Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012995.1 Corchorus capsularis cultivar CVL-1 contig13016, 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: 14233
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:3864 original size:78 final size:78
Alignment explanation
Indices: 3782--4020 Score: 352
Period size: 78 Copynumber: 3.2 Consensus size: 78
3772 TTGTTTAGGT
* *
3782 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAAC-
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACT
3845 ----TATTTT---A
65 ATTATATTTTACCA
* *
3852 TTTTACTATTTTACTCAATTAAAAACTCTATTTTTATATAATTAAATATAATATCCCTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
3917 TTATATTTTACCA
66 TTATATTTTACCA
* *
3930 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
3995 TTATATTTTACCA
66 TTATATTTTACCA
4008 TTTTACTATTTTA
1 TTTTACTATTTTA
4021 ATTAAAAAAC
Statistics
Matches: 152, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
70 56 0.37
71 2 0.01
75 6 0.04
78 88 0.58
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.50
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATATTTTACCA
Found at i:3865 original size:70 final size:70
Alignment explanation
Indices: 3782--4014 Score: 306
Period size: 70 Copynumber: 3.2 Consensus size: 70
3772 TTGTTTAGGT
* *
3782 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACT
3846 ATTTTA
65 ATTTTA
* *
3852 TTTTACTATTTTACTCAATTAAAAACTCTATTTTTATATAATTAAATATAATATCCCTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAAC--
3917 TTATATTTTACCA
64 ---TATTTT---A
* *
3930 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
*
3995 TTATA
66 TTTTA
*
4000 TTTTACCATTTTACT
1 TTTTACTATTTTACT
4015 ATTTTAATTA
Statistics
Matches: 144, Mismatches: 10, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
70 71 0.49
71 2 0.01
73 5 0.03
75 6 0.04
78 60 0.42
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.50
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
TTTTA
Found at i:4712 original size:7 final size:7
Alignment explanation
Indices: 4700--4737 Score: 67
Period size: 7 Copynumber: 5.3 Consensus size: 7
4690 TACAAGGAAG
4700 AAAGAAA
1 AAAGAAA
4707 AAAGAAA
1 AAAGAAA
4714 AAGAGAAA
1 AA-AGAAA
4722 AAAGAAA
1 AAAGAAA
4729 AAAGAAA
1 AAAGAAA
4736 AA
1 AA
4738 GAGGAAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:4722 original size:15 final size:14
Alignment explanation
Indices: 4700--4737 Score: 67
Period size: 15 Copynumber: 2.6 Consensus size: 14
4690 TACAAGGAAG
4700 AAAGAAAAAAGAAA
1 AAAGAAAAAAGAAA
4714 AAGAGAAAAAAGAAA
1 AA-AGAAAAAAGAAA
4729 AAAGAAAAA
1 AAAGAAAAA
4738 GAGGAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAGAAA
Found at i:4748 original size:15 final size:14
Alignment explanation
Indices: 4693--4748 Score: 58
Period size: 15 Copynumber: 3.8 Consensus size: 14
4683 GCATTAATAC
4693 AAGGAAGAAAGAAAA
1 AAGGAA-AAAGAAAA
*
4708 AAGAAAAAGAGAAAA
1 AAGGAAAA-AGAAAA
*
4723 AAGAAAAAAGAAAA
1 AAGGAAAAAGAAAA
*
4737 AGAGGAAGAAGA
1 A-AGGAAAAAGA
4749 GGTGAAACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 9 0.25
15 27 0.75
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
AAGGAAAAAGAAAA
Found at i:4748 original size:22 final size:22
Alignment explanation
Indices: 4694--4748 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
4684 CATTAATACA
4694 AGGAAGAAAGAAAAAAGAAAAAG
1 AGGAAG-AAGAAAAAAGAAAAAG
* *
4717 AGAAAAAAGAAAAAAGAAAAAG
1 AGGAAGAAGAAAAAAGAAAAAG
4739 AGGAAGAAGA
1 AGGAAGAAGA
4749 GGTGAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (22 bp):
AGGAAGAAGAAAAAAGAAAAAG
Found at i:8740 original size:551 final size:548
Alignment explanation
Indices: 7030--9890 Score: 3749
Period size: 551 Copynumber: 5.2 Consensus size: 548
7020 TTTTTCTTAT
* * * * * *
7030 AATATTGCATTAGTCGTAGCAGTAT-CTTATTTAATAGACTATTCTGAAAAGTTAGCCCGTTGGT
1 AATATTGCATTAGTCGTAGCGGTATCCTGATTCAATAGACTATTCTGAACAGTTAGACCATTGGT
* * * * ** * * * * *
7094 GGAAAATGATGCATTCATCGCAAAATCCTAATAGTATGCAATAACCAGTCCACACATTTGACTGC
66 GGAAAAGGTTGCATTCACCGCAGAATCCTTGTAGTCTGCAATAACCAGCCCACACGTTAGGCTG-
* * * * * * *
7159 TT-AAGTCAAACCTAAAAATGGTAATTAACCATTTATGTA-AGCATTGAAA-AATAAGACATATT
130 TTCAAGTCAAGCCTAAAAATGAT-ATTAACCATTTATGTACA-CGTT-AAAGTACAAGTCATTTT
* * *
7221 TTGACTTACTAACAATGAAACAAATATTAATTGTAGATAGAAAACAAATTAACAATATCATTGCT
192 TTGACTTCCTAACAATGAAACAAATATTAATTCTAGATAGAAAACAAATTAACAATATCATTACT
* * * **
7286 TGACAAATTATCACCTATTAAAAAGTCACCGTATAATAATAAGGAATGTTTTTCGAGTTGATCAT
257 TGACAAATTATCAGCTATTAAAAAGACACCGTATAATTATAAGGAATGTTTACCGAGTTGATCAT
* * * *
7351 CAATATACTAAGCATACATGGTTTAAAATAAATATTTAGACTCTGATATCATACATGATAAAC-A
322 CAATATACTAAGCATACATGGCTTAAAATAAATATTTGGACTCTGATATCATATAAGATAAACAA
*
7415 AAAAA-AAATGTCGCGAGCCCTTAGATATTTATAACAAACTTTTTATTGATCCATTGATATGTTA
387 AAAAATAAATGTCGCGGGCCCTTAGATATTTATAACAAACTTTTTATTGATCCATTGATATGTTA
* * *
7479 AAGTATTTTTTATGA-GATGTTACGCAATAAAGAGACAATTTTTGAACTTTTTGTGTATA-CTGA
452 AAGTATTTTTTATGAGGATTTTACGCGATAATGAGACAATTTTTGAACTTTTTGTGTATAGCTGA
*
7542 AGCAATACAAATAATATTTAATTTGACAAATTA
517 AGCAATACAAATAATATTTAATTGGA-AAATTA
* *
7575 AATATTGCATTAGTCGTAACGGTATCCTGATTCAATAGACTATTCTGAACAGTTAGACCTTTGGT
1 AATATTGCATTAGTCGTAGCGGTATCCTGATTCAATAGACTATTCTGAACAGTTAGACCATTGGT
* * *
7640 GGAAAAGGTTGCATTCACCGCAAAACCCTTGTAGTCTGCAATAACCAGCCCACGCGTTAGGCTGT
66 GGAAAAGGTTGCATTCACCGCAGAATCCTTGTAGTCTGCAATAACCAGCCCACACGTTAGGCTGT
* * * * * * * *
7705 TTAGGCCACGCCT-AGAA--AT-TTAACTATTTATGTACACGTTAATGTAGAAGTCATTTTTTTG
131 TCAAGTCAAGCCTAAAAATGATATTAACCATTTATGTACACGTTAAAGTACAAGTCA-TTTTTTG
* * * * * *
7766 AGTTCTTAGCAATGAAATAAATATTAATTCTAGAAAGAAAACAAATTAACAATATCATTACTTAA
195 ACTTCCTAACAATGAAACAAATATTAATTCTAGATAGAAAACAAATTAACAATATCATTACTTGA
* * *
7831 CAAATTATCAGCTATTAAAAAGACACCGTAT-A--ATAAGGAATGTTTACCAAGTCGATTATCAA
260 CAAATTATCAGCTATTAAAAAGACACCGTATAATTATAAGGAATGTTTACCGAGTTGATCATCAA
* *
7893 TATACTAAGCATACATTGCATAAAATAAATATTTGGACTCTGATATCATATAAGATAAACAAAAA
325 TATACTAAGCATACATGGCTTAAAATAAATATTTGGACTCTGATATCATATAAGATAAACAAAAA
*
7958 AATAAATGTCGGGGGCCCTTAGATATTTATAACAAACTTTTTATTGATCCATTGATATGTTAAAG
390 AATAAATGTCGCGGGCCCTTAGATATTTATAACAAACTTTTTATTGATCCATTGATATGTTAAAG
* * *
8023 TATTTTTTATGA-GATGTTTTACGCGTTAATTAGACAATTTTTGAACTCTTTGTGTATAGCTGAA
455 TATTTTTTATGAGGA--TTTTACGCGATAATGAGACAATTTTTGAACTTTTTGTGTATAGCTGAA
* * *
8087 GCAACACAAATAATATCTAATTGGACAAGTTA
518 GCAATACAAATAATATTTAATTGGA-AAATTA
* * * *
8119 AATATTGCATTAGTCATAGCGGTATCCTGATTCAATAGACTATTCTGAACATTTAAACCGTTGGT
1 AATATTGCATTAGTCGTAGCGGTATCCTGATTCAATAGACTATTCTGAACAGTTAGACCATTGGT
* *
8184 GGAAAAGGTTGCATTCACCGCAGAACCCTTGTAGTATGCAATAACCAGCCCACACGTTAGGCTGT
66 GGAAAAGGTTGCATTCACCGCAGAATCCTTGTAGTCTGCAATAACCAGCCCACACGTTAGGCTGT
8249 TCAAGTCAAGCCTAAAAATGATAATTAACCATTTATGTACACGTTAAAGTA-AAGTCATTTTTTG
131 TCAAGTCAAGCCTAAAAATGAT-ATTAACCATTTATGTACACGTTAAAGTACAAGTCATTTTTTG
* *
8313 ACTTCCTAGCAATGAAACAAATATTAATTCTAGATAGAAAACAAATTGACAATATCATTACTTGA
195 ACTTCCTAACAATGAAACAAATATTAATTCTAGATAGAAAACAAATTAACAATATCATTACTTGA
* *
8378 CAAATTATCAGCTATTGAAAAGACACCGTATAATTATAAGGAATGTTTAACGAGTTGATCATCAA
260 CAAATTATCAGCTATTAAAAAGACACCGTATAATTATAAGGAATGTTTACCGAGTTGATCATCAA
* * * *
8443 TATACTAAGCATATATGGCTTAAAATAAATGTTTAGACACTGATATCATATAAGATAAACAAAAA
325 TATACTAAGCATACATGGCTTAAAATAAATATTTGGACTCTGATATCATATAAGATAAACAAAAA
* * *
8508 AATAAATGTCGCGGGCCTTTAAATATTTATAACAAACTTTTTATTGATCCATTGACATGTTAAAG
390 AATAAATGTCGCGGGCCCTTAGATATTTATAACAAACTTTTTATTGATCCATTGATATGTTAAAG
* * * *
8573 ATTTTTTTTATAAGGACTTTTACGCGATAATGAGAGAATTTTTGAATTTTTTGTGTATAGCTGAA
455 -TATTTTTTATGAGGA-TTTTACGCGATAATGAGACAATTTTTGAACTTTTTGTGTATAGCTGAA
* *
8638 GTATTACAAATAATATTTAATTGGAAAACTTA
518 GCAATACAAATAATATTTAATTGGAAAA-TTA
* * *
8670 AATATTGCATTAGTCGTAGCGGTATCCTGATTCATTAGACTATTCTAAACTGTTAGACCATTGGT
1 AATATTGCATTAGTCGTAGCGGTATCCTGATTCAATAGACTATTCTGAACAGTTAGACCATTGGT
*
8735 GGAAAAGGTTGCATTCACCACAGAATCCTTGTAGTCTGCAATAACCAGCCCACGA-GTTAGGCTG
66 GGAAAAGGTTGCATTCACCGCAGAATCCTTGTAGTCTGCAATAACCAGCCCAC-ACGTTAGGCTG
* * * * * **
8799 TTCAAGCCACGCCT-AGAA--AT-TTAACTATTTATGTACATGTTAAAGTGGAAGTCATTTTTTG
130 TTCAAGTCAAGCCTAAAAATGATATTAACCATTTATGTACACGTTAAAGTACAAGTCATTTTTTG
* * * *
8860 ACTTCTTAACAATGAAACAAATATTAATTCTAGATAGAAAACAAATTAACAAAATCACTACTTTA
195 ACTTCCTAACAATGAAACAAATATTAATTCTAGATAGAAAACAAATTAACAATATCATTACTTGA
*
8925 CAAATTATCAGCTATTAAAAAGACACTGTATAATTATAAGGAATGTTTACCGAGTTGATCATCAA
260 CAAATTATCAGCTATTAAAAAGACACCGTATAATTATAAGGAATGTTTACCGAGTTGATCATCAA
* * * * *
8990 TATACTAAGCATACATGGCTTAAAATATATACTCGGACTCTGATATAATATAAGATAAACAACAA
325 TATACTAAGCATACATGGCTTAAAATAAATATTTGGACTCTGATATCATATAAGATAAACAAAAA
* * *
9055 AATAAATGTTGCGGGCCCTTAGATATTTATAACAAACTTTTTATTGATCCATCGACATGTTAAA-
390 AATAAATGTCGCGGGCCCTTAGATATTTATAACAAACTTTTTATTGATCCATTGATATGTTAAAG
* * *
9119 AATTTTTTTATGAGGTGTTTTACGCGATAATGAGACAATTTTTGAATTTTTTGTGTATAGCTGAA
455 TA-TTTTTTATGAGG-ATTTTACGCGATAATGAGACAATTTTTGAACTTTTTGTGTATAGCTGAA
** * *
9184 GTTATTCAAATAATATTCAATTGGAAAAGTTA
518 GCAATACAAATAATATTTAATTGGAAAA-TTA
* * * *
9216 AAAATTACATTAGTTGTAGCGGTATCCTGATTCATTAGACTATTCTGAACAGTTAGACCATTGGT
1 AATATTGCATTAGTCGTAGCGGTATCCTGATTCAATAGACTATTCTGAACAGTTAGACCATTGGT
* * *
9281 GG-AAAGGATTGCATTCTCCACAGAATCCTTGTAGTCTGCAATAACTAGCCCACACGTTAGGCTG
66 GGAAAAGG-TTGCATTCACCGCAGAATCCTTGTAGTCTGCAATAACCAGCCCACACGTTAGGCTG
* * * * ** * * * *
9345 CTCAGGTCAAGCCCAGAAATGGCCATTAGCCATTTATGTACATGTTAATGTACAAGTCATGTTTT
130 TTCAAGTCAAGCCTAAAAAT-GATATTAACCATTTATGTACACGTTAAAGTACAAGTCATTTTTT
* * * *
9410 GACTTCCTAACAATGAATCAAATATTAACTATAGATAGAAAACAAATTAACAATATCACTACTTG
194 GACTTCCTAACAATGAAACAAATATTAATTCTAGATAGAAAACAAATTAACAATATCATTACTTG
* * * * ** *
9475 AGAAATTATCACCTATT-AAAAGTCACCGTATAATTATTAGGAATGTTTTTCGAGTCGATCATCA
259 ACAAATTATCAGCTATTAAAAAGACACCGTATAATTATAAGGAATGTTTACCGAGTTGATCATCA
* *
9539 ATATACAAAGCATACATGGTTTAAAATAAATATTTGGACTCTGATATCATATAAGATAAACAAAA
324 ATATACTAAGCATACATGGCTTAAAATAAATATTTGGACTCTGATATCATATAAGATAAACAAAA
* * * * * *
9604 AAATAATTGCCACAGGCCCTTAGATATTTATAACAAACATTTTATTGATCTATTGATATGATATA
389 AAATAAATGTCGCGGGCCCTTAGATATTTATAACAAACTTTTTATTGATCCATTGATATG-T-TA
* * * *
9669 AAGTATTTTTTATGAGGATTTATACGCGATAATAAGATAATTTTTGAACTTTTAGGGTATAGCTG
452 AAGTATTTTTTATGAGGATTT-TACGCGATAATGAGACAATTTTTGAACTTTTTGTGTATAGCTG
* * *
9734 AAGCAATACAAACAATATTCAATTGGACAAATTT
516 AAGCAATACAAATAATATTTAATTGGA-AAATTA
* * * * * *
9768 AGTATTGCATTATTCGTAACGGTATCCTGATTTATTAGATTATTCTGAACAGTTAGACCATTGGT
1 AATATTGCATTAGTCGTAGCGGTATCCTGATTCAATAGACTATTCTGAACAGTTAGACCATTGGT
*
9833 GGAAAAGGTTGCATTAACC-CAGAATCCTTGTAGTCTGCAATAACCAGCCCACACGTTA
66 GGAAAAGGTTGCATTCACCGCAGAATCCTTGTAGTCTGCAATAACCAGCCCACACGTTA
9891 CACGTCAAAG
Statistics
Matches: 2040, Mismatches: 238, Indels: 70
0.87 0.10 0.03
Matches are distributed among these distances:
539 79 0.04
540 8 0.00
541 98 0.05
542 92 0.05
543 37 0.02
544 164 0.08
545 37 0.02
546 325 0.16
547 350 0.17
548 9 0.00
549 25 0.01
550 301 0.15
551 356 0.17
552 150 0.07
553 9 0.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (548 bp):
AATATTGCATTAGTCGTAGCGGTATCCTGATTCAATAGACTATTCTGAACAGTTAGACCATTGGT
GGAAAAGGTTGCATTCACCGCAGAATCCTTGTAGTCTGCAATAACCAGCCCACACGTTAGGCTGT
TCAAGTCAAGCCTAAAAATGATATTAACCATTTATGTACACGTTAAAGTACAAGTCATTTTTTGA
CTTCCTAACAATGAAACAAATATTAATTCTAGATAGAAAACAAATTAACAATATCATTACTTGAC
AAATTATCAGCTATTAAAAAGACACCGTATAATTATAAGGAATGTTTACCGAGTTGATCATCAAT
ATACTAAGCATACATGGCTTAAAATAAATATTTGGACTCTGATATCATATAAGATAAACAAAAAA
ATAAATGTCGCGGGCCCTTAGATATTTATAACAAACTTTTTATTGATCCATTGATATGTTAAAGT
ATTTTTTATGAGGATTTTACGCGATAATGAGACAATTTTTGAACTTTTTGTGTATAGCTGAAGCA
ATACAAATAATATTTAATTGGAAAATTA
Done.