Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014731.1 Corchorus olitorius cultivar O-4 contig14764, 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: 25994
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:443 original size:159 final size:160
Alignment explanation
Indices: 2--639 Score: 813
Period size: 159 Copynumber: 4.0 Consensus size: 160
1 C
*
2 CTGCTTCAAAAACCCCGGAACCCACCACCCCTCTCCGCCGGTCCTCCAGGCTTCTCAATCGAGCA
1 CTGCTTCAAAAACCCCGGAA-CCACCACCCCTCTCCGCCGGTCCTCAAGGCTTCTCAATCGAGCA
* * * *
67 ACTCCCTCAAAACCACAAAATTTGAGTACCCAGAAGTCAGAATCCACGAAAACAACCTCTCGCTC
65 ACTCCCTCAAAACCACAAGATTTGAGTGCCCAGAAGTCAGAATCCAAGAAAAC-CCCTCTCGCTC
132 CGCAGATAAAATTTCGAAGAAATTGATAAGCT
129 CGCAGATAAAATTTCGAAGAAATTGATAAGCT
* **
164 CTGCTTCAAAAACTCCGGAACCCACCACCCCTCTCCGCCGGTCCTCAAGGCTTCTCAATTTAGCA
1 CTGCTTCAAAAACCCCGGAA-CCACCACCCCTCTCCGCCGGTCCTCAAGGCTTCTCAATCGAGCA
* *
229 ACTCCCTCGAAACCACGAA-ATTTGAGTGCCCAGAAGTCAGAATCCACGAAAACCCCATCTCGCT
65 ACTCCCTCAAAACCAC-AAGATTTGAGTGCCCAGAAGTCAGAATCCAAGAAAACCCC-TCTCGCT
*
293 CCGCAGATAAAATTTCGAAGAAATTGATGAGCT
128 CCGCAGATAAAATTTCGAAGAAATTGATAAGCT
* *
326 CTGCTTCAAAAACCCCGGAA-C-CCACCCCTCTCCGCAGGTCCTTAAGGCTTCTCAATCGAGCAA
1 CTGCTTCAAAAACCCCGGAACCACCACCCCTCTCCGCCGGTCCTCAAGGCTTCTCAATCGAGCAA
* * * * *
389 CTCCATCAAAACCACAAGATTTTAGTGCCC-GAAAGCCAGAATCCAAGAAAACCCCCGCTCACTC
66 CTCCCTCAAAACCACAAGATTTGAGTGCCCAG-AAGTCAGAATCCAAGAAAA-CCCCTCTCGCTC
* *
453 CGCATATAAAATTT-GCAGGAAATTGATAAGCT
129 CGCAGATAAAATTTCG-AAGAAATTGATAAGCT
** * * * * * * *
485 CTGCCCCCAAAACCCCAGAA-C-CCACTCCTCTCCGCCGATCCTCAAGGATTCTAAATCTAGCAA
1 CTGCTTCAAAAACCCCGGAACCACCACCCCTCTCCGCCGGTCCTCAAGGCTTCTCAATCGAGCAA
* * * * *
548 CTCCTTCAAAATCACAAGATTTGAGAGCCCAAAAGTCAGAATCCAAGAAAACCCCTGCTTGCTCC
66 CTCCCTCAAAACCACAAGATTTGAGTGCCCAGAAGTCAGAATCCAAGAAAACCCCT-CTCGCTCC
* * *
613 ACAGATAAAATTTCCAAGAAACTGATA
130 GCAGATAAAATTTCGAAGAAATTGATA
640 CAACCAAGCA
Statistics
Matches: 419, Mismatches: 48, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
158 8 0.02
159 235 0.56
160 5 0.01
161 2 0.00
162 167 0.40
163 2 0.00
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.19
Consensus pattern (160 bp):
CTGCTTCAAAAACCCCGGAACCACCACCCCTCTCCGCCGGTCCTCAAGGCTTCTCAATCGAGCAA
CTCCCTCAAAACCACAAGATTTGAGTGCCCAGAAGTCAGAATCCAAGAAAACCCCTCTCGCTCCG
CAGATAAAATTTCGAAGAAATTGATAAGCT
Found at i:11240 original size:96 final size:95
Alignment explanation
Indices: 11135--11315 Score: 240
Period size: 95 Copynumber: 1.9 Consensus size: 95
11125 AAATTTTATA
* *
11135 TTTTTCGATTATATCCATTTTTTTCAAATGTATTTCCAAATTATCATTATTAAAATAT-TTTAAT
1 TTTTTCGATTATA-CCATTTTTTT-AAATATATTTCCAAATTATCATTATTAAAATATATTTAAA
*
11199 TATGTCATTATT-AAATATAATTTTATGTATT
64 TATGCCATTATTAAAATATAATTTTATGTATT
* * ** * *
11230 TTTTTCCGATTGTACTATTTTTTTAAATATATTTTTAAATTTTCATTATTAAATTATATTTAAAT
1 TTTTT-CGATTATACCATTTTTTTAAATATATTTCCAAATTATCATTATTAAAATATATTTAAAT
11295 ATGCCATTATTAAAATATAAT
65 ATGCCATTATTAAAATATAAT
11316 AATAATTTTG
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
94 28 0.38
95 30 0.41
96 16 0.22
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (95 bp):
TTTTTCGATTATACCATTTTTTTAAATATATTTCCAAATTATCATTATTAAAATATATTTAAATA
TGCCATTATTAAAATATAATTTTATGTATT
Found at i:12167 original size:335 final size:328
Alignment explanation
Indices: 11379--12549 Score: 1305
Period size: 335 Copynumber: 3.5 Consensus size: 328
11369 AAATATAATT
* *
11379 TTTAATTAGAAATTAATTCGGAAAAAGGTAGGAAAAGCGATATTAGAAGCGTGAGAAGCCCTTCA
1 TTTAATTAGAAATTAATTCGGAAAAA--TAGAAAAAACGATATTAGAAGCGTGAGAAGCCCTTCA
* * * * * *
11444 GTCTTTTTGGCATTGAGTTATATATATTTTGT-TTAGTATTGTGGCCCAAAATTGAGGAGAAATT
64 ATCTTTTTGACGTTGAATTATATAT-TTTT-TATGAGTATTGTGGCCAAAAATTGA-GAGAAATT
* * ** * *
11508 TCTCGGGTCAATTTTTGCACAA-TTTAGTTGAAATCATGTACTAACTATCGCGGTTTTTGACTAA
126 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGACTAA
* * * * * *
11572 AAACGCGTTCCGGAGCCCCGGTTCTGTTTTACACGATTTTTGGCACCAAGTCTCATTGAAATATC
191 AAACGCGTTTCGGA-CCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATC
* * * * *
11637 TATATCCATCTAACCAAATCTTACCCACATTGGATTTAAAGATTTATTTTTACCAA-CATATATA
255 TATATCCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTA-CAAGCATCTA-A
* *
11701 TGAATCATGTTTCGA
318 T---CCGT-TTTCGA
* * * *
11716 TTCAATTAGGAATTAATTCGGAAAAAATAGAAAAAATGATATTAGAAGCGTGA-ATAGCCTTTCA
1 TTTAATTAGAAATTAATTCGG-AAAAATAGAAAAAACGATATTAGAAGCGTGAGA-AGCCCTTCA
* * * * *
11780 ATCTTTTTTATGTTGAATTATATA-TTTCTATGAGTATCGTGGCCAAAAATTGAGAAAAATTCTT
64 ATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGAGAAATT-TT
* * *
11844 TTGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGGCTAAAA
128 TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGACTAAAA
*
11909 ACGCGTTTCGTGACCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATCTA
193 ACGCGTTTCG-GACCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTA
** * * *
11974 TATTTATCTAACAAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCC
257 TATCCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACAAGCATCT-AATCC
12039 GTTTTCGA
321 GTTTTCGA
* * *
12047 TTTAATCAGAAATTAATTCGGAAAAATAGAAAAAAAAAACAATATTAGAAGTGTGAGAAGCCCTT
1 TTTAATTAGAAATTAATTCGGAAAAATAG----AAAAAACGATATTAGAAGCGTGAGAAGCCCTT
* * * * ** *
12112 CAATATTTTTGACGTTGAGTTATATATTTTTTATGAATATGGTGGCCGGAAATTGAAGAGAAATG
62 CAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTG-AGAGAAATT
* * * * *
12177 TTTCGTGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTA-TAAACCATCACAGTTTTTTACTA
126 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-AACTATCACGGTTTTTGACTA
*** *
12241 AAAACGCGTTTCGGGGTTCCGGCTTTA-TTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATA
190 AAAACGCGTTTC-GGACCCCGGC-TCAGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATA
12305 TCTATATCCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGA
253 TCTATATCCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACAAGCATCT-A
*
12370 ATCATGTTTTCGA
317 ATC-CGTTTTCGA
* * * *
12383 TTTAATTAGAAATTAATTCGGAAAAATAGGAAAACCGATATTAGAAGCGTGAAAAGCCTTTCAAT
1 TTTAATTAGAAATTAATTCGGAAAAATAGAAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAAT
* * ** * *
12448 CTTTTTTACGTCGAATTATATATTTTTTATGAGTATTGTGGAAAAAAATTTAG-GAAAACTCTTT
66 CTTTTTGACGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGAG-AAA-TTTTT
* * * * *
12512 CGGGTAAATTTTCGCAAATTTTTAACCGAAATCATGTA
129 CGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
12550 TTAATCATCA
Statistics
Matches: 705, Mismatches: 108, Indels: 47
0.82 0.13 0.05
Matches are distributed among these distances:
330 9 0.01
331 29 0.04
332 107 0.15
333 8 0.01
334 92 0.13
335 338 0.48
336 98 0.14
337 19 0.03
338 5 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (328 bp):
TTTAATTAGAAATTAATTCGGAAAAATAGAAAAAACGATATTAGAAGCGTGAGAAGCCCTTCAAT
CTTTTTGACGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGAGAGAAATTTTTCG
GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTGACTAAAAACG
CGTTTCGGACCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATC
CATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTAATCCGTTTT
CGA
Done.