Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012384.1 Corchorus capsularis cultivar CVL-1 contig12405, 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: 30220
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2652 original size:7 final size:7
Alignment explanation
Indices: 2642--2671 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2632 GTAAATTATA
2642 AAAAAAT
1 AAAAAAT
2649 AAAAAAT
1 AAAAAAT
2656 AAAAAAT
1 AAAAAAT
*
2663 ACAAAAT
1 AAAAAAT
2670 AA
1 AA
2672 TGGAAGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:17548 original size:2 final size:2
Alignment explanation
Indices: 17541--17586 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
17531 ATATGTAGTA
*
17541 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17581 -T AT AT A
1 AT AT AT A
17587 GACCAGTCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20700 original size:22 final size:22
Alignment explanation
Indices: 20653--20701 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
20643 AGATTTCGAG
* **
20653 AACCTTTTTATAAATTTTTTTC
1 AACCTTCTTATAAATTTAGTTC
20675 AACCTTCTTATGAAATTTAGTT-
1 AACCTTCTTAT-AAATTTAGTTC
20697 AACCT
1 AACCT
20702 CCCTAAGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (22 bp):
AACCTTCTTATAAATTTAGTTC
Found at i:20791 original size:29 final size:30
Alignment explanation
Indices: 20736--20793 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
20726 ATATGAAATT
*
20736 TTGATAACCAACACTATGAGATGTTGATAC
1 TTGATAACCAACACTATGAGATATTGATAC
** *
20766 TTGATAACCTCCA-TATGATATATTGATA
1 TTGATAACCAACACTATGAGATATTGATA
20794 ACCACGTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (30 bp):
TTGATAACCAACACTATGAGATATTGATAC
Found at i:20861 original size:22 final size:22
Alignment explanation
Indices: 20836--20950 Score: 97
Period size: 22 Copynumber: 5.1 Consensus size: 22
20826 GAATTGTTAG
*
20836 TAATCACACTTTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
20858 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
20880 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
20902 TAAATCTTC-CTATAAAATTTTGA
1 T-AATC-ACACTATGAAATTTTGA
* * * *
20925 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
20948 TAA
1 TAA
20951 CTTTCTTATG
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
22 43 0.53
23 36 0.44
24 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:20919 original size:23 final size:23
Alignment explanation
Indices: 20888--20972 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
20878 GATAACCTCG
*
20888 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
20911 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
20934 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
20956 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
20973 CTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:20969 original size:22 final size:22
Alignment explanation
Indices: 20849--20974 Score: 94
Period size: 22 Copynumber: 5.6 Consensus size: 22
20839 TCACACTTTG
** *
20849 AAATTTTGATAA-TCACACTATG
1 AAATTTTGATAACTTTC-CTATA
* * *
20871 AAATTGTGATAAC-CTCGCTATG
1 AAATTTTGATAACTTTC-CTATA
*
20893 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAACT-TTCCTATA
* *
20916 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACTTTCCTATA
* *
20939 AAATTTTGATAACTTTCTTATG
1 AAATTTTGATAACTTTCCTATA
*
20961 AAATCTTGATAACT
1 AAATTTTGATAACT
20975 ACAAATTTTG
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
22 50 0.59
23 31 0.36
24 4 0.05
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACTTTCCTATA
Found at i:20971 original size:45 final size:45
Alignment explanation
Indices: 20849--20972 Score: 130
Period size: 45 Copynumber: 2.8 Consensus size: 45
20839 TCACACTTTG
* * *
20849 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
20893 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
* *
20939 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
20973 CTACAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
44 11 0.16
45 31 0.46
46 26 0.38
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:21020 original size:22 final size:22
Alignment explanation
Indices: 20842--21030 Score: 79
Period size: 22 Copynumber: 8.8 Consensus size: 22
20832 TTAGTAATCA
* * * *
20842 CACTTTGAAATTTTGATAATCA
1 CACTATGAAGTTTTGATAACCT
* *
20864 CACTATGAAATTGTGATAACCT
1 CACTATGAAGTTTTGATAACCT
* * *
20886 CGCTATGAAATTTTGATAAATCTT
1 CACTATGAAGTTTTGAT-AA-CCT
* *
20910 C-CTATAAAATTTTGATAAACCT
1 CACTATGAAGTTTTGAT-AACCT
* * * *
20932 CCCTATAAAATTTTGATAACTTT
1 CACTATGAAGTTTTGATAAC-CT
* * *
20955 C-TTATGAAATCTTGATAA-CT
1 CACTATGAAGTTTTGATAACCT
20975 -AC-A--AA-TTTTGATAACCT
1 CACTATGAAGTTTTGATAACCT
* ** *
20992 CCCTATGATTTTTTGATAATCT
1 CACTATGAAGTTTTGATAACCT
*
21014 CATTATGAAGTTTTGAT
1 CACTATGAAGTTTTGAT
21031 CTACATACTA
Statistics
Matches: 133, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
16 8 0.06
17 4 0.03
18 1 0.01
19 2 0.02
20 1 0.01
21 1 0.01
22 77 0.58
23 36 0.27
24 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
CACTATGAAGTTTTGATAACCT
Found at i:21141 original size:19 final size:20
Alignment explanation
Indices: 21085--21135 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
21075 AACTAAAATA
21085 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
21105 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
21124 TGAAATTTTGAT
1 TGAAATTTTGAT
21136 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:21293 original size:22 final size:22
Alignment explanation
Indices: 21217--21431 Score: 122
Period size: 22 Copynumber: 9.7 Consensus size: 22
21207 GAAATACCAC
21217 TATGAAATTTTTG-TAAT-TACATT
1 TATGAAA-TTTTGATAATCT-C-TT
* *
21240 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCTCTT
21261 TATGAAATTTTGATAATCTCTT
1 TATGAAATTTTGATAATCTCTT
* * * *
21283 TATAAAATTTTGTTGA-CCCTT
1 TATGAAATTTTGATAATCTCTT
* * *
21304 CTATGAAATTCTGATAATCACAT
1 -TATGAAATTTTGATAATCTCTT
* * * *
21327 TACGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCTC-TT
* **
21350 T-TGAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAATC-TCTT
21371 TATGAAATTTTGATAATCT-TT
1 TATGAAATTTTGATAATCTCTT
* *
21392 CTAT-AAATTTTGATATTCTGATCTC
1 -TATGAAATTTTGATAATC---TCTT
21417 TATGAAATTTTGATA
1 TATGAAATTTTGATA
21432 GTCATTCTAT
Statistics
Matches: 147, Mismatches: 30, Indels: 28
0.72 0.15 0.14
Matches are distributed among these distances:
21 26 0.18
22 97 0.66
23 8 0.05
24 4 0.03
25 12 0.08
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTCTT
Found at i:21401 original size:21 final size:22
Alignment explanation
Indices: 21241--21470 Score: 123
Period size: 22 Copynumber: 10.5 Consensus size: 22
21231 AATTACATTT
* *
21241 TGAAAATTTGATAACCTCTT-TA
1 TGAAATTTTGATAATCT-TTCTA
21263 TGAAATTTTGATAATCTCTT-TA
1 TGAAATTTTGATAATCT-TTCTA
* * * * *
21285 TAAAATTTTGTTGACCCTTCTA
1 TGAAATTTTGATAATCTTTCTA
* **
21307 TGAAATTCTGATAATCACAT-TA
1 TGAAATTTTGATAATC-TTTCTA
* * * ** *
21329 CGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAATCTTTCTA
***
21351 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAATC-TTTCTA
21373 TGAAATTTTGATAATCTTTCTA
1 TGAAATTTTGATAATCTTTCTA
*
21395 T-AAATTTTGATATTCTGATCTCTA
1 TGAAATTTTGATAATCT--T-TCTA
* *
21419 TGAAATTTTGATAGTCATTCTA
1 TGAAATTTTGATAATCTTTCTA
* *
21441 TGAGA-TTTGATAA-CCTTCTA
1 TGAAATTTTGATAATCTTTCTA
*
21461 TCAAATTTTG
1 TGAAATTTTG
21471 GTACTTCTTA
Statistics
Matches: 161, Mismatches: 37, Indels: 21
0.74 0.17 0.10
Matches are distributed among these distances:
20 9 0.06
21 28 0.17
22 101 0.63
23 5 0.03
24 5 0.03
25 13 0.08
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAATCTTTCTA
Found at i:21522 original size:22 final size:21
Alignment explanation
Indices: 21493--21547 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
21483 AAATTGAGAC
21493 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTC-TATGAAA
** *
21514 TTTTGATAACCACACTATAAAA
1 TTTTGATAACC-TTCTATGAAA
21536 TTTTGATAACCT
1 TTTTGATAACCT
21548 CCCCATGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.14
22 23 0.82
23 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (21 bp):
TTTTGATAACCTTCTATGAAA
Found at i:21558 original size:22 final size:22
Alignment explanation
Indices: 21508--21558 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
21498 TAACCTTCAT
*
21508 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
21530 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
21552 ATGAAAT
1 ATGAAAT
21559 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:21729 original size:24 final size:22
Alignment explanation
Indices: 21665--21804 Score: 97
Period size: 22 Copynumber: 6.3 Consensus size: 22
21655 TTGTAATAAT
* *
21665 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
21687 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
**
21709 TAA-CATGATCCTATGAAATTTTGG
1 TAACCA--A-CCTATGAAATTTTAA
* *
21733 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* *
21755 TAACC-TCCTCATGAAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
21777 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
21799 TAACCA
1 TAACCA
21805 CATAGAGACC
Statistics
Matches: 94, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.05
22 70 0.74
23 4 0.04
24 14 0.15
25 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:21758 original size:68 final size:66
Alignment explanation
Indices: 21665--21806 Score: 151
Period size: 68 Copynumber: 2.1 Consensus size: 66
21655 TTGTAATAAT
* * * *
21665 TAACCACCCTATGAAATTTCAATAACCAACCT-AAGAGATTTTAATAACATGATCCTATGAAATT
1 TAACCACACTATGAAATTTCAATAACC-ACCTCAAGAAATTATAATAAC--CATCCTATGAAATT
*
21729 TTGG
63 TTGA
* ** * * *
21733 TAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTG
1 TAACCACACTATGAAATTTCAATAACCACCTCAAGAAATTATAATAACCATCCTATGAAATTTTG
21798 A
66 A
21799 TAACCACA
1 TAACCACA
21807 TAGAGACCAT
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
66 23 0.37
67 3 0.05
68 36 0.58
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (66 bp):
TAACCACACTATGAAATTTCAATAACCACCTCAAGAAATTATAATAACCATCCTATGAAATTTTG
A
Found at i:22010 original size:20 final size:20
Alignment explanation
Indices: 21973--22015 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
21963 TATTGACATT
21973 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTAAAAAG
21992 TAAAATATT-AAATTTAAAAAG
1 TAAAA-ATTGAAA-TTAAAAAG
22013 TAA
1 TAA
22016 TAGTAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (20 bp):
TAAAAATTGAAATTAAAAAG
Found at i:22226 original size:31 final size:31
Alignment explanation
Indices: 22152--22216 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
22142 AAGACCAAAG
22152 ACAAAG-CAAAATTAAATACAACGATTGGAA
1 ACAAAGACAAAATTAAATACAACGATTGGAA
**
22182 ACAAAGACAAAATTAAATAGGACG-TTGGAA
1 ACAAAGACAAAATTAAATACAACGATTGGAA
22212 ACAAA
1 ACAAA
22217 ATGCCAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.57, C:0.12, G:0.15, T:0.15
Consensus pattern (31 bp):
ACAAAGACAAAATTAAATACAACGATTGGAA
Found at i:22307 original size:26 final size:27
Alignment explanation
Indices: 22278--22329 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
22268 GATTAAAAAA
22278 TAATGGAAAATTA-AAATATTATTTAG
1 TAATGGAAAATTAGAAATATTATTTAG
* * *
22304 TAATGGCAATTTAGAAATATTTTTTA
1 TAATGGAAAATTAGAAATATTATTTA
22330 AAGAAAAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (27 bp):
TAATGGAAAATTAGAAATATTATTTAG
Found at i:22352 original size:31 final size:31
Alignment explanation
Indices: 22317--22382 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
22307 TGGCAATTTA
* * *
22317 GAAATATTTTTTAAAGAA-AAGGGTATAATTG
1 GAAATATATTTTAAA-AAGAAGGGTACAATCG
22348 GAAATATATTTTAAAAAGAAGGGTACAATCG
1 GAAATATATTTTAAAAAGAAGGGTACAATCG
22379 GAAA
1 GAAA
22383 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.29
Consensus pattern (31 bp):
GAAATATATTTTAAAAAGAAGGGTACAATCG
Done.