Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012301.1 Corchorus capsularis cultivar CVL-1 contig12322, 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: 1811
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Found at i:93 original size:35 final size:36
Alignment explanation
Indices: 4--614 Score: 884
Period size: 35 Copynumber: 17.3 Consensus size: 36
1 TAT
4 TTCAAGAAGTTTTCAGAGG-CAGAGTTGATCTCATA
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
*
39 -TCAAGAAG-TTTCAGAGGTCAGAGTTGATCTCGTA
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
73 TT-AAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
107 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
* *
142 TCCAAGAAGTTTTCAGAGGTCATAGTTGATCTC--A
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
176 TTCAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
1 TTC-AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
* *
213 TACAAGTAAG-TTTCAAGAGGTCAGAGTTGATCTCATT
1 TTCAAG-AAGTTTTC-AGAGGTCAGAGTTGATCTCATA
*
250 TTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
285 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
321 -TCAAGTAAGTTTTCAGAGGTCAGAGTTGATCTC--A
1 TTCAAG-AAGTTTTCAGAGGTCAGAGTTGATCTCATA
355 TTCAGAGGAAGTTTTCAGAGGTCAGAGTTGATCTCA-A
1 TTCA-A-GAAGTTTTCAGAGGTCAGAGTTGATCTCATA
* * *
392 TCCAAGAAG-TTTCAAGAGGTTAGAGTTGATCTCATT
1 TTCAAGAAGTTTTC-AGAGGTCAGAGTTGATCTCATA
*
428 TTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
463 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
* *
498 TCCAAGAAGTTTTCAGAGGTCAGAGTTAATCTCAT-
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
*
533 TCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
*
568 TGCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-
1 TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
*
603 TCCAAGAAGTTT
1 TTCAAGAAGTTT
615 CCCACGATCA
Statistics
Matches: 533, Mismatches: 23, Indels: 40
0.89 0.04 0.07
Matches are distributed among these distances:
33 9 0.02
34 38 0.07
35 328 0.62
36 114 0.21
37 44 0.08
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (36 bp):
TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATA
Found at i:318 original size:178 final size:175
Alignment explanation
Indices: 7--603 Score: 1006
Period size: 178 Copynumber: 3.4 Consensus size: 175
1 TATTTC
*
7 AAGAAGTTTTCAGAGG-CAGAGTTGATCTCATATCAAGAAGTTTCAGAGGTCAGAGTTGATCTCG
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATCAAGAAGTTTCAGAGGTCAGAGTTGATCTCA
*
71 TATT-AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTG
66 TTTTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTG
*
135 ATCTCATTCCAAGAAGTTTTCAGAGGTCATAGTTGATCTCATTCA
131 ATCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCA
180 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATACAAGTAAGTTTCAAGAGGTCAGAGTTGATC
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATAT-CAAG-AAGTTTC-AGAGGTCAGAGTTGATC
245 TCATTTTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAG
63 TCATTTTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAG
310 TTGATCTCATAT-CAAGTAAGTTTTCAGAGGTCAGAGTTGATCTCATTCA
128 TTGATCTCAT-TCCAAG-AAGTTTTCAGAGGTCAGAGTTGATCTCATTCA
* *
359 GAGGAAGTTTTCAGAGGTCAGAGTTGATCTCA-ATCCAAGAAGTTTCAAGAGGTTAGAGTTGATC
1 -AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATAT-CAAGAAGTTTC-AGAGGTCAGAGTTGATC
423 TCATTTTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAG
63 TCATTTTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAG
* *
488 TTGATCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTAATCTCATTCC
128 TTGATCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCA
536 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCAT-TGCAAGAAGTTTTCAGAGGTCAGAGTTGATCT
1 AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATAT-CAAGAAG-TTTCAGAGGTCAGAGTTGATCT
600 CATT
64 CATT
604 CCAAGAAGTT
Statistics
Matches: 402, Mismatches: 11, Indels: 19
0.93 0.03 0.04
Matches are distributed among these distances:
173 16 0.04
174 17 0.04
175 4 0.01
176 66 0.16
177 57 0.14
178 174 0.43
179 38 0.09
180 30 0.07
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (175 bp):
AAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATCAAGAAGTTTCAGAGGTCAGAGTTGATCTCA
TTTTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTG
ATCTCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTCA
Found at i:697 original size:35 final size:35
Alignment explanation
Indices: 587--873 Score: 329
Period size: 35 Copynumber: 8.3 Consensus size: 35
577 TTTTCAGAGG
* * * *
587 TCAGAGTTGATCTCA-TTCCAAGAAGTTTCCCACGA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
* *
622 TCAGAGTTGATCGCATTTTTAGTA-TTTTCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
656 TCAGAGTTGATCGCATTTTCAGTA-TTCTCTAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTT-TCCAACGA
691 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
726 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
**
761 TCAGAGTTGATCATATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * *
796 TCAAAG-TGA-CACA-TTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * * * * *
828 ACAGAGGTGATCTCA--TTCAAGAAATTTCCAATGA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
862 TCAGAGTTGATC
1 TCAGAGTTGATC
874 CGAGGAGTTC
Statistics
Matches: 222, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
32 22 0.10
33 9 0.04
34 60 0.27
35 127 0.57
36 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (35 bp):
TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
Found at i:753 original size:139 final size:136
Alignment explanation
Indices: 587--873 Score: 321
Period size: 139 Copynumber: 2.1 Consensus size: 136
577 TTTTCAGAGG
* * * * *
587 TCAGAGTTGATCTCATTCCAAGAAGTTTCCCACGATCAGAGTTGATCGCATTTTTAGTA-TTTTC
1 TCAGAGTTGATCGCATTCCAAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCC
* * * * * * *
651 AACGATCAGAGTTGATCGCATTTTCAGTA-TTCTCTAACGATCAGAGTTGATCGCATTTTC-AGT
66 AACGATCAAAG-TGA-CACA-TTTCAGTAGTT-TCCAACAAACAGAGGTGATCGCA--TTCAAGA
*
714 AGTTTCCAACGA
125 AATTTCCAACGA
* * *
726 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGATCAGAGTTGATCATATTTTCAGTAGTTTC
1 TCAGAGTTGATCGCA-TTCCAAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTC
*
790 CAACGATCAAAGTGACACATTTCAGTAGTTTCCAACAAACAGAGGTGATCTCATTCAAGAAATTT
65 CAACGATCAAAGTGACACATTTCAGTAGTTTCCAACAAACAGAGGTGATCGCATTCAAGAAATTT
*
855 CCAATGA
130 CCAACGA
862 TCAGAGTTGATC
1 TCAGAGTTGATC
874 CGAGGAGTTC
Statistics
Matches: 126, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
135 3 0.02
136 24 0.19
137 26 0.21
138 5 0.04
139 51 0.40
140 17 0.13
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (136 bp):
TCAGAGTTGATCGCATTCCAAGAAGTTTCCAACGATCAGAGTTGATCACATTTTCAGTAGTTTCC
AACGATCAAAGTGACACATTTCAGTAGTTTCCAACAAACAGAGGTGATCGCATTCAAGAAATTTC
CAACGA
Done.