Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019702.1 Corchorus olitorius cultivar O-4 contig19735, 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: 47981
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:8765 original size:30 final size:31
Alignment explanation
Indices: 8729--8807 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 31
8719 TGGTATGTTA
* * *
8729 ACACGTGGTGTGCCACGTGTCCTTTTTT-GT
1 ACACGTGGCGTGCCACATGTCATTTTTTGGT
*
8759 ACACGTGGCGTGTCACATGTCATTTTTTGGT
1 ACACGTGGCGTGCCACATGTCATTTTTTGGT
* *
8790 ATACGTGGCATGCCACAT
1 ACACGTGGCGTGCCACAT
8808 CGGATGCCGT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 24 0.59
31 17 0.41
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.35
Consensus pattern (31 bp):
ACACGTGGCGTGCCACATGTCATTTTTTGGT
Found at i:13457 original size:1 final size:1
Alignment explanation
Indices: 13451--13487 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
13441 GACATTGAAG
**
13451 TTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13488 AATTAGACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:16754 original size:53 final size:54
Alignment explanation
Indices: 16673--16780 Score: 164
Period size: 53 Copynumber: 2.0 Consensus size: 54
16663 GGATTGGGAC
*
16673 TGTTCCCTCTTAATTAATGAATGAAACCAAATAAAGGGTGTTTTTATGTTTCTA
1 TGTTCCCTCTTAATTAATGAATGAAACCAAATAAAGGGTGTTTTGATGTTTCTA
* ** *
16727 TGTT-CCTTTTAATTAATGGGTGAAACCAGATAAAGGGTGTTTTGATGTTTCTA
1 TGTTCCCTCTTAATTAATGAATGAAACCAAATAAAGGGTGTTTTGATGTTTCTA
16780 T
1 T
16781 TCTATGTTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 45 0.92
54 4 0.08
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.42
Consensus pattern (54 bp):
TGTTCCCTCTTAATTAATGAATGAAACCAAATAAAGGGTGTTTTGATGTTTCTA
Found at i:26785 original size:17 final size:17
Alignment explanation
Indices: 26763--26796 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
26753 ATAAGTTAGA
26763 GGATAGAGTATACAAAC
1 GGATAGAGTATACAAAC
26780 GGATAGAGTATACAAAC
1 GGATAGAGTATACAAAC
26797 AAATCTCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
GGATAGAGTATACAAAC
Found at i:35680 original size:19 final size:19
Alignment explanation
Indices: 35656--35695 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
35646 ATAGACATGT
35656 TAGGCGACATAATGGAAGG
1 TAGGCGACATAATGGAAGG
35675 TAGGCGACATAATGGAAGG
1 TAGGCGACATAATGGAAGG
35694 TA
1 TA
35696 ACCCTTTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.35, T:0.17
Consensus pattern (19 bp):
TAGGCGACATAATGGAAGG
Found at i:44751 original size:154 final size:154
Alignment explanation
Indices: 44455--44760 Score: 445
Period size: 154 Copynumber: 2.0 Consensus size: 154
44445 AGATTGACGG
* * * *
44455 GCTTCTCACGCTTCTAATATCGTTATTCCATTTTTTTTCTGATTTAATTTTTAATTAAATCGAAA
1 GCTTCTCACGCTTCTAATATCGTTATTCCAGTATTTTTCAGAATTAATTTTTAATTAAATCGAAA
* *** * *
44520 CAAGATTCGAATGCTTGTTTTACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAAT
66 CAACATTCGAATGCTTGTAAAACAAATCCTTATATCCAATGTGACTAAGATTTGGTTCGATGAAT
*
44585 GTAGATATTTCAAGGAGTCTTTCC
131 ATAGATATTTCAAGGAGTCTTTCC
* *
44609 GCTT-TCACGCTTCTAATATCGTTTTTTCC-GTATTTTTCAGAATTAATTTTTAATTAAATTGAA
1 GCTTCTCACGCTTCTAATATCG-TTATTCCAGTATTTTTCAGAATTAATTTTTAATTAAATCGAA
* *
44672 ACAACATTTGTATGCTTGTAAAAACAAATCCTTATATCCAATGTGACTAAGATTTGGTTCGATGA
65 ACAACATTCGAATGCTTGT-AAAACAAATCCTTATATCCAATGTGACTAAGATTTGGTTCGATGA
44737 ATATAGATATTTCAAGGAGTCTTT
129 ATATAGATATTTCAAGGAGTCTTT
44761 ACGCCAAAAA
Statistics
Matches: 135, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
153 62 0.46
154 73 0.54
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (154 bp):
GCTTCTCACGCTTCTAATATCGTTATTCCAGTATTTTTCAGAATTAATTTTTAATTAAATCGAAA
CAACATTCGAATGCTTGTAAAACAAATCCTTATATCCAATGTGACTAAGATTTGGTTCGATGAAT
ATAGATATTTCAAGGAGTCTTTCC
Found at i:45267 original size:327 final size:325
Alignment explanation
Indices: 44611--46041 Score: 1184
Period size: 327 Copynumber: 4.5 Consensus size: 325
44601 GTCTTTCCGC
* *
44611 TTTCACGCTTCTAATATCGTTTTTTCCGTA-TTTTTCAGAATTAATTTTTAATTAAATTGAAACA
1 TTTCACGCTTCTAATATCG-TTTTT-C-TATTTTTTCCGAATTAATTTTTAATTAAATCGAAACA
* * * *
44675 ACATT-TGTATGCTTGTAAAAACAAATCCTTATATCCAATGTGACTAAGATTTGGTTCGATGAAT
63 AGATTCAG-ATGCTTGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTCGATGAAT
* * * ** * *
44739 ATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCTGGTCTCCAGAACACG
127 ATAGATATTTCAAAGAGTCTTTACGACAAAAATCATGCAAAACTGAGCAGGGACTCCAGAACACA
* * ** ** *
44804 TTTTTAGACAAAAATGGTTAGTACACGCTTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGT
192 TTTTTAGACAAAAACGGTTAGTAAACAATTTCAACTAAAATTTTGCAAAAACTGACCCGAAAAAT
* ** * * *
44869 TTTTGCTCAATTTTTTGCCAGAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAG
257 TTTTCCTCAATCATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGAATGAAG
44934 GGTT
322 GGTT
* *
44938 TTTCACGCTTCTAATATCGTTTTTCTATTTTTTCCGAATTAATTTCTAAATAAATCGAAACAAGA
1 TTTCACGCTTCTAATATCGTTTTTCTATTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGA
** * * *
45003 TTCAGATTTTTGTAAAAACAAATCGTTAAATCCAATGTGGCTGAGATTTGATTCGATGAATATAG
66 TTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTCGATGAATATAG
* * * *
45068 ATATTTCAATGAGTTTTTACGACAAAAAT-ACT-CAAAACTGAGCAGGGAC-CCTGGAACGCATT
131 ATATTTCAAAGAGTCTTTACGACAAAAATCA-TGCAAAACTGAGCAGGGACTCC-AGAACACATT
* * *
45130 TTTAGCCAAAAACGGTGATGAGTAAACAATTTCAACTAAAATTTTGCAAAAATTGACTCGAAAAA
194 TTTAGACAAAAACGGT--T-AGTAAACAATTTCAACTAAAATTTTGCAAAAACTGACCCGAAAAA
*
45195 TTTTTCCTCAATCATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCTAAAAA-ACATGA
256 TTTTTCCTCAATCATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA-ATGA
*
45259 ATGGTT
320 AGGGTT
* * *
45265 TTTCACGCTTCTAATATCGTTTTTC-CTTTTTTCCGAATTTATTTTTAATTTAATCGAAACAAGA
1 TTTCACGCTTCTAATATCGTTTTTCTATTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGA
* * ** * * * * **
45329 TTCAAATGCTCGTAAAAGTAAATCCTTTAATCCATTGTTACTGAGAATTGGTTAAATGAATATAG
66 TTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTCGATGAATATAG
* * * * * *
45394 ATATTTCAAAGAGTCTTT-CTGTCAAAAATCATGCAAAACTTAGTC-GAGGCCTCGA-AACGCGT
131 ATATTTCAAAGAGTCTTTAC-GACAAAAATCATGCAAAACTGAG-CAG-GGACTCCAGAACACAT
* * * * **** ** * *
45456 TTTTTGCCAAAAACTGTGA-TTGTTAA--T--AC-ATGATTTCGGTTAAAAACTGACCC-AAAGA
193 TTTTAGACAAAAACGGTTAGTAAACAATTTCAACTAAAATTT-TG-CAAAAACTGACCCGAAA-A
* * ** * * * * *
45514 ATATTT-ATCAATTGTTTTG-CAAAATATTCAGAAAAAATACATAATTGAACGCCAAAAAGATTG
255 ATTTTTCCTCAA-TCATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGAATG
* *
45577 ACGGGCT
319 AAGGGTT
* * *
45584 TTTCACGCTTCTAATATCATTTTTTCCATTTTTTTCGAATTAA--TTTAATT-AAT---------
1 TTTCACGCTTCTAATATC-GTTTTTCTATTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAG
* * * * *
45637 -TTCTA-A----T-T-AAATCGAA----T--ATCCAATGTGCCTGAGATTTGATTTGATGAATAT
65 ATTC-AGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTCGATGAATAT
* * * * *
45688 AGATATTTCAAGGAGTCTTTGCG-CAAAAAATCATTG-AAAATTGAGCCGGAACTCC-GAAACAC
129 AGATATTTCAAAGAGTCTTTACGAC-AAAAATCA-TGCAAAACTGAGCAGGGACTCCAG-AACAC
* * * *
45750 GTTTTTAGCCAAAAAACCGTGATTGATAGTATACACGATTTCAGCTAAAATTTTGCAAAAACTGA
191 ATTTTTAGAC-AAAAA-CG-G--T--TAGTA-A-ACAATTTCAACTAAAATTTTGCAAAAACTGA
*
45815 CCC-AAAAATTTTTTCCTCAA-CTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
247 CCCGAAAAA-TTTTTCCTCAATC-ATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
45878 AAAA-AATTGAAGGGTT
310 AAAAGAA-TGAAGGGTT
* *
45894 TTTCACGCTTCTAATATCGTTTTTCCA-TTTTTCCGAATTTATTTTTAATTAAATCGAAACAAGA
1 TTTCACGCTTCTAATATCGTTTTTCTATTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGA
* * * * ** *
45958 TTCAGTTGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGTTGAGATTTGGTTAGATGAATATAG
66 TTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTCGATGAATATAG
*
46023 ATATTTCAAGGAGTCTTTA
131 ATATTTCAAAGAGTCTTTA
46042 TACCAAAAAC
Statistics
Matches: 876, Mismatches: 154, Indels: 142
0.75 0.13 0.12
Matches are distributed among these distances:
295 6 0.01
296 76 0.09
297 8 0.01
298 2 0.00
299 1 0.00
301 1 0.00
302 5 0.01
303 2 0.00
304 1 0.00
306 1 0.00
308 19 0.02
309 34 0.04
310 73 0.08
311 8 0.01
318 8 0.01
319 75 0.09
320 29 0.03
321 17 0.02
323 5 0.01
324 38 0.04
325 116 0.13
326 118 0.13
327 178 0.20
328 4 0.00
329 1 0.00
331 1 0.00
333 49 0.06
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (325 bp):
TTTCACGCTTCTAATATCGTTTTTCTATTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGA
TTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTCGATGAATATAG
ATATTTCAAAGAGTCTTTACGACAAAAATCATGCAAAACTGAGCAGGGACTCCAGAACACATTTT
TAGACAAAAACGGTTAGTAAACAATTTCAACTAAAATTTTGCAAAAACTGACCCGAAAAATTTTT
CCTCAATCATTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGAATGAAGGGTT
Found at i:46326 original size:276 final size:280
Alignment explanation
Indices: 45806--46326 Score: 753
Period size: 288 Copynumber: 1.8 Consensus size: 280
45796 AAAATTTTGC
*
45806 AAAAACTGACCCAAAAATTTTTTCCTCAACTTTTTGCCACAATACTCAGAAAAAATATATAATTC
1 AAAAACTGACCCAAAAACTTTTTCCTCAACTTTTTGCCACAATACTCAGAAAAAATATATAATTC
* * *
45871 AACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTCCGAATTTAT
66 AACCCCAAAAAAATTCAAGGGTTTTTCAAGCTTCTAATATCGTTTTTCCA---TT-C--A--TAT
* * * * ** *
45936 TTTTAATTAAATCGAAACAAGATTCAGTTGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGTTG
123 TTCTAATTAAATCGAAACAAGATTCAGGTGCACGTAAAAAGAAATCCTTAAATCCAATGTGACTA
* * *
46001 AGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATACCAAAAACCATTTAGCTAAAAA
188 AGATTTGATTAGATGAATAAAAATATTTCAAGGAGTCTTTATACCAAAAACCATTTAGCTAAAAA
46066 TCGTGATGATTAGTACACAATTTCGGCT
253 TCGTGATGATTAGTACACAATTTCGGCT
* * *
46094 AAAAACTGACCCGAAAACTTTTTCCTCAATTTTTTGCCACAATACTCGGAAAAAATATATAATTC
1 AAAAACTGACCCAAAAACTTTTTCCTCAACTTTTTGCCACAATACTCAGAAAAAATATATAATTC
46159 AACCCCAAAAAAATTCAAGGGTTTTTCAAGCTTCTAATATCGTTTTT-CA-T-A-ATTTCTAATT
66 AACCCCAAAAAAATTCAAGGGTTTTTCAAGCTTCTAATATCGTTTTTCCATTCATATTTCTAATT
* * *
46220 GAATCGAAACAAGATTCAGGTGCACGTAAAAATAAATCCTTAAATTCAATGTGACTAAGATTTGA
131 AAATCGAAACAAGATTCAGGTGCACGTAAAAAGAAATCCTTAAATCCAATGTGACTAAGATTTGA
*
46285 TTAGATGAATAAAAATATTTCAAGGAGTCTTTATGCCAAAAA
196 TTAGATGAATAAAAATATTTCAAGGAGTCTTTATACCAAAAA
46327 TAATGCAAAA
Statistics
Matches: 212, Mismatches: 21, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
276 103 0.49
279 1 0.00
283 1 0.00
287 2 0.01
288 105 0.50
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (280 bp):
AAAAACTGACCCAAAAACTTTTTCCTCAACTTTTTGCCACAATACTCAGAAAAAATATATAATTC
AACCCCAAAAAAATTCAAGGGTTTTTCAAGCTTCTAATATCGTTTTTCCATTCATATTTCTAATT
AAATCGAAACAAGATTCAGGTGCACGTAAAAAGAAATCCTTAAATCCAATGTGACTAAGATTTGA
TTAGATGAATAAAAATATTTCAAGGAGTCTTTATACCAAAAACCATTTAGCTAAAAATCGTGATG
ATTAGTACACAATTTCGGCT
Found at i:47958 original size:2 final size:2
Alignment explanation
Indices: 47951--47980 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47941 ACTCATAAAA
47951 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
47981 T
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
Done.