Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016385.1 Corchorus olitorius cultivar O-4 contig16418, 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: 9391
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--30 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31 CTAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1775 original size:81 final size:78
Alignment explanation
Indices: 1682--1863 Score: 240
Period size: 81 Copynumber: 2.3 Consensus size: 78
1672 ACGATGTTGT
*
1682 TGGCTTATCGTTCACCATAGGAGGAGCTAATTGATTTTGAGCATCCG-GAATTACTTTCTCCCAT
1 TGGCTTATCGTTCACCATAGGAGGA---AATTGATTTTGAGCATCCGAG-ACTACTTTCTCCCAT
1746 CTCTCCCAAGTAATTTC
62 CTCTCCCAAGTAATTTC
* * *
1763 TGGCTTATCGTTCAGTACCATTGGAGGAACTTGATTTTGAGCATCCGAGACTACTTTTTCCCATC
1 TGGCTTATCGTTC---ACCATAGGAGGAAATTGATTTTGAGCATCCGAGACTACTTTCTCCCATC
1828 TCTCCCAAGTAATTTC
63 TCTCCCAAGTAATTTC
* *
1844 TGGCTTAGCGTTCGCCATAG
1 TGGCTTATCGTTCACCATAG
1864 CATGATCTTG
Statistics
Matches: 90, Mismatches: 7, Indels: 11
0.83 0.06 0.10
Matches are distributed among these distances:
78 5 0.06
81 73 0.81
82 1 0.01
84 11 0.12
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.35
Consensus pattern (78 bp):
TGGCTTATCGTTCACCATAGGAGGAAATTGATTTTGAGCATCCGAGACTACTTTCTCCCATCTCT
CCCAAGTAATTTC
Found at i:4156 original size:333 final size:329
Alignment explanation
Indices: 3520--4256 Score: 903
Period size: 333 Copynumber: 2.2 Consensus size: 329
3510 TCCTATTTTA
* * * *
3520 TTTCGATTTAATCAGATATTAATTTGGTAAAAATAGGAAAAATGATATTAAAAGCGTG-AAAGCC
1 TTTCGATTTAATCAAAAATTAATTTGGAAAAAATAGGAAAAATGATATTAGAAGCGTGAAAAGCC
** * *
3584 CTTCGATC--TTTTTGGTATTGAATTAATTATTTCTTATGAGTATTTTGGTCAAAAATTGAGGAA
66 CTTTAATCTTTTTTTGGTATTGAATTAATAATTTCTTATGAGTATTTTGGCCAAAAATTGAGGAA
* * * * *
3647 AAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACGTCACGGTTTTTTGGCTA
131 AAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATCTACATCACGGTTATTTCGCTA
* * * * * * * * * *
3712 AAATCGCGTTCCGGTCCCTTGGTTCAGTTTTGCATGGTTTTTGGCGCCAAGACTCCTTTAAATAT
196 AAAACGCGTTACGGGCCC-TAGATCAATTTTGCATGATTTTTGGCACCAAGAATCCTTGAAATAT
* * * *
3777 CTATATTCATCTAGTCAAATCTCAGCCACACTAGATTTATGGATATGTTTGTATGAGCATCTGAA
260 CAATATTCATCTAATCAAATCCCAGCCACACTAGATTTAAGGATATGTTTGTATGAGCATCTGAA
3842 TCTTG
325 TCTTG
* *
3847 TTTCGATTTAATCAAAAATTAATTTAGAAAAAATAGGAAAAATGATATTAGAAGGGTGAAAAGCC
1 TTTCGATTTAATCAAAAATTAATTTGGAAAAAATAGGAAAAATGATATTAGAAGCGTGAAAAGCC
* * *
3912 CTTTAATCTTTTTTTTGTGTTGAATTATATAATTT-TTATGAG-ATTTTGGCCAAGAATTGAGGA
66 CTTTAATCTTTTTTTGGTATTGAATTA-ATAATTTCTTATGAGTATTTTGGCCAAAAATTGAGGA
* * *
3975 AAAATATTTTGGGTTAATTTTTGCAAAATTTTAGTCGAAATCATATACTAATCATCACGG-TATT
130 AAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC--AT-CT-A-CATCACGGTTATT
* *
4039 TCGCTAAAAACGCGTTTAGGGGCTCC-AGATCAATTTTGCATGATTTTTGGCACCGAGAATCCTT
190 TCGCTAAAAACGCG-TTACGGGC-CCTAGATCAATTTTGCATGATTTTTGGCACCAAGAATCCTT
* * * * *
4103 GAATTATCAATATTCATTTAATCAAATCCCAGCCACATTGGATTTAAGGATATGTTTTTATGAGC
253 GAAATATCAATATTCATCTAATCAAATCCCAGCCACACTAGATTTAAGGATATGTTTGTATGAGC
4168 ATCTGAATCTTG
318 ATCTGAATCTTG
* * * * * *
4180 TTTCAATTTAATCAAAAATTCATTTGGAAAAAAAAAGAAAAATGATATTAGAAGCATGAAAATCC
1 TTTCGATTTAATCAAAAATTAATTTGGAAAAAATAGGAAAAATGATATTAGAAGCGTGAAAAGCC
*
4245 CTTTAATATTTT
66 CTTTAATCTTTT
4257 GGCGTAGAAT
Statistics
Matches: 348, Mismatches: 51, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
327 52 0.15
328 12 0.03
329 58 0.17
330 22 0.06
331 7 0.02
332 1 0.00
333 182 0.52
334 12 0.03
335 2 0.01
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (329 bp):
TTTCGATTTAATCAAAAATTAATTTGGAAAAAATAGGAAAAATGATATTAGAAGCGTGAAAAGCC
CTTTAATCTTTTTTTGGTATTGAATTAATAATTTCTTATGAGTATTTTGGCCAAAAATTGAGGAA
AAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATCTACATCACGGTTATTTCGCTA
AAAACGCGTTACGGGCCCTAGATCAATTTTGCATGATTTTTGGCACCAAGAATCCTTGAAATATC
AATATTCATCTAATCAAATCCCAGCCACACTAGATTTAAGGATATGTTTGTATGAGCATCTGAAT
CTTG
Found at i:7907 original size:332 final size:329
Alignment explanation
Indices: 7180--8111 Score: 1327
Period size: 332 Copynumber: 2.8 Consensus size: 329
7170 ATTATATATT
* * * *
7180 TTTTGCATGATTTTTGGCCCCAAGACTCATTGAATTATCTATATTCATCA-TCCAAAATCTTAGC
1 TTTTGCAAGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCATTCC-AAATCTCAGC
* *
7244 CACCTTGGATTTAAGGATTTGATTTTACGAGCACTTGAATCATGTTTCAATTTAATCGGAAATTA
65 CACATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCAATTTAATCGGAAATTA
* * * *
7309 AATAGGAAAA-ATAAAAAAATGATATTAGAATCATGCAAAGCCCTTCAATCTTTTTTGGCGTTGA
130 ATTAGAAAAATATAAAAAAATGATATTAGAAGCGTGCAAAGCCCTTCAATC-TTTTTGGCGTTGA
* * *
7373 ATTATATATTTTTTTACGACTATTGCGGTTAAAAATTGAGGAAAAATCTGTCGGGTCAATTTTTG
194 ATTATATA-TTTTTTATGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTG
* *
7438 C---------CGAAATCGTGTACTAACCATCACGATTCTTGGCTGAAAACGCGTTCCAGGGCCCC
258 CAAAATTTTGCGAAATCGTGTACTAACCATCACGATTCCTGGATGAAAACGCGTTCCAGGGCCCC
7494 AGCTCAG
323 AGCTCAG
* *
7501 TTTTGCATA-ATTTTTTGCGCCAAGACTCATTGAAATATCTATATTCATCATCCCAAATCTCAGC
1 TTTTGCA-AGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCATTCCAAATCTCAGC
* *
7565 CACATTGGATTTAAGGATTTTATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATTA
65 CACATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCAATTTAATCGGAAATTA
* *
7630 ATTCAGAAAAATATTAAAAAAATTATATTAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCATTG
130 ATT-AGAAAAATA-TAAAAAAATGATATTAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCGTTG
*
7695 AATTAGATA-TTTTTATGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTG
193 AATTATATATTTTTTATGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTG
* * *
7759 CAAATATTTTGCTGAAATCGTGTACTAACCATTATGATTCCTGGATGAAAACGCGTTCCGGGGCC
258 CAAA-ATTTTGC-GAAATCGTGTACTAACCATCACGATTCCTGGATGAAAACGCGTTCCAGGGCC
*
7824 CCGGCTCAG
321 CCAGCTCAG
* *
7833 TTTTGCAAGATTTTTGGCGTCAAGACTCATTCAAATATCTATATTCATCATTCCAAATCTCAGCC
1 TTTTGCAAGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCATTCCAAATCTCAGCC
** ** *
7898 ATGTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATAATTCCATTTAATCGGAAATTAA
66 ACATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCAATTTAATCGGAAATTAA
* *
7963 TTTGGAAAAATA-AAAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAA
131 -TTAGAAAAATATAAAAAAATGATATTAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCGTTGAA
*
8027 TTATATATTTTTTACT-AGTATTGCGGTTGAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGC
195 TTATATATTTTTTA-TGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGC
8091 AAAATTATTGCCGAAATCGTG
259 AAAATT-TTG-CGAAATCGTG
8112 CGGGGCCACG
Statistics
Matches: 547, Mismatches: 42, Indels: 34
0.88 0.07 0.05
Matches are distributed among these distances:
321 170 0.31
322 8 0.01
323 20 0.04
324 36 0.07
330 58 0.11
331 70 0.13
332 183 0.33
333 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (329 bp):
TTTTGCAAGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCATTCCAAATCTCAGCC
ACATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCAATTTAATCGGAAATTAA
TTAGAAAAATATAAAAAAATGATATTAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCGTTGAAT
TATATATTTTTTATGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAA
AATTTTGCGAAATCGTGTACTAACCATCACGATTCCTGGATGAAAACGCGTTCCAGGGCCCCAGC
TCAG
Found at i:8740 original size:330 final size:327
Alignment explanation
Indices: 8122--9390 Score: 1626
Period size: 330 Copynumber: 3.9 Consensus size: 327
8112 CGGGGCCACG
* * * * *
8122 GCTCAGTTTTGCATGATTTTAGGCGCCAAGACTCATTGGATTATCCT-TATTCATCATTCCAGAT
1 GCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATAT-CTATATTCATCATCCCAAAT
* ** * * *
8186 CTCAACCATGTTGGATTTAAGGATTTTATTTTACGAGCATTTAAATCATGTTTCGATTTAATCGG
65 CTCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTTAAATCATATTTCAATTTAATCGG
* * * * *
8251 AAATTAATTCGGAAAATTTAAAAAAAATGATATTAGAAGCGTGGAAAGGCCTGCAATATTTTTGG
130 AAATTAATTCGGAAAA-AT-AAAAAAATGATATTAGAAGCGTGCAAAGCCCTTCAATCTTTTTGG
* *
8316 CGTTGAATTATATATTTTTTACGAGAATTACGGTTAAAAATTGAGGAAAAATCA-TTCGGGTCAA
193 CGTTGAATTATATA-TTTTTACGAGTATTGCGGTTAAAAATTGAGGAAAAAT-ATTTCGGGTCAA
* * * *
8380 TTTCTGCAAAATTTTTACCGAAACCGTGTACTAACAATCACGATTCTTGGCTGAAAACGCGTTCC
256 TTT-TGC-AAATTTTTGCCGAAATCGTGTACTAACCATCACGATTATTGGCTGAAAACGCGTTCC
*
8445 AGGGCCCCG
319 AGGGCCCCA
* * * *
8454 GCTCAGTTTTGTATGATTTTTGGGGTCAAGACTCATTCAAATATCTATATTCATCATCCCAAATC
1 GCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCATCCCAAATC
* * *
8519 TCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATACTTCAATTTAGTCGGA
66 TCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTTAAATCATATTTCAATTTAATCGGA
* * *
8584 AATCAATTCGGAAAAATAAAAAAATGATATTAGAAGCGTGCAAAGCCCTTTAATCTTTTTGGCAT
131 AATTAATTCGGAAAAATAAAAAAATGATATTAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCGT
*
8649 TGAATTATATAATTTTTACGAGTATTGCGGTTAAAAATTGGGGAAAAATATTTCGGGTCAATATT
196 TGAATTATAT-ATTTTTACGAGTATTGCGGTTAAAAATTGAGGAAAAATATTTCGGGTCAAT-TT
* **
8714 TGCAATATTTTTGCCGAAATCGTGTACTAACCATCACGATTATTGGCTGAAAACGCATTCGGGGG
259 TGCAA-ATTTTTGCCGAAATCGTGTACTAACCATCACGATTATTGGCTGAAAACGCGTTCCAGGG
*
8779 CCCTA
323 CCCCA
* ** *
8784 GCTCAGTTTTGCATGATTTTTAGC-CACAAGACTCATTGATTTATCTATATTCATCATTCCAAAT
1 GCTCAGTTTTGCATGATTTTTGGCGC-CAAGACTCATTGAAATATCTATATTCATCATCCCAAAT
* * *
8848 CTCAGCCACGTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATATTTCAATTTATTCGG
65 CTCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTTAAATCATATTTCAATTTAATCGG
* * *
8913 AAATTAATTTGGAAAAATAAATAAAATGATATTAGATGCGTGCCAAG-CCTTCAATCTTTTTGGC
130 AAATTAATTCGGAAAAATAAA-AAAATGATATTAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGC
* * *
8977 GTTG---TATAT-TTTTGACGACTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGG-------
194 GTTGAATTATATATTTTTACGAGTATTGCGGTTAAAAATTGAGGAAAAATATTTCGGGTCAATTT
* *
9031 T-C-AATTTTTGCCGAAATCGTGTACTAACCATCAC-AGTTATTGTCTGAAAACGCGTTTCAGGG
259 TGCAAATTTTTGCCGAAATCGTGTACTAACCATCACGA-TTATTGGCTGAAAACGCGTTCCAGGG
9093 CCCCA
323 CCCCA
* *
9098 GCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATATTCATCGTCCCAAATC
1 GCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCATCCCAAATC
* * * * *
9163 TCAGCCGCATTGGATTTAAGGATCTGATATTACAAGCATTTAAATCATATTTCCATTTAATCGGA
66 TCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTTAAATCATATTTCAATTTAATCGGA
*
9228 AATTAATTCGGAAAAAT-AAAAAATGATATTAGAAGCGTTG-AATGCCCTTCAATCTTTTTGGCG
131 AATTAATTCGGAAAAATAAAAAAATGATATTAGAAGCG-TGCAAAGCCCTTCAATCTTTTTGGCG
** * * * **
9291 TTGAATTATATATTTTTAAAAATATTGCGGTTGAAAATTGTA-GAAAAATCTTTCTTGTCAATTT
195 TTGAATTATATATTTTTACGAGTATTGCGGTTAAAAATTG-AGGAAAAATATTTCGGGTCAATTT
* *
9355 TGCAAAATTTTGCCGAAATCGTGCACTAACCATCAC
259 TGCAAATTTTTGCCGAAATCGTGTACTAACCATCAC
9391 A
Statistics
Matches: 821, Mismatches: 91, Indels: 56
0.85 0.09 0.06
Matches are distributed among these distances:
312 19 0.02
313 26 0.03
314 187 0.23
315 2 0.00
316 6 0.01
317 37 0.05
318 1 0.00
324 1 0.00
325 42 0.05
326 30 0.04
327 5 0.01
329 3 0.00
330 310 0.38
331 29 0.04
332 123 0.15
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (327 bp):
GCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTCATCATCCCAAATC
TCAGCCACATTGGATTTAAGGATTTGATTTTACGAGCATTTAAATCATATTTCAATTTAATCGGA
AATTAATTCGGAAAAATAAAAAAATGATATTAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCGT
TGAATTATATATTTTTACGAGTATTGCGGTTAAAAATTGAGGAAAAATATTTCGGGTCAATTTTG
CAAATTTTTGCCGAAATCGTGTACTAACCATCACGATTATTGGCTGAAAACGCGTTCCAGGGCCC
CA
Done.