Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009695.1 Corchorus capsularis cultivar CVL-1 contig09716, 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: 23481
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 6--59 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1 GCAAG
6 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
48 TC TC TC TC TC TC
1 TC TC TC TC TC TC
60 AGAGAAAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5195 original size:50 final size:50
Alignment explanation
Indices: 5136--5234 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
5126 TCTCCTTGGG
* *
5136 TGCTCTCAACACTGGCCTCTCTAGATCGATTGGAGATACTGATTTAAGCA
1 TGCTCTCAACACTGGCCTCTCTAGATCGATTGGAGATAATGATTGAAGCA
* * *
5186 TGCTCTCAACGCTGGCTTCTCTGGATCGATTGGAGATAATGATTGAAGC
1 TGCTCTCAACACTGGCCTCTCTAGATCGATTGGAGATAATGATTGAAGC
5235 CCAAAATCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (50 bp):
TGCTCTCAACACTGGCCTCTCTAGATCGATTGGAGATAATGATTGAAGCA
Found at i:5941 original size:70 final size:70
Alignment explanation
Indices: 5854--5994 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
5844 TGACGCAGCG
5854 TGTAGCGTGAAATCAAACTCACCAAGAATCCACTTGGATGAAAGTTGATAAAAATTCCATACCAG
1 TGTAGCGTGAAATCAAACTCACCAAGAATCCACTTGGATGAAAGTTGATAAAAATTCCATACCAG
5919 GAAAA
66 GAAAA
5924 TGTAGCGTGAAATCAAACTCACCAAGAATCCACTTGGATGAAAGTTGATAAAAATTCCATACCAG
1 TGTAGCGTGAAATCAAACTCACCAAGAATCCACTTGGATGAAAGTTGATAAAAATTCCATACCAG
5989 GAAAA
66 GAAAA
5994 T
1 T
5995 AAACTGAGAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (70 bp):
TGTAGCGTGAAATCAAACTCACCAAGAATCCACTTGGATGAAAGTTGATAAAAATTCCATACCAG
GAAAA
Found at i:12845 original size:29 final size:29
Alignment explanation
Indices: 12803--12875 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
12793 GACCATTAAG
* *
12803 ATTATAGAA-AAAAATCTAAAATAATTCCA
1 ATTAAAGAACAAAAA-CGAAAATAATTCCA
* * *
12832 ATTAAAGAACAAAAAGGACAATAATTTCA
1 ATTAAAGAACAAAAACGAAAATAATTCCA
12861 ATTAAAGAACAAAAA
1 ATTAAAGAACAAAAA
12876 GATAAAGGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 33 0.87
30 5 0.13
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.22
Consensus pattern (29 bp):
ATTAAAGAACAAAAACGAAAATAATTCCA
Found at i:14259 original size:15 final size:16
Alignment explanation
Indices: 14216--14264 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
14206 AGCCCCAACG
14216 CGAAAATACCCGAACC
1 CGAAAATACCCGAACC
*
14232 TGAAAATACCCGAACC
1 CGAAAATACCCGAACC
*
14248 CG-AAATATCCGAACC
1 CGAAAATACCCGAACC
14263 CG
1 CG
14265 CCCAATTGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 14 0.47
16 16 0.53
ACGTcount: A:0.41, C:0.35, G:0.14, T:0.10
Consensus pattern (16 bp):
CGAAAATACCCGAACC
Found at i:15010 original size:31 final size:31
Alignment explanation
Indices: 14972--15030 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
14962 TTTGTAAAAC
* *
14972 TTTTGAAACATCTATTATGCCCTTATTTAAT
1 TTTTGAAACATCAATTATACCCTTATTTAAT
* *
15003 TTTTGAAACGTCAATTATATCCTTATTT
1 TTTTGAAACATCAATTATACCCTTATTT
15031 GTCTAACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (31 bp):
TTTTGAAACATCAATTATACCCTTATTTAAT
Found at i:19894 original size:78 final size:76
Alignment explanation
Indices: 19763--19998 Score: 292
Period size: 78 Copynumber: 3.2 Consensus size: 76
19753 TTTTTTTAAT
*
19763 TAAAATAGTAAAATGGTAAAATATAAGTAATAAGGATATTAGATTTAATTATATAAAAATAGAAT
1 TAAAATAGTAAAATGATAAAATATAAGTAATAAGGATATTAGATTTAATTATATAAAAATAGAAT
19828 TTTTAGTTGAG
66 TTTTAGTTGAG
19839 TAAAATAGTAAAATGATAAAATATAA-TAGCTATAAGGATATTAGATTTAATTATATAAAAATAG
1 TAAAATAGTAAAATGATAAAATATAAGTA---ATAAGGATATTAGATTTAATTATATAAAAATAG
*
19903 ATTTTTTAGTTGAG
63 AATTTTTAGTTGAG
* * * * * *
19917 TAAAATAGT-AAA--AT-AAA-AT-AGTTATAAAGATATTATATTGAATTAAAT-AAAATAGAGT
1 TAAAATAGTAAAATGATAAAATATAAGTAATAAGGATATTAGATTTAATTATATAAAAATAGAAT
*
19975 TTTTAGTTAAG
66 TTTTAGTTGAG
19986 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
19999 ACCTAAACAA
Statistics
Matches: 145, Mismatches: 9, Indels: 18
0.84 0.05 0.10
Matches are distributed among these distances:
69 25 0.17
70 26 0.18
72 1 0.01
73 3 0.02
74 3 0.02
75 4 0.03
76 25 0.17
77 3 0.02
78 55 0.38
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (76 bp):
TAAAATAGTAAAATGATAAAATATAAGTAATAAGGATATTAGATTTAATTATATAAAAATAGAAT
TTTTAGTTGAG
Found at i:19929 original size:70 final size:69
Alignment explanation
Indices: 19845--19998 Score: 195
Period size: 70 Copynumber: 2.2 Consensus size: 69
19835 TGAGTAAAAT
* * * * *
19845 AGTAAAAT-GATAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGATTTTT
1 AGTAAAATAG-TAAAATAAAATAGCTATAAAGATATTAGATTGAATTAAAT-AAAATAGAGTTTT
*
19909 TAGTTG
64 TAGTTA
* *
19915 AGTAAAATAGTAAAATAAAATAGTTATAAAGATATTATATTGAATTAAATAAAATAGAGTTTTTA
1 AGTAAAATAGTAAAATAAAATAGCTATAAAGATATTAGATTGAATTAAATAAAATAGAGTTTTTA
19980 GTTA
66 GTTA
19984 AGTAAAACTA-TAAAA
1 AGTAAAA-TAGTAAAA
19999 ACCTAAACAA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
69 29 0.39
70 44 0.59
71 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (69 bp):
AGTAAAATAGTAAAATAAAATAGCTATAAAGATATTAGATTGAATTAAATAAAATAGAGTTTTTA
GTTA
Found at i:20379 original size:28 final size:30
Alignment explanation
Indices: 20339--20399 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 30
20329 TTTTTTTACG
20339 TTAAACCTCTTATTATTA-TA-ATTAATTA
1 TTAAACCTCTTATTATTATTATATTAATTA
* *
20367 TTAAACTTCTTATTATTATTATTTTAATTA
1 TTAAACCTCTTATTATTATTATATTAATTA
20397 TTA
1 TTA
20400 TTAGTGGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 17 0.59
29 2 0.07
30 10 0.34
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (30 bp):
TTAAACCTCTTATTATTATTATATTAATTA
Done.