Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008975.1 Corchorus capsularis cultivar CVL-1 contig08996, 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: 30031
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:795 original size:53 final size:52
Alignment explanation
Indices: 666--850 Score: 203
Period size: 53 Copynumber: 3.4 Consensus size: 52
656 CCCAACAATT
** * * *
666 AAAAGTCCTCAAACACAAGGGCATTTATAAGTCCCTAGACACAGAGGCAATTCTAGATT
1 AAAAGTCCTCAAACACAAGGG----TATTCGTCCCTAAACACAGAGGC-A-TCTA-CTC
725 AAAAGTCCTCAAACACAAGGGTATTCGTCCCTAAACACAGAGGCACCTCT-CTC
1 AAAAGTCCTCAAACACAAGGGTATTCGTCCCTAAACACAGAGGCA--TCTACTC
*
778 AAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATCTACATC
1 AAAAGTCCTCAAACACAAGGGTATTCGTCCCTAAACACAGAGGCATCTAC-TC
*
831 -AAAGTCCTCAAGCACAAGGG
1 AAAAGTCCTCAAACACAAGGG
851 CATCTATATT
Statistics
Matches: 115, Mismatches: 8, Indels: 13
0.85 0.06 0.10
Matches are distributed among these distances:
51 3 0.03
52 20 0.17
53 47 0.41
54 1 0.01
55 23 0.20
59 21 0.18
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (52 bp):
AAAAGTCCTCAAACACAAGGGTATTCGTCCCTAAACACAGAGGCATCTACTC
Found at i:885 original size:30 final size:30
Alignment explanation
Indices: 805--906 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
795 AGGGTATTCA
* *
805 TCCCTAAACACAGAGGCATCTACATCAAAG
1 TCCCTAAACACAGAGGCATCTATATTAAAG
*
835 T-CCTCAAGCACA-AGGGCATCTATATTAAAG
1 TCCCT-AAACACAGA-GGCATCTATATTAAAG
* *
865 TCCCTAAACACAGAGACATCTATACTAAAG
1 TCCCTAAACACAGAGGCATCTATATTAAAG
*
895 TCCCCAAACACA
1 TCCCTAAACACA
907 TATAACACAG
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
29 4 0.07
30 53 0.87
31 4 0.07
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (30 bp):
TCCCTAAACACAGAGGCATCTATATTAAAG
Found at i:2587 original size:29 final size:29
Alignment explanation
Indices: 2537--2598 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
2527 GTATACCTTA
*
2537 ATTAAAACTTTATTAATATTTAATCTTTTT
1 ATTAAAACTTTATTAATATTTAAT-TTGTT
*
2567 ATTAAAAC-TTATT-TTGATTTAATTTGTT
1 ATTAAAACTTTATTAAT-ATTTAATTTGTT
2595 ATTA
1 ATTA
2599 GATTATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 9 0.31
29 12 0.41
30 8 0.28
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.56
Consensus pattern (29 bp):
ATTAAAACTTTATTAATATTTAATTTGTT
Found at i:5419 original size:6 final size:6
Alignment explanation
Indices: 5408--5432 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5398 CATGCATTTA
5408 ATCTAT ATCTAT ATCTAT ATCTAT A
1 ATCTAT ATCTAT ATCTAT ATCTAT A
5433 CTAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
ATCTAT
Found at i:8452 original size:446 final size:437
Alignment explanation
Indices: 7386--8452 Score: 1081
Period size: 438 Copynumber: 2.4 Consensus size: 437
7376 GTATTTTTCC
* * * * * * * * *
7386 CTATTTGTCCGATTAACGTGATTCAAGTGTCAATTAAAAGGTAATTTCATAATCTACAATTTTCA
1 CTATTTATCCAATTAAGGTAATTCAGGTGTCTATTAAAAAGTAATTTCATGATCTACAACTTTCA
* * ** * * ** * *
7451 T-ACAGAACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTCCGAAATTTTGTGGTT
66 TGAAAG-ACTCAAAAGCAAATTTTAATGTTTCAATTCAAAAAAATACTTCATAAATTTGGTCGTT
** ***** * * * * ** * *
7515 TTGATTGCCGGCCAATTTAATATCGTCTAATTTTTTG-TCCACATGCCCGATTGAAGTTATTGAA
130 TCAATTGATAATCTATTTAATACCATATAA-TTTTTGATCCACATATCCGATTAAAGTTATTCAA
* * *
7579 GTGTCGGTTAAAAGGATATTGCATGATTTACGACTTTCATGAAGGACCCGAAAGCTAAATTTGAT
194 GTGTCGGTTAAAAGGATACTGCATGATCTACGACTTTCATGAAGAACCCGAAAGCTAAATTTGAT
* * *
7644 CTACAAGTTTCATGAAGGGTTCAAAAGAGAGTTTTTATGTTCAAAATCTCCATTAACAAACATTT
259 CTACAAGTTTCATAAAGGGTTCAAAAGAGAATTTTTATGTTCAAAATATCCATTAACAAACATTT
* * * *
7709 TCTTATTTGGATTATTTATCAAATGGCCCTCATATTTTTCTACTTTATACTACTTAGTCCTTTAC
324 TCTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCCTTTAC
*
7774 AAATTCTATCTTAATCTAACATTTAAGATTTATATTTTTTATTCTTTGTT
389 AAATTATATCTTAATCT-ACATTTAAGATTTATATTTTTTATTCTTTGTT
* * * * * *
7824 TTATTTATCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCA
1 CTATTTATCCAATTAAGGTAATTCAGGTGTCTATTAAAAAGTAATTTCATGATCTACAACTTTCA
* * *
7889 TGAAGGACTCAAAAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTCATAAATTTGGTCGTTT
66 TGAAAGACTCAAAAGCAAATTTTAATGTTTCAATTCAAAAAAATACTTCATAAATTTGGTCGTTT
* ** *
7954 CAATTGTTGGTCTATTTAATACCATATAATTTTTGATCCACATGTCCGATTAAAGTTATTCAAGT
131 CAATTGATAATCTATTTAATACCATATAATTTTTGATCCACATATCCGATTAAAGTTATTCAAGT
* * * * * *
8019 GTCGGTTAAAAGGTTACTGTATGGTCTACGACTTTCGTGAAGAACCTGAAAG-TTAATTTGATCT
196 GTCGGTTAAAAGGATACTGCATGATCTACGACTTTCATGAAGAACCCGAAAGCTAAATTTGATCT
* * * * *
8083 ACGAGTTTCATAAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATATCCATTAAGAAATATTTT
261 ACAAGTTTCATAAAGGGTTCAAAAGAGAATTTTTATG-TTCAAAATATCCATTAACAAACATTTT
* *
8148 CTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTATTTTATATTTTATGCTACTTAGTT
325 CTTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTA-CTT-TA---TA--CTACTTAGTC
* *
8213 CTTTATAAATTATATC-TAA-CT-CGATTTAACG-TTTCATTTTTTTTTATTTTCTTTGTT
383 CTTTACAAATTATATCTTAATCTAC-ATTTAA-GATTT-A-TATTTTTTA--TTCTTTGTT
* * *
8270 CTATTTGTCCAATTAAGGTAATTTAGGTGTCTATTAAAAAGTAATTTTATGATCTACAACTTTCA
1 CTATTTATCCAATTAAGGTAATTCAGGTGTCTATTAAAAAGTAATTTCATGATCTACAACTTTCA
* * * * * * * *
8335 TGAAAGATTCAAAAGCTATTTTTCATGTTTCAATTCTAAAAATTACTT-TTGAAATTTTGT-GAT
66 TGAAAGACTCAAAAGCAAATTTTAATGTTTCAATTCAAAAAAATACTTCAT-AAATTTGGTCG-T
* ** * * * *
8398 TTCTATTGATAATCTATTTAATTTCATATTATTTTTTATCCAGATATTCGATTAA
129 TTCAATTGATAATCTATTTAATACCATATAATTTTTGATCCACATATCCGATTAA
8453 TAAAGATTCA
Statistics
Matches: 525, Mismatches: 86, Indels: 28
0.82 0.13 0.04
Matches are distributed among these distances:
437 50 0.10
438 260 0.50
439 4 0.01
440 2 0.00
441 1 0.00
442 9 0.02
443 6 0.01
444 11 0.02
445 25 0.05
446 157 0.30
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (437 bp):
CTATTTATCCAATTAAGGTAATTCAGGTGTCTATTAAAAAGTAATTTCATGATCTACAACTTTCA
TGAAAGACTCAAAAGCAAATTTTAATGTTTCAATTCAAAAAAATACTTCATAAATTTGGTCGTTT
CAATTGATAATCTATTTAATACCATATAATTTTTGATCCACATATCCGATTAAAGTTATTCAAGT
GTCGGTTAAAAGGATACTGCATGATCTACGACTTTCATGAAGAACCCGAAAGCTAAATTTGATCT
ACAAGTTTCATAAAGGGTTCAAAAGAGAATTTTTATGTTCAAAATATCCATTAACAAACATTTTC
TTATTTGAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCCTTTACAA
ATTATATCTTAATCTACATTTAAGATTTATATTTTTTATTCTTTGTT
Found at i:10958 original size:12 final size:12
Alignment explanation
Indices: 10941--10978 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
10931 CTACACACAT
10941 ATATATAATATA
1 ATATATAATATA
10953 ATATATAA-ATA
1 ATATATAATATA
10964 TATATATAATATA
1 -ATATATAATATA
10977 AT
1 AT
10979 GAGTGATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATATAATATA
Found at i:13616 original size:25 final size:26
Alignment explanation
Indices: 13581--13659 Score: 76
Period size: 25 Copynumber: 3.1 Consensus size: 26
13571 TACTAATTAT
*
13581 CTTCTTCTTACTGGTTACCATTTTTA
1 CTTCTTCTTACTGATTACCATTTTTA
*
13607 CTTCTT-TTACTGAATACCATTTGTTA
1 CTTCTTCTTACTGATTACCATTT-TTA
* *
13633 C-TCTTGC-TACT-TTTATCATTTTTA
1 CTTCTT-CTTACTGATTACCATTTTTA
13657 CTT
1 CTT
13660 TGATTATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
24 4 0.09
25 26 0.59
26 14 0.32
ACGTcount: A:0.18, C:0.22, G:0.06, T:0.54
Consensus pattern (26 bp):
CTTCTTCTTACTGATTACCATTTTTA
Found at i:13698 original size:16 final size:16
Alignment explanation
Indices: 13677--13730 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
13667 TTTCTTACTC
13677 TTTTTACTTAATACCA
1 TTTTTACTTAATACCA
*
13693 TTTTTATTTAATACCA
1 TTTTTACTTAATACCA
* *
13709 CTTCTTACTTGATACCA
1 -TTTTTACTTAATACCA
13726 TTTTT
1 TTTTT
13731 GACCCTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 19 0.59
17 13 0.41
ACGTcount: A:0.26, C:0.19, G:0.02, T:0.54
Consensus pattern (16 bp):
TTTTTACTTAATACCA
Found at i:13774 original size:47 final size:46
Alignment explanation
Indices: 13720--13891 Score: 221
Period size: 47 Copynumber: 3.8 Consensus size: 46
13710 TTCTTACTTG
*
13720 ATACCATTTTTGACCCTT-TTACTCAATACCATTTTTTAATTAATGCC
1 ATACCATTTTTGA-CCTTCTTACTCAATACCATATTTTAATT-ATGCC
*
13767 ATACCATTTTTGACCTTCTTACTCAATACCATATTTTACTTGATGCC
1 ATACCATTTTTGACCTTCTTACTCAATACCATATTTTAATT-ATGCC
* *
13814 ATACCATTTTTTACCTTCTTACTCAATACCATATTTT-ACT-TG--
1 ATACCATTTTTGACCTTCTTACTCAATACCATATTTTAATTATGCC
* *
13856 ATACCATTCTTGACCTTCTTACTTAATACCAT-TTTT
1 ATACCATTTTTGACCTTCTTACTCAATACCATATTTT
13892 GACATTTTTA
Statistics
Matches: 115, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
41 4 0.03
42 29 0.25
44 2 0.02
46 5 0.04
47 75 0.65
ACGTcount: A:0.26, C:0.24, G:0.04, T:0.45
Consensus pattern (46 bp):
ATACCATTTTTGACCTTCTTACTCAATACCATATTTTAATTATGCC
Found at i:13844 original size:25 final size:25
Alignment explanation
Indices: 13709--13852 Score: 113
Period size: 25 Copynumber: 6.0 Consensus size: 25
13699 TTTAATACCA
** *
13709 CTTCTTACTTGATACCATTTTTGACC
1 CTTCTTACTCAATACCATTTTTTA-C
13735 CTT-TTACTCAATACCATTTTTTA-
1 CTTCTTACTCAATACCATTTTTTAC
* ** * *
13758 ATTAATGC-C-ATACCATTTTTGAC
1 CTTCTTACTCAATACCATTTTTTAC
*
13781 CTTCTTACTCAATACCATATTTTA-
1 CTTCTTACTCAATACCATTTTTTAC
** *
13805 CTTGATGC-C-ATACCATTTTTTAC
1 CTTCTTACTCAATACCATTTTTTAC
*
13828 CTTCTTACTCAATACCATATTTTAC
1 CTTCTTACTCAATACCATTTTTTAC
13853 TTGATACCAT
Statistics
Matches: 90, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
22 24 0.27
23 13 0.14
24 9 0.10
25 41 0.46
26 3 0.03
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.45
Consensus pattern (25 bp):
CTTCTTACTCAATACCATTTTTTAC
Found at i:13884 original size:25 final size:25
Alignment explanation
Indices: 13849--13910 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
13839 ATACCATATT
* *
13849 TTACTTGATACCATTCTTGACCTTC
1 TTACTTAATACCATTCTTGACATTC
* *
13874 TTACTTAATACCATTTTTGACATTT
1 TTACTTAATACCATTCTTGACATTC
*
13899 TTACTCAATACC
1 TTACTTAATACC
13911 CTATTTTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (25 bp):
TTACTTAATACCATTCTTGACATTC
Found at i:13903 original size:67 final size:68
Alignment explanation
Indices: 13814--13960 Score: 224
Period size: 67 Copynumber: 2.2 Consensus size: 68
13804 ACTTGATGCC
* *
13814 ATACCATTTTTTACCTTCTTACTCAATACCATATTTTACTTGATACCA-TTCTTGACCTTCTTAC
1 ATACCATTTTTGACATTCTTACTCAATACCATATTTTACTTGATACCATTTCTTGACCTTCTTAC
*
13878 TTA
66 TCA
* * *
13881 ATACCATTTTTGACATTTTTACTCAATACCCTATTTTACTTGATACCATTTTTTGACCTTCTTAC
1 ATACCATTTTTGACATTCTTACTCAATACCATATTTTACTTGATACCATTTCTTGACCTTCTTAC
13946 TCA
66 TCA
13949 ATACCATATTTT
1 ATACCAT-TTTT
13961 ACTCTTAATT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
67 44 0.61
68 24 0.33
69 4 0.06
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (68 bp):
ATACCATTTTTGACATTCTTACTCAATACCATATTTTACTTGATACCATTTCTTGACCTTCTTAC
TCA
Found at i:13976 original size:43 final size:43
Alignment explanation
Indices: 13874--13963 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
13864 CTTGACCTTC
* *
13874 TTACTTAATACCA-TTTTTGACATTTTTACTCAATACCCTATT
1 TTACTTAATACCATTTTTTGACATTCTTACTCAATACCATATT
* *
13916 TTACTTGATACCATTTTTTGACCTTCTTACTCAATACCATATT
1 TTACTTAATACCATTTTTTGACATTCTTACTCAATACCATATT
13959 TTACT
1 TTACT
13964 CTTAATTCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 12 0.28
43 31 0.72
ACGTcount: A:0.27, C:0.22, G:0.03, T:0.48
Consensus pattern (43 bp):
TTACTTAATACCATTTTTTGACATTCTTACTCAATACCATATT
Found at i:14222 original size:40 final size:38
Alignment explanation
Indices: 14152--14284 Score: 142
Period size: 39 Copynumber: 3.4 Consensus size: 38
14142 ATTACCAGAT
* * *
14152 ATTTCACTAATTACTCTTTACTTTCTCTCTTAATCATCA
1 ATTT-ACTAATTAATCTTTACTTTCACTCTTAATTATCA
*
14191 ATTTACTAATTAATCCTTCTACTTTGACTCTTAATTATCA
1 ATTTACTAATTAAT-CTT-TACTTTCACTCTTAATTATCA
* * * *
14231 ATTTACTGAA-TGATCTTTTACTTCCCCCCTTAATTATCA
1 ATTTACT-AATTAATC-TTTACTTTCACTCTTAATTATCA
14270 ATTTACTAATTAATC
1 ATTTACTAATTAATC
14285 CTTTTATTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
38 11 0.14
39 36 0.46
40 30 0.38
41 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.02, T:0.47
Consensus pattern (38 bp):
ATTTACTAATTAATCTTTACTTTCACTCTTAATTATCA
Found at i:15229 original size:2 final size:2
Alignment explanation
Indices: 15222--15247 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15212 TCTATCTAAC
15222 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
15248 TCTACCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17530 original size:25 final size:26
Alignment explanation
Indices: 17496--17544 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
17486 ATCAATCAAG
*
17496 AAACCCAAAGACT-AAAAGTGAAAGA
1 AAACCAAAAGACTAAAAAGTGAAAGA
17521 AAACCAAAAGACTAAAAAGTGAAA
1 AAACCAAAAGACTAAAAAGTGAAA
17545 TTAAAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.63, C:0.14, G:0.14, T:0.08
Consensus pattern (26 bp):
AAACCAAAAGACTAAAAAGTGAAAGA
Found at i:17655 original size:22 final size:22
Alignment explanation
Indices: 17614--17659 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
17604 AAAGAAACTT
17614 AAGAATTATTCTAAAAAGAGGA
1 AAGAATTATTCTAAAAAGAGGA
*
17636 AAGAATTATTCTAAAGAGAGGA
1 AAGAATTATTCTAAAAAGAGGA
17658 AA
1 AA
17660 TGATTTGGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22
Consensus pattern (22 bp):
AAGAATTATTCTAAAAAGAGGA
Done.