Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014518.1 Corchorus capsularis cultivar CVL-1 contig14539, 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: 23905
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:5959 original size:45 final size:45
Alignment explanation
Indices: 5901--6072 Score: 122
Period size: 45 Copynumber: 3.8 Consensus size: 45
5891 AAGACCTCAA
* * *
5901 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAATAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAATAC
* * * *
5946 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCACT-T
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAATAC
* * * * * * *
5990 TATAAAAAT-TTAAAAACCTCCATATAAAAATTTTGATAATC-ACAC
1 TAT-GAAATGTTGATAACCTCCATAT-GAAATATTGATAACCAATAC
*
6035 TATGAAAT-TGTGATAACCTCGC-TATGAAATTTTGATAA
1 TATGAAATGT-TGATAACCTC-CATATGAAATATTGATAA
6073 ATCTTTCTAT
Statistics
Matches: 99, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
44 37 0.37
45 61 0.62
46 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.35
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAATAC
Found at i:5980 original size:22 final size:22
Alignment explanation
Indices: 5857--6392 Score: 197
Period size: 22 Copynumber: 24.8 Consensus size: 22
5847 TAAACTTTCT
* *
5857 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCCA
* * *
5879 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTCCA
*
5901 TATGAAATTTTGATAACTTCCCA
1 TATGAAATTTTGATAACCT-CCA
*
5924 -ATGAAATTTTGATAACCAATAC-
1 TATGAAATTTTGATAACC--TCCA
* *
5946 TATGAGATGTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCA
* * * **
5968 TATGATATATTGATAACCACTT
1 TATGAAATTTTGATAACCTCCA
* * * *
5990 TATAAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
*
6012 TATAAAAATTTTGATAA--TCACA
1 TAT-GAAATTTTGATAACCTC-CA
*
6034 CTATGAAATTGTGATAACCTCGC-
1 -TATGAAATTTTGATAACCTC-CA
* *
6057 TATGAAATTTTGATAAATCTTTC-
1 TATGAAATTTTGAT-AA-CCTCCA
* * * *
6080 TATAAAATTTTAATAAAGCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* * * * *
6103 TTTAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTCCA
* *
6125 TATGAAATCTTCATAA----C-
1 TATGAAATTTTGATAACCTCCA
* * *
6142 TA-CAAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCTCCA
**
6163 TATGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* * *
6184 TTATGAAATTTTGTTAATCTCCT
1 -TATGAAATTTTGATAACCTCCA
* * * *
6207 TGTGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
*
6229 TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CA
* **
6251 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
* *
6272 CTATGAAAATTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTCCA
*
6295 TATGAAATTTTGATATCCT-CA
1 TATGAAATTTTGATAACCTCCA
* *
6316 -CTG-AATTTTGATATCCTCC-
1 TATGAAATTTTGATAACCTCCA
* * *
6335 -CTG-AATTTTGGTATCCTCC-
1 TATGAAATTTTGATAACCTCCA
*
6354 -ATGAAATTTTGATTA-CTCCA
1 TATGAAATTTTGATAACCTCCA
* * *
6374 TCATAAAAGTTTAATAACC
1 T-ATGAAATTTTGATAACC
6393 ATCCTAATTT
Statistics
Matches: 384, Mismatches: 95, Indels: 69
0.70 0.17 0.13
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
19 38 0.10
20 12 0.03
21 16 0.04
22 227 0.59
23 72 0.19
24 6 0.02
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:6087 original size:23 final size:23
Alignment explanation
Indices: 5990--6118 Score: 75
Period size: 23 Copynumber: 5.7 Consensus size: 23
5980 ATAACCACTT
* * * *
5990 TATAAAAATTT-AAAAACCTCCA
1 TATAAAATTTTGATAAAGCTCCC
* * *
6012 TATAAAAATTTTGAT-AATCACAC
1 TAT-AAAATTTTGATAAAGCTCCC
* * * *
6035 TATGAAATTGTGAT-AACCTCGC
1 TATAAAATTTTGATAAAGCTCCC
* * **
6057 TATGAAATTTTGATAAATCTTTC
1 TATAAAATTTTGATAAAGCTCCC
*
6080 TATAAAATTTTAATAAAGCTCCC
1 TATAAAATTTTGATAAAGCTCCC
*
6103 TTTAAAATTTTGATAA
1 TATAAAATTTTGATAA
6119 CTTTCTTATG
Statistics
Matches: 82, Mismatches: 22, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
22 30 0.37
23 51 0.62
24 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (23 bp):
TATAAAATTTTGATAAAGCTCCC
Found at i:6087 original size:89 final size:90
Alignment explanation
Indices: 5927--6119 Score: 209
Period size: 89 Copynumber: 2.1 Consensus size: 90
5917 CTTCCCAATG
* * *
5927 AAATTTTGATAACCAATACTATGAGATGTTGATAACCTCCATATGATATATTGATAACCACTTTA
1 AAATTTTGATAACCAACACTATGAAATGTTGATAACCTCCATATGAAATATTGATAA-CACTTTA
5992 TAAAAA-TTTAA-AAACCTCCATATAA
65 TAAAAATTTTAATAAACCTCCAT-TAA
* *
6017 AAATTTTGATAATC-ACACTATGAAAT-TGTGATAACCTCGC-TATGAAATTTTGATAA-ATCTT
1 AAATTTTGATAACCAACACTATGAAATGT-TGATAACCTC-CATATGAAATATTGATAACA-CTT
* * * *
6078 TCTATAAAATTTTAATAAAGCTCCCTTTA
63 TATA-AAAATTTTAATAAACCTCCATTAA
6107 AAATTTTGATAAC
1 AAATTTTGATAAC
6120 TTTCTTATGA
Statistics
Matches: 87, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
87 1 0.01
88 7 0.08
89 38 0.44
90 33 0.38
91 8 0.09
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (90 bp):
AAATTTTGATAACCAACACTATGAAATGTTGATAACCTCCATATGAAATATTGATAACACTTTAT
AAAAATTTTAATAAACCTCCATTAA
Found at i:6374 original size:19 final size:19
Alignment explanation
Indices: 6300--6366 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
6290 CTTCATATGA
6300 AATTTTGATATCCT-CACTG
1 AATTTTGATATCCTCCA-TG
*
6319 AATTTTGATATCCTCCCTG
1 AATTTTGATATCCTCCATG
*
6338 AATTTTGGTATCCTCCATG
1 AATTTTGATATCCTCCATG
6357 AAATTTTGAT
1 -AATTTTGAT
6367 TACTCCATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 33 0.79
20 9 0.21
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.43
Consensus pattern (19 bp):
AATTTTGATATCCTCCATG
Found at i:6561 original size:66 final size:66
Alignment explanation
Indices: 6472--6619 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 66
6462 AATCAGATTT
* * * * * * * * ** *
6472 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATC-TTTATAAAATTTTGTTGACCCCTC
1 TGAAATTTTGATAATCACATTATGAAATTTAGATAACATCGCTT-TAAAATTTTGATAACAACAC
6536 TA
65 TA
* * *
6538 TGAAATTTTGATAATCACATTATGTAATTTAGATAACCTCGCTTTGAAATTTTGATAACAACACT
1 TGAAATTTTGATAATCACATTATGAAATTTAGATAACATCGCTTTAAAATTTTGATAACAACACT
6603 A
66 A
6604 TGAAATTTTGATAATC
1 TGAAATTTTGATAATC
6620 TTCATATAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (66 bp):
TGAAATTTTGATAATCACATTATGAAATTTAGATAACATCGCTTTAAAATTTTGATAACAACACT
A
Found at i:6567 original size:44 final size:43
Alignment explanation
Indices: 6449--6617 Score: 142
Period size: 44 Copynumber: 3.8 Consensus size: 43
6439 AAATACCACC
* * * * **
6449 ATGAAATTTTTG-TAATCAGATTTTGAAAATTTGATAACCTCTTT
1 ATGAAA-TTTTGATAA-CACATTATGAAATTTTGATAACCCCGCT
* * * * *
6493 ATGAAATTTTGATAACATCTTTATAAAATTTTGTTGACCCCTCT
1 ATGAAATTTTGATAACA-CATTATGAAATTTTGATAACCCCGCT
* * *
6537 ATGAAATTTTGATAATCACATTATGTAATTTAGATAACCTCGCT
1 ATGAAATTTTGATAA-CACATTATGAAATTTTGATAACCCCGCT
* *
6581 TTGAAATTTTGATAACAACACTATGAAATTTTGATAA
1 ATGAAATTTTGATAAC-ACATTATGAAATTTTGATAA
6618 TCTTCATATA
Statistics
Matches: 100, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
43 8 0.08
44 90 0.90
45 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (43 bp):
ATGAAATTTTGATAACACATTATGAAATTTTGATAACCCCGCT
Found at i:6610 original size:88 final size:88
Alignment explanation
Indices: 6449--6613 Score: 210
Period size: 88 Copynumber: 1.9 Consensus size: 88
6439 AAATACCACC
* * * * **
6449 ATGAAATTTTTGTAATCAGATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATCTT
1 ATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACAC
6514 TATAAAATTTTGTTGACCCCTCT
66 TATAAAATTTTGTTGACCCCTCT
*
6537 ATGAAA-TTTTGATAATCACATTATG-TAATTTAGATAACCTCGCTT-TGAAATTTTGATAACAA
1 ATGAAATTTTTG-TAATCACATTATGAAAATTT-GATAACCTC-CTTATGAAATTTTGATAACAA
*
6599 CACTATGAAATTTTG
63 CACTATAAAATTTTG
6614 ATAATCTTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
87 10 0.15
88 54 0.82
89 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (88 bp):
ATGAAATTTTTGTAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACAACAC
TATAAAATTTTGTTGACCCCTCT
Found at i:6753 original size:22 final size:22
Alignment explanation
Indices: 6472--6834 Score: 96
Period size: 22 Copynumber: 16.3 Consensus size: 22
6462 AATCAGATTT
* *
6472 TGAAAATTTGATAACC-TCTTTA
1 TGAAATTTTGATAACCTTC-ATA
6494 TGAAATTTTGATAACATCTT--TA
1 TGAAATTTTGATAAC--CTTCATA
* * * *
6516 TAAAATTTTGTTGACCCCTC-TA
1 TGAAATTTTGAT-AACCTTCATA
* *
6538 TGAAATTTTGATAATC-ACATTA
1 TGAAATTTTGATAACCTTCA-TA
* * * *
6560 TGTAATTTAGATAACC-TCGCTT
1 TGAAATTTTGATAACCTTC-ATA
**
6582 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAACCTTCA-TA
*
6604 TGAAATTTTGATAATCTTCATA
1 TGAAATTTTGATAACCTTCATA
* * *
6626 T-AAAATTTGATAATCATATCTTTA
1 TGAAATTTTGATAA-CCT-TC-ATA
**
6650 TGAAATTTCAATAATCAC-TC-TA
1 TGAAATTTTGATAA-C-CTTCATA
*
6672 TGAGA-TTTGATAACCTTC-TA
1 TGAAATTTTGATAACCTTCATA
* * *
6692 TCAAATTTTGGTACTCCTT-ATGAAA
1 TGAAATTTTGATA-ACCTTCAT---A
*
6717 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTCATA
*
6740 TGAAATTTTGATAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* * **
6762 TAAAATTTTGATAACCTCCCGA
1 TGAAATTTTGATAACCTTCATA
* *
6784 TGAAGTATT-AGTAACCTTC-TAA
1 TGAAATTTTGA-TAACCTTCAT-A
* *
6806 TGAAATTTTGTTAACC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
6828 TGAAATT
1 TGAAATT
6835 CGTATAACCT
Statistics
Matches: 250, Mismatches: 57, Indels: 68
0.67 0.15 0.18
Matches are distributed among these distances:
19 1 0.00
20 9 0.04
21 37 0.15
22 159 0.64
23 10 0.04
24 6 0.02
25 17 0.07
26 6 0.02
27 5 0.02
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:6930 original size:22 final size:22
Alignment explanation
Indices: 6898--6945 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
6888 TTGTGATAAT
*
6898 TAACCACCCTATA-AAATTTCAA
1 TAACCAACCTA-AGAAATTTCAA
*
6920 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTAAGAAATTTCAA
6942 TAAC
1 TAAC
6946 TTGATCCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTCAA
Found at i:6983 original size:22 final size:21
Alignment explanation
Indices: 6951--7005 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
6941 ATAACTTGAT
* *
6951 CCTATGAAATTTTGGTAACCA
1 CCTATGGAATTTTGATAACCA
*
6972 CACTATGGAATTTTGATAACCT
1 C-CTATGGAATTTTGATAACCA
6994 CCTCATGGAATT
1 CCT-ATGGAATT
7006 ATAATAGCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (21 bp):
CCTATGGAATTTTGATAACCA
Found at i:7853 original size:14 final size:15
Alignment explanation
Indices: 7834--7866 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
7824 TTATTAATAA
7834 ATTAGTAAATAT-TT
1 ATTAGTAAATATATT
*
7848 ATTAGTATATATATT
1 ATTAGTAAATATATT
7863 ATTA
1 ATTA
7867 TTTATTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTAGTAAATATATT
Found at i:7924 original size:2 final size:2
Alignment explanation
Indices: 7919--7971 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
7909 TTTATTTAAC
* * *
7919 AT AT AT AT AT AT AT GT AT AC AT A- AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7960 AT AT AT AT AT AT
1 AT AT AT AT AT AT
7972 TTCGGGCCCG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12901 original size:29 final size:30
Alignment explanation
Indices: 12868--12939 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
12858 ACTTGTAGCA
12868 TTTGGACGTTTTGTCCCT-TAAACTTCAAT
1 TTTGGACGTTTTGTCCCTATAAACTTCAAT
* * *
12897 TTTGGACATTTT-TCCCTATGAATTTCAAT
1 TTTGGACGTTTTGTCCCTATAAACTTCAAT
12926 TTTGGGACGTTTTG
1 TTT-GGACGTTTTG
12940 CCCCCTCAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 5 0.14
29 23 0.64
30 8 0.22
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (30 bp):
TTTGGACGTTTTGTCCCTATAAACTTCAAT
Found at i:13085 original size:28 final size:29
Alignment explanation
Indices: 13041--13113 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
13031 ATGCTGAGGG
*
13041 GGCAAAACATCTCAAAATTGAAATTCA-GA
1 GGCAAAACGTC-CAAAATTGAAATTCATGA
* *
13070 GGTAAAATGTCCAAAATTGAAATTCATGA
1 GGCAAAACGTCCAAAATTGAAATTCATGA
13099 GGCAAAACGTCCAAA
1 GGCAAAACGTCCAAA
13114 CGCTACAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 15 0.39
29 23 0.61
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (29 bp):
GGCAAAACGTCCAAAATTGAAATTCATGA
Found at i:14746 original size:11 final size:11
Alignment explanation
Indices: 14732--14769 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
14722 ATTCATAACA
14732 AATTTATAATT
1 AATTTATAATT
14743 AATTTATAATT
1 AATTTATAATT
14754 -ATTTGATAATT
1 AATTT-ATAATT
*
14765 TATTT
1 AATTT
14770 TATATAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:15856 original size:29 final size:29
Alignment explanation
Indices: 15801--15856 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
15791 ATCTGAGCTG
* *
15801 AAATTGAAACATTAGGCCCTGATTCAACC
1 AAATTGAAACATTAGGCCCTAAATCAACC
*
15830 AAATTGAAAGATTTA-GCCCTAAATCAA
1 AAATTGAAACA-TTAGGCCCTAAATCAA
15857 ACATTTCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (29 bp):
AAATTGAAACATTAGGCCCTAAATCAACC
Found at i:17141 original size:15 final size:15
Alignment explanation
Indices: 17108--17140 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
17098 ATAATACTAG
17108 TTTTCCTTCTTTTTT
1 TTTTCCTTCTTTTTT
17123 TTTTCCTT-TTTTTT
1 TTTTCCTTCTTTTTT
17137 TTTT
1 TTTT
17141 TTGTCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTCCTTCTTTTTT
Found at i:17150 original size:17 final size:16
Alignment explanation
Indices: 17108--17142 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17098 ATAATACTAG
*
17108 TTTTCC-TTCTTTTTT
1 TTTTCCTTTTTTTTTT
17123 TTTTCCTTTTTTTTTT
1 TTTTCCTTTTTTTTTT
17139 TTTT
1 TTTT
17143 GTCTTTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTCCTTTTTTTTTT
Done.