGGAACAAG
27823 AA
1 AA
27825 GCACCAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.16
Consensus pattern (18 bp):
AAACTCTTAAGGAACAAG
Found at i:28235 original size:26 final size:27
Alignment explanation
Indices: 28206--28265 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 27
28196 TGAATTTCAT
28206 GAAGTTGTTGAAGTCCCAATCATGAA-
1 GAAGTTGTTGAAGTCCCAATCATGAAG
*
28232 GAAGTTCTTGAAGTCCCAATCATGAAG
1 GAAGTTGTTGAAGTCCCAATCATGAAG
28259 GAAGTTG
1 GAAGTTG
28266 AAGAGGTGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 25 0.81
27 6 0.19
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (27 bp):
GAAGTTGTTGAAGTCCCAATCATGAAG
Found at i:28621 original size:16 final size:16
Alignment explanation
Indices: 28602--28663 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
28592 AACCCGCCTG
28602 AACCCGAACCCGAAAA
1 AACCCGAACCCGAAAA
*
28618 AACCCGAATCCGAAAA
1 AACCCGAACCCGAAAA
* * *
28634 AGCTCAAACCCGAAAA
1 AACCCGAACCCGAAAA
*
28650 AACCCGAATCCGAA
1 AACCCGAACCCGAA
28664 TCCGAAAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.48, C:0.34, G:0.13, T:0.05
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:28839 original size:16 final size:15
Alignment explanation
Indices: 28794--28844 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
28784 TCTGGCCAAA
28794 ACCCAAATTGAACCCG
1 ACCCAAATT-AACCCG
* *
28810 AACCCGAATTAACCTG
1 -ACCCAAATTAACCCG
28826 ACCCAAATTCAACCCG
1 ACCCAAATT-AACCCG
28842 ACC
1 ACC
28845 TGACTTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 8 0.28
16 13 0.45
17 8 0.28
ACGTcount: A:0.37, C:0.39, G:0.10, T:0.14
Consensus pattern (15 bp):
ACCCAAATTAACCCG
Found at i:31951 original size:35 final size:35
Alignment explanation
Indices: 31901--32274 Score: 538
Period size: 35 Copynumber: 10.7 Consensus size: 35
31891 AGTAATAAGT
* *
31901 AACTTAATTCGGGGTAATTAAGTAATTCAGGAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
31936 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
31971 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
32006 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
*
32041 AACTTAATTCAGGGTAATTAAGTGATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* * *
32076 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAGTC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
*
32111 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* * *
32146 AACTTAATTCAGGGTAATTAAGTGAGTCGGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
32181 AACTTAA-TCTAGGATAATTAAGTGATTCAGTAATC
1 AACTTAATTC-AGGGTAATTAAGTAATTCAGTAATC
* * *
32216 AACTGTAATTTAGGGTAATTAAGTGAGTT-AATAAGT-
1 AACT-TAATTCAGGGTAATTAAGT-AATTCAGTAA-TC
32252 AACTTAATTCAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
32275 TTAGTAAGAA
Statistics
Matches: 308, Mismatches: 26, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
34 2 0.01
35 279 0.91
36 23 0.07
37 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
Done.