Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007645.1 Corchorus capsularis cultivar CVL-1 contig07666, 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: 45568
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:14712 original size:28 final size:29
Alignment explanation
Indices: 14660--14728 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 29
14650 GTGGCCAAAA
** *
14660 AATAATAT-TTTATTATTAATGAT-AAT-
1 AATAATATATTTATTAAGAATAATAAATC
14686 AATAATATATTGTATTAAGAATAATAAATC
1 AATAATATATT-TATTAAGAATAATAAATC
14716 AATAA-ATATTTAT
1 AATAATATATTTAT
14729 ATTATAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 8 0.22
27 2 0.06
28 13 0.36
29 8 0.22
30 5 0.14
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (29 bp):
AATAATATATTTATTAAGAATAATAAATC
Found at i:14795 original size:65 final size:62
Alignment explanation
Indices: 14751--14866 Score: 207
Period size: 62 Copynumber: 1.9 Consensus size: 62
14741 ATTATTATCG
14751 TTAGTATTATTATGATTATATTATTATTATAGAAAATATATATATAATAAATAAATAAATAA
1 TTAGTATTATTATGATTATATTATTATTATAGAAAATATATATATAATAAATAAATAAATAA
*
14813 TTAGTATTATTATGATTATATTATTATTATATAAAATATATA-ATAAATAAATAA
1 TTAGTATTATTATGATTATATTATTATTATAGAAAATATATATAT-AATAAATAA
14867 TCTTATCATC
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
61 2 0.04
62 50 0.96
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (62 bp):
TTAGTATTATTATGATTATATTATTATTATAGAAAATATATATATAATAAATAAATAAATAA
Found at i:18225 original size:126 final size:125
Alignment explanation
Indices: 18000--18270 Score: 470
Period size: 126 Copynumber: 2.2 Consensus size: 125
17990 CACAGTGTTG
*
18000 GAAACCAAGCAAGCAAAAGGTTCACTTCCTGCTGACTTCTTTGATAAGGATGAAGCAAGGTTACC
1 GAAACCAAGCAAGC-AAAGGTTCACTTCCTGCTGACTTCTTTGATAAGGATGAAACAAGGTTACC
*
18065 TGCAAATGGTATGAAGCCTTCCAGGGAGAATAAACAGGCATCAGTGAAGGCTACCGCTCCA
65 TGCAAATGGTATGAAGCCTGCCAGGGAGAATAAACAGGCATCAGTGAAGGCTACCGCTCCA
18126 GAAACCAAGCAAGCGAAAGGTTCACTTCCTGCTGACTTCTTTGATAAGGATGAAACAAGGTTACC
1 GAAACCAAGCAAGC-AAAGGTTCACTTCCTGCTGACTTCTTTGATAAGGATGAAACAAGGTTACC
* * *
18191 TGCAAATGGTATGAAGCCTGCTAGGGAGAATAAACAGGCATCAGTGCAGGCTACTGCTCCA
65 TGCAAATGGTATGAAGCCTGCCAGGGAGAATAAACAGGCATCAGTGAAGGCTACCGCTCCA
*
18252 GAAACCAAACAAGCAAAGG
1 GAAACCAAGCAAGCAAAGG
18271 GAGCACTACC
Statistics
Matches: 138, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
125 5 0.04
126 133 0.96
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (125 bp):
GAAACCAAGCAAGCAAAGGTTCACTTCCTGCTGACTTCTTTGATAAGGATGAAACAAGGTTACCT
GCAAATGGTATGAAGCCTGCCAGGGAGAATAAACAGGCATCAGTGAAGGCTACCGCTCCA
Found at i:24421 original size:16 final size:16
Alignment explanation
Indices: 24400--24433 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
24390 ACAATTCAGA
24400 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
24416 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
24432 AA
1 AA
24434 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:26691 original size:60 final size:61
Alignment explanation
Indices: 26600--26778 Score: 270
Period size: 60 Copynumber: 2.9 Consensus size: 61
26590 CAGTTAACCC
* *
26600 AAAAAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAG-AA
1 AAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTAA
* * *
26660 AAAAAAAAAAAAAAACTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTACGCAAAAGTTAG
1 AAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAG-TAA
** *
26722 AGCAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAA
1 AAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAA
26779 CTTAGAGCAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 54 0.50
62 53 0.50
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.15
Consensus pattern (61 bp):
AAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTAA
Found at i:26733 original size:62 final size:62
Alignment explanation
Indices: 26601--26797 Score: 281
Period size: 62 Copynumber: 3.2 Consensus size: 62
26591 AGTTAACCCA
* * **
26601 AAAAAAAAAAGAAGCTCGCTAAGTTGAAAATCCTGCAAAGGACGACTTAGGCAAAAG--AAAAA
1 AAAAAAAAAA-AA-CTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGC
*
26663 AAAAAAAAAAAACTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTACGCAAAAGTTAGAGC
1 AAAAAAAAAAAACTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGC
** *
26725 AAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAACTTAGAGC
1 AAAAAAAAAAAACTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGC
*
26787 ACAAAAAAAAA
1 AAAAAAAAAAA
26798 TGAATGAACT
Statistics
Matches: 122, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
60 41 0.34
61 2 0.02
62 79 0.65
ACGTcount: A:0.50, C:0.16, G:0.19, T:0.14
Consensus pattern (62 bp):
AAAAAAAAAAAACTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGCAAAAGTTAGAGC
Found at i:29446 original size:8 final size:7
Alignment explanation
Indices: 29418--29442 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29408 GTGCAGTGAA
29418 TTTTATT
1 TTTTATT
29425 TTTTATT
1 TTTTATT
29432 TTTTATT
1 TTTTATT
29439 TTTT
1 TTTT
29443 TATTATCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:41298 original size:16 final size:16
Alignment explanation
Indices: 41282--41318 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41272 CTAATATATA
41282 AATATAT-AAATAAAT
1 AATATATAAAATAAAT
*
41297 AATAAATAAAATAAAT
1 AATATATAAAATAAAT
41313 AATATA
1 AATATA
41319 CTCCATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATATATAAAATAAAT
Found at i:41308 original size:12 final size:11
Alignment explanation
Indices: 41273--41314 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
41263 TCCTACCTCC
*
41273 TAATATATAAA
1 TAATAAATAAA
41284 TATATAAATAAA
1 TA-ATAAATAAA
41296 TAATAAAT-AA
1 TAATAAATAAA
41306 -AATAAATAA
1 TAATAAATAA
41315 TATACTCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 7 0.25
10 3 0.11
11 8 0.29
12 10 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:41764 original size:5 final size:5
Alignment explanation
Indices: 41754--41779 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
41744 ATATTTGACC
41754 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
41780 GAGAAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:43166 original size:224 final size:223
Alignment explanation
Indices: 42763--43218 Score: 688
Period size: 224 Copynumber: 2.0 Consensus size: 223
42753 AGTAATAATG
* *
42763 ATATGATAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTATAAGACTACACAAGTGGGT
1 ATATGACAAATTATACAATACACCGTCAGTGGAGTTTA--AGAC---AAGACTACACAAGCGGGT
* *
42828 CCTGAAGGGTGACATGTGTCTCCTAGGGACTAGATTGAAACATTTAAAACTCAATTAATTCAAAA
61 CATGAAGGGTGACACGTGTCTCCTAGGGACTAGATTGAAACATTTAAAACTCAATTAATTCAAAA
42893 AACGGACATGTGTCAACTCCACAACCCACTTATGGAGACCAAAATTTACACCGTCGGTGTATCAA
126 AACGGACATGTGTCAACTCCACAACCCACTTATGGAGACCAAAATTTACACCGTCGGTGTATCAA
42958 ATAATCA-CCATAATATATATATATATATATATATA
191 ATAATCACCCATAATA-ATATATATA-ATAT-TATA
*
42993 ATATGACAAATTATACAATACATCGTCAGTGGAGTTT-AG-C-AGACTACACAAGCGGGTCATGA
1 ATATGACAAATTATACAATACACCGTCAGTGGAGTTTAAGACAAGACTACACAAGCGGGTCATGA
* *
43055 AGGGTGACACGTGTC-CTCTGGGGACTAGATTGAAATATTTTAAAACTCAATTAATTCAAAAAAA
66 AGGGTGACACGTGTCTC-CTAGGGACTAGATTGAAACA-TTTAAAACTCAATTAATTC-AAAAAA
* *
43119 CGGACATGTGTCAACTCCACAACCCGCTTATGGAGTCCAAAATTTACACCGTCGGTGTATCAAAT
128 CGGACATGTGTCAACTCCACAACCCACTTATGGAGACCAAAATTTACACCGTCGGTGTATCAAAT
*
43184 AATTACCCATAATAATATATATAATATTATA
193 AATCACCCATAATAATATATATAATATTATA
43215 ATAT
1 ATAT
43219 AATAATATAC
Statistics
Matches: 212, Mismatches: 10, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
221 1 0.00
222 60 0.28
223 23 0.11
224 82 0.39
225 8 0.04
226 1 0.00
227 2 0.01
230 35 0.17
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (223 bp):
ATATGACAAATTATACAATACACCGTCAGTGGAGTTTAAGACAAGACTACACAAGCGGGTCATGA
AGGGTGACACGTGTCTCCTAGGGACTAGATTGAAACATTTAAAACTCAATTAATTCAAAAAACGG
ACATGTGTCAACTCCACAACCCACTTATGGAGACCAAAATTTACACCGTCGGTGTATCAAATAAT
CACCCATAATAATATATATAATATTATA
Found at i:43227 original size:8 final size:8
Alignment explanation
Indices: 43192--43227 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
43182 ATAATTACCC
43192 ATAATAAT
1 ATAATAAT
43200 ATATATAAT
1 ATA-ATAAT
*
43209 ATTATAAT
1 ATAATAAT
43217 ATAATAAT
1 ATAATAAT
43225 ATA
1 ATA
43228 CTCCCTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATAATAAT
Done.