Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013521.1 Corchorus capsularis cultivar CVL-1 contig13542, 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: 40618
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3278 original size:18 final size:18
Alignment explanation
Indices: 3255--3290 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3245 TACCTGAACA
3255 AATTTAAGAACATCTTTT
1 AATTTAAGAACATCTTTT
3273 AATTTAAGAACATCTTTT
1 AATTTAAGAACATCTTTT
3291 GTTCCGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
AATTTAAGAACATCTTTT
Found at i:10662 original size:322 final size:328
Alignment explanation
Indices: 9568--10976 Score: 859
Period size: 331 Copynumber: 4.3 Consensus size: 328
9558 TTGAAAATAT
* ** *
9568 GAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTG-GCGTTAAATTATATATTTTTT
1 GAAAAACAATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGAG-GTCGAATTATATATATTTT
* * * *
9632 ATGAGTATTTTAGCCAAAAAAAATTGAGGAAAAATTTTTCGGGT-TATTCTTTGCAAAATTTTAG
65 ATGAGTACTTTAGCC---AAAAATTGAGGAAAAATCTTTCGGGTCAATT-ATTGCAAAATTTTAG
* * * * * * * * * * * **
9696 CCAAAATCGTGTACTAACCATCACGATTTTTTTGCTAAATACGCGTTTCAGGGCCCCGGGTCAGT
126 CCGAAATCATATACCAACCATCAC-A-ATTTTGGCTAAAAACGCGTTCCAAGGTCACGACTCAGT
* * * * * * * *
9761 TTTGCATGATTTTTTGTGGCAAAATTCCTTGAAATATCTATATTCATCTAACCAATTCTTAGCCA
189 ATTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAAACAA-AC-T---CA
* * ** * * * * *
9826 TA-TTGGATTTAAGAATTTGTTTTTACAAGCATTTGAATCATGTTTCGATTTAAT---TAGTTAA
249 TACATGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCAATTTAATAAAAAATTAA
** **
9887 TTTGGGAAAAAAAAATG
314 -TTCAGAAAAAATTA-G
** * **
9904 AGAAAAATGATATT--AAGCGTGAGAAA-TCCTTCAATCTTTTTG-GCGTTAAATTATATA-ATT
1 -GAAAAACAATATTAAAAGCGTGA-AAAGTCCTCCAATCTTTTTGAG-GTCGAATTATATATA-T
* * * * * *
9964 TTTATGATTA-TTATGGCTAAAAATTGA-GAAAATAT-TAT-GGGTCAATTTTTGTAAAATTTTA
62 TTTATGAGTACTT-TAGCCAAAAATTGAGGAAAA-ATCTTTCGGGTCAATTATTGCAAAATTTTA
* * ** ***** * * * ** * * *
10025 GCCGAAATCGTGTACCATCACGGTTTTTTTTTTTTGATAAAAACGCGTTCCGAGACCCCGAGTTA
125 GCCGAAATCATATACCA--AC-CATCACAATTTTGGCTAAAAACGCGTTCCAAGGTCACGACTCA
* * * ***
10090 GTTTTGCATGATTTTTGGCGCCAAGACTCCTTAAAATATATCTATATTCATCTTTCCAAATCTTA
187 GTATTGCATGATTTTTGGCGTCAAGACTCCTT-GAA-ATATCTATATTCATCTAAACAAA-C-T-
* ** * * * *
10155 GCCATA-TTGTTTTTAAGGATTTGTTTTTACGAG----T--A------TTCGATTTAATCATAAA
247 --CATACATGGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCAATTTAATAAAAAA
** *
10207 TTAATTTGGAAATAAAATAG
310 TTAATTCAGAAA-AAATTAG
* * *** * * *
10227 CAAAAACAATATTAAATGCGTGAAAA-AAATACAAT-TTTTTG-CGTTGAA-T-TATATATTTTA
1 GAAAAACAATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGAGGTCGAATTATATATATTTTA
** * ** * * ** *
10287 TGAGTGTTTTCGTTAGAAATTGAGGAAAAATCTTTTGGGTCAATTATTGCAAAATTTTAGTTGGA
66 TGAGTACTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTATTGCAAAATTTTAGCCGAA
** * * ** *
10352 ATCATATACCAACCATCACGGTTTTCGGCTAAAAACGCGTTTCAAGG-CCCGTTTCAGTTTTGCA
131 ATCATATACCAACCATCACAATTTT-GGCTAAAAACGCGTTCCAAGGTCACGACTCAGTATTGCA
*
10416 TGATTTTT-GTGTCAAGACTCCTTGAAATATCTATATTCATCTAAACAAA-TC-T-CA-GGATTT
195 TGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAAACAAACTCATACATGGATTT
* * * *
10476 AAGGATTTGTTTTTATGAGCATTTGAATCTTGTTTCGATTTAATAAAAAATTTATTCGGAAAAAA
260 AAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCAATTTAATAAAAAATTAATTCAGAAAAAA
10541 -TAG
325 TTAG
* * ** * * * *
10544 GATAAACAATATTAGAAGTTTTAAAA-TCCTTTCAATCTTTTTTATGTCGAATTATATAT-TTTT
1 GAAAAACAATATTAAAAGCGTGAAAAGTCC-TCCAATCTTTTTGAGGTCGAATTATATATATTTT
* *
10607 CATGAGTACTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCG
65 -ATGAGTACTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTATTGCAAAATTTTAGCCG
* * * ** * *
10672 AAATTATGTACTAACCATCACAATTTTGGCTAAAAACGCGTTCCGGGGTCATGACTCTGTATTGC
129 AAATCATATACCAACCATCACAATTTTGGCTAAAAACGCGTTCCAAGGTCACGACTCAGTATTGC
* * * *
10737 ATGATTTTTGGCGTCGAGACTCCTTGAATTATCTTTATTCATCTAATCAAATCTCAGTCACATTG
194 ATGATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAAACAAA-CTCA-T-ACA-TG
* * * *
10802 GATTTGAGGATTTGTTTTTATGTGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCAGA
255 GATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCAATTTAATAAAAAATTAATTCAGA
*
10867 AAAAATTAT
320 AAAAATTAG
* * *
10876 GAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGGGTTGAATTATATATATTTTA
1 GAAAAACAATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGAGGTCGAATTATATATATTTTA
* *
10941 TGAGTATTTTTGCCAAAAATTGAGGAAAAATCTTTC
66 TGAGTACTTTAGCCAAAAATTGAGGAAAAATCTTTC
10977 AAGTCATTTT
Statistics
Matches: 855, Mismatches: 162, Indels: 115
0.76 0.14 0.10
Matches are distributed among these distances:
307 22 0.03
308 1 0.00
309 1 0.00
311 1 0.00
312 1 0.00
313 1 0.00
315 20 0.02
316 2 0.00
317 35 0.04
318 35 0.04
319 74 0.09
320 16 0.02
321 72 0.08
322 114 0.13
323 52 0.06
324 17 0.02
325 2 0.00
327 2 0.00
329 3 0.00
330 32 0.04
331 128 0.15
332 95 0.11
333 61 0.07
334 2 0.00
335 51 0.06
336 3 0.00
337 12 0.01
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (328 bp):
GAAAAACAATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGAGGTCGAATTATATATATTTTA
TGAGTACTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTATTGCAAAATTTTAGCCGAA
ATCATATACCAACCATCACAATTTTGGCTAAAAACGCGTTCCAAGGTCACGACTCAGTATTGCAT
GATTTTTGGCGTCAAGACTCCTTGAAATATCTATATTCATCTAAACAAACTCATACATGGATTTA
AGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCAATTTAATAAAAAATTAATTCAGAAAAAAT
TAG
Found at i:15356 original size:109 final size:109
Alignment explanation
Indices: 15149--15444 Score: 416
Period size: 109 Copynumber: 2.7 Consensus size: 109
15139 ACTATTATAG
* *
15149 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
* *
15214 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGAAATACTAAAATTTTGTCTAATATACAA
15263 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
15328 TTACCTAAAAAA-TTGGAAATATTTAAATTTTGTCTAATATACAA
66 TTACC-AAAAAATTTGGAAATACTAAAATTTTGTCTAATATACAA
* **
15372 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
15436 TTTTTACCA
63 TTTTTACCA
15445 TTTTAATTTA
Statistics
Matches: 169, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
108 1 0.01
109 116 0.69
110 15 0.09
111 16 0.09
114 21 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGAAATACTAAAATTTTGTCTAATATACAA
Found at i:19132 original size:27 final size:26
Alignment explanation
Indices: 19101--19173 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
19091 CACTAGTAAG
*
19101 TTCATCTCTAGATTTTCCTACGGTGAA
1 TTCATCTCTAGATTTTCCTACGAT-AA
* * * *
19128 TTCATCTCCAGTTTTTCTTGCGATAA
1 TTCATCTCTAGATTTTCCTACGATAA
*
19154 TTGATTCTCTAGATTTTCCT
1 TTCA-TCTCTAGATTTTCCT
19174 GTGGCATCCA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 5 0.14
27 31 0.86
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (26 bp):
TTCATCTCTAGATTTTCCTACGATAA
Found at i:20171 original size:13 final size:12
Alignment explanation
Indices: 20148--20190 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
20138 TAAATACAGG
20148 TATCGACGGATA
1 TATCGACGGATA
20160 TATCGAACGGATA
1 TATCG-ACGGATA
20173 TATCGACGGATA
1 TATCGACGGATA
20185 TATCGA
1 TATCGA
20191 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:32454 original size:21 final size:21
Alignment explanation
Indices: 32429--32473 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
32419 CCTTCTTGAT
32429 GAAGGATTTGTTTGTGAAGGA
1 GAAGGATTTGTTTGTGAAGGA
32450 GAAGGATTTGTTTGTGAAGGA
1 GAAGGATTTGTTTGTGAAGGA
32471 GAA
1 GAA
32474 CAATTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (21 bp):
GAAGGATTTGTTTGTGAAGGA
Found at i:32466 original size:66 final size:65
Alignment explanation
Indices: 32390--32522 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 65
32380 TTCTGATCTC
32390 TTTGTTTGTGAAGGAGAACAATCTGATTTCCTTCTTGATGAAGGATTTGTTTGTGAAGGAGAAGG
1 TTTGTTTGTGAAGGAGAACAATCTGATTTCCTTCTTGATGAAGGATTTGTTTGTGAAGGAG-AGG
32455 A
65 A
* *
32456 TTTGTTTGTGAAGGAGAACAATTTGATTTCCTTCTTGATGAAGGCTTTGTTTGTGAAGGAGAGGA
1 TTTGTTTGTGAAGGAGAACAATCTGATTTCCTTCTTGATGAAGGATTTGTTTGTGAAGGAGAGGA
32521 TT
1 TT
32523 CTGATCTTGT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 6 0.09
66 59 0.91
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.38
Consensus pattern (65 bp):
TTTGTTTGTGAAGGAGAACAATCTGATTTCCTTCTTGATGAAGGATTTGTTTGTGAAGGAGAGGA
Found at i:32479 original size:21 final size:21
Alignment explanation
Indices: 32434--32480 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
32424 TTGATGAAGG
**
32434 ATTTGTTTGTGAAGGAGAAGG
1 ATTTGTTTGTGAAGGAGAACA
32455 ATTTGTTTGTGAAGGAGAACA
1 ATTTGTTTGTGAAGGAGAACA
32476 ATTTG
1 ATTTG
32481 ATTTCCTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (21 bp):
ATTTGTTTGTGAAGGAGAACA
Found at i:35344 original size:8 final size:8
Alignment explanation
Indices: 35331--35376 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
35321 ACCTCCCATT
35331 TTTTACAC
1 TTTTACAC
35339 TTTTAC-C
1 TTTTACAC
35346 TTTTAC-C
1 TTTTACAC
* *
35353 CTTTGCAC
1 TTTTACAC
35361 TTTTTACAC
1 -TTTTACAC
35370 TTTTACA
1 TTTTACA
35377 TTGAGCCTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 12 0.38
8 14 0.44
9 6 0.19
ACGTcount: A:0.20, C:0.26, G:0.02, T:0.52
Consensus pattern (8 bp):
TTTTACAC
Found at i:35434 original size:33 final size:33
Alignment explanation
Indices: 35380--35457 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
35370 TTTTACATTG
* * *
35380 AGCCTCCTCATTAGGATGGCTCAGCCACGGCGA
1 AGCCTCCCCACTAGGATGGCTCAACCACGGCGA
* *
35413 AGCCTCCCCACTAGGGA-GGCTCAACCACGGTGG
1 AGCCTCCCCACTA-GGATGGCTCAACCACGGCGA
35446 AGCCTCCCCACT
1 AGCCTCCCCACT
35458 GAGACGGCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 36 0.92
34 3 0.08
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (33 bp):
AGCCTCCCCACTAGGATGGCTCAACCACGGCGA
Found at i:36329 original size:16 final size:16
Alignment explanation
Indices: 36308--36366 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
36298 CAGGTTCGGA
36308 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
36324 CGGGTTTGGGT-TCTGT
1 CGGGTTCGGGTAT-TTT
36340 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
36356 TGGGTTCGGGT
1 CGGGTTCGGGT
36367 TCGGATCGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 1 0.03
16 34 0.94
17 1 0.03
ACGTcount: A:0.03, C:0.12, G:0.42, T:0.42
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:36336 original size:32 final size:32
Alignment explanation
Indices: 36300--36378 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 32
36290 TAATTGGGCA
*
36300 GGTTCGGACGGGTTCGGGTATTTTCGGGTTTG
1 GGTTCGGACGGGTTCGGGTATTTTCGGGTTCG
* * *
36332 GGTTCTGTCGGGTTCGGGTATTTTTGGGTTCG
1 GGTTCGGACGGGTTCGGGTATTTTCGGGTTCG
36364 GGTTCGGATCGGGTT
1 GGTTCGGA-CGGGTT
36379 TGAGTTTGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 34 0.85
33 6 0.15
ACGTcount: A:0.05, C:0.13, G:0.43, T:0.39
Consensus pattern (32 bp):
GGTTCGGACGGGTTCGGGTATTTTCGGGTTCG
Found at i:36975 original size:31 final size:31
Alignment explanation
Indices: 36940--37011 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
36930 TAAATTGTAG
*
36940 CAAATTAAAACAAAT-TAAGTATTAAATTAAA
1 CAAATTAAAA-AAATGCAAGTATTAAATTAAA
* ** * *
36971 CAAATCATCAAAATGCAAGTCTTAGATTAAA
1 CAAATTAAAAAAATGCAAGTATTAAATTAAA
37002 CAAATTAAAA
1 CAAATTAAAA
37012 GCTAATGGAC
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGCAAGTATTAAATTAAA
Found at i:37200 original size:16 final size:15
Alignment explanation
Indices: 37179--37239 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
37169 TATTTTGATC
37179 TCGGGTTCGGGTTGTT
1 TCGGGTTCGGGTT-TT
37195 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGT-TTT
* *
37211 TTGGGTTCGGGTAATT
1 TCGGGTTCGGGT-TTT
*
37227 TCAGGTTCGGGTT
1 TCGGGTTCGGGTT
37240 CGGACGGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 38 0.97
17 1 0.03
ACGTcount: A:0.07, C:0.11, G:0.39, T:0.43
Consensus pattern (15 bp):
TCGGGTTCGGGTTTT
Done.