Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012597.1 Corchorus olitorius cultivar O-4 contig12630, 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: 10327
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:314 original size:154 final size:153
Alignment explanation
Indices: 1--884 Score: 1322
Period size: 154 Copynumber: 5.7 Consensus size: 153
*
1 AAAACGGAACTAATGCGCCCCCGAAAAGGCCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
1 AAAACGGAACTAATG-GGCCCCG-AAAGGCCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAAC
* * *
66 TTCACAGTGGAAATATCTCACCAAAATGATTATAGTTAGTTCATAAACAACT-TAAAGAAAAGCT
63 TTCACAGTGGACA-ATCTCACCAAAATGATTATAGTTAGTCCATAAACAA-TGGAAAGAAAAGCT
* * *
130 TTGAGCTTTGCCAAATCGAAGACAATTC
126 TTGAGGTTTGCCAAATCGAAGTCGATTC
* * *
158 AAAACGGAACTAGTGGGCCCCGAAAGGCCCAAAATAAGAAGTGTTCCGAATGAGCTAAAAACTTC
1 AAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* * * *
223 ACAGTGGACTAATTTCACAAAAATGATTATAGTTAGTCCCTAAACAATGGAAAGAAAAACTTTGA
66 ACAGTGGAC-AATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGA
*
288 GGTTTGCCAAATCGAAGTCGAATC
130 GGTTTGCCAAATCGAAGTCGATTC
* *
312 AAAACGGAACTAATGGG-CCCGAAAGGCCCAAAATAAGAAGTGTTCCGAATGAGCTAAAAACTTC
1 AAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* *
376 ATAGTAGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGA
66 ACAGTGGAC-AATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGA
*
441 GGTTTGCCAAATCGATGTCGATTC
130 GGTTTGCCAAATCGAAGTCGATTC
* * * * *
465 GAAACGGATCTAATGGGCCCCGGAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTT
1 AAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* *
530 ACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGATAGAAAAGCTTTGA
66 ACAGTGGACA-ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGA
595 GGTTTGCCAAATCGAAGTCGATTC
130 GGTTTGCCAAATCGAAGTCGATTC
* * *
619 AAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAACGAGCTAAAAACTCC
1 AAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* ** * *
684 ACAGTTGACTAATCTCGTCAAATTGATTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGA
66 ACAGTGGAC-AATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGA
749 GGTTTGCCAAATCGAAGTCGATTC
130 GGTTTGCCAAATCGAAGTCGATTC
* *
773 AAAACAGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTC
1 AAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
*
838 ACATTGGACATATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
66 ACAGTGGACA-ATCTCACCAAAATGATTATAGTTAGTCCATAAACAA
885 GTAGCACATG
Statistics
Matches: 659, Mismatches: 62, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
153 146 0.22
154 483 0.73
155 10 0.02
156 6 0.01
157 14 0.02
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (153 bp):
AAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
ACAGTGGACAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAG
GTTTGCCAAATCGAAGTCGATTC
Found at i:595 original size:307 final size:307
Alignment explanation
Indices: 1--884 Score: 1342
Period size: 307 Copynumber: 2.9 Consensus size: 307
*
1 AAAACGGAACTAATGCGCCCCCGAAAAGGCCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
1 AAAACGGAACTAATG-G-GCCCG-AAAGGCCC-AAAATAACAAGTGTTCCAAATGAGCTAAAAAC
* * *
66 TTCACAGTGGA-AATATCTCACCAAAATGATTATAGTTAGTTCATAAACAACT-TAAAGAAAAGC
62 TTCACAGTAGACTA-ATCTCACCAAAATGATTATAGTTAGTTCATAAACAA-TGGAAAGAAAAGC
* * * *
129 TTTGAGCTTTGCCAAATCGAAGACAATTCAAAACGGAACTAGTGGGCCCCGAAAGGCCCAAAATA
125 TTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATA
* * * *
194 AGAAGTGTTCCGAATGAGCTAAAAACTTCACAGTGGAC-TAATTTCACAAAAATGATTATAGTTA
190 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAT-ATCTCACCAAAATGATTATAGTTA
*
258 GTCCCTAAACAATGGAAAGAAAAACTTTGAGGTTTGCCAAATCGAAGTCGAATC
254 GTCCATAAACAATGGAAAGAAAAACTTTGAGGTTTGCCAAATCGAAGTCGAATC
* *
312 AAAACGGAACTAATGGGCCCGAAAGGCCCAAAATAAGAAGTGTTCCGAATGAGCTAAAAACTTCA
1 AAAACGGAACTAATGGGCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
* *
377 TAGTAGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCTTTGAG
66 CAGTAGACTAATCTCACCAAAATGATTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGAG
* * * *
442 GTTTGCCAAATCGATGTCGATTCGAAACGGATCTAATGGGCCCCGGAAGGCCCAAAATAACAAGT
131 GTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT
* * *
507 GTTCCAAATGAGCTAAAAATTTTACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATA
196 GTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGTCCATA
* * *
572 AACAATGGATAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTC
261 AACAATGGAAAGAAAAACTTTGAGGTTTGCCAAATCGAAGTCGAATC
* * *
619 AAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAACGAGCTAAAAACTCC
1 AAAACGGAACTAATGGG-CCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* ** *
684 ACAGTTGACTAATCTCGTCAAATTGATTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGA
65 ACAGTAGACTAATCTCACCAAAATGATTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGA
*
749 GGTTTGCCAAATCGAAGTCGATTCAAAACAGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAG
130 GGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAG
* *
814 TGTTCTAAATGAGCTAAAAACTTCACATTGGACATATCTCACCAAAATGATTATAGTTAGTCCAT
195 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGTCCAT
879 AAACAA
260 AAACAA
885 GTAGCACATG
Statistics
Matches: 521, Mismatches: 48, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
306 1 0.00
307 263 0.50
308 237 0.45
309 4 0.01
310 1 0.00
311 15 0.03
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (307 bp):
AAAACGGAACTAATGGGCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
CAGTAGACTAATCTCACCAAAATGATTATAGTTAGTTCATAAACAATGGAAAGAAAAGCTTTGAG
GTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT
GTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGTCCATA
AACAATGGAAAGAAAAACTTTGAGGTTTGCCAAATCGAAGTCGAATC
Found at i:3418 original size:77 final size:77
Alignment explanation
Indices: 3291--3521 Score: 462
Period size: 77 Copynumber: 3.0 Consensus size: 77
3281 TGAATAGAAG
3291 GATAGATTTACCGATTGAAGATGACAACCTATGCTCTGATTACCAATTGATACGAATCTAGTTGT
1 GATAGATTTACCGATTGAAGATGACAACCTATGCTCTGATTACCAATTGATACGAATCTAGTTGT
3356 GTAAAGATTCAA
66 GTAAAGATTCAA
3368 GATAGATTTACCGATTGAAGATGACAACCTATGCTCTGATTACCAATTGATACGAATCTAGTTGT
1 GATAGATTTACCGATTGAAGATGACAACCTATGCTCTGATTACCAATTGATACGAATCTAGTTGT
3433 GTAAAGATTCAA
66 GTAAAGATTCAA
3445 GATAGATTTACCGATTGAAGATGACAACCTATGCTCTGATTACCAATTGATACGAATCTAGTTGT
1 GATAGATTTACCGATTGAAGATGACAACCTATGCTCTGATTACCAATTGATACGAATCTAGTTGT
3510 GTAAAGATTCAA
66 GTAAAGATTCAA
3522 ATCCACCCTT
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 154 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (77 bp):
GATAGATTTACCGATTGAAGATGACAACCTATGCTCTGATTACCAATTGATACGAATCTAGTTGT
GTAAAGATTCAA
Found at i:9539 original size:127 final size:127
Alignment explanation
Indices: 9326--9575 Score: 482
Period size: 127 Copynumber: 2.0 Consensus size: 127
9316 TTGTGATAGC
9326 TTGTTTGTTTGTGAATCTTGTGATCTTAGGTGTTCAATTGCAGGTCAAACTGAAGGTCTAAGGTC
1 TTGTTTGTTTGTGAATCTTGTGATCTTAGGTGTTCAATTGCAGGTCAAACTGAAGGTCTAAGGTC
9391 GACGAAAGAAGAAGATTGCTTAGTGAAGATCATCAACATACACATCTAGAAGTTGAAGAAGA
66 GACGAAAGAAGAAGATTGCTTAGTGAAGATCATCAACATACACATCTAGAAGTTGAAGAAGA
*
9453 TTGTTTGTTTGTGAATCTTGTGATCTTAGGTGTTCAATTGCTGGTCAAACTGAAGGTCTAAGGTC
1 TTGTTTGTTTGTGAATCTTGTGATCTTAGGTGTTCAATTGCAGGTCAAACTGAAGGTCTAAGGTC
*
9518 GACGAAAGAAGAAGATTGCTTAGTGAAGATCATCGACATACACATCTAGAAGTTGAAG
66 GACGAAAGAAGAAGATTGCTTAGTGAAGATCATCAACATACACATCTAGAAGTTGAAG
9576 TTGTTCAAGT
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 121 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (127 bp):
TTGTTTGTTTGTGAATCTTGTGATCTTAGGTGTTCAATTGCAGGTCAAACTGAAGGTCTAAGGTC
GACGAAAGAAGAAGATTGCTTAGTGAAGATCATCAACATACACATCTAGAAGTTGAAGAAGA
Found at i:10286 original size:13 final size:12
Alignment explanation
Indices: 10262--10317 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
10252 TTTAATACAG
*
10262 ATATCCACAGAT
1 ATATCGACAGAT
10274 ATATCGAACAGAT
1 ATATCG-ACAGAT
*
10287 ATATCGACGGAT
1 ATATCGACAGAT
* *
10299 ATATTGACGGAT
1 ATATCGACAGAT
10311 ATATCGA
1 ATATCGA
10318 GGTATCGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
12 27 0.69
13 12 0.31
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (12 bp):
ATATCGACAGAT
Found at i:10299 original size:25 final size:24
Alignment explanation
Indices: 10262--10317 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
10252 TTTAATACAG
*
10262 ATATCCACAGATATATCGAACAGAT
1 ATATCGACAGATATATCG-ACAGAT
* * *
10287 ATATCGACGGATATATTGACGGAT
1 ATATCGACAGATATATCGACAGAT
10311 ATATCGA
1 ATATCGA
10318 GGTATCGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (24 bp):
ATATCGACAGATATATCGACAGAT
Done.