Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009083.1 Corchorus capsularis cultivar CVL-1 contig09104, 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: 39005
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--32 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 T
2 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33 AAATGTTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:788 original size:22 final size:21
Alignment explanation
Indices: 762--802 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
752 AATTTTTCAA
762 AAGAAAAACAAATAGAAAGAAG
1 AAGAAAAACAAATA-AAAGAAG
* *
784 AAGAAGAAGAAATAAAAGA
1 AAGAAAAACAAATAAAAGA
803 GTATGTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (21 bp):
AAGAAAAACAAATAAAAGAAG
Found at i:9509 original size:109 final size:109
Alignment explanation
Indices: 9272--9568 Score: 434
Period size: 109 Copynumber: 2.7 Consensus size: 109
9262 ACTATTATAG
* *
9272 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
9337 TATTTTTACCAAAAAAATTTAGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACC-AAAAAATTTAGATATACTAAAATTTTTTCTAATATACAA
9387 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
9452 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTAGATATACTAAAATTTTTTCTAATATACAA
* * **
9496 TTTTATTATACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
9560 TTTTTACCA
63 TTTTTACCA
9569 TTTTAATTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
108 1 0.01
109 82 0.48
110 47 0.27
111 18 0.11
112 2 0.01
115 21 0.12
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTAGATATACTAAAATTTTTTCTAATATACAA
Found at i:10713 original size:22 final size:22
Alignment explanation
Indices: 10688--10730 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
10678 CATAAATGAA
10688 AGATGAAGAAGAAGATAGAATC
1 AGATGAAGAAGAAGATAGAATC
*
10710 AGATGAGGAAGAAGATAGAAT
1 AGATGAAGAAGAAGATAGAAT
10731 TATAGAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (22 bp):
AGATGAAGAAGAAGATAGAATC
Found at i:11917 original size:2 final size:2
Alignment explanation
Indices: 11910--11939 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11900 ATGTAGAATC
11910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11940 ATCATAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21484 original size:118 final size:118
Alignment explanation
Indices: 21276--21512 Score: 420
Period size: 118 Copynumber: 2.0 Consensus size: 118
21266 ATTACACCAA
* *
21276 GTAAATTCCCATGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAATCCAACCCCTTAGACAG
1 GTAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAACCCAACCCCTTAGACAG
* *
21341 AATTTGCCTAGATATGTAATTAAAGCACAATGACAACTTTTAGTGTCAAATGG
66 AATTTGCCTAGACATGTAATTAAAGCACAATGACAACTTCTAGTGTCAAATGG
*
21394 GTAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAACCCAACTCCTTAGACAG
1 GTAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAACCCAACCCCTTAGACAG
*
21459 AATTTGCCTAGACATGTAATTAAAGCACCATGACAACTTCTAGTGTCAAATGG
66 AATTTGCCTAGACATGTAATTAAAGCACAATGACAACTTCTAGTGTCAAATGG
21512 G
1 G
21513 AATTAGTTAT
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (118 bp):
GTAAATTCCCAGGAAAGATGGAGGAGTCACAAACGGTCTCACTTAAAACCCAACCCCTTAGACAG
AATTTGCCTAGACATGTAATTAAAGCACAATGACAACTTCTAGTGTCAAATGG
Found at i:21628 original size:30 final size:30
Alignment explanation
Indices: 21566--21918 Score: 465
Period size: 30 Copynumber: 11.7 Consensus size: 30
21556 CATGGTGTAT
* **
21566 ATGACAACTTCTGGTGTCAATTAAATAAATC
1 ATGACAACTTCCGGTGTCAATTGCA-AAATC
* **
21597 ATGACATCTTCAAGTGTCAATTGCAAAATC
1 ATGACAACTTCCGGTGTCAATTGCAAAATC
*
21627 ATGACAACTTCGGGTGTCAATTGCAAAATC
1 ATGACAACTTCCGGTGTCAATTGCAAAATC
*
21657 ATGACAACTTCTGGTGTCAATTGCAAAAATC
1 ATGACAACTTCCGGTGTCAATTGC-AAAATC
*
21688 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCCGGTGTCAATTGCAAAATC
21718 ATGACAACTTCCGGTGTCAATTGCAAAATC
1 ATGACAACTTCCGGTGTCAATTGCAAAATC
*
21748 ATGACAACTTCCAGTGTCAATTGCAAAATC
1 ATGACAACTTCCGGTGTCAATTGCAAAATC
21778 ATGACAACTTCCGGTGTCAATTGCAAAATC
1 ATGACAACTTCCGGTGTCAATTGCAAAATC
*
21808 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCCGGTGTCAATTGCAAAATC
* * * *
21838 ATGACAACTTCC-GTGTCATTTGTAAGACC
1 ATGACAACTTCCGGTGTCAATTGCAAAATC
* ** * * * *
21867 ATGAAAACTTCTAGTGTCATTTGTAAGATT
1 ATGACAACTTCCGGTGTCAATTGCAAAATC
*
21897 ATTGACAACTTCTGGTGTCAAT
1 A-TGACAACTTCCGGTGTCAAT
21919 GGAGATTTAT
Statistics
Matches: 294, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
29 23 0.08
30 204 0.69
31 67 0.23
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (30 bp):
ATGACAACTTCCGGTGTCAATTGCAAAATC
Found at i:21721 original size:91 final size:91
Alignment explanation
Indices: 21566--21918 Score: 480
Period size: 91 Copynumber: 3.9 Consensus size: 91
21556 CATGGTGTAT
* * *
21566 ATGACAACTTCTGGTGTCAATT-AAATAAATCATGACATCTTCAAGTGTCAATTGCAAAATCATG
1 ATGACAACTTCTGGTGTCAATTGCAA-AAATCATGACAACTTCTAGTGTCAATTGCAAAATCATG
*
21630 ACAACTTCGGGTGTCAATTGCAAAATC
65 ACAACTTCTGGTGTCAATTGCAAAATC
*
21657 ATGACAACTTCTGGTGTCAATTGCAAAAATCATGACAACTTCTGGTGTCAATTGCAAAATCATGA
1 ATGACAACTTCTGGTGTCAATTGCAAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGA
*
21722 CAACTTCCGGTGTCAATTGCAAAATC
66 CAACTTCTGGTGTCAATTGCAAAATC
** **
21748 ATGACAACTTCCAGTGTCAATTGC-AAAATCATGACAACTTCCGGTGTCAATTGCAAAATCATGA
1 ATGACAACTTCTGGTGTCAATTGCAAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGA
21812 CAACTTCTGGTGTCAATTGCAAAATC
66 CAACTTCTGGTGTCAATTGCAAAATC
* * * * * * * * * *
21838 ATGACAACTTC-CGTGTCATTTG-TAAGACCATGAAAACTTCTAGTGTCATTTGTAAGATTATTG
1 ATGACAACTTCTGGTGTCAATTGCAAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCA-TG
21901 ACAACTTCTGGTGTCAAT
65 ACAACTTCTGGTGTCAAT
21919 GGAGATTTAT
Statistics
Matches: 239, Mismatches: 20, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
89 37 0.15
90 95 0.40
91 105 0.44
92 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (91 bp):
ATGACAACTTCTGGTGTCAATTGCAAAAATCATGACAACTTCTAGTGTCAATTGCAAAATCATGA
CAACTTCTGGTGTCAATTGCAAAATC
Found at i:25228 original size:2 final size:2
Alignment explanation
Indices: 25223--25277 Score: 50
Period size: 2 Copynumber: 30.0 Consensus size: 2
25213 TTTCCAACAT
*
25223 TA TA TA TA TA TA TA TA T- TA TA T- TT TA TA TA TA TCA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
25263 T- TA TA -A TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA
25278 ATAATGATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
1 6 0.13
2 37 0.82
3 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:25254 original size:24 final size:24
Alignment explanation
Indices: 25222--25267 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
25212 TTTTCCAACA
25222 TTATATATAT-ATATATATTATATT
1 TTATATATATCATAT-TATTATATT
25246 TTATATATATCATATTATTATA
1 TTATATATATCATATTATTATA
25268 ATAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATATATATCATATTATTATATT
Found at i:25968 original size:41 final size:38
Alignment explanation
Indices: 25918--26008 Score: 119
Period size: 41 Copynumber: 2.3 Consensus size: 38
25908 TGCGTTACTC
25918 TATTGTTGAAGACAATTTAAGAATGTATTTTTTAAAGGATT
1 TATT-TTGAAGA-AATTTAAGAATGTA-TTTTTAAAGGATT
* *
25959 TGTTTTTGAATGATATTTAAGAATGTATTTTTAAAGGATT
1 T-ATTTTGAA-GAAATTTAAGAATGTATTTTTAAAGGATT
25999 TATTTTGAAG
1 TATTTTGAAG
26009 GATATATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
38 1 0.02
39 7 0.16
40 14 0.31
41 19 0.42
42 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (38 bp):
TATTTTGAAGAAATTTAAGAATGTATTTTTAAAGGATT
Found at i:26016 original size:41 final size:41
Alignment explanation
Indices: 25932--26013 Score: 132
Period size: 40 Copynumber: 2.0 Consensus size: 41
25922 GTTGAAGACA
* *
25932 ATTTAAGAATGTATTTTTTAAAGGATTTGTTTTTGAATGAT
1 ATTTAAGAATGTATTTTTTAAAGGATTTGATTTTGAAGGAT
25973 ATTTAAGAATGTA-TTTTTAAAGGATTT-ATTTTGAAGGAT
1 ATTTAAGAATGTATTTTTTAAAGGATTTGATTTTGAAGGAT
26012 AT
1 AT
26014 ATTATGATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 12 0.31
40 14 0.36
41 13 0.33
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (41 bp):
ATTTAAGAATGTATTTTTTAAAGGATTTGATTTTGAAGGAT
Found at i:33725 original size:12 final size:12
Alignment explanation
Indices: 33692--33730 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
33682 TCACAATTTC
33692 TTTTCTTCTA-T
1 TTTTCTTCTAGT
33703 TTTTC-TCTAGT
1 TTTTCTTCTAGT
*
33714 TTTTCTTATAGT
1 TTTTCTTCTAGT
33726 TTTTC
1 TTTTC
33731 CTAAGGATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 4 0.16
11 11 0.44
12 10 0.40
ACGTcount: A:0.10, C:0.15, G:0.05, T:0.69
Consensus pattern (12 bp):
TTTTCTTCTAGT
Found at i:35303 original size:94 final size:94
Alignment explanation
Indices: 35138--35329 Score: 348
Period size: 94 Copynumber: 2.0 Consensus size: 94
35128 AAGTTTTGGA
*
35138 TTGAGTCTCCTCAAGCTTTGATTCCACAATCTCCGCACAAACAGGTTTGATAACAGCCACAGGTT
1 TTGAGTCTCCTCAAGCTTTGATTCCACAATCTCCGCACAAACAGGTTTAATAACAGCCACAGGTT
35203 TAATGGGGGCAACTCCTCCCATATGAATC
66 TAATGGGGGCAACTCCTCCCATATGAATC
* *
35232 TTGAGTCTCCTCAGGCTTTGATTCCACAATCTTCGCACAAACAGGTTTAATAACAGCCACAGGTT
1 TTGAGTCTCCTCAAGCTTTGATTCCACAATCTCCGCACAAACAGGTTTAATAACAGCCACAGGTT
*
35297 TGATGGGGGCAACTCCTCCCATATGAATC
66 TAATGGGGGCAACTCCTCCCATATGAATC
35326 TTGA
1 TTGA
35330 AGTTATCACC
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (94 bp):
TTGAGTCTCCTCAAGCTTTGATTCCACAATCTCCGCACAAACAGGTTTAATAACAGCCACAGGTT
TAATGGGGGCAACTCCTCCCATATGAATC
Found at i:35843 original size:8 final size:8
Alignment explanation
Indices: 35830--35855 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
35820 GTGCCACTTT
35830 CTAACTAG
1 CTAACTAG
35838 CTAACTAG
1 CTAACTAG
35846 CTAACTAG
1 CTAACTAG
35854 CT
1 CT
35856 GATGCCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (8 bp):
CTAACTAG
Done.