Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013919.1 Corchorus capsularis cultivar CVL-1 contig13940, 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: 16986
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:3078 original size:21 final size:21
Alignment explanation
Indices: 3037--3080 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3027 TAATCCTATG
*
3037 TTGGAGGTCTCTTATTTATAT
1 TTGGAGGTCTCTTATTAATAT
*
3058 TTGGAGGTTTCTT-TATAATAT
1 TTGGAGGTCTCTTAT-TAATAT
3079 TT
1 TT
3081 TGATTTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (21 bp):
TTGGAGGTCTCTTATTAATAT
Found at i:6494 original size:21 final size:19
Alignment explanation
Indices: 6469--6507 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
6459 TATGACTCAT
6469 ATGCTATGAATGCTATGATTG
1 ATGCTATGAAT-CT-TGATTG
*
6490 ATGCTTTGAATCTTGATT
1 ATGCTATGAATCTTGATT
6508 TGCTTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (19 bp):
ATGCTATGAATCTTGATTG
Found at i:12405 original size:31 final size:29
Alignment explanation
Indices: 12333--12407 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
12323 CCAAATTGCT
12333 AGTTCAGGGGG-AAAACGTCCAAAATTAA
1 AGTTCAGGGGGCAAAACGTCCAAAATTAA
* *
12361 AGTTTAGGAGGCAAAACGT-CAAAATCGTAGA
1 AGTTCAGGGGGCAAAACGTCCAAAAT--TA-A
12392 AGTTCAGGGGGCAAAA
1 AGTTCAGGGGGCAAAA
12408 AGGACATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 15 0.38
29 7 0.18
30 2 0.05
31 15 0.38
ACGTcount: A:0.41, C:0.13, G:0.28, T:0.17
Consensus pattern (29 bp):
AGTTCAGGGGGCAAAACGTCCAAAATTAA
Found at i:13242 original size:444 final size:441
Alignment explanation
Indices: 12415--13297 Score: 1543
Period size: 444 Copynumber: 2.0 Consensus size: 441
12405 AAAAGGACAT
*
12415 TAAGCCTATAATATTTATAGTTAAGTTTTATGGGCTTTAATCACATATAAACCACTCACATAATT
1 TAAGCCTATAATATTTATAGTTAAGTTTTATGGGCTTTAATCACATATAAACCAATCACATAATT
*
12480 ACCTAATAATAAACTAATGAAATTATGACACTTAAACAATTTTATATATTAATACTTGGTTTAAT
66 ACCTAATAATAAACTAATGAAATTATGACACTTAAACAATTTTATATAATAATACTTGGTTTAAT
* *
12545 TTACAGTATATATTGTATAATAATTCTAACTTTATATAATGATATCATAAATAATGTAGTTTATT
131 TTACAGTATATATTGTATAATAATTCTAACTTTATATAATAATATCATAAATAATGCAGTTTATT
** *
12610 AAATTTACAATACTTAACTTCAGAAAAGTTATACCGCTATGAATTTATTAGAAATGCATAAATAA
196 AAATTTACAATACTTAACCACAGAAAAGTTATACCGCTATGAATTTATAAGAAATGCATAAATAA
* * *
12675 TAAGTTTTAATGGAGTATCAAAGAAACTATATGTGTTCTTGGTATGAGTTTTATATGCACTATGA
261 TAAGTTTTAATGGAGTATCAAAGAAACTATACGTGTTCTTGGTATGAGTTTAATATGCACCATGA
12740 GCAGTATCTGGTTAGTATTTGAATAAACTTTTGAGAAACTGCTTGGATAATATTTTTTTTTCCTT
326 GCAGTATCTGGTTAGTATTTGAATAAACTTTTGAGAAACTGCTTGGATAATA-TTTTTTTTCCTT
* *
12805 TTTTCTTCGAAACAAAGCTTAGCTCCAAGAAAGAAAGATGTCGTAAGTCTCG
390 TTTTCTTCAAAACAAAGCTTAGCTCCAAGAAAGAAAGATGTCGCAAGTCTCG
*
12857 TAAGCCTATAATATTTATAGTTAAGTTTTATGGGTTTTAATCACATATATAAACCAATCACATAA
1 TAAGCCTATAATATTTATAGTTAAGTTTTATGGGCTTTAATCAC--ATATAAACCAATCACATAA
*
12922 TTACCTAATAATAAACTAATGAAATTATGACAGTTAAACAATTTTATATAATAATACTTGGTTTA
64 TTACCTAATAATAAACTAATGAAATTATGACACTTAAACAATTTTATATAATAATACTTGGTTTA
*
12987 ATTTACAGTATATATTGTATAATAATTCTAACTTTATATAATAATATTATAAATAATGCAGTTTA
129 ATTTACAGTATATATTGTATAATAATTCTAACTTTATATAATAATATCATAAATAATGCAGTTTA
13052 TTAAATTT-CTAATACTTAACCACAGAAAAGTTATACCGCTATGAATTTATAAGAAATGCATAAA
194 TTAAATTTAC-AATACTTAACCACAGAAAAGTTATACCGCTATGAATTTATAAGAAATGCATAAA
* * *
13116 TTATAAGTTTTAATGGAGTATCAAAGAAACTATGCGTGTTCTTGGTATGGGTTTAATATGCACCA
258 TAATAAGTTTTAATGGAGTATCAAAGAAACTATACGTGTTCTTGGTATGAGTTTAATATGCACCA
**
13181 TGAGTGGTATCTGGTTAGTATTTGAATAAACTTTTGAGAAACTGCTTGGATAATATTTTTTTTCC
323 TGAGCAGTATCTGGTTAGTATTTGAATAAACTTTTGAGAAACTGCTTGGATAATATTTTTTTTCC
13246 TTTTTTCTTCAAAACAAAGCTTAGCTCCAAGAAAGAAAGATGTCGCAAGTCT
388 TTTTTTCTTCAAAACAAAGCTTAGCTCCAAGAAAGAAAGATGTCGCAAGTCT
13298 TGTATCCTTG
Statistics
Matches: 418, Mismatches: 20, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
442 43 0.10
443 61 0.15
444 314 0.75
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (441 bp):
TAAGCCTATAATATTTATAGTTAAGTTTTATGGGCTTTAATCACATATAAACCAATCACATAATT
ACCTAATAATAAACTAATGAAATTATGACACTTAAACAATTTTATATAATAATACTTGGTTTAAT
TTACAGTATATATTGTATAATAATTCTAACTTTATATAATAATATCATAAATAATGCAGTTTATT
AAATTTACAATACTTAACCACAGAAAAGTTATACCGCTATGAATTTATAAGAAATGCATAAATAA
TAAGTTTTAATGGAGTATCAAAGAAACTATACGTGTTCTTGGTATGAGTTTAATATGCACCATGA
GCAGTATCTGGTTAGTATTTGAATAAACTTTTGAGAAACTGCTTGGATAATATTTTTTTTCCTTT
TTTCTTCAAAACAAAGCTTAGCTCCAAGAAAGAAAGATGTCGCAAGTCTCG
Found at i:13517 original size:12 final size:12
Alignment explanation
Indices: 13500--13526 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13490 TATATAATAA
13500 ATTGATTTTAAT
1 ATTGATTTTAAT
13512 ATTGATTTTAAT
1 ATTGATTTTAAT
13524 ATT
1 ATT
13527 TATGAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
ATTGATTTTAAT
Found at i:15421 original size:138 final size:138
Alignment explanation
Indices: 15254--15528 Score: 478
Period size: 138 Copynumber: 2.0 Consensus size: 138
15244 ATTATAGTTG
* * *
15254 ATTATTAATATCTTTCCATAATTTCAAAAAATTAAATATTGGATTTAAAAAATCTTTCCATAATT
1 ATTAGTAATATCTTTCCATAATTTCAAAAAATTAAATATTAGATTGAAAAAATCTTTCCATAATT
15319 AATAAAAAACTTCAATGACTAAAAAGAATACTCATTAAAAAATTATTATACTATAATACTAAGGG
66 AATAAAAAACTTCAATGACTAAAAAGAATACTCATTAAAAAATTATTATACTATAATACTAAGGG
15384 TATTTTAA
131 TATTTTAA
* *
15392 ATTAGTAATATCTTTTCATAATTTCAAAAAATTAAATATTAGATTGACAAAATCTTTCCATAATT
1 ATTAGTAATATCTTTCCATAATTTCAAAAAATTAAATATTAGATTGAAAAAATCTTTCCATAATT
* * *
15457 ATTAAAAAAGTTCAATGACTAAAAAGAATTCTCATTAAAAAATTATTATACTATAATACTAAGGG
66 AATAAAAAACTTCAATGACTAAAAAGAATACTCATTAAAAAATTATTATACTATAATACTAAGGG
15522 TATTTTA
131 TATTTTA
15529 GAAGTTTCGC
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 129 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (138 bp):
ATTAGTAATATCTTTCCATAATTTCAAAAAATTAAATATTAGATTGAAAAAATCTTTCCATAATT
AATAAAAAACTTCAATGACTAAAAAGAATACTCATTAAAAAATTATTATACTATAATACTAAGGG
TATTTTAA
Done.