Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011733.1 Corchorus capsularis cultivar CVL-1 contig11754, 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: 11939
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Found at i:5728 original size:29 final size:29
Alignment explanation
Indices: 5695--5754 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
5685 TATTAATCTA
5695 AAAATGAGCATTGTGTGCTCTTATGTCTC
1 AAAATGAGCATTGTGTGCTCTTATGTCTC
5724 AAAATGAGCATTGTGTGCTCTTATGTCTC
1 AAAATGAGCATTGTGTGCTCTTATGTCTC
5753 AA
1 AA
5755 TTTTTATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (29 bp):
AAAATGAGCATTGTGTGCTCTTATGTCTC
Found at i:6161 original size:62 final size:62
Alignment explanation
Indices: 6064--6215 Score: 205
Period size: 62 Copynumber: 2.5 Consensus size: 62
6054 ATATTCATAC
* * * * * *
6064 GAAATTATAATAACCTTCCTATTAAGTTAAGATAATTACACTATTTTTGATAATGTCCTTGT
1 GAAATTTTGATAACCTTCCTATGAAATTAAGATAATTACACTATTTTTGATAACGTCCTTAT
* * * * *
6126 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTTCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTAAGATAATTACACTATTTTTGATAACGTCCTTAT
6188 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACCTTCCTATGAAATT
6216 TCAATAACGA
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 78 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATGAAATTAAGATAATTACACTATTTTTGATAACGTCCTTAT
Found at i:6195 original size:21 final size:22
Alignment explanation
Indices: 6185--6747 Score: 209
Period size: 22 Copynumber: 25.7 Consensus size: 22
6175 ATGACGTTCT
6185 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** ** *
6207 TATGAAATTTCAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
6229 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* *
6251 TAT-AAATTTTGTTTTAACCTTCT
1 TATGAAATTTTG--ATAACCTTCC
* * *
6274 TATGAAATTTTGTTTACCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
6296 TAAGGAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATA-ACCTTC-C
6318 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
* **
6339 AAATGAAATTTTGATAACCAACAC
1 -TATGAAATTTTGATAACCTTC-C
* *
6363 TAT-AAGATGTTGATAGCC-TCC
1 TATGAA-ATTTTGATAACCTTCC
* * *
6384 ATATGATATATTGATAATCACGT--
1 -TATGAAATTTTGATAA-C-CTTCC
* * * *
6407 TATGAAAATTTAAAAATC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
6428 ATATG-AATTGTCAGTAATC-ACAC
1 -TATGAAATTTTGA-TAACCTTC-C
* * *
6451 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
6473 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
6495 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
6518 TATAAAATTTTGATAAATCTACC
1 TATGAAATTTTGAT-AACCTTCC
*
6541 TATAAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
*
6562 TTATGAAATCTTGATAA-----C
1 -TATGAAATTTTGATAACCTTCC
* *
6580 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
6601 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * * *
6623 TATGAGATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
6645 TATGAAATTTTGATTTA-CATGC
1 TATGAAATTTTGA-TAACCTTCC
* * * *
6667 TATAAAATTTTGACAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
6689 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* * *
6711 TATGATATTTTGATAACCCTCA
1 TATGAAATTTTGATAACCTTCC
6733 TATGAAATTTTGATA
1 TATGAAATTTTGATA
6748 TTCTCCCTGA
Statistics
Matches: 404, Mismatches: 100, Indels: 74
0.70 0.17 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 1 0.00
19 1 0.00
20 1 0.00
21 26 0.06
22 270 0.67
23 79 0.20
24 12 0.03
25 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:6271 original size:23 final size:24
Alignment explanation
Indices: 6243--6288 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
6233 AAATTTCGAG
*
6243 AACCTTTTTAT-AAATTTTGTTTT
1 AACCTTCTTATGAAATTTTGTTTT
6266 AACCTTCTTATGAAATTTTGTTT
1 AACCTTCTTATGAAATTTTGTTT
6289 ACCTCCCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.57
Consensus pattern (24 bp):
AACCTTCTTATGAAATTTTGTTTT
Found at i:6906 original size:44 final size:44
Alignment explanation
Indices: 6856--6999 Score: 134
Period size: 44 Copynumber: 3.3 Consensus size: 44
6846 AAGTACCACA
* *
6856 ATGAAATTTTGGTAATCACATTTTGAAAATTTTATAACCTCTTT
1 ATGAAATTTTGATAATCACATTATGAAAATTTTATAACCTCTTT
* * * * * *
6900 ATGAAATTTTGATAACCGC-TCTAT-AAAATTTTGTCGACCCCTCT
1 ATGAAATTTTGATAATCACAT-TATGAAAATTTTAT-AACCTCTTT
* *
6944 ATGAAATTTTGATAATCACATTATG-TAATTTTGATAACCTCGCTT
1 ATGAAATTTTGATAATCACATTATGAAAATTTT-ATAACCTC-TTT
6989 -TGAAATTTTGA
1 ATGAAATTTTGA
7000 AATTGGACCA
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
43 10 0.13
44 65 0.83
45 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (44 bp):
ATGAAATTTTGATAATCACATTATGAAAATTTTATAACCTCTTT
Found at i:6968 original size:22 final size:22
Alignment explanation
Indices: 6856--6999 Score: 91
Period size: 22 Copynumber: 6.5 Consensus size: 22
6846 AAGTACCACA
* *
6856 ATGAAATTTTGGTAATCACATT
1 ATGAAATTTTGATAACCACATT
* * *
6878 TTGAAAATTTT-ATAACCTCTTT
1 ATG-AAATTTTGATAACCACATT
*
6900 ATGAAATTTTGATAACCGC-TCT
1 ATGAAATTTTGATAACCACAT-T
* * *
6922 ATAAAATTTTG-TCGACC-CCTCT
1 ATGAAATTTTGAT-AACCACAT-T
*
6944 ATGAAATTTTGATAATCACATT
1 ATGAAATTTTGATAACCACATT
* * *
6966 ATGTAATTTTGATAACCTCGCTT
1 ATGAAATTTTGATAACCAC-ATT
6989 -TGAAATTTTGA
1 ATGAAATTTTGA
7000 AATTGGACCA
Statistics
Matches: 96, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
21 10 0.10
22 74 0.77
23 12 0.12
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACATT
Found at i:7098 original size:37 final size:37
Alignment explanation
Indices: 7057--7148 Score: 105
Period size: 38 Copynumber: 2.5 Consensus size: 37
7047 ATCTAAACTC
* * *
7057 AAATAGGACGTTGGAGACGAAGACAAAA-AGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAGA-AAAAATT
** *
7094 AAATACAATGGTTGGAAACAAAGACAAAAGAAAAAATT
1 AAATAGGA-CGTTGGAAACAAAGACAAAAGAAAAAATT
7132 AAATAGGACGTTGGAAA
1 AAATAGGACGTTGGAAA
7149 TAAAAAGTCA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
37 14 0.32
38 29 0.66
39 1 0.02
ACGTcount: A:0.54, C:0.09, G:0.22, T:0.15
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAGAAAAAATT
Found at i:7303 original size:32 final size:32
Alignment explanation
Indices: 7267--7334 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
7257 TTTAGTAATG
* * *
7267 ACAATTTAGAAATATGTTTTTTACAA-AAGGGT
1 ACAATTTAGAAATAT-ATTTTAAAAATAAGGGT
*
7299 ACAA-TTGGAAATATATTTTAAAAATAAGGGT
1 ACAATTTAGAAATATATTTTAAAAATAAGGGT
7330 ACAAT
1 ACAAT
7335 CGGAAAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
30 7 0.23
31 19 0.63
32 4 0.13
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.34
Consensus pattern (32 bp):
ACAATTTAGAAATATATTTTAAAAATAAGGGT
Found at i:8596 original size:28 final size:27
Alignment explanation
Indices: 8551--8620 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 27
8541 TCACTCTCTT
*
8551 CTCTTT-TCCATATTTTTTT-AGGGAA
1 CTCTTTCTCCATATTTTTTTGAAGGAA
*
8576 TTCTTTCTCCATATTTGTTTTGAAGGAA
1 CTCTTTCTCCATATTT-TTTTGAAGGAA
8604 CTCTTTCTCCATATTTT
1 CTCTTTCTCCATATTTT
8621 GTATCTCTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
25 5 0.13
26 9 0.23
27 5 0.13
28 20 0.51
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.53
Consensus pattern (27 bp):
CTCTTTCTCCATATTTTTTTGAAGGAA
Found at i:8704 original size:2 final size:2
Alignment explanation
Indices: 8697--8729 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8687 GGTAGTAAAT
8697 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
8730 TATATGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:10087 original size:24 final size:24
Alignment explanation
Indices: 10035--10087 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
10025 AAGTCTTAAA
* *
10035 AATTTGGTAACACCTTACCTTTTT
1 AATTTAGTAACACCTTACCTCTTT
* *
10059 AATTTAGTAACACGTTATCTCTTT
1 AATTTAGTAACACCTTACCTCTTT
*
10083 GATTT
1 AATTT
10088 TATTAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.47
Consensus pattern (24 bp):
AATTTAGTAACACCTTACCTCTTT
Found at i:11000 original size:26 final size:26
Alignment explanation
Indices: 10953--11017 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
10943 ATATTGATGA
*
10953 AAGGTATACTAAAATTTGTAAGAATGC
1 AAGGT-TACTAAAATTTCTAAGAATGC
10980 AAGGTTACTGAAAA-TTCTAAGAATGC
1 AAGGTTACT-AAAATTTCTAAGAATGC
*
11006 GAGGTTACTAAA
1 AAGGTTACTAAA
11018 TTTATGTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 3 0.09
26 23 0.66
27 9 0.26
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (26 bp):
AAGGTTACTAAAATTTCTAAGAATGC
Found at i:11803 original size:197 final size:200
Alignment explanation
Indices: 11431--11938 Score: 718
Period size: 197 Copynumber: 2.5 Consensus size: 200
11421 ACTTAATTAA
* * * *
11431 TTAAATAATTATGAAATG-GAGTGTATGTCAACTTCTTAACCCGCTTATGAAGTCCAAATTTTAC
1 TTAATTAATTATGAAATGAGA-TATATGTCAACTTCTTAACCTGC-TATGAAGTCCAAAATTTAC
*
11495 ACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACTATACATACACCGTCAGTGGAG
64 ATTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATAC-ATA-ATACACCGTCAGTGGAG
* *
11560 TTTAGCAGATTGCACGTGCATGGTTTAAGGGTTGACATGGGTCCCCTTAGGGAATATGTATTAAT
127 TTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGGGTCCCCTTAGGGAATATGTATTAAT
*
11625 ATTATATAT
192 ATTAAATAT
* *
11634 TTAATTAATGATGAAATGAGATATATGTCAACTTCTTAACCTGC-ATGGAGTCCAAAATTTACAT
1 TTAATTAATTATGAAATGAGATATATGTCAACTTCTTAACCTGCTATGAAGTCCAAAATTTACAT
* * * * *
11698 TGACAATTTATTGTATAATATTCCTATAAGAAAAATTATAC-T-ATACACTGTCAGTGGATTTTA
66 TGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACATAATACACCGTCAGTGGAGTTTA
* **
11761 GCAGACTGCACGTGCGGGGTTTAAGGGTTGACATTTGTCCCCTTAGGGAATATGTATTAATATTA
131 GCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGGGTCCCCTTAGGGAATATGTATTAATATTA
11826 AATAT
196 AATAT
* * * *
11831 TTAATTAATTATGAAATGAGGTTTATGTCAACTTCTTAATCTGCTTATGAAGTTCAAAATTTACA
1 TTAATTAATTATGAAATGAGATATATGTCAACTTCTTAACCTGC-TATGAAGTCCAAAATTTACA
* * *
11896 TTAACAGTGTATTGTATAATAATCTTATAAGAACAATTATACA
65 TTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACA
11939 A
Statistics
Matches: 271, Mismatches: 30, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
197 123 0.45
199 54 0.20
201 55 0.20
203 37 0.14
204 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (200 bp):
TTAATTAATTATGAAATGAGATATATGTCAACTTCTTAACCTGCTATGAAGTCCAAAATTTACAT
TGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACATAATACACCGTCAGTGGAGTTTA
GCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGGGTCCCCTTAGGGAATATGTATTAATATTA
AATAT
Done.