Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012595.1 Corchorus capsularis cultivar CVL-1 contig12616, 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: 91282
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:163 original size:2 final size:2
Alignment explanation
Indices: 158--184 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
148 ATCTAGTGTG
158 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
185 TATTTGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1824 original size:19 final size:20
Alignment explanation
Indices: 1800--1846 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1790 TTTTATTGGC
*
1800 TTTTTTGTAATT-GTCTATT
1 TTTTTTGTAATTCATCTATT
* *
1819 TTTTTTCTATTTCATCTATT
1 TTTTTTGTAATTCATCTATT
1839 TTTTTTGT
1 TTTTTTGT
1847 TCAAATTTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.13, C:0.09, G:0.06, T:0.72
Consensus pattern (20 bp):
TTTTTTGTAATTCATCTATT
Found at i:2855 original size:167 final size:166
Alignment explanation
Indices: 2474--2908 Score: 645
Period size: 167 Copynumber: 2.6 Consensus size: 166
2464 TGAGTCATTT
* * *
2474 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * ** * *
2539 TTAAGTAATCTGTCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
66 TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCAAAAGCAAGCCTTG
* * *
2604 ATGGGGATCTTTTATTAATTCCACCACTCTATTCAA
131 ATAGGGATCTTTTAGTAATTCCACCACTCTATTAAA
* * * *
2640 GTCCATTGAGAAATGACAAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
2705 TTAAGTAATCTATCAAGTAGGAAAAAACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCCTT
66 TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACT-CAAAAGCAAGCCTT
* *
2770 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
130 GATAGGGATCTTTTAGTAATTCCACCACTCTATTAAA
*
2807 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTGGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
*
2872 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAT
66 TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAAT
2909 TAATTCCCTC
Statistics
Matches: 238, Mismatches: 30, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
166 102 0.43
167 136 0.57
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
TTAAGTAATCTGTCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCAAAAGCAAGCCTTG
ATAGGGATCTTTTAGTAATTCCACCACTCTATTAAA
Found at i:3456 original size:6 final size:6
Alignment explanation
Indices: 3445--3477 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3435 TTAAACTTTG
3445 TTTTCT TTTTCT TTTTCT TTTT-T TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
3478 ATTTATTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTCT
Found at i:3465 original size:11 final size:12
Alignment explanation
Indices: 3445--3477 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
3435 TTAAACTTTG
3445 TTTTCTTTTTCT
1 TTTTCTTTTTCT
3457 TTTTCTTTTT-T
1 TTTTCTTTTTCT
3468 TTTTCTTTTT
1 TTTTCTTTTT
3478 ATTTATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:3470 original size:17 final size:17
Alignment explanation
Indices: 3445--3477 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3435 TTAAACTTTG
3445 TTTTCTTTTTCTTTTTC
1 TTTTCTTTTTCTTTTTC
*
3462 TTTTTTTTTTCTTTTT
1 TTTTCTTTTTCTTTTT
3478 ATTTATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTCTTTTTCTTTTTC
Found at i:6686 original size:71 final size:71
Alignment explanation
Indices: 6570--6712 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
6560 GCTCTGTTTC
6570 AGATTTAGGCAATTAAGCTTAAATACCCCTGTTTAATAAAAGGGTTTAAATTCTATTAGGATCAT
1 AGATTTAGGCAATTAAGCTTAAATACCCCTGTTTAATAAAAGGGTTTAAATTCTATTAGGATCAT
6635 CCTAAA
66 CCTAAA
*
6641 AGATTTAGGCAATTAAGCTTAAATACCCCTGTTTAATAAAAGGGTTTAAATTTTATTAGGATCAT
1 AGATTTAGGCAATTAAGCTTAAATACCCCTGTTTAATAAAAGGGTTTAAATTCTATTAGGATCAT
6706 CCTAAA
66 CCTAAA
6712 A
1 A
6713 AGGTGATTTT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (71 bp):
AGATTTAGGCAATTAAGCTTAAATACCCCTGTTTAATAAAAGGGTTTAAATTCTATTAGGATCAT
CCTAAA
Found at i:7455 original size:3 final size:3
Alignment explanation
Indices: 7441--7469 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
7431 CTTAAACTCT
7441 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7470 CGCCTTCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:10055 original size:99 final size:100
Alignment explanation
Indices: 9940--10127 Score: 333
Period size: 99 Copynumber: 1.9 Consensus size: 100
9930 TTTAGCCTCA
* *
9940 TAAATGTCTTTACATATTTTGTTATTGCATATGAAGTACTTATGG-AAAAAACCCTGAAAAATCA
1 TAAATGTCTTTACATATTTTGTTATTGCATATGAAGTACTCATGGAAAAAAACCCTGAAAAACCA
10004 ATATCCTATCAATCTTCAAATTTTCAATGTCTTTT
66 ATATCCTATCAATCTTCAAATTTTCAATGTCTTTT
*
10039 TAAATGTCTTTACATATTTTGTTATTGCATATGAAGTACTCATGGAAAAAAACCCTGAAAAGCCA
1 TAAATGTCTTTACATATTTTGTTATTGCATATGAAGTACTCATGGAAAAAAACCCTGAAAAACCA
*
10104 ATATCCTTTCAATCTTCAAATTTT
66 ATATCCTATCAATCTTCAAATTTT
10128 ATCTCTGTTC
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
99 44 0.52
100 40 0.48
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (100 bp):
TAAATGTCTTTACATATTTTGTTATTGCATATGAAGTACTCATGGAAAAAAACCCTGAAAAACCA
ATATCCTATCAATCTTCAAATTTTCAATGTCTTTT
Found at i:10769 original size:1 final size:1
Alignment explanation
Indices: 10763--10801 Score: 69
Period size: 1 Copynumber: 39.0 Consensus size: 1
10753 TCAAACATTT
*
10763 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10802 GAAGAAGAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:10802 original size:6 final size:6
Alignment explanation
Indices: 10763--10839 Score: 59
Period size: 6 Copynumber: 13.2 Consensus size: 6
10753 TCAAACATTT
* * * *
10763 AAAAA- AAAAA- AAAAAA AAAAAA AAAAAA AAAAAG AAAAAG AAGAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * * * *
10809 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
10840 GAACCTACCT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
5 10 0.14
6 59 0.86
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:10806 original size:3 final size:3
Alignment explanation
Indices: 10794--10839 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
10784 AAAAAAAAAA
*
10794 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
10840 GAACCTACCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:24490 original size:16 final size:16
Alignment explanation
Indices: 24469--24500 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
24459 TTTCAACTAT
24469 ATTTGTATTGTTCATA
1 ATTTGTATTGTTCATA
24485 ATTTGTATTGTTCATA
1 ATTTGTATTGTTCATA
24501 CAGCAACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (16 bp):
ATTTGTATTGTTCATA
Found at i:26935 original size:52 final size:52
Alignment explanation
Indices: 26857--26961 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
26847 GTACTTAACA
26857 GCCTTCTGTCCTACCTGGATGATTGAGCATTTAATAGTACTAGCATTTTCAT
1 GCCTTCTGTCCTACCTGGATGATTGAGCATTTAATAGTACTAGCATTTTCAT
26909 GCCTTCTGTCCTACCTGGATGATTGAGCATTTAATAGTACTAGCATTTTCAT
1 GCCTTCTGTCCTACCTGGATGATTGAGCATTTAATAGTACTAGCATTTTCAT
26961 G
1 G
26962 TTGAAGTTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (52 bp):
GCCTTCTGTCCTACCTGGATGATTGAGCATTTAATAGTACTAGCATTTTCAT
Found at i:35298 original size:31 final size:31
Alignment explanation
Indices: 35260--35368 Score: 143
Period size: 31 Copynumber: 3.6 Consensus size: 31
35250 CCCTAACTGA
35260 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
* *
35291 TTATATCCTTAATTGCTCGAAATCAAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
** * *
35322 TTATATCCTTAATTGCTT--TTTTG-TAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
35350 TTATATCCTTAATTGCTTG
1 TTATATCCTTAATTGCTTG
35369 CGGCAGCAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 22 0.32
29 1 0.01
31 46 0.67
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACG
Found at i:35444 original size:3 final size:3
Alignment explanation
Indices: 35436--35494 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
35426 CCCGTATTTT
* * *
35436 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ACA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
35484 ATA ATC ATA AT
1 ATA ATA ATA AT
35495 TTTCATAACT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:36521 original size:31 final size:31
Alignment explanation
Indices: 36476--36554 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
36466 TACAAAACAT
* *
36476 GCAATTTAGGATATAATGTTTTTGATTTCGA
1 GCAATTAAGGATATAATGTTTTCGATTTCGA
* *
36507 GCAATTAAGTATATAACGTTTTCGATTTCGA
1 GCAATTAAGGATATAATGTTTTCGATTTCGA
36538 GCAATTAAGGATATAAT
1 GCAATTAAGGATATAAT
36555 CAGTTAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (31 bp):
GCAATTAAGGATATAATGTTTTCGATTTCGA
Found at i:36707 original size:31 final size:29
Alignment explanation
Indices: 36672--36738 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 29
36662 TCTAACGGAC
*
36672 TATATCCTTAATTGCTCGATTTTCTTAACGT
1 TATATCCTTAATTGCTCG-TTTT-GTAACGT
* *
36703 TATATCCTTAATTGTTTGTTTTGTAACGT
1 TATATCCTTAATTGCTCGTTTTGTAACGT
36732 TATATCC
1 TATATCC
36739 CAAATTGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.39
30 4 0.12
31 16 0.48
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.51
Consensus pattern (29 bp):
TATATCCTTAATTGCTCGTTTTGTAACGT
Found at i:40148 original size:16 final size:16
Alignment explanation
Indices: 40129--40178 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
40119 TTCTTTTCCC
40129 TTCCTTCCTATTTCTT
1 TTCCTTCCTATTTCTT
* *
40145 TTCCCTTGCTACTTCATT
1 TT-CCTTCCTATTTC-TT
40163 TT-CTTCCTATTTCTT
1 TTCCTTCCTATTTCTT
40178 T
1 T
40179 CCTCTCTACC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 3 0.11
16 11 0.39
17 10 0.36
18 4 0.14
ACGTcount: A:0.08, C:0.30, G:0.02, T:0.60
Consensus pattern (16 bp):
TTCCTTCCTATTTCTT
Found at i:42231 original size:14 final size:15
Alignment explanation
Indices: 42197--42231 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
42187 TCATTAGTCC
42197 ATTTTTGCCCTTAGA
1 ATTTTTGCCCTTAGA
42212 ATTTTTGCCCTTAGA
1 ATTTTTGCCCTTAGA
42227 ATTTT
1 ATTTT
42232 CTTCTAGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.11, T:0.51
Consensus pattern (15 bp):
ATTTTTGCCCTTAGA
Found at i:44580 original size:41 final size:41
Alignment explanation
Indices: 44535--44617 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
44525 ATAGCTGATC
* *
44535 CATTTTGGTATCGCGATTAGAAGGGTTAGTTACTGAAAGTT
1 CATTTTGGTATCACGATTAGAAGGGTTAGTTACTAAAAGTT
44576 CATTTTGGTATCACGATTAGAAGGGTTAGTTACTAAAAGTT
1 CATTTTGGTATCACGATTAGAAGGGTTAGTTACTAAAAGTT
44617 C
1 C
44618 TCTCAATCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTTGGTATCACGATTAGAAGGGTTAGTTACTAAAAGTT
Found at i:55510 original size:6 final size:6
Alignment explanation
Indices: 55499--55525 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
55489 TAGCTGACCC
55499 AATCAA AATCAA AATCAA AATCAA AAT
1 AATCAA AATCAA AATCAA AATCAA AAT
55526 AATTTTGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (6 bp):
AATCAA
Found at i:78815 original size:30 final size:30
Alignment explanation
Indices: 78780--78842 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
78770 TATACTAAAT
* *
78780 ACACAAACAAGTAAATTATAAAGAAAACTC
1 ACACAAACAAATAAATTATAAAAAAAACTC
78810 ACACAAACAAATAAATTATAAAAAAAACTC
1 ACACAAACAAATAAATTATAAAAAAAACTC
78840 ACA
1 ACA
78843 TTTCGTGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.63, C:0.17, G:0.03, T:0.16
Consensus pattern (30 bp):
ACACAAACAAATAAATTATAAAAAAAACTC
Found at i:85984 original size:16 final size:16
Alignment explanation
Indices: 85963--85996 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
85953 CCTGTTAATC
85963 TATAACTATTAAAGAA
1 TATAACTATTAAAGAA
*
85979 TATAACTATTAAGGAA
1 TATAACTATTAAAGAA
85995 TA
1 TA
85997 GCTTACCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (16 bp):
TATAACTATTAAAGAA
Done.