Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017160.1 Corchorus olitorius cultivar O-4 contig17193, 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: 68937
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:4191 original size:21 final size:21
Alignment explanation
Indices: 4165--4204 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
4155 TCCTCTACTG
4165 TTGTATCATATATAAACCCGT
1 TTGTATCATATATAAACCCGT
4186 TTGTATCATATATAAACCC
1 TTGTATCATATATAAACCC
4205 TATGTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (21 bp):
TTGTATCATATATAAACCCGT
Found at i:19536 original size:11 final size:11
Alignment explanation
Indices: 19512--19546 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
19502 TTGACAGCGC
19512 AACAAAAACAA
1 AACAAAAACAA
* *
19523 AACGAAAACGA
1 AACAAAAACAA
19534 AACAAAAACAA
1 AACAAAAACAA
19545 AA
1 AA
19547 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:19974 original size:34 final size:34
Alignment explanation
Indices: 19931--20034 Score: 208
Period size: 34 Copynumber: 3.1 Consensus size: 34
19921 ATAGAACTGT
19931 AACCTCTCTTCAGGCCTTTCATGTCCATATGAAG
1 AACCTCTCTTCAGGCCTTTCATGTCCATATGAAG
19965 AACCTCTCTTCAGGCCTTTCATGTCCATATGAAG
1 AACCTCTCTTCAGGCCTTTCATGTCCATATGAAG
19999 AACCTCTCTTCAGGCCTTTCATGTCCATATGAAG
1 AACCTCTCTTCAGGCCTTTCATGTCCATATGAAG
20033 AA
1 AA
20035 GAGAGTAAAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 70 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (34 bp):
AACCTCTCTTCAGGCCTTTCATGTCCATATGAAG
Found at i:21759 original size:20 final size:20
Alignment explanation
Indices: 21734--21773 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
21724 GATCTTTGAT
21734 TTGTCATCTGTGGAAAATTA
1 TTGTCATCTGTGGAAAATTA
21754 TTGTCATCTGTGGAAAATTA
1 TTGTCATCTGTGGAAAATTA
21774 AGCACTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGTCATCTGTGGAAAATTA
Found at i:23143 original size:23 final size:20
Alignment explanation
Indices: 23123--23166 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
23113 GAAATAATCA
23123 TATAAAATAATAATAACTAAT
1 TATAAAA-AATAATAACTAAT
* *
23144 TTTTAAAAATAATAACTAAT
1 TATAAAAAATAATAACTAAT
23164 TAT
1 TAT
23167 TAATTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TATAAAAAATAATAACTAAT
Found at i:23156 original size:20 final size:20
Alignment explanation
Indices: 23131--23169 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
23121 CATATAAAAT
*
23131 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
23151 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
23170 TTTATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:23948 original size:6 final size:6
Alignment explanation
Indices: 23937--23978 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
23927 CAACCGTCCC
* *
23937 CCAACA CCAACA CCAACG CCAACG CCAACG CCAACG CCAACG
1 CCAACG CCAACG CCAACG CCAACG CCAACG CCAACG CCAACG
23979 GTAGATGAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.38, C:0.50, G:0.12, T:0.00
Consensus pattern (6 bp):
CCAACG
Found at i:26201 original size:8 final size:8
Alignment explanation
Indices: 26188--26214 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
26178 AAAAGCCTTA
26188 GACAGTTG
1 GACAGTTG
26196 GACAGTTG
1 GACAGTTG
26204 GACAGTTG
1 GACAGTTG
26212 GAC
1 GAC
26215 TTGGACTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (8 bp):
GACAGTTG
Found at i:31340 original size:17 final size:17
Alignment explanation
Indices: 31318--31353 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
31308 TAACAAAGCA
31318 TTCCACTTT-GTTTAGCT
1 TTCCACTTTAG-TTAGCT
31335 TTCCACTTTAGTTAGCT
1 TTCCACTTTAGTTAGCT
31352 TT
1 TT
31354 TTGGGCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.14, C:0.22, G:0.11, T:0.53
Consensus pattern (17 bp):
TTCCACTTTAGTTAGCT
Found at i:34855 original size:2 final size:2
Alignment explanation
Indices: 34848--34877 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34838 GGATTCAGAA
34848 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34878 TTGCTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35127 original size:21 final size:19
Alignment explanation
Indices: 35102--35159 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
35092 GCTGCTCTAA
35102 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
35123 TAATCTAATATGTACAGTG
1 TAATCTCATCTGTACAGTC
35142 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
35160 TGCTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:44779 original size:21 final size:21
Alignment explanation
Indices: 44749--44797 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
44739 AGTTTAACAT
*
44749 GGTTTAACATTCAAAATTTGG
1 GGTTTGACATTCAAAATTTGG
*
44770 GGTTTGACATTCAAAATTTTG
1 GGTTTGACATTCAAAATTTGG
44791 GGTTTGA
1 GGTTTGA
44798 TCGGAGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (21 bp):
GGTTTGACATTCAAAATTTGG
Found at i:46675 original size:460 final size:459
Alignment explanation
Indices: 46092--47011 Score: 1786
Period size: 460 Copynumber: 2.0 Consensus size: 459
46082 GAAGCCGAAT
46092 TTGGAGGGTTCATCCCAAATCAATGATGCACAACATTGTGCAAAAGAAGCTTATGTTATAACAAA
1 TTGGAGGGTTCATCCCAAATCAATGATGCACAACATTGTGCAAAAGAAGCTTATGTTATAACAAA
*
46157 AGGATTTTGAAATGCTTTCAAACTATGAAAACTCGTAGAAAAATGTTGTAATGTATCATTTCTCA
66 AGGATTTTGAAATGCTTTCAAACTATGAAAACTCGTAGAAAAAGGTTGTAATGTATCATTTCTCA
46222 TAGAATTCTTATGCACTTGGAATATATGGTTTTTATAATTTTAAAATATAAATTTGAAACTATGT
131 TAGAATTCTTATGCACTTGGAATATATGGTTTTTATAATTTTAAAATATAAATTTGAAACTATGT
*
46287 ATATTAATTTGCCCCCACTGTCTAAAATTCCTGGATCCGCCACTGGGAATACAAATTTTGTACTT
196 ATATTAATTTGCCCCCACTGTCTAAAATTCCTGGATCCACCACTGGGAATACAAATTTTGTACTT
46352 CCATTTTTTCAATATTAAATATTTATTAGCATTTTGTTTTTATTTTTTATTAAATCCTCATTTAA
261 CCATTTTTTCAATATTAAATATTTATTAGCATTTTGTTTTTATTTTTTATTAAATCCTCATTTAA
46417 ATAATATTTCATTTTTCTAAATTGTTTTTTCTCTCTCCTTACCCAACCACTTTCTAACCTTTTAT
326 ATAATATTTCATTTTTCTAAATTGTTTTTTCTCTCTCCTTACCCAACCACTTTCTAACCTTTTAT
*
46482 TTTCCTCTTTTCGGATCAAACTAGCTATCAAACCTGAAAAAATATGAACCATCTATGAACAACAT
391 TTTCCTCTTTTCGGATCAAACTAGCTATCAAACCAGAAAAAATATGAACCATCTATGAACAACAT
46547 GAAC
456 GAAC
46551 TTGGAGGGTTCATCCCAAATCAATGATGCACAACATTGTGCAAAAGAAGCTTATGTTGATAACAA
1 TTGGAGGGTTCATCCCAAATCAATGATGCACAACATTGTGCAAAAGAAGCTTATGTT-ATAACAA
*
46616 AAGGATTTTGAAATGTTTTCAAACTATGAAAACTCGTAGAAAAAGGTTGTAATGTATCATTTCTC
65 AAGGATTTTGAAATGCTTTCAAACTATGAAAACTCGTAGAAAAAGGTTGTAATGTATCATTTCTC
46681 ATAGAATTCTTATGCACTTGGAATATATGGTTTTTATAATTTTAAAATATAAATTTGAAACTATG
130 ATAGAATTCTTATGCACTTGGAATATATGGTTTTTATAATTTTAAAATATAAATTTGAAACTATG
46746 TATATTAATTTGCCCCCACTGTCTAAAATTCCTGGATCCACCACTGGGAATACAAATTTTGTACT
195 TATATTAATTTGCCCCCACTGTCTAAAATTCCTGGATCCACCACTGGGAATACAAATTTTGTACT
46811 TCCATTTTTTCAATATTAAATATTTATTAGCATTTTGTTTTTATTTTTTATTAAATCCTCATTTA
260 TCCATTTTTTCAATATTAAATATTTATTAGCATTTTGTTTTTATTTTTTATTAAATCCTCATTTA
46876 AATAATATTTCATTTTTCTAAATTGTTTTTTCTCTCTCCTTACCCAACCACTTTCTAACCTTTTA
325 AATAATATTTCATTTTTCTAAATTGTTTTTTCTCTCTCCTTACCCAACCACTTTCTAACCTTTTA
*
46941 TTTTCCTCTTTTCGGATGAAACTAGCTATCAAACCAGAAAAAATATGAACCATCTATGAACAACA
390 TTTTCCTCTTTTCGGATCAAACTAGCTATCAAACCAGAAAAAATATGAACCATCTATGAACAACA
47006 TGAAC
455 TGAAC
47011 T
1 T
47012 GTAAAGAACA
Statistics
Matches: 455, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
459 57 0.13
460 398 0.87
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (459 bp):
TTGGAGGGTTCATCCCAAATCAATGATGCACAACATTGTGCAAAAGAAGCTTATGTTATAACAAA
AGGATTTTGAAATGCTTTCAAACTATGAAAACTCGTAGAAAAAGGTTGTAATGTATCATTTCTCA
TAGAATTCTTATGCACTTGGAATATATGGTTTTTATAATTTTAAAATATAAATTTGAAACTATGT
ATATTAATTTGCCCCCACTGTCTAAAATTCCTGGATCCACCACTGGGAATACAAATTTTGTACTT
CCATTTTTTCAATATTAAATATTTATTAGCATTTTGTTTTTATTTTTTATTAAATCCTCATTTAA
ATAATATTTCATTTTTCTAAATTGTTTTTTCTCTCTCCTTACCCAACCACTTTCTAACCTTTTAT
TTTCCTCTTTTCGGATCAAACTAGCTATCAAACCAGAAAAAATATGAACCATCTATGAACAACAT
GAAC
Found at i:48075 original size:8 final size:8
Alignment explanation
Indices: 48062--48087 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
48052 AAGCAATTCT
48062 ATTGGAGA
1 ATTGGAGA
48070 ATTGGAGA
1 ATTGGAGA
48078 ATTGGAGA
1 ATTGGAGA
48086 AT
1 AT
48088 CATTCTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.27
Consensus pattern (8 bp):
ATTGGAGA
Found at i:65985 original size:30 final size:30
Alignment explanation
Indices: 65951--66301 Score: 405
Period size: 30 Copynumber: 11.5 Consensus size: 30
65941 AAATGACACC
*
65951 TGTCATGGTCTTACAATTGACACCAGAAGT
1 TGTCATGATCTTACAATTGACACCAGAAGT
* *
65981 TGTCATGCTCTTACAAATGACACCAGAAGT
1 TGTCATGATCTTACAATTGACACCAGAAGT
*
66011 TGTCATGATCTTACAAATGACACCAGAAGT
1 TGTCATGATCTTACAATTGACACCAGAAGT
66041 TGTCATGATCTTACAATTGACACCAGAAGT
1 TGTCATGATCTTACAATTGACACCAGAAGT
66071 TGTCATGATCTTACAATTGACACCAGAAGT
1 TGTCATGATCTTACAATTGACACCAGAAGT
* * *
66101 TGTCATGATGTTGCAATTGACACCATAAGT
1 TGTCATGATCTTACAATTGACACCAGAAGT
* *
66131 TGTCATGATCTTGCAATTGACACCATAAGT
1 TGTCATGATCTTACAATTGACACCAGAAGT
* * ** *
66161 TGTCATGATCTTGCAATTGATACTTGAAGA
1 TGTCATGATCTTACAATTGACACCAGAAGT
* *
66191 TGTCATAATTTTATTCAATTGACACCAGAAGT
1 TGTCATGATCTTA--CAATTGACACCAGAAGT
* * * *** *
66223 TGTCATGATAAATTTCCAATAGACATTTGAAGA
1 TGTCATGAT---CTTACAATTGACACCAGAAGT
* *
66256 TGTCATAATTTTATTCAATTGACACCAGAAGT
1 TGTCATGATCTTA--CAATTGACACCAGAAGT
*
66288 TGTCATGATTTTAC
1 TGTCATGATCTTAC
66302 CTTTCAAAAT
Statistics
Matches: 279, Mismatches: 35, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
30 211 0.76
32 45 0.16
33 20 0.07
35 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Consensus pattern (30 bp):
TGTCATGATCTTACAATTGACACCAGAAGT
Done.