Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009498.1 Corchorus capsularis cultivar CVL-1 contig09519, 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: 37777
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:432 original size:24 final size:20
Alignment explanation
Indices: 386--425 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
376 GTTTAGAAGC
*
386 AATTAATTAAAAGCATCAAA
1 AATTAATTAAAAACATCAAA
406 AATTAATTAAAAACAATCAA
1 AATTAATTAAAAAC-ATCAA
426 GAGAAATGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (20 bp):
AATTAATTAAAAACATCAAA
Found at i:525 original size:73 final size:74
Alignment explanation
Indices: 428--571 Score: 218
Period size: 73 Copynumber: 2.0 Consensus size: 74
418 ACAATCAAGA
* * * *
428 GAAATGTGTAGTTACGAAAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAGAGGGACTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAAGAATAGGGGAAACTCATAGAGGGACTTTT
493 TAGTCATTC
66 TAGTCATTC
** *
502 GAAAAGTGTAATTACG-AAAAGGGTAGAAGGAAAAAGAATAGGGGATCCTCATAGAGGGGCTTTT
1 GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAAGAATAGGGGAAACTCATAGAGGGACTTTT
566 TAGTCA
66 TAGTCA
572 CCCGAAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
73 49 0.78
74 14 0.22
ACGTcount: A:0.39, C:0.08, G:0.31, T:0.22
Consensus pattern (74 bp):
GAAAAGTGTAATTACGAAAAAGGGTAGAAGGAAAAAGAATAGGGGAAACTCATAGAGGGACTTTT
TAGTCATTC
Found at i:5357 original size:3 final size:3
Alignment explanation
Indices: 5349--5375 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5339 GACGCGCTTC
5349 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
5376 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:8609 original size:10 final size:10
Alignment explanation
Indices: 8590--8619 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
8580 AGATGAGGAC
8590 TCTAGAATTT
1 TCTAGAATTT
*
8600 TCTGGAATTT
1 TCTAGAATTT
8610 TCTAGAATTT
1 TCTAGAATTT
8620 ATCAGCAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (10 bp):
TCTAGAATTT
Found at i:21116 original size:22 final size:21
Alignment explanation
Indices: 21076--21213 Score: 84
Period size: 22 Copynumber: 6.3 Consensus size: 21
21066 TTTTCACTGG
*
21076 AATTTTGATAATCATACTATGA
1 AATTTTG-TAATCACACTATGA
* *
21098 AATGTTTGTAAGCACACTATAA
1 AAT-TTTGTAATCACACTATGA
*
21120 AATTTTG-AAACATC-CATATGA
1 AATTTTGTAATCA-CAC-TATGA
*
21141 AATGTTAGTAATCACACTGA-GA
1 AAT-TTTGTAATCACACT-ATGA
*
21163 AATTTTAATAATCACACTATGA
1 AATTTT-GTAATCACACTATGA
* * * * *
21185 CATTATGATAACCTCATTATGA
1 AATTTTG-TAATCACACTATGA
21207 AATTTTG
1 AATTTTG
21214 ATAAACCTTC
Statistics
Matches: 89, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
20 5 0.06
21 15 0.17
22 59 0.66
23 10 0.11
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.36
Consensus pattern (21 bp):
AATTTTGTAATCACACTATGA
Found at i:21144 original size:43 final size:44
Alignment explanation
Indices: 21076--21184 Score: 125
Period size: 43 Copynumber: 2.5 Consensus size: 44
21066 TTTTCACTGG
*
21076 AATTTTGATAATCATACTATGAAATGTTTGTAAGCACACTATAA
1 AATTTTGATAATCATACTATGAAATGTTAGTAAGCACACTATAA
* * *
21120 AATTTTGA-AA-CATCCATATGAAATGTTAGTAATCACACTGA-GA
1 AATTTTGATAATCATAC-TATGAAATGTTAGTAAGCACACT-ATAA
* *
21163 AATTTTAATAATCACACTATGA
1 AATTTTGATAATCATACTATGA
21185 CATTATGATA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
42 4 0.07
43 31 0.57
44 16 0.30
45 3 0.06
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (44 bp):
AATTTTGATAATCATACTATGAAATGTTAGTAAGCACACTATAA
Found at i:21215 original size:22 final size:22
Alignment explanation
Indices: 21026--21217 Score: 69
Period size: 22 Copynumber: 8.8 Consensus size: 22
21016 GTATAAATTG
* *
21026 TTATGAAATTTTGAAAACCTCG
1 TTATGAAATTTTGATAACCTCA
* *
21048 CTATGAAATTTTGATAA-CT-T
1 TTATGAAATTTTGATAACCTCA
*
21068 TTCACTGGAATTTTGATAA--TCA
1 TT-A-TGAAATTTTGATAACCTCA
* *
21090 TACTATGAAATGTTTG-TAAGCACA
1 T--TATGAAAT-TTTGATAACCTCA
* * *
21114 CTATAAAATTTTGA-AACATCCA
1 TTATGAAATTTTGATAACCT-CA
* * *
21136 -TATGAAATGTT-AGTAATCACA
1 TTATGAAATTTTGA-TAACCTCA
* * * *
21157 CTGA-GAAATTTTAATAATCACA
1 -TTATGAAATTTTGATAACCTCA
* * *
21179 CTATGACATTATGATAACCTCA
1 TTATGAAATTTTGATAACCTCA
21201 TTATGAAATTTTGATAA
1 TTATGAAATTTTGATAA
21218 ACCTTCCCAT
Statistics
Matches: 124, Mismatches: 30, Indels: 32
0.67 0.16 0.17
Matches are distributed among these distances:
20 2 0.02
21 22 0.18
22 90 0.73
23 7 0.06
24 3 0.02
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCTCA
Found at i:21266 original size:22 final size:22
Alignment explanation
Indices: 21233--21280 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
21223 CCCATTGACA
21233 AACCTCGCTATAAAATTTTAAT
1 AACCTCGCTATAAAATTTTAAT
*
21255 AACCTC-CTTATAAAATTTTGAT
1 AACCTCGC-TATAAAATTTTAAT
21277 AACC
1 AACC
21281 ATAAACTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (22 bp):
AACCTCGCTATAAAATTTTAAT
Found at i:21684 original size:22 final size:23
Alignment explanation
Indices: 21637--21827 Score: 87
Period size: 22 Copynumber: 8.5 Consensus size: 23
21627 CCTCGTTATA
* * * *
21637 AAATTTTGACAA-CTGCATTATT
1 AAATTTTGATAACCTACACTATG
* *
21659 AAATTTTAATAACCT-CCCTATG
1 AAATTTTGATAACCTACACTATG
21681 AAATTTTGATAA-CTACACTATG
1 AAATTTTGATAACCTACACTATG
* * *
21703 AAATTTTGATAACTTTC-CTATA
1 AAATTTTGATAACCTACACTATG
* * *
21725 AAAATTTGATAATCTTATCTCTATG
1 AAATTTTGATAA-CCTA-CACTATG
* *
21750 AAATGTTGATAA--TAACTCTATG
1 AAATTTTGATAACCT-ACACTATG
* *
21772 AGATTTTGATTACCT-C-CT-TG
1 AAATTTTGATAACCTACACTATG
* * *
21792 TCAAATTTCGATAAAC-ACACTATA
1 --AAATTTTGATAACCTACACTATG
*
21816 AAAATTTGATAA
1 AAATTTTGATAA
21828 TCTTCTTATG
Statistics
Matches: 130, Mismatches: 25, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
20 2 0.02
21 4 0.03
22 97 0.75
23 10 0.08
24 3 0.02
25 14 0.11
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAACCTACACTATG
Found at i:21734 original size:44 final size:44
Alignment explanation
Indices: 21624--21761 Score: 132
Period size: 44 Copynumber: 3.1 Consensus size: 44
21614 TTTTGAAATT
** * * * * *
21624 TAACCTCGTTATAAAATTTTGACAACTGCATTATTAAATTTTAA
1 TAACCTCCCTATAAAATTTTGATAACTACACTATGAAATTTTGA
*
21668 TAACCTCCCTATGAAATTTTGATAACTACACTATGAAATTTTGA
1 TAACCTCCCTATAAAATTTTGATAACTACACTATGAAATTTTGA
* * * * *
21712 TAACTTTCCTATAAAAATTTGATAATCTTATCTCTATGAAATGTTGA
1 TAACCTCCCTATAAAATTTTGATAA-C-TA-CACTATGAAATTTTGA
21759 TAA
1 TAA
21762 TAACTCTATG
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
44 57 0.74
45 1 0.01
46 2 0.03
47 17 0.22
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (44 bp):
TAACCTCCCTATAAAATTTTGATAACTACACTATGAAATTTTGA
Found at i:21923 original size:22 final size:22
Alignment explanation
Indices: 21889--22216 Score: 196
Period size: 22 Copynumber: 14.9 Consensus size: 22
21879 CTAAACTTGG
* *
21889 TAACCACATTATGAAATTTTGA
1 TAACTACACTATGAAATTTTGA
21911 TAACTACACTATGAAATTTTGA
1 TAACTACACTATGAAATTTTGA
** * *
21933 TAACCT-TGCTAT-AAAATTTCA
1 TAA-CTACACTATGAAATTTTGA
* * *
21954 GTAACCTTC-CCATGAAATTTTGT
1 -TAA-CTACACTATGAAATTTTGA
* *
21977 TAACCACACTATGAAATTCTGA
1 TAACTACACTATGAAATTTTGA
* *
21999 TAATCT-CGCTATGAAATTCTGA
1 TAA-CTACACTATGAAATTTTGA
* * * *
22021 TAACCATACTTTGAAATTTTAA
1 TAACTACACTATGAAATTTTGA
*
22043 TAACCTTC-CTAAT-AAATTTT-A
1 TAA-CTACACT-ATGAAATTTTGA
* * *
22064 GTAACGTTC-CTATGAATTTTTAA
1 -TAAC-TACACTATGAAATTTTGA
22087 TAAACTGATC-CTATGAAATTTTGA
1 T-AACT-A-CACTATGAAATTTTGA
* *
22111 TAACCACTCTATGAAATTTTGA
1 TAACTACACTATGAAATTTTGA
* * *
22133 TAACCTTCA-TATGAAATTGTGG
1 TAA-CTACACTATGAAATTTTGA
*
22155 TAACCACACTATGAAATTTTGA
1 TAACTACACTATGAAATTTTGA
22177 TAACTACAC--TGAAATTTTGA
1 TAACTACACTATGAAATTTTGA
*
22197 TAACCT-CCCTATGAAATTTT
1 TAA-CTACACTATGAAATTTT
22217 TCTAATCAGA
Statistics
Matches: 240, Mismatches: 44, Indels: 44
0.73 0.13 0.13
Matches are distributed among these distances:
20 16 0.07
21 20 0.08
22 170 0.71
23 20 0.08
24 14 0.06
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
TAACTACACTATGAAATTTTGA
Found at i:21950 original size:44 final size:44
Alignment explanation
Indices: 21889--22216 Score: 244
Period size: 44 Copynumber: 7.5 Consensus size: 44
21879 CTAAACTTGG
* *
21889 TAACCACATTATGAAATTTTGATAA-CTACACTATGAAATTTTGA
1 TAACCATACTATGAAATTTTGATAACCTAC-CTATGAAATTTTGA
* * * * * * *
21933 TAACCTTGCTAT-AAAATTTCAGTAACCTTCCCATGAAATTTTGT
1 TAACCATACTATGAAATTTTGA-TAACCTACCTATGAAATTTTGA
* * * *
21977 TAACCACACTATGAAATTCTGATAATCT-CGCTATGAAATTCTGA
1 TAACCATACTATGAAATTTTGATAACCTAC-CTATGAAATTTTGA
* * *
22021 TAACCATACTTTGAAATTTTAATAACCTTCCTAAT-AAATTTT-A
1 TAACCATACTATGAAATTTTGATAACCTACCT-ATGAAATTTTGA
** * * * *
22064 GTAACGTTCCTATGAATTTTTAATAAACTGATCCTATGAAATTTTGA
1 -TAACCATACTATGAAATTTTGATAACCT-A-CCTATGAAATTTTGA
* * * *
22111 TAACCACT-CTATGAAATTTTGATAACCTTCATATGAAATTGTGG
1 TAACCA-TACTATGAAATTTTGATAACCTACCTATGAAATTTTGA
*
22155 TAACCACACTATGAAATTTTGATAA-CTA-C-ACTGAAATTTTGA
1 TAACCATACTATGAAATTTTGATAACCTACCTA-TGAAATTTTGA
*
22197 TAACC-TCCCTATGAAATTTT
1 TAACCAT-ACTATGAAATTTT
22217 TCTAATCAGA
Statistics
Matches: 221, Mismatches: 48, Indels: 32
0.73 0.16 0.11
Matches are distributed among these distances:
41 1 0.00
42 26 0.12
43 11 0.05
44 136 0.62
45 14 0.06
46 31 0.14
47 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (44 bp):
TAACCATACTATGAAATTTTGATAACCTACCTATGAAATTTTGA
Found at i:21975 original size:66 final size:66
Alignment explanation
Indices: 21898--22215 Score: 267
Period size: 66 Copynumber: 4.8 Consensus size: 66
21888 GTAACCACAT
*
21898 TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGCTATAAAATTTCAGTAACCTTC
1 TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGCTATGAAATTTCAGTAACCTTC
21963 C
66 C
* * * * * * * *
21964 CATGAAATTTTGTTAACCACACTATGAAATTCTGATAATCTCGCTATGAAA-TTCTGATAACCAT
1 TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGCTATGAAATTTCAG-TAACCTT
*
22028 AC
65 CC
* * * * * * * * *
22030 TTTGAAATTTTAATAACCTTC-CTAAT-AAATTTT-AGTAACGTTCCTATGAATTTTTAATAAAC
1 TATGAAATTTTGATAA-CTACACT-ATGAAATTTTGA-TAACCTTGCTATGAAATTTCAGTAACC
22092 TGATCC
63 T--TCC
* * *
22098 TATGAAATTTTGATAACCACTCTATGAAATTTTGATAACCTT-CATATGAAATTGT-GGTAACC-
1 TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGC-TATGAAATT-TCAGTAACCT
*
22160 ACAC
64 TC-C
**
22164 TATGAAATTTTGATAACTACAC--TGAAATTTTGATAACCTCCCTATGAAATTT
1 TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGCTATGAAATTT
22216 TTCTAATCAG
Statistics
Matches: 197, Mismatches: 41, Indels: 31
0.73 0.15 0.12
Matches are distributed among these distances:
63 1 0.01
64 26 0.13
65 7 0.04
66 107 0.54
67 11 0.06
68 43 0.22
69 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (66 bp):
TATGAAATTTTGATAACTACACTATGAAATTTTGATAACCTTGCTATGAAATTTCAGTAACCTTC
C
Found at i:22683 original size:33 final size:34
Alignment explanation
Indices: 22622--22708 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 34
22612 CTTTTACACT
* ** *
22622 GAGCCTCCCCACTAGAACGG-TTCAGCCACGGCG
1 GAGCCTCCCCACTGGGGCGGCTTCAGCCACGGCA
22655 GAGCCTCCCCACTGGGGCGGCTTC-GCCACGGCA
1 GAGCCTCCCCACTGGGGCGGCTTCAGCCACGGCA
* **
22688 G-GCCGCCCCGGTGGGGCGGCT
1 GAGCCTCCCCACTGGGGCGGCT
22709 AGACCAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
32 17 0.37
33 26 0.57
34 3 0.07
ACGTcount: A:0.13, C:0.40, G:0.36, T:0.11
Consensus pattern (34 bp):
GAGCCTCCCCACTGGGGCGGCTTCAGCCACGGCA
Found at i:24427 original size:2 final size:2
Alignment explanation
Indices: 24415--24450 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
24405 ATGCTCTTGC
24415 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24451 ATAATAACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:26993 original size:2 final size:2
Alignment explanation
Indices: 26988--27015 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26978 ATCGATCTAC
26988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27016 GCATATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35169 original size:3 final size:3
Alignment explanation
Indices: 35163--35190 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
35153 AATAATAATA
35163 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
35191 CTACTAGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:35705 original size:2 final size:2
Alignment explanation
Indices: 35698--35730 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
35688 GTATTATCTT
35698 TA TA TA TA TA TA TA TA TA TA TA T- TA TA CTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
35731 CTTATATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35735 original size:12 final size:11
Alignment explanation
Indices: 35697--35737 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
35687 AGTATTATCT
35697 TTATATATATA
1 TTATATATATA
35708 TATATATATATA
1 T-TATATATATA
*
35720 TTATACTATATC
1 TTATA-TATATA
35732 TTATAT
1 TTATAT
35738 CTTATATATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 6 0.22
12 21 0.78
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (11 bp):
TTATATATATA
Found at i:37433 original size:2 final size:2
Alignment explanation
Indices: 37426--37450 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37416 AGATTTAGCC
37426 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
37451 AAGTCCTCAA
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
Done.