Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014623.1 Corchorus olitorius cultivar O-4 contig14656, 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: 7003
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Found at i:338 original size:188 final size:190
Alignment explanation
Indices: 1--380 Score: 538
Period size: 188 Copynumber: 2.0 Consensus size: 190
*
1 AGAAAGACTCATTGAAATATCTATATTCATCTAATCAAATCTCAGCCACAATGGATTTAAAAAAT
1 AGAAAGACTCATTAAAATATCTATATTCATCTAATCAAATCTCAGCCACAATGGATTTAAAAAAT
* *
66 TTATTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGA
66 TTATTTTTACGAG---CTAAATCTATGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGA
131 AAAACGATATTGAAAGCGTG-AAAACTCCTTCAATTTTTTTGGCGTTGAATTATATATATATTTA
128 AAAACGATATTGAAAGCGTGAAAAAC-CCTTCAATTTTTTTGGCGTTGAATTATATAT-TATTTA
* * * ** *
195 AGAAAGACTCATTAAAATATCTATATTTATTTAATTAAATC-CTAGCCACGTTGGATTT-AAGAA
1 AGAAAGACTCATTAAAATATCTATATTCATCTAATCAAATCTC-AGCCACAATGGATTTAAAAAA
* *
258 TTTGTTTTTACGAG-TAAATC-ATGTTTCGATTTAATTAGAAATAAATTCGGGAAAAAAAGGAAA
65 TTTATTTTTACGAGCTAAATCTATGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGAAA
* *
321 AACTATATT-ATAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTTAATTATATATTATTT
130 AACGATATTGA-AAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTATTT
381 CTGAGTATTC
Statistics
Matches: 170, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
187 6 0.04
188 86 0.51
189 10 0.06
193 18 0.11
194 50 0.29
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (190 bp):
AGAAAGACTCATTAAAATATCTATATTCATCTAATCAAATCTCAGCCACAATGGATTTAAAAAAT
TTATTTTTACGAGCTAAATCTATGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAGGAAAA
ACGATATTGAAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTATTTA
Found at i:842 original size:323 final size:323
Alignment explanation
Indices: 278--1042 Score: 726
Period size: 323 Copynumber: 2.3 Consensus size: 323
268 CGAGTAAATC
* * * *
278 ATGTTTCGATTTAA-TT--AGAAATAAATTCGG--GAAAAAAAGGAAAAACTATATTATAAGCGT
1 ATGTTCCGATTTAATTTACAGAAATAAATTCGGAAAAAAAAAAGGAAAAACGATATTAGAAGCGT
* * * * * * * * * *
338 GAAAAACCCTTCAATTTTTTTGGCGTTTAATTATATATTATTTCTGAGTATTCTGGCAAAAAATT
66 AAAAAACCCGTCAA-TTTTTTGACATTGAATTATATATTTTTTCTAAATATT-TAGTAAAAAATT
* * *
403 GAAGAAAAACTTCTCGGGTCATTTTTTGCAAAATTTTAGTCGAAATCGTGTACTAACCATCACGG
129 G-TGAAAAACTTTTCGGGTCA------GC----TTTTAGACGAAATCGTGTACTAACCATCACGG
* *** * * *
468 TTTTTAGCTAAAAACGCATTCAGCAGTGGCGGCTTAATTTTGCAAGATTTTTTGAACAAAGACTC
183 TTTTCAGCTAAAAACGCATTCAGCAGCCCCGACTTAATTTTGCAAGATTTTTGGAACAAAAACTC
* * * * *
533 CTTGAAATATCTATA-TTATCGAACCAAATGTTAGCCACACTAGATATATATAAGGATTTGTATT
248 CATGAAATATCTATATTTATCGAACCAAATCTAAGCCACAAT-G-GAT-T-TAAGGATTTGTATT
* *
597 TACGAGCATCTCAAT
309 TACAAGAATCTCAAT
* ** * * * *
612 CTTGTTTTGATTTAA-TTA-A-TAATTAATTC-G-AAAACAAATGGAAAAACGATATTAGAAGCG
1 -ATGTTCCGATTTAATTTACAGAAATAAATTCGGAAAAAAAAAAGGAAAAACGATATTAGAAGCG
* * ** *
672 TGAAAAGCGTGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTAAATATTTAGTAAAAAATT
65 TAAAAAACCCGTCAAT-TTTTTGACATTGAATTATATATTTTTTCTAAATATTTAGTAAAAAATT
* *
737 GTGAAAAACTTTTCGGGTCAGCTTTTAGACGAAATCGTGTACTAACCATCACTGTTTTCGGCTAA
129 GTGAAAAACTTTTCGGGTCAGCTTTTAGACGAAATCGTGTACTAACCATCACGGTTTTCAGCTAA
* ** * * * *
802 AAACGCGTTTC-GGGGCCCCGACTTAGTTTTGCATGATTTTTGGCAGAAAAACTCCATGAAATAT
194 AAACGC-ATTCAGCAGCCCCGACTTAATTTTGCAAGATTTTTGGAACAAAAACTCCATGAAATAT
* * * *
866 CTTTATTTATCTAACCAAATCTAAGCCACAATGGATTTAAGGATTTGTTTTTACAAGAATCTGAA
258 CTATATTTATCGAACCAAATCTAAGCCACAATGGATTTAAGGATTTGTATTTACAAGAATCTCAA
931 T
323 T
*
932 ATGTTCCGATTTAATTTACTAGAAATAAATTCGGAAAAAAAAAAAGGAAAAACGATATTAGAAGT
1 ATGTTCCGATTTAATTTAC-AGAAATAAATTCGG-AAAAAAAAAAGGAAAAACGATATTAGAAGC
*
997 GTAAAAAACCCGTCAATTTTTTGACTTTGAATTATATATTTTTTCT
64 GTAAAAAACCCGTCAATTTTTTGACATTGAATTATATATTTTTTCT
1043 GACTATTGTC
Statistics
Matches: 354, Mismatches: 64, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
319 11 0.03
320 28 0.08
321 1 0.00
322 3 0.01
323 98 0.28
324 26 0.07
325 27 0.08
326 39 0.11
327 2 0.01
333 17 0.05
334 13 0.04
335 88 0.25
336 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (323 bp):
ATGTTCCGATTTAATTTACAGAAATAAATTCGGAAAAAAAAAAGGAAAAACGATATTAGAAGCGT
AAAAAACCCGTCAATTTTTTGACATTGAATTATATATTTTTTCTAAATATTTAGTAAAAAATTGT
GAAAAACTTTTCGGGTCAGCTTTTAGACGAAATCGTGTACTAACCATCACGGTTTTCAGCTAAAA
ACGCATTCAGCAGCCCCGACTTAATTTTGCAAGATTTTTGGAACAAAAACTCCATGAAATATCTA
TATTTATCGAACCAAATCTAAGCCACAATGGATTTAAGGATTTGTATTTACAAGAATCTCAAT
Found at i:3223 original size:23 final size:24
Alignment explanation
Indices: 3188--3232 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
3178 TTAGATGTTT
3188 ATGAGAATAACGAAAAAACCAATA
1 ATGAGAATAACGAAAAAACCAATA
*
3212 ATGA-AATGACGAAAAAACCAA
1 ATGAGAATAACGAAAAAACCAA
3233 ACTAAATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.11
Consensus pattern (24 bp):
ATGAGAATAACGAAAAAACCAATA
Found at i:4633 original size:62 final size:62
Alignment explanation
Indices: 4559--5267 Score: 1112
Period size: 62 Copynumber: 11.2 Consensus size: 62
4549 GAAGGAAGAC
*
4559 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAG
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
* *
4621 AGAAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAG
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
4683 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
* * *
4745 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGATGACAG
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
*
4807 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAGAGG
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACAC--G-AGA-AGA--
*
4872 AAGG
60 CA-G
*
4876 AAGGAAGGAAGAGGCCTCCGCAGAAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
1 -AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
* *
4939 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAGAGG
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGAC--A-G
*
5004 AAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAA
1 -AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
*
5067 AGGAAGGAAGAGGCCTCCGCAGGTGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
* * *
5129 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGATGACAGAGG
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGAC--A-G
* *
5194 AAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAG
1 -AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
5257 AGGAAGGAAGA
1 AGGAAGGAAGA
5268 CACGAAGGTA
Statistics
Matches: 606, Mismatches: 25, Indels: 32
0.91 0.04 0.05
Matches are distributed among these distances:
62 416 0.69
63 2 0.00
64 6 0.01
65 4 0.01
66 122 0.20
67 3 0.00
68 2 0.00
69 1 0.00
70 50 0.08
ACGTcount: A:0.35, C:0.21, G:0.40, T:0.04
Consensus pattern (62 bp):
AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
Found at i:5192 original size:190 final size:188
Alignment explanation
Indices: 4559--5267 Score: 1156
Period size: 190 Copynumber: 3.7 Consensus size: 188
4549 GAAGGAAGAC
* * *
4559 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAGAGA
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAGAGA
* *
4624 --AAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGGCACGAAGGTACACGAGAAGACAGAGGA
66 GGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAAAGGA
4687 AGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
131 AGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
*
4745 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGATGAC--AGA
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAGAGA
* *
4808 GGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAGAGGA
66 GGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACAC--G-AGA-AGA--C
*
4873 AGGAAGGAAGGAAGAGGCCTCCGCAGAAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACA
125 A--AAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACA
4938 G
188 G
4939 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAGAGG
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAGA-G
5004 AAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAAAG
65 -AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAAAG
*
5069 GAAGGAAGAGGCCTCCGCAGGTGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
129 GAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
*
5129 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGATGACAGAGG
1 AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAGA-G
* * *
5194 AAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAGAG
65 -AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAAAG
5259 GAAGGAAGA
129 GAAGGAAGA
5268 CACGAAGGTA
Statistics
Matches: 491, Mismatches: 18, Indels: 24
0.92 0.03 0.05
Matches are distributed among these distances:
184 3 0.01
186 103 0.21
188 1 0.00
189 3 0.01
190 199 0.41
192 2 0.00
194 123 0.25
195 3 0.01
196 2 0.00
197 1 0.00
198 51 0.10
ACGTcount: A:0.35, C:0.21, G:0.40, T:0.04
Consensus pattern (188 bp):
AGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTAGACGGGAAGACAGAGA
GGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAAAGGA
AGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGGCACGAAGGTACACGAGAAGACAG
Found at i:5277 original size:34 final size:34
Alignment explanation
Indices: 5229--5323 Score: 147
Period size: 34 Copynumber: 2.8 Consensus size: 34
5219 GGCGAGGCCA
* *
5229 ACAGGCACGAAGGTAGACGGGAAGACAGAGGAAGG
1 ACAGACACGAAGGTACACGGGAAGACAGAGGAA-G
*
5264 A-AGACACGAAGGTACACGAGAAGACAGAGGAAG
1 ACAGACACGAAGGTACACGGGAAGACAGAGGAAG
5297 ACAGACACGAAGGTACACGGGAAGACA
1 ACAGACACGAAGGTACACGGGAAGACA
5324 CAGTGGTGCT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
33 2 0.04
34 52 0.95
35 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.36, T:0.03
Consensus pattern (34 bp):
ACAGACACGAAGGTACACGGGAAGACAGAGGAAG
Found at i:6241 original size:45 final size:45
Alignment explanation
Indices: 6185--6285 Score: 157
Period size: 45 Copynumber: 2.2 Consensus size: 45
6175 AAGTTAGAAT
* * *
6185 CCATGACTGCCAAATGCTTCAAGGAGATCAAAGAGAGCTTTGGCC
1 CCATGATTGCCAAATGCTTCAACGAAATCAAAGAGAGCTTTGGCC
* *
6230 CCATGATTGCCAAATGCTTTAACGAAATCAAAGAGAGCTTTGGCT
1 CCATGATTGCCAAATGCTTCAACGAAATCAAAGAGAGCTTTGGCC
6275 CCATGATTGCC
1 CCATGATTGCC
6286 GAGTGCACAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (45 bp):
CCATGATTGCCAAATGCTTCAACGAAATCAAAGAGAGCTTTGGCC
Found at i:6375 original size:3 final size:3
Alignment explanation
Indices: 6367--6396 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6357 ATTTTCCAGG
6367 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
6397 AGAAAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Done.