Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013378.1 Corchorus olitorius cultivar O-4 contig13411, 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: 23834
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1264 original size:16 final size:16
Alignment explanation
Indices: 1243--1277 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1233 TGACAAGCAA
1243 TTTTCCTTTTTATCTG
1 TTTTCCTTTTTATCTG
1259 TTTTCCTTTTTATCTG
1 TTTTCCTTTTTATCTG
1275 TTT
1 TTT
1278 GCCTCCCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTCCTTTTTATCTG
Found at i:1419 original size:19 final size:19
Alignment explanation
Indices: 1369--1419 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1359 CATAAGATTT
1369 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
1387 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
1406 TTAATAATTAATTA
1 TTAATAATTAATTA
1420 ATTTCAGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:14127 original size:25 final size:26
Alignment explanation
Indices: 14097--14167 Score: 119
Period size: 25 Copynumber: 2.8 Consensus size: 26
14087 TTGCTGCAGG
14097 AAGTGGCGCAGGGCCTGAGAG-AAGA
1 AAGTGGCGCAGGGCCTGAGAGAAAGA
*
14122 AAGTGGCACAGGGCCTGAG-GAAAGA
1 AAGTGGCGCAGGGCCTGAGAGAAAGA
14147 AAGTGGCGCAGGGCCTGAGAG
1 AAGTGGCGCAGGGCCTGAGAG
14168 CAAATAAGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 1 0.02
25 40 0.95
26 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.44, T:0.08
Consensus pattern (26 bp):
AAGTGGCGCAGGGCCTGAGAGAAAGA
Found at i:17044 original size:11 final size:10
Alignment explanation
Indices: 17028--17079 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
17018 AAGTTCGTGT
17028 TTGAAGACTTA
1 TTGAAGA-TTA
*
17039 TTGAAGATAA
1 TTGAAGATTA
17049 TTTGAAGA-T-
1 -TTGAAGATTA
17058 TTGAAGATTA
1 TTGAAGATTA
17068 TTGAAGAATTA
1 TTGAAG-ATTA
17079 T
1 T
17080 CTCAAGAAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 7 0.20
9 1 0.03
10 8 0.23
11 19 0.54
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.38
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:17063 original size:19 final size:18
Alignment explanation
Indices: 17039--17074 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17029 TGAAGACTTA
17039 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
17058 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
17075 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:23224 original size:4 final size:4
Alignment explanation
Indices: 23207--23421 Score: 123
Period size: 4 Copynumber: 55.2 Consensus size: 4
23197 GACCAAAAAG
* * *
23207 ATTT -TTT A-TT ATTT ATTT A-CT ATTT ATCT ATTT ATTT ATTT -TTA
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * **
23251 ACTATT ATCT ATTT ATTT A-CT ATTT ATCT ATTT ATTT ATTTT AACT A-TT
1 A-T-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT
* * *
23300 ATCT ATTT ATTT A-TT ATTT ATCTT ATTT ATTT ATTT -TTA ACTATT ATAT
1 ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT A-T-TT ATTT
* * * * * *
23349 ATTT ATTT A-CT ATTT ATTCT TTTT ATTT ATTA ATTT AGTC A-TT ATCT
1 ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATTT ATTT
23396 ATTT ATTT ATTT A-TT A-TT ATTT -TTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
23422 GCTACCTATT
Statistics
Matches: 160, Mismatches: 32, Indels: 38
0.70 0.14 0.17
Matches are distributed among these distances:
3 32 0.20
4 109 0.68
5 15 0.09
6 4 0.03
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (4 bp):
ATTT
Found at i:23239 original size:8 final size:8
Alignment explanation
Indices: 23215--23460 Score: 85
Period size: 8 Copynumber: 30.8 Consensus size: 8
23205 AGATTTTTTA
*
23215 TTATTTAT
1 TTATCTAT
23223 TTA-CTAT
1 TTATCTAT
23230 TTATCTAT
1 TTATCTAT
*
23238 TTATTTATTT
1 TTATCTA--T
*
23248 TTAACTA-
1 TTATCTAT
23255 TTATCTAT
1 TTATCTAT
23263 TTATTTACTAT
1 TTA--T-CTAT
23274 TTATCTAT
1 TTATCTAT
*
23282 TTATTTATT
1 TTATCTA-T
*
23291 TTAACTA-
1 TTATCTAT
23298 TTATCTAT
1 TTATCTAT
*
23306 TTATTTA-
1 TTATCTAT
*
23313 TTATTTAT
1 TTATCTAT
*
23321 CTTATTTAT
1 -TTATCTAT
23330 TTAT-T-T
1 TTATCTAT
*
23336 TTAACTA-
1 TTATCTAT
*
23343 TTATATAT
1 TTATCTAT
23351 TTATTTACTAT
1 TTA--T-CTAT
*
23362 TTAT-TCT
1 TTATCTAT
23369 TT-T-TAT
1 TTATCTAT
23375 TTAT-TAAT
1 TTATCT-AT
23383 TTAGTC-A-
1 TTA-TCTAT
23390 TTATCTAT
1 TTATCTAT
*
23398 TTATTTAT
1 TTATCTAT
23406 TTAT-TA-
1 TTATCTAT
*
23412 TTAT-TTT
1 TTATCTAT
23419 TTAGCTACCTAT
1 TTA--T--CTAT
23431 TTATCTA-
1 TTATCTAT
*
23438 TTATTCTCT
1 TTA-TCTAT
*
23447 GTATCTAT
1 TTATCTAT
23455 TTATCT
1 TTATCT
23461 CTATACCTAT
Statistics
Matches: 184, Mismatches: 23, Indels: 62
0.68 0.09 0.23
Matches are distributed among these distances:
6 16 0.09
7 50 0.27
8 71 0.39
9 20 0.11
10 9 0.05
11 13 0.07
12 5 0.03
ACGTcount: A:0.26, C:0.09, G:0.01, T:0.64
Consensus pattern (8 bp):
TTATCTAT
Found at i:23272 original size:44 final size:44
Alignment explanation
Indices: 23212--23404 Score: 284
Period size: 45 Copynumber: 4.3 Consensus size: 44
23202 AAAAGATTTT
23212 TTAT-TATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
23255 TTATCTATTTATTTACTATTTATCTATTTATTTA-TTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
*
23298 TTATCTATTTATTTATTATTTATCTTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATC-TATTTATTTATTTTTAACTA
* * *
23343 TTATATATTTATTTACTATTTATTCTTTTTATTTATTAATTT-AGTCA
1 TTATCTATTTATTTACTATTTA-TCTATTTATTTATT--TTTAACT-A
23390 TTATCTATTTATTTA
1 TTATCTATTTATTTA
23405 TTTATTATTA
Statistics
Matches: 137, Mismatches: 6, Indels: 10
0.90 0.04 0.07
Matches are distributed among these distances:
43 36 0.26
44 39 0.28
45 40 0.29
46 4 0.03
47 18 0.13
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (44 bp):
TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
Found at i:23357 original size:88 final size:90
Alignment explanation
Indices: 23212--23421 Score: 299
Period size: 88 Copynumber: 2.4 Consensus size: 90
23202 AAAAGATTTT
* *
23212 TTAT-TATTTATTTACTATTTATCTATTTATTTATTTTTAACTATTATCTATTTATTTACTATTT
1 TTATCTATTTATTTATTATTTATCTATTTATTTATTTTTAACTATTATATATTTATTTACTATTT
23276 A-TCTATTTATTTATT-TTAACT-A
66 ATTCTATTTATTTATTATTAACTCA
23298 TTATCTATTTATTTATTATTTATCTTATTTATTTATTTTTAACTATTATATATTTATTTACTATT
1 TTATCTATTTATTTATTATTTATC-TATTTATTTATTTTTAACTATTATATATTTATTTACTATT
* * *
23363 TATTCTTTTTATTTATTAATTTAGTCA
65 TATTCTATTTATTTATT-ATTAACTCA
23390 TTATCTATTTATTTATT-TATTAT-TATTT-TTTA
1 TTATCTATTTATTTATTAT-TTATCTATTTATTTA
23422 GCTACCTATT
Statistics
Matches: 112, Mismatches: 5, Indels: 11
0.88 0.04 0.09
Matches are distributed among these distances:
86 4 0.04
87 18 0.16
88 41 0.37
89 17 0.15
90 5 0.04
91 5 0.04
92 22 0.20
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (90 bp):
TTATCTATTTATTTATTATTTATCTATTTATTTATTTTTAACTATTATATATTTATTTACTATTT
ATTCTATTTATTTATTATTAACTCA
Found at i:23461 original size:16 final size:17
Alignment explanation
Indices: 23432--23472 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
23422 GCTACCTATT
*
23432 TATCTA-TTATTCTCTG
1 TATCTATTTATTCTCTA
23448 TATCTATTTA-TCTCTA
1 TATCTATTTATTCTCTA
*
23464 TACCTATTT
1 TATCTATTT
23473 TTTTTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.22, C:0.20, G:0.02, T:0.56
Consensus pattern (17 bp):
TATCTATTTATTCTCTA
Done.