Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008838.1 Corchorus capsularis cultivar CVL-1 contig08859, 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: 42978
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:8074 original size:97 final size:99
Alignment explanation
Indices: 7892--8090 Score: 296
Period size: 97 Copynumber: 2.0 Consensus size: 99
7882 TTTTTTTTTC
* * *
7892 TTTGTTTAATCTATACTAATTTCATAATTGATTTCTCAAGCTTGACGTCTTTTTTTGACTATTCT
1 TTTGTTTAATCTATACTAATTTCATAATTGATTTCACAAGCTTGAC--CTTTTGTAGACTATTCT
7957 TTGTTTGATTTATGATTAATTAAAGCTTGGAGCCTT
64 TTGTTTGATTTATGATTAATTAAAGCTTGGAGCCTT
* *
7993 TTTG-TTAATCTATACTAATTTCA-ATATTGATTTCACAAGTTTGA-CTTTTGTAGGCTATTCTT
1 TTTGTTTAATCTATACTAATTTCATA-ATTGATTTCACAAGCTTGACCTTTTGTAGACTATTCTT
*
8055 TGTTTGATTTATGATTAATTAAAGCTTGGCGCCTT
65 TGTTTGATTTATGATTAATTAAAGCTTGGAGCCTT
8090 T
1 T
8091 GAACGGTGTT
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
97 50 0.55
99 1 0.01
100 36 0.40
101 4 0.04
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.50
Consensus pattern (99 bp):
TTTGTTTAATCTATACTAATTTCATAATTGATTTCACAAGCTTGACCTTTTGTAGACTATTCTTT
GTTTGATTTATGATTAATTAAAGCTTGGAGCCTT
Found at i:17434 original size:15 final size:15
Alignment explanation
Indices: 17414--17449 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
17404 GCTCATGAAA
17414 ATAAAAACATAAATT
1 ATAAAAACATAAATT
17429 ATAAAAACATAAATT
1 ATAAAAACATAAATT
17444 ATAAAA
1 ATAAAA
17450 TAAATAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (15 bp):
ATAAAAACATAAATT
Found at i:21570 original size:142 final size:144
Alignment explanation
Indices: 21306--21586 Score: 444
Period size: 142 Copynumber: 2.0 Consensus size: 144
21296 GAATTTAATA
*
21306 AAATAAAAGTAGAGCTTTTAGTATAATAAAACTGTAAAGTTTAAACAATATATCATTTAAGAAAT
1 AAATAAAAGTAGAGCTTTTAGTAGAATAAAACTGTAAAGTTTAAACAATATATCATTTAAGAAAT
* * *
21371 ATATTTAAAAATTCTAATATATCTAATTTTTTAATTAAAATAGTAAAATGGTAAAAAT-AAAATA
66 ATATTTAAAAATTATAATATATCTAATTTTATAATGAAAATAGTAAAATGGTAAAAATAAAAATA
21435 GTTATAAAGATATT
131 GTTATAAAGATATT
* *
21449 AAATAAAA-TAGAGTTTTTTAGTAGAATAAAACTGTAAATTTTAAAC-A-ATATCATTTAAGAAA
1 AAATAAAAGTAGAG-CTTTTAGTAGAATAAAACTGTAAAGTTTAAACAATATATCATTTAAGAAA
* *
21511 TATATTTAGAAATTTATAATATATCTAATTTTATAATGAAAATAGTAAAATGTTAAAAATAAAAA
65 TATATTTA-AAAATTATAATATATCTAATTTTATAATGAAAATAGTAAAATGGTAAAAATAAAAA
21576 TAGTTATAAAG
129 TAGTTATAAAG
21587 CTATACTATA
Statistics
Matches: 127, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
141 23 0.18
142 52 0.41
143 52 0.41
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.36
Consensus pattern (144 bp):
AAATAAAAGTAGAGCTTTTAGTAGAATAAAACTGTAAAGTTTAAACAATATATCATTTAAGAAAT
ATATTTAAAAATTATAATATATCTAATTTTATAATGAAAATAGTAAAATGGTAAAAATAAAAATA
GTTATAAAGATATT
Found at i:38866 original size:19 final size:19
Alignment explanation
Indices: 38842--38904 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
38832 ATGTTTGGTT
38842 CGTGGTATCTTAGGTATCA
1 CGTGGTATCTTAGGTATCA
* * * *
38861 CGTGGTAATGTCA-TTAT-T
1 CGTGGT-ATCTTAGGTATCA
38879 CGTGGTATCTTAGGTATCA
1 CGTGGTATCTTAGGTATCA
38898 CGTGGTA
1 CGTGGTA
38905 ATGTCATTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 4 0.12
18 9 0.27
19 16 0.48
20 4 0.12
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (19 bp):
CGTGGTATCTTAGGTATCA
Found at i:38890 original size:37 final size:37
Alignment explanation
Indices: 38840--38912 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
38830 TTATGTTTGG
38840 TTCGTGGTATCTTAGGTATCACGTGGTAATGTCATTA
1 TTCGTGGTATCTTAGGTATCACGTGGTAATGTCATTA
38877 TTCGTGGTATCTTAGGTATCACGTGGTAATGTCATT
1 TTCGTGGTATCTTAGGTATCACGTGGTAATGTCATT
38913 CACACTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.41
Consensus pattern (37 bp):
TTCGTGGTATCTTAGGTATCACGTGGTAATGTCATTA
Found at i:39431 original size:2 final size:2
Alignment explanation
Indices: 39424--39448 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39414 TCCCTTTTAT
39424 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 T
39449 TAAATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42921 original size:33 final size:34
Alignment explanation
Indices: 42815--42935 Score: 140
Period size: 34 Copynumber: 3.6 Consensus size: 34
42805 GATGACTCGT
** **
42815 GCCGCCCCAAAAGGGCGGCTT-ACCA-TGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATTGAACAG
**
42847 GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATTGAACAG
* *
42881 GCCGCCCCACTAGGGCGGCTTCACTA-TGAATAG
1 GCCGCCCCACTAGGGCGGCTTCACCATTGAACAG
*
42914 GCCGCCCCACTGGGGCGGCTTC
1 GCCGCCCCACTAGGGCGGCTTC
42936 GCCAGGGCAG
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
32 19 0.24
33 29 0.36
34 32 0.40
ACGTcount: A:0.17, C:0.37, G:0.32, T:0.14
Consensus pattern (34 bp):
GCCGCCCCACTAGGGCGGCTTCACCATTGAACAG
Found at i:42971 original size:32 final size:33
Alignment explanation
Indices: 42815--42967 Score: 184
Period size: 32 Copynumber: 4.7 Consensus size: 33
42805 GATGACTCGT
**
42815 GCCGCCCCAAAAGGGCGGCTT-ACCATGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATGGGCAG
42847 GCCGCCCCACTAGGGCGGCTTCACCATTGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCA-TGGGCAG
* ***
42881 GCCGCCCCACTAGGGCGGCTTCACTATGAATAG
1 GCCGCCCCACTAGGGCGGCTTCACCATGGGCAG
* *
42914 GCCGCCCCACTGGGGCGGCTTCGCCA-GGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATGGGCAG
** *
42946 GCCGCCCCGGTGGGGCGGCTTC
1 GCCGCCCCACTAGGGCGGCTTC
42968 GCCACAGCAG
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
32 42 0.40
33 31 0.30
34 32 0.30
ACGTcount: A:0.14, C:0.37, G:0.35, T:0.13
Consensus pattern (33 bp):
GCCGCCCCACTAGGGCGGCTTCACCATGGGCAG
Done.