Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015881.1 Corchorus capsularis cultivar CVL-1 contig15902, 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: 20811
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1354 original size:219 final size:219
Alignment explanation
Indices: 975--1414 Score: 880
Period size: 219 Copynumber: 2.0 Consensus size: 219
965 GTTCCAAAAC
975 AACAAGTTAAATTAGTTTTCATGTTGAGTGGCAAAATCAAAGAACCAAAGTTGCTCAAACCATTG
1 AACAAGTTAAATTAGTTTTCATGTTGAGTGGCAAAATCAAAGAACCAAAGTTGCTCAAACCATTG
1040 AAACTTACTCCTTACCTTTAACTCTCATATATCCATCTTTAGTGGCCAAGAAATCCACTATTCAA
66 AAACTTACTCCTTACCTTTAACTCTCATATATCCATCTTTAGTGGCCAAGAAATCCACTATTCAA
1105 CCCAAGACCAAGAACAACTTCGTAAGAGGAAGCTCATGCCTCAATTGCATGTTGGTTTCCATACA
131 CCCAAGACCAAGAACAACTTCGTAAGAGGAAGCTCATGCCTCAATTGCATGTTGGTTTCCATACA
1170 ATAATTCTTGAACCATTATGTGGG
196 ATAATTCTTGAACCATTATGTGGG
1194 AACAAGTTAAATTAGTTTTCATGTTGAGTGGCAAAATCAAAGAACCAAAGTTGCTCAAACCATTG
1 AACAAGTTAAATTAGTTTTCATGTTGAGTGGCAAAATCAAAGAACCAAAGTTGCTCAAACCATTG
1259 AAACTTACTCCTTACCTTTAACTCTCATATATCCATCTTTAGTGGCCAAGAAATCCACTATTCAA
66 AAACTTACTCCTTACCTTTAACTCTCATATATCCATCTTTAGTGGCCAAGAAATCCACTATTCAA
1324 CCCAAGACCAAGAACAACTTCGTAAGAGGAAGCTCATGCCTCAATTGCATGTTGGTTTCCATACA
131 CCCAAGACCAAGAACAACTTCGTAAGAGGAAGCTCATGCCTCAATTGCATGTTGGTTTCCATACA
1389 ATAATTCTTGAACCATTATGTGGG
196 ATAATTCTTGAACCATTATGTGGG
1413 AA
1 AA
1415 ATGGTTTCGA
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 221 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.29
Consensus pattern (219 bp):
AACAAGTTAAATTAGTTTTCATGTTGAGTGGCAAAATCAAAGAACCAAAGTTGCTCAAACCATTG
AAACTTACTCCTTACCTTTAACTCTCATATATCCATCTTTAGTGGCCAAGAAATCCACTATTCAA
CCCAAGACCAAGAACAACTTCGTAAGAGGAAGCTCATGCCTCAATTGCATGTTGGTTTCCATACA
ATAATTCTTGAACCATTATGTGGG
Found at i:19454 original size:36 final size:34
Alignment explanation
Indices: 19412--19530 Score: 138
Period size: 36 Copynumber: 3.4 Consensus size: 34
19402 CTCTTTTTAG
*
19412 ATTAAGTTGTTTATTGACTTCACTTAATTACCTTGA
1 ATTAAGTTCTTTATTGAC-TCACTTAATTACC-TGA
19448 ATTAAGTTCTTTATT--CT-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCACTTAATTA-CCTGA
*
19480 ATTAAG-CCTTTTATTGACCTCACTTAATTATCCTGA
1 ATTAAGTTC-TTTATTGA-CTCACTTAATTA-CCTGA
19516 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
19531 TTACTTAATT
Statistics
Matches: 72, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
31 1 0.01
32 24 0.33
33 3 0.04
34 1 0.01
35 2 0.03
36 40 0.56
37 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (34 bp):
ATTAAGTTCTTTATTGACTCACTTAATTACCTGA
Found at i:19474 original size:32 final size:32
Alignment explanation
Indices: 19433--19545 Score: 122
Period size: 32 Copynumber: 3.4 Consensus size: 32
19423 TATTGACTTC
19433 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
* *
19465 ACTTAATTACCCTGAATTAAG-CCTTTTATTGACCT
1 ACTTAATTACCTTGAATTAAGTTC-TTTATT---CT
*
19500 CACTTAATTATCC-TGAATTAAGTTCTTTATTTT
1 -ACTTAATTA-CCTTGAATTAAGTTCTTTATTCT
*
19533 ACTTAATTTCCTT
1 ACTTAATTACCTT
19546 TCCTGAAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
31 3 0.04
32 35 0.51
33 1 0.01
35 2 0.03
36 24 0.35
37 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (32 bp):
ACTTAATTACCTTGAATTAAGTTCTTTATTCT
Found at i:19615 original size:36 final size:36
Alignment explanation
Indices: 19565--19936 Score: 356
Period size: 36 Copynumber: 10.1 Consensus size: 36
19555 TAATCTTGTG
* *
19565 TTTTTTACTTAATTTCCTTTG-AATTAAGCCAGTCTT
1 TTTTTTACCTAATTTCC-TTGAAACTAAGCCAGTCTT
** * *
19601 TCCTTTACCTAATTTCATTGAAATTAAGCCAGTCTT
1 TTTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTT
* *
19637 TTCTTTACCTAGTTTCCTTGAAACTAAGCCAGCCTCTTTTT
1 TTTTTTACCTAATTTCCTTGAAACTAAGCCAG--TC---TT
* * *
19678 TTTTTTACTTAGTTTCCTTGAAACTAAGTCAGTC-T
1 TTTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTT
* * * *
19713 TCTTTTACCTAATTTCTTTGAAATTAAGCCAGTATT
1 TTTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTT
* *
19749 TTCTTTACCTAGTTTCCTTGAAACTAAGCCAGCCTCTTTT
1 TTTTTTACCTAATTTCCTTGAAACTAAGCCAG--TC--TT
* *
19789 TTTTTTACTTAGTTT-CTTGAAACTAAGCCAGTC-T
1 TTTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTT
* * *
19823 TCTTTTACCTAATTTCCTTGAAATTAAACCAGTCTT
1 TTTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTT
* *
19859 TTCTTTACTTAATTTCCTTGAAACTAAGCCAGTCATT
1 TTTTTTACCTAATTTCCTTGAAACTAAGCCAGTC-TT
* * * *
19896 TCTTTTACCTAATTACCTTGAAATTAAGTCAGTCTT
1 TTTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTT
*
19932 CTTTT
1 TTTTT
19937 AGTCTTTCTT
Statistics
Matches: 278, Mismatches: 44, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
34 13 0.05
35 47 0.17
36 119 0.43
37 32 0.12
38 3 0.01
39 18 0.06
40 15 0.05
41 31 0.11
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (36 bp):
TTTTTTACCTAATTTCCTTGAAACTAAGCCAGTCTT
Found at i:19734 original size:112 final size:111
Alignment explanation
Indices: 19565--19937 Score: 531
Period size: 110 Copynumber: 3.4 Consensus size: 111
19555 TAATCTTGTG
* *
19565 TTTTTTACTTAATTTCCTTTG-AATTAAGCCAGTCTTTCCTTTACCTAATTTCATTGAAATTAAG
1 TTTTTTACTTAATTTCC-TTGAAACTAAGCCAGTC-TTCTTTTACCTAATTTCATTGAAATTAAG
19629 CCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGCCTCTTTTT
64 CCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGCCTC-TTTT
* * *
19678 TTTTTTACTTAGTTTCCTTGAAACTAAGTCAGTCTTCTTTTACCTAATTTCTTTGAAATTAAGCC
1 TTTTTTACTTAATTTCCTTGAAACTAAGCCAGTCTTCTTTTACCTAATTTCATTGAAATTAAGCC
*
19743 AGTATTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGCCTCTTTT
66 AGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGCCTCTTTT
* * *
19789 TTTTTTACTTAGTTT-CTTGAAACTAAGCCAGTCTTCTTTTACCTAATTTCCTTGAAATTAAACC
1 TTTTTTACTTAATTTCCTTGAAACTAAGCCAGTCTTCTTTTACCTAATTTCATTGAAATTAAGCC
* * *
19853 AGTCTTTTCTTTACTTAATTTCCTTGAAACTAAGCCAG--TC-ATT
66 AGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGCCTCTTTT
* * * * *
19896 TCTTTTACCTAATTACCTTGAAATTAAGTCAGTCTTCTTTTA
1 TTTTTTACTTAATTTCCTTGAAACTAAGCCAGTCTTCTTTTA
19938 GTCTTTCTTT
Statistics
Matches: 239, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
107 13 0.05
108 26 0.11
110 81 0.34
111 19 0.08
112 73 0.31
113 27 0.11
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (111 bp):
TTTTTTACTTAATTTCCTTGAAACTAAGCCAGTCTTCTTTTACCTAATTTCATTGAAATTAAGCC
AGTCTTTTCTTTACCTAGTTTCCTTGAAACTAAGCCAGCCTCTTTT
Found at i:19940 original size:11 final size:12
Alignment explanation
Indices: 19924--20097 Score: 140
Period size: 11 Copynumber: 15.2 Consensus size: 12
19914 TGAAATTAAG
19924 TCAGTCTTCTTT
1 TCAGTCTTCTTT
19936 T-AGTCTT-TCTT
1 TCAGTCTTCT-TT
19947 TCAGTCTT-TCTT
1 TCAGTCTTCT-TT
19959 TCAGTCTT-TTT
1 TCAGTCTTCTTT
*
19970 CTCAGTTTTCTCTT
1 -TCAGTCTTCT-TT
* *
19984 TCAATCTT-GTT
1 TCAGTCTTCTTT
19995 TCAGTCTTCTCTT
1 TCAGTCTTCT-TT
* *
20008 TCAGACTT-GTT
1 TCAGTCTTCTTT
*
20019 TCAGTCTTTTTT
1 TCAGTCTTCTTT
20031 TCAGTCTTCTTT
1 TCAGTCTTCTTT
*
20043 TCAATCTTC-TT
1 TCAGTCTTCTTT
20054 TC---CTT-TTT
1 TCAGTCTTCTTT
20062 TCAGTCTT-TTT
1 TCAGTCTTCTTT
20073 TCAGTCTTC-TT
1 TCAGTCTTCTTT
*
20084 TCAGTCTTTTTT
1 TCAGTCTTCTTT
20096 TC
1 TC
20098 CTTGACATTA
Statistics
Matches: 135, Mismatches: 13, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
8 7 0.05
10 1 0.01
11 57 0.42
12 52 0.39
13 16 0.12
14 2 0.01
ACGTcount: A:0.10, C:0.23, G:0.08, T:0.59
Consensus pattern (12 bp):
TCAGTCTTCTTT
Found at i:19947 original size:12 final size:12
Alignment explanation
Indices: 19924--20097 Score: 147
Period size: 12 Copynumber: 15.2 Consensus size: 12
19914 TGAAATTAAG
19924 TCAGTC-TTCTT
1 TCAGTCTTTCTT
*
19935 TTAGTCTTTCTT
1 TCAGTCTTTCTT
19947 TCAGTCTTTCTT
1 TCAGTCTTTCTT
19959 TCAGTCTTT-TT
1 TCAGTCTTTCTT
*
19970 CTCAGTTTTCTCTT
1 -TCAGTCTT-TCTT
* *
19984 TCAATC-TTGTT
1 TCAGTCTTTCTT
19995 TCAGTCTTCTCTT
1 TCAGTCTT-TCTT
* *
20008 TCAGAC-TTGTT
1 TCAGTCTTTCTT
*
20019 TCAGTCTTTTTT
1 TCAGTCTTTCTT
20031 TCAGTC-TTCTTT
1 TCAGTCTTTC-TT
*
20043 TCAATC-TTCTT
1 TCAGTCTTTCTT
20054 TC---CTTT-TT
1 TCAGTCTTTCTT
20062 TCAGTCTTT-TT
1 TCAGTCTTTCTT
20073 TCAGTC-TTCTT
1 TCAGTCTTTCTT
*
20084 TCAGTCTTTTTT
1 TCAGTCTTTCTT
20096 TC
1 TC
20098 CTTGACATTA
Statistics
Matches: 134, Mismatches: 15, Indels: 27
0.76 0.09 0.15
Matches are distributed among these distances:
8 5 0.04
9 2 0.01
10 2 0.01
11 49 0.37
12 61 0.46
13 13 0.10
14 2 0.01
ACGTcount: A:0.10, C:0.23, G:0.08, T:0.59
Consensus pattern (12 bp):
TCAGTCTTTCTT
Found at i:19964 original size:24 final size:23
Alignment explanation
Indices: 19924--20097 Score: 162
Period size: 24 Copynumber: 7.6 Consensus size: 23
19914 TGAAATTAAG
*
19924 TCAGTC-TTCTTTTAGTCTTTCTT
1 TCAGTCTTTCTTTCAGTC-TTCTT
*
19947 TCAGTCTTTCTTTCAGTCTTTTT
1 TCAGTCTTTCTTTCAGTCTTCTT
* * *
19970 CTCAGTTTTCTCTTTCAATCTTGTT
1 -TCAGTCTT-TCTTTCAGTCTTCTT
* *
19995 TCAGTCTTCTCTTTCAGACTTGTT
1 TCAGTCTT-TCTTTCAGTCTTCTT
*
20019 TCAGTCTTTTTTTCAGTCTTCTTT
1 TCAGTCTTTCTTTCAGTCTTC-TT
* *
20043 TCAATC-TTCTTTC---CTTTTT
1 TCAGTCTTTCTTTCAGTCTTCTT
20062 TCAGTCTTT-TTTCAGTCTTCTT
1 TCAGTCTTTCTTTCAGTCTTCTT
*
20084 TCAGTCTTTTTTTC
1 TCAGTCTTTCTTTC
20098 CTTGACATTA
Statistics
Matches: 126, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
19 11 0.09
20 5 0.04
22 14 0.11
23 30 0.24
24 53 0.42
25 13 0.10
ACGTcount: A:0.10, C:0.23, G:0.08, T:0.59
Consensus pattern (23 bp):
TCAGTCTTTCTTTCAGTCTTCTT
Found at i:20204 original size:33 final size:33
Alignment explanation
Indices: 20160--20357 Score: 181
Period size: 33 Copynumber: 5.9 Consensus size: 33
20150 TTTGCTGACT
*
20160 TTACTTAATTCTTGTGAAATTAAGCCTTTGCTAA
1 TTACTTAATTCTTGTGAAATTAAGTCTTTG-TAA
* *
20194 TT-CTTAATTCTTGTAAAATTAAGACTTTG-AA
1 TTACTTAATTCTTGTGAAATTAAGTCTTTGTAA
* * *
20225 CTTGCTT-ATCTCATGTGAAATTATGTCTTTGATAA
1 -TTACTTAAT-TCTTGTGAAATTAAGTCTTTG-TAA
* *
20260 TTCACTTAATTCTTGTGAGATTAAGTTTTTG-AA
1 TT-ACTTAATTCTTGTGAAATTAAGTCTTTGTAA
* * *
20293 CTTGCTTAACTCTTGTGAAATTATGTCTTTGATAA
1 -TTACTTAATTCTTGTGAAATTAAGTCTTTG-TAA
*
20328 TTCACTTAATTCTTGTGAGATTAAGT-TTTG
1 TT-ACTTAATTCTTGTGAAATTAAGTCTTTG
20358 GATCTTGCTT
Statistics
Matches: 133, Mismatches: 20, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
31 2 0.02
32 4 0.03
33 70 0.53
34 12 0.09
35 43 0.32
36 2 0.02
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (33 bp):
TTACTTAATTCTTGTGAAATTAAGTCTTTGTAA
Found at i:20291 original size:68 final size:68
Alignment explanation
Indices: 20163--20367 Score: 279
Period size: 68 Copynumber: 3.0 Consensus size: 68
20153 GCTGACTTTA
* * * * * * * **
20163 CTTAATTCTTGTGAAATTAAGCCTTTGCTAATT--CTTAATTCTTGTAAAATTAAGACTTTGAAC
1 CTTAACTCATGTGAAATTATGTCTTTGATAATTCACTTAATTCTTGTGAGATTAAGTTTTTGAAC
20226 TTG
66 TTG
*
20229 CTTATCTCATGTGAAATTATGTCTTTGATAATTCACTTAATTCTTGTGAGATTAAGTTTTTGAAC
1 CTTAACTCATGTGAAATTATGTCTTTGATAATTCACTTAATTCTTGTGAGATTAAGTTTTTGAAC
20294 TTG
66 TTG
* * *
20297 CTTAACTCTTGTGAAATTATGTCTTTGATAATTCACTTAATTCTTGTGAGATTAAGTTTTGGATC
1 CTTAACTCATGTGAAATTATGTCTTTGATAATTCACTTAATTCTTGTGAGATTAAGTTTTTGAAC
20362 TTG
66 TTG
20365 CTT
1 CTT
20368 GCTTTTCTTA
Statistics
Matches: 123, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
66 27 0.22
68 96 0.78
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (68 bp):
CTTAACTCATGTGAAATTATGTCTTTGATAATTCACTTAATTCTTGTGAGATTAAGTTTTTGAAC
TTG
Done.