Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014690.1 Corchorus olitorius cultivar O-4 contig14723, 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: 26732
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1170 original size:323 final size:311
Alignment explanation
Indices: 3--2348 Score: 1592
Period size: 323 Copynumber: 7.2 Consensus size: 311
1 GG
* *
3 CCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATTTTGCAAAAAAAAATTGAGAAA
1 CCGTCAATATTTTTGGCGTTGAATTATATATTTTTCTGAATA-TTTG---GAAAAAATTGAGAAA
* * * * *
68 AACTTTCCGGGTCA---GT-TTTTAGCCGAAATCATGTACT-ACCATCAAGGGTTTTGGCTAAAA
62 AACTTTTCGGGTCATTTTTATTTTAGCCGAAATCATGTACTAACCTTCACGGTTTTTGGCTAAAA
* * * *
128 ACGCGTTTCATG-GCCCCGGCTTAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCT
127 ACGCGTTTCAGGAGCCCCGGCTCAGTTTTGCATAATTTTTGGC-GAAAGACTCCTTGAAATATCT
* * * * * * *
192 ATATTCATCTAACCAAATCCCAGCCACAATGGATTTAAAGATTTGAT-TTTACGAGCATATGAAA
191 ATATTCATCTAACCAAATCTCAGACACATTGTATATAAGGATTTG-TGTTTACGAGCATCT-AAA
** * *
256 -CTTTATTTTAATTTAATTAGAAATAAATTCGGGGAAAAAAATGAAAAAAACGATATTAG-AGGA
254 TC-TTATTTCGATTTAATTAGAAATTAATTC---G--------G--AAAAACGATATTAGAAGCA
319 GTGAAAAAC
305 -TG-AAAAC
* ** * * * * * *
328 CCTTTTATTTTTTTGGCGTTGAATCAT-TTTTTTTCTGAGTATTGTGGAAAAAAATTGGGGGAAA
1 CCGTCAATATTTTTGGCGTTGAATTATATATTTTTCTGAATATT-TGG-AAAAAATT-GAGAAAA
* * ** * * *
392 ACCTTTCGGGTTAATTTCCGCAAAATTTTAGCCGAAATCGTGTACTAA-CTATCATGATTTTTTG
63 ACTTTTCGGG-TCATTT-----TTATTTTAGCCGAAATCATGTACTAACCT-TCACG-GTTTTTG
* ** * * *
456 GCTAAAAACGCG-TTCCGGAGTTCCGGCTCAATTTTGCATGATTTTTGGCGTAAAGGCTCCTTGA
120 GCTAAAAACGCGTTTCAGGAGCCCCGGCTCAGTTTTGCATAATTTTTGGCG-AAAGACTCCTTGA
* * *
520 AATATCTATATTCATCGAACCAAATCTCA-ACAACATTGTATATAAGGATTTGTTTTTAAGAGCA
184 AATATCTATATTCATCTAACCAAATCTCAGAC-ACATTGTATATAAGGATTTGTGTTTACGAGCA
584 TC-AGAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAATTCTAAAAATGATATTAGAAG
248 TCTA-AATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAA--C-------GATATTAGAAG
*
648 CGTGAAAAGC
303 CATGAAAA-C
* * * * * *
658 CCGTCAATTTTTTTGGCGTTGGATTA-ACTATCTTTTTTAAATATTTTGCAAAAAATTGAGAAAC
1 CCGTCAATATTTTTGGCGTTGAATTATA-TAT-TTTTCTGAATA-TTTGGAAAAAATTGAGAAAA
** * ** * * *
722 ACTTTTCGGGT--TAGTT-TTTCA-CCGAAATTGTGTACTGATCATCACGGTTTTTGGCTAAAAA
63 ACTTTTCGGGTCATTTTTATTTTAGCCGAAATCATGTACTAACCTTCACGGTTTTTGGCTAAAAA
* * *
783 TGTGTTTC-GG-GCCCCGTCTCAGTTTTGCATAATTTTTGGCGAAAAGACTCCTTGAAATATCTA
128 CGCGTTTCAGGAGCCCCGGCTCAGTTTTGCATAATTTTTGGCG-AAAGACTCCTTGAAATATCTA
* * * * *
846 TATTCATTTAACCAAATCTCAGACACAATGGATTTAAGGATTTGTGTTTACGAGCATCTCAATCT
192 TATTCATCTAACCAAATCTCAGACACATTGTATATAAGGATTTGTGTTTACGAGCATCTAAATCT
*
911 TAATTTCGATTTAATTAGAAATAAATTCGGAAAAACGATATTAGAAGCATGAAAAC
257 T-ATTTCGATTTAATTAGAAATTAATTCGGAAAAACGATATTAGAAGCATGAAAAC
* * * * * *
967 CCTTCAATTTTTTTGGCGTTAAATTATATATTTTTCAGAGTATTGTGGCAAAAAATTGGAGAACA
1 CCGTCAATATTTTTGGCGTTGAATTATATATTTTTCTGAATATT-TGG-AAAAAATT-GAGAAAA
* * * *
1032 ACTTTTCGAGTCAGTTTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCTTCACGGCTTTTG
63 ACTTTTCGGGTCA---TTTTT-----ATTTTAGCCGAAATCATGTACTAACCTTCACGGTTTTTG
* * * * * * *
1097 GTTAAAAGCGCGTTAC-GGAGCCCCTGCTCAATTTTGCATAATATTTGGCGCAAAGACTCATTGA
120 GCTAAAAACGCGTTTCAGGAGCCCCGGCTCAGTTTTGCATAATTTTTGGCG-AAAGACTCCTTGA
* * * **
1161 AATATCTATATTCATCGAATCAAATCTCAGCCACATTGTATATAATAATTTG-GTTTTACGAGCA
184 AATATCTATATTCATCTAACCAAATCTCAGACACATTGTATATAAGGATTTGTG-TTTACGAGCA
* * *
1225 -CTTAAATCTTGTTTCGATTTAAATATAAATTAATTCGGAAAAAATAATGGGAAAACGATATTAG
248 TC-TAAATCTTATTTCGATTTAATTAGAAATTAATTCGG--------A----AAAACGATATTAG
*
1289 AAGCATGAAAAGG
300 AAGCATGAAAA-C
*
1302 CCGTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGAAAAATATTGAGAAAAA
1 CCGTCAATATTTTTGGCGTTGAATTATATA-TTTTTCTGAATATTTGGAAAAA-ATTGAG-AAAA
* * *
1367 ACTCTTAGGGTCA---TT-TTTTAGCCGAAATCATGTACTAACCGTCACGGTTTTTGGCTAAAAA
63 ACTTTTCGGGTCATTTTTATTTTAGCCGAAATCATGTACTAACCTTCACGGTTTTTGGCTAAAAA
* * * * *
1428 CGCGTTTCA-TAGCCCCGGCTTAGTTTTGAATGAGTTTTGGCAGAAAGACTCCTTGAAAT-TCCT
128 CGCGTTTCAGGAGCCCCGGCTCAGTTTTGCATAATTTTTGGC-GAAAGACTCCTTGAAATAT-CT
* * * * * *
1491 ATATTCATCTAACCAGATCTCGGCCACATTGTATATAAGAATTTATTTTTACGAGCATCTAAATC
191 ATATTCATCTAACCAAATCTCAGACACATTGTATATAAGGATTTGTGTTTACGAGCATCTAAATC
*
1556 TTATTTCGATTTAATTAGAAATTAATTCGGGAAGAAATGAAAGAACGATATTAGAAGCGTGAAAT
256 TTATTTCGATTTAATTAGAAATTAATTC-----G----GAAA-AACGATATTAGAAGCATGAAA-
*
1621 GC
310 AC
* *
1623 CCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTGAATATTTTGCAAAAAAAATTGAGAAAA
1 CCGTCAATATTTTTGGCGTTGAATTATATATTTTTCTGAATA-TTTG--GAAAAAATTGAGAAAA
* * *
1688 ACTTTTCGGGTCAGTTTTTA----A-CCGAAATCATGTACTAACCATCACGGGTTTTGGCTGAAA
63 ACTTTTCGGGTCA-TTTTTATTTTAGCCGAAATCATGTACTAACCTTCACGGTTTTTGGCTAAAA
* * * * *
1748 ACGCGTTTCATG-GCCCCAGCTTAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCT
127 ACGCGTTTCAGGAGCCCCGGCTCAGTTTTGCATAATTTTTGGC-GAAAGACTCCTTGAAATATCT
* * * * * *
1812 ATATTCATCTAACCAAAT-TCCAGGCACAATGGATTTAAAGATTTGAT-TCTACGAGCATCTGAA
191 ATATTCATCTAACCAAATCT-CAGACACATTGTATATAAGGATTTG-TGTTTACGAGCATCT-AA
* * * * *
1875 A-CTTTATTTTGATTTAATTAGAAATAAATTCAGGGAAAAAAATGAAAAAAAGGTAACTAGAGGC
253 ATC-TTATTTCGATTTAATTAGAAATTAATTC--GG--AAAAACG------A--T-ATTAGAAGC
*
1939 GTGAAAAAC
304 ATG-AAAAC
* * * * * *
1948 CCTTTAATGTTTTTGGCGTTGAATCATATTTTTTTCTGAGTATTGTGGAATAAAATTGAGGAAAA
1 CCGTCAATATTTTTGGCGTTGAATTATATATTTTTCTGAATATT-TGGAA-AAAATTGA-GAAAA
* * * * * *
2013 ACCTTTCGGGTTAATTTCCGCATAATTTTAGCCGAAATCGTGTACTAA-CTATCATGATTTTTTG
63 ACTTTTCGGG-TCATTT-----TTATTTTAGCCGAAATCATGTACTAACCT-TCACG-GTTTTTG
* ** * *
2077 GCTAAAAACGCG-TTCTGGAGTTCCGGCTCAATTTTGCATAATTTTTGGCATAAAGACTCCTTGA
120 GCTAAAAACGCGTTTCAGGAGCCCCGGCTCAGTTTTGCATAATTTTTGGC-GAAAGACTCCTTGA
* * *
2141 AATATCTGTATTCATCGAACCAAATCTCA-ACAACATTGTATATAAGGATTTGTTTTTACGAGCA
184 AATATCTATATTCATCTAACCAAATCTCAGAC-ACATTGTATATAAGGATTTGTGTTTACGAGCA
* * *
2205 TTTAAATCTTGTTTCGATTTAAATAGAAATTAATTCGGAAAAAAATAATGGAAAAACGAATATTA
248 TCTAAATCTTATTTCGATTTAATTAGAAATTAATTC-------------GGAAAAACG-ATATTA
*
2270 GAAGTC-TGAAAAGG
299 GAAG-CATGAAAA-C
* *
2284 CCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGAAAAAAATTGAGAAAAA
1 CCGTCAATATTTTTGGCGTTGAATTATATA-TTTTTCTGAATA-TTTGGAAAAAATTGAGAAAAA
2349 AAACTTTTTG
Statistics
Matches: 1617, Mismatches: 249, Indels: 300
0.75 0.11 0.14
Matches are distributed among these distances:
307 2 0.00
308 9 0.01
309 35 0.02
310 34 0.02
315 4 0.00
316 3 0.00
317 4 0.00
318 100 0.06
319 54 0.03
320 37 0.02
321 222 0.14
322 113 0.07
323 291 0.18
324 30 0.02
325 90 0.06
326 5 0.00
327 1 0.00
328 1 0.00
329 7 0.00
330 48 0.03
331 13 0.01
332 11 0.01
333 24 0.01
334 73 0.05
335 216 0.13
336 159 0.10
337 18 0.01
338 2 0.00
339 2 0.00
344 6 0.00
346 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (311 bp):
CCGTCAATATTTTTGGCGTTGAATTATATATTTTTCTGAATATTTGGAAAAAATTGAGAAAAACT
TTTCGGGTCATTTTTATTTTAGCCGAAATCATGTACTAACCTTCACGGTTTTTGGCTAAAAACGC
GTTTCAGGAGCCCCGGCTCAGTTTTGCATAATTTTTGGCGAAAGACTCCTTGAAATATCTATATT
CATCTAACCAAATCTCAGACACATTGTATATAAGGATTTGTGTTTACGAGCATCTAAATCTTATT
TCGATTTAATTAGAAATTAATTCGGAAAAACGATATTAGAAGCATGAAAAC
Found at i:3729 original size:17 final size:17
Alignment explanation
Indices: 3697--3728 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3687 CCAAAACAAC
3697 ATAAATGGGTCTAAAAT
1 ATAAATGGGTCTAAAAT
3714 ATAAATGGG-CTAAAA
1 ATAAATGGGTCTAAAA
3729 AGTAACAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (17 bp):
ATAAATGGGTCTAAAAT
Found at i:4200 original size:16 final size:16
Alignment explanation
Indices: 4175--4205 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4165 TAGTCGAAGA
4175 TTTCACTTTTTTTTCC
1 TTTCACTTTTTTTTCC
*
4191 TTTCATTTTTTTTTC
1 TTTCACTTTTTTTTC
4206 TGTTAAGGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCACTTTTTTTTCC
Found at i:4702 original size:16 final size:16
Alignment explanation
Indices: 4681--4713 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4671 CCCTTCTTTT
4681 TTTATGACATGACTAA
1 TTTATGACATGACTAA
4697 TTTATGACATGACTAA
1 TTTATGACATGACTAA
4713 T
1 T
4714 GATTTACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (16 bp):
TTTATGACATGACTAA
Found at i:21778 original size:63 final size:63
Alignment explanation
Indices: 21705--21828 Score: 212
Period size: 63 Copynumber: 2.0 Consensus size: 63
21695 GAATTCAATT
* * * *
21705 CAAACTAAGAAATTACCTTACATAATCTACTTAACAAACTATTTAACAAATAAACAAATAACC
1 CAAACTAAGAAATTACCTTAAATAACCTACCTAACAAACTATTTAACAAACAAACAAATAACC
21768 CAAACTAAGAAATTACCTTAAATAACCTACCTAACAAACTATTTAACAAACAAACAAATAA
1 CAAACTAAGAAATTACCTTAAATAACCTACCTAACAAACTATTTAACAAACAAACAAATAA
21829 ATAAACGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.54, C:0.21, G:0.02, T:0.23
Consensus pattern (63 bp):
CAAACTAAGAAATTACCTTAAATAACCTACCTAACAAACTATTTAACAAACAAACAAATAACC
Found at i:25933 original size:29 final size:31
Alignment explanation
Indices: 25901--25967 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
25891 ATGCAATTTG
25901 GGATATAACGTTAT-AAAACA-AGCAATTAA
1 GGATATAACGTTATGAAAACAGAGCAATTAA
*
25930 GGATATAACGTTATGAAAAGAGAGCAATTAA
1 GGATATAACGTTATGAAAACAGAGCAATTAA
25961 GGATATA
1 GGATATA
25968 GTCCGTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 5 0.14
31 16 0.46
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.24
Consensus pattern (31 bp):
GGATATAACGTTATGAAAACAGAGCAATTAA
Found at i:26133 original size:31 final size:31
Alignment explanation
Indices: 26098--26176 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
26088 CTAACTGATT
* *
26098 ATATCCTTAATTACTTGAAATCGAAAACGTC
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
*
26129 ATATCCTTAATTGCTTGAAATAGAAAACGTT
1 ATATCCTTAATTGCTTGAAATAGAAAACGTC
*
26160 ATATCATTAATTGCTTG
1 ATATCCTTAATTGCTTG
26177 TTTTGTAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAGAAAACGTC
Found at i:26221 original size:31 final size:29
Alignment explanation
Indices: 26096--26232 Score: 112
Period size: 31 Copynumber: 4.5 Consensus size: 29
26086 GCCTAACTGA
* * *
26096 TTATATCCTTAATTACTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTG-TATAG-AAACG
* *
26127 TCATATCCTTAATTGCTTGAAATAGAAAACG
1 TTATATCCTTAATTGCTTG-TATAG-AAACG
* * * *
26158 TTATATCATTAATTGCTTGTTTTGTAACG
1 TTATATCCTTAATTGCTTGTATAGAAACG
**
26187 TTATATCCTTAATTGCTTGTGGCAGCAAACG
1 TTATATCCTTAATTGCTTGT-ATAG-AAACG
*
26218 TTATATCCTAAATTG
1 TTATATCCTTAATTG
26233 ATTATTTGAC
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 23 0.26
30 3 0.03
31 63 0.71
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (29 bp):
TTATATCCTTAATTGCTTGTATAGAAACG
Done.