Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013685.1 Corchorus olitorius cultivar O-4 contig13718, 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: 31255
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Found at i:4952 original size:21 final size:20
Alignment explanation
Indices: 4906--4948 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4896 CTCTCACAAG
* *
4906 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
4926 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
4946 TTT
1 TTT
4949 TCTACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:7971 original size:33 final size:33
Alignment explanation
Indices: 7918--7982 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
7908 TCTCAATCTG
* * * *
7918 TTGTGACAGATGCCATTCTTCCTATTCAACCAA
1 TTGTGACAAATACCACTCTTCCTACTCAACCAA
*
7951 TTGTGACAAATACCACTCTTCCTGCTCAACCA
1 TTGTGACAAATACCACTCTTCCTACTCAACCA
7983 GTTTTTCCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.31
Consensus pattern (33 bp):
TTGTGACAAATACCACTCTTCCTACTCAACCAA
Found at i:14085 original size:22 final size:22
Alignment explanation
Indices: 14060--14136 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
14050 TATTTTTATG
* *
14060 AAATTTTAATAATTACCCTATT
1 AAATTTTGATAATTACCCTATA
* * *
14082 AAATTTTGACAATTACCATATG
1 AAATTTTGATAATTACCCTATA
14104 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAATTACCCTATA
*
14125 AAATTGTGATAA
1 AAATTTTGATAA
14137 ATTCCATAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 15 0.32
22 32 0.68
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.40
Consensus pattern (22 bp):
AAATTTTGATAATTACCCTATA
Found at i:14144 original size:43 final size:44
Alignment explanation
Indices: 14056--14158 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 44
14046 TGAATATTTT
* * * *
14056 TATGAAATTTTAATAATTACCCTATTAAATTTTGACAATTACCA
1 TATGAAATTTTGATAATTACCCTATAAAATTGTGAAAATTACCA
14100 TATGAAATTTTGATAATTA-CCTATAAAATTGTGATAAATT-CCA
1 TATGAAATTTTGATAATTACCCTATAAAATTGTGA-AAATTACCA
* *
14143 TAAGAAACTTTGATAA
1 TATGAAATTTTGATAA
14159 CCTAACAATG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 30 0.58
44 22 0.42
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGATAATTACCCTATAAAATTGTGAAAATTACCA
Found at i:16763 original size:468 final size:470
Alignment explanation
Indices: 15859--16794 Score: 1653
Period size: 469 Copynumber: 2.0 Consensus size: 470
15849 AATTACAAAA
*
15859 GCAACAATCAATATCTATCATCATCGTTTTTTTTTGCTATATTTATTATCATTAATAATTTGGAT
1 GCAACAATCAATATCTATCATCATCGATTTTTTTTGCTATATTTATTATCATTAATAATTTGGAT
15924 AAGTAGTTAGAAATATATATAAAATAGTTTGAGCAGGATTTAAATTTATAATTAAATCATAAATA
66 AAGTAGTTAGAAATATATATAAAATAGTTTGAGCAGGATTTAAATTTATAATTAAATCATAAATA
* *
15989 AATAATAATATATACAGTAGAAATTGGGTTGGCCAATAATGATATAATAATATATATAAAACATA
131 AATAATAATATATACAGTAGAAATTGGGTTGACCAATAATAATATAATAATATATATAAAACATA
* * *
16054 AAAGTCTATTTTTAAGTAATGATATTTTTTTTAAAAAAAAAGTAAAAACAATTTAGAAATATTTT
196 AAAGTCTATTTTTAAGTAATGACAATTTTTTAAAAAAAAAAGTAAAAACAATTTAGAAATATTTT
16119 GGAAAAAAAGGGTACAATCGGAAAACATAAAATTTCCCATTATTCATACTCTTCTATTTAGTATA
261 GGAAAAAAAGGGTACAATCGGAAAACATAAAATTTCCCATTATTCATACTCTTCTATTTAGTATA
* *
16184 GATTTGGAGAAACTATTGATTTTGTCTCATTTCGGTCCAGTAGACCTATTAGGCCCGTTTGAGTC
326 GATTTGGAGAAACTATTGATTTTGTCTCATTTCAGTCCAGTAGACCTATTAGGCCCCTTTGAGTC
*
16249 CATGAAGGCCAAATTGCCAAGCCAGATGTCTTGAAACCTAAATATGATATTCTTAGACCCAATTC
391 CATGAAGCCCAAATTGCCAAGCCAGATGTCTTGAAACCTAAATATGATATTCTTAGACCCAATTC
16314 GTTCATATGGAAGAT
456 GTTCATATGGAAGAT
* * *
16329 GCAACAATCAATATTTATCATCATC-ATTTTTTTTGTTATATTTATTATCGTTAATAATTTGGAT
1 GCAACAATCAATATCTATCATCATCGATTTTTTTTGCTATATTTATTATCATTAATAATTTGGAT
16393 AAGTAGTTAGAAATATATATAAAATAGTTTGAGCAGGATTTAAATTTATAATTAAATCATAAATA
66 AAGTAGTTAGAAATATATATAAAATAGTTTGAGCAGGATTTAAATTTATAATTAAATCATAAATA
* * * *
16458 CATAATAATATATATATTAGAAATTGGGTTGACCAATAATAATATCATAATATATATAAAACATA
131 AATAATAATATATACAGTAGAAATTGGGTTGACCAATAATAATATAATAATATATATAAAACATA
16523 AAAGTCTATTTTTAAGTAATGACAATTTTTTAAAAAAAAAAGTAAAGAA-AATTTAGAAATATTT
196 AAAGTCTATTTTTAAGTAATGACAATTTTTTAAAAAAAAAAGTAAA-AACAATTTAGAAATATTT
** *
16587 T-TTAAAAAAGGGTACAATCGGAAAACATAAAATTTTCCATTATTCATACTCTTCTATTTAGTAT
260 TGGAAAAAAAGGGTACAATCGGAAAACATAAAATTTCCCATTATTCATACTCTTCTATTTAGTAT
16651 AGATTTGGAGAAACTATTGATTTTGTCTCATTTCAGTCCAGTAGACCTATTAGGCCCCTTTGAGT
325 AGATTTGGAGAAACTATTGATTTTGTCTCATTTCAGTCCAGTAGACCTATTAGGCCCCTTTGAGT
* *
16716 CCATGAAGCCCAAATTGCCAAGTCAGATGTCTTGAAACCTAAATATGATATTGTTAGACCCAATT
390 CCATGAAGCCCAAATTGCCAAGCCAGATGTCTTGAAACCTAAATATGATATTCTTAGACCCAATT
16781 CGTTCATATGGAAG
455 CGTTCATATGGAAG
16795 CCCAAAGAAA
Statistics
Matches: 444, Mismatches: 21, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
468 199 0.45
469 219 0.49
470 26 0.06
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (470 bp):
GCAACAATCAATATCTATCATCATCGATTTTTTTTGCTATATTTATTATCATTAATAATTTGGAT
AAGTAGTTAGAAATATATATAAAATAGTTTGAGCAGGATTTAAATTTATAATTAAATCATAAATA
AATAATAATATATACAGTAGAAATTGGGTTGACCAATAATAATATAATAATATATATAAAACATA
AAAGTCTATTTTTAAGTAATGACAATTTTTTAAAAAAAAAAGTAAAAACAATTTAGAAATATTTT
GGAAAAAAAGGGTACAATCGGAAAACATAAAATTTCCCATTATTCATACTCTTCTATTTAGTATA
GATTTGGAGAAACTATTGATTTTGTCTCATTTCAGTCCAGTAGACCTATTAGGCCCCTTTGAGTC
CATGAAGCCCAAATTGCCAAGCCAGATGTCTTGAAACCTAAATATGATATTCTTAGACCCAATTC
GTTCATATGGAAGAT
Found at i:23364 original size:17 final size:17
Alignment explanation
Indices: 23342--23402 Score: 95
Period size: 17 Copynumber: 3.4 Consensus size: 17
23332 GTCAACGTTA
23342 GGATTATGATTTTATAT
1 GGATTATGATTTTATAT
23359 GGATTATGATTTTATAT
1 GGATTATGATTTTATAT
23376 GGATTATCTGATTTTATTAT
1 GGATTA--TGATTTTA-TAT
23396 GGATTAT
1 GGATTAT
23403 CTAGTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
17 23 0.56
18 1 0.02
19 8 0.20
20 9 0.22
ACGTcount: A:0.28, C:0.02, G:0.18, T:0.52
Consensus pattern (17 bp):
GGATTATGATTTTATAT
Found at i:23413 original size:20 final size:19
Alignment explanation
Indices: 23351--23412 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
23341 AGGATTATGA
*
23351 TTTTATATGGATTAT-GA-
1 TTTTATATGGATTATCTAG
23368 TTTTATATGGATTATCT-G
1 TTTTATATGGATTATCTAG
23386 ATTTTATTATGGATTATCTAG
1 -TTTTA-TATGGATTATCTAG
23407 TTTTAT
1 TTTTAT
23413 TTAATTTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 15 0.38
19 6 0.15
20 17 0.44
21 1 0.03
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (19 bp):
TTTTATATGGATTATCTAG
Done.