Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005056.1 Corchorus capsularis cultivar CVL-1 contig05074, 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: 38575
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:739 original size:327 final size:323
Alignment explanation
Indices: 80--748 Score: 787
Period size: 327 Copynumber: 2.0 Consensus size: 323
70 ATATATATAT
* ** ** **
80 ATATATATATTTCAAGGAGTCTTGGTGCCAAAAATATGCAAAACTGAGTCGGGGTCTTGGAACGC
1 ATATAGATATTTCAAGGAGTCTTGACGCCAAAAATATGCAAAACTGAGTCGGAATCCCGGAACGC
*
145 GTTTTTAGCCAAAAACCGTGATATATAGTAAACGATTTCGGCTAAAATTTTGCAAAAAATGACCC
66 GTTTTTAGCCAAAAACCGTG--A-ATAGTAAACAATTTCGGCTAAAATTTTGCAAAAAATGACCC
* * * *
210 GAAATATTTCTCATTTTTGCCCACTATACTCGTAAAAAAAATATTATTCAACACCAAAAAGATTG
128 GAAATATTTCTAATTTTTGCCCACAATACTCGTAAAAAAAATATAATTCAACACCAAAAAGAGTG
* **
275 AAAGGCATTTCACGCCTCTAATATTGTTTTTCCTATTTTTTAAAATTAATTTCTAATAAAATCGA
193 AAAGGCATTTAACGCCTCTAATATTCATTTTCCTATTTTTTAAAATTAATTTCTAATAAAATCGA
* *
340 AACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATTTAATGTGGCTAACATTTGGCTAGATG
258 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTAACATTTGGCTAGATG
405 A
323 A
* * *
406 ATATAGATATTTCAAGGAGTCTTGACGCCAAAAATCATGGAAAATTGAGTTGGAATCCCGGAACG
1 ATATAGATATTTCAAGGAGTCTTGACGCCAAAAAT-ATGCAAAACTGAGTCGGAATCCCGGAACG
* * *
471 TGTTTTTA-CCAAAAACCCGTG-A-AGTACACAATTTCGGTTAAAATTTTGCAAAAAATTGACCC
65 CGTTTTTAGCCAAAAA-CCGTGAATAGTAAACAATTTCGGCTAAAATTTTGCAAAAAA-TGACCC
* * * *
533 GAATGATTTTTCCATAATTTTTTG-CCACAATACTTGTAAAAAATATATAATTCATC-CCTAAAA
128 GAA--ATATTT-C-TAA-TTTTTGCCCACAATACTCGTAAAAAAAATATAATTCAACACC-AAAA
* * * * **
596 ATAGTG-AAGAGCTTTTAACGCTTCTAATA-TCATTTTCCTTCTTTTTTCCGAATTAATTTCTAA
187 AGAGTGAAAG-GCATTTAACGCCTCTAATATTCATTTTCC-TATTTTTT-AAAATTAATTTCTAA
* * * * * *
659 TTAAATTGAAACAAGATTCAGATGCTCGTAAAAA-AGATCCTTAAATTCAATTTGGCTTAGATTT
249 TAAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTAACATTT
*
723 GGTTAGATGA
314 GGCTAGATGA
733 ATATAGATATTTCAAG
1 ATATAGATATTTCAAG
749 TGCAAAACTG
Statistics
Matches: 291, Mismatches: 40, Indels: 23
0.82 0.11 0.06
Matches are distributed among these distances:
322 30 0.10
323 10 0.03
325 5 0.02
326 52 0.18
327 144 0.49
328 50 0.17
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (323 bp):
ATATAGATATTTCAAGGAGTCTTGACGCCAAAAATATGCAAAACTGAGTCGGAATCCCGGAACGC
GTTTTTAGCCAAAAACCGTGAATAGTAAACAATTTCGGCTAAAATTTTGCAAAAAATGACCCGAA
ATATTTCTAATTTTTGCCCACAATACTCGTAAAAAAAATATAATTCAACACCAAAAAGAGTGAAA
GGCATTTAACGCCTCTAATATTCATTTTCCTATTTTTTAAAATTAATTTCTAATAAAATCGAAAC
AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTAACATTTGGCTAGATGA
Found at i:2972 original size:68 final size:68
Alignment explanation
Indices: 2863--2998 Score: 211
Period size: 68 Copynumber: 2.0 Consensus size: 68
2853 AATCAAATTT
* * * *
2863 AACTAAACTTCACGAAATGAACACCGTCGAAATTTTTGATAACTTCTGGATCTTCATAATTAAAC
1 AACTAAACTACACGAAACGAACACCATCGAAATTTTTGATAACTTCCGGATCTTCATAATTAAAC
2928 AAG
66 AAG
*
2931 AACTAAACTACAC-AAAGCGAACACCATCGAAATTTTTGATAACTTCCGGATCTTCATAATTAAG
1 AACTAAACTACACGAAA-CGAACACCATCGAAATTTTTGATAACTTCCGGATCTTCATAATTAAA
2995 CAAG
65 CAAG
2999 CTCTTTCCCA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 3 0.05
68 59 0.95
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (68 bp):
AACTAAACTACACGAAACGAACACCATCGAAATTTTTGATAACTTCCGGATCTTCATAATTAAAC
AAG
Found at i:3319 original size:13 final size:13
Alignment explanation
Indices: 3301--3326 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3291 TTTGGAATTC
3301 TAAATAATATTTA
1 TAAATAATATTTA
3314 TAAATAATATTTA
1 TAAATAATATTTA
3327 GAATATTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAATAATATTTA
Found at i:6057 original size:2 final size:2
Alignment explanation
Indices: 6040--6077 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
6030 TATTATTTGC
*
6040 TA TA T- TA TA TA CA 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 TA TA TA TA TA TA T
6078 TGCAGGGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23470 original size:14 final size:15
Alignment explanation
Indices: 23451--23482 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
23441 ATATACCAAC
23451 GAGAAGGGGAGAG-G
1 GAGAAGGGGAGAGAG
23465 GAGAAGGGGAGAGAG
1 GAGAAGGGGAGAGAG
23480 GAG
1 GAG
23483 CGGCTAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (15 bp):
GAGAAGGGGAGAGAG
Found at i:28067 original size:55 final size:55
Alignment explanation
Indices: 27983--28094 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
27973 TACCGTATCA
*
27983 ATGATTCCATCAAATGTGCCCATAGCAGCCTAAACAGAGTGAATAGTCAAGTTAT
1 ATGATTCCATCAAATGTGCCCATAGCAGCCTAAACAGAGTAAATAGTCAAGTTAT
*
28038 ATGATTCCGTCAAATGTGCCCATAGCAGCCTAAACAGAGTAAATAGTCAAGTTAT
1 ATGATTCCATCAAATGTGCCCATAGCAGCCTAAACAGAGTAAATAGTCAAGTTAT
28093 AT
1 AT
28095 TTTCAGTGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (55 bp):
ATGATTCCATCAAATGTGCCCATAGCAGCCTAAACAGAGTAAATAGTCAAGTTAT
Found at i:31240 original size:53 final size:53
Alignment explanation
Indices: 31182--31288 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
31172 CGGCTGTTTT
** *
31182 ATTTTATAAATTATTTTAAGAAAATTCAGTTCAGAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTATCATAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
*
31235 ATTTTATAAATTCTCATAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
1 ATTTTATAAATTATCATAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
31288 A
1 A
31289 ACAATAACAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (53 bp):
ATTTTATAAATTATCATAAGAAAATTCAGTTAAGAAATCAAATTTTGTTGTGA
Found at i:32229 original size:14 final size:14
Alignment explanation
Indices: 32212--32251 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
32202 GTCGGGTTGG
*
32212 ATTTGGGTTCGGTT
1 ATTTGGGTTAGGTT
32226 ATTTGGGTTAGGTT
1 ATTTGGGTTAGGTT
32240 AGTTTCGGGTTA
1 A-TTT-GGGTTA
32252 AGGAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 3 0.13
16 6 0.26
ACGTcount: A:0.12, C:0.05, G:0.35, T:0.47
Consensus pattern (14 bp):
ATTTGGGTTAGGTT
Done.