Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015662.1 Corchorus olitorius cultivar O-4 contig15695, 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: 16540
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:1981 original size:37 final size:37
Alignment explanation
Indices: 1940--2011 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
1930 ACATAATTAT
* *
1940 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
1977 TCATAAAGTTATGTCTATATGAAAAGACATGTATT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATT
2012 TTGATCAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:11933 original size:27 final size:28
Alignment explanation
Indices: 11898--11955 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
11888 TTTTAATAAG
* *
11898 TATTCTTTTT-AG-TCATTTAACTTTTT
1 TATTTTTTTTGAGATCATTCAACTTTTT
*
11924 TATTTTTTTTGAGATGATTCAACTTTTT
1 TATTTTTTTTGAGATCATTCAACTTTTT
11952 TATT
1 TATT
11956 AATTATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
27 2 0.07
28 16 0.59
ACGTcount: A:0.21, C:0.09, G:0.07, T:0.64
Consensus pattern (28 bp):
TATTTTTTTTGAGATCATTCAACTTTTT
Found at i:13649 original size:331 final size:326
Alignment explanation
Indices: 13019--14806 Score: 1725
Period size: 331 Copynumber: 5.5 Consensus size: 326
13009 CGAAATCGTA
* * *
13019 TTGTTTCGATTTAATTAAAAATTAATTCGGAAAATAAATGGAAAAACGATAATAGAAGCGTG-AA
1 TTGTTTCGATTTAATTAGAAATAAATTC-GAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAA
*
13083 AACCCTTCAATCTTTTTGGCATTGAATTATATGTTTTTTTCTGAGTATTGTGGCAAAAAATTGAG
64 AACCCTTCAATCTTTTTGGCATTGAATTATAT-ATTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* * * *
13148 AAAAATTTTTTCGTGTCAG----TT-----TTTAGCAGAAATCGTGTACTAATTATCACCGTTTT
128 -AAAA-TTTTTCGGGTCAGTTTTTTGCAAATTTAGCCGAAATCGTGTACT-A-CATCACGGTTTT
* * * *** * * * * * *
13204 TGGCTAAAAACGCGTTCAGGGGTCTCCAATCAGTTTTGAATGGTTTTTGGCATC-CAGAATCCTT
189 TGGCTAAAAACGCGTTCTGGAGTCACGGCTCAATTTTGCATGATTTTTGGC-GCAAAGACTCCTT
* * *
13268 GAAATATCTATATTC-TTGTAATCAAATCTCAGCCACATTGGATTTAAGGATTCGTTTTTACGAG
253 GAAATATCTATATTCATCG-AACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
*
13332 CATTTGAATC
317 CATCTGAATC
* * *
13342 TTGTTTTGATTTTATTATAAATAAATTC-AGAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATAAATTCGA-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* *
13405 ACCCTTCAATTTTTTTTGCGA-TGAATTATATATTTTTTTCTGAGTATTGTGGCAAAAAATTGAG
65 ACCCTTCAATCTTTTTGGC-ATTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* *
13469 GAAATCTTTTCGGGTTAGTTTTTTTGCAAAATTCTAGCCGAAATCGTGTACTACCATCACGGTTT
128 AAAAT-TTTTCGGGTCAG-TTTTTTGC-AAATT-TAGCCGAAATCGTGTACTA-CATCACGGTTT
* * ***
13534 TTGGCAAAAAACGCGTTCTGGATTCACGGCTCAATTTTATTTGATTTTTGGCGCAAAGACTCCTT
188 TTGGCTAAAAACGCGTTCTGGAGTCACGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTT
** *
13599 GAAATATCTATATTCATCGAACCAAATCTCAGGTACATTGGATTTAAGGATTT-TTTTTACGAGT
253 GAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
* *
13663 TTCTGAATT
318 ATCTGAATC
* * * * *
13672 TTGTTTCAATTTAATTAGAAATTAATTTGGAAAAAAAATGGAAAACCGATATTAGAAGCCTGAAA
1 TTGTTTCGATTTAATTAGAAA-TAAATTCG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAA
* * * * * * *
13737 AGCCCGTCAATCTTTTTGGCATTAAATTATATATTTTTTATGACTATTGTAGCAAAAAAATGAGA
64 AACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-
* * * *
13802 AAAAATTTTTCGGGTTAGTTTTTAGC--A---A----AAATCGTGTAC-ACGTTACGGTTTTTGG
128 -AAAATTTTTCGGGTCAGTTTTTTGCAAATTTAGCCGAAATCGTGTACTACATCACGGTTTTTGG
* * * * * * ** *
13857 CTAAAAACGTGTT-TCGGGGCCCCGGTTCAATTTTGCATGATTTTTGGTAG-AAAGAAACCTTTA
192 CTAAAAACGCGTTCT-GGAGTCACGGCTCAATTTTGCATGATTTTTGG-CGCAAAGACTCCTTGA
* * * * * *
13920 AATATCTATATTCATCTAACCAAATCTTAGCTACATTGGATTCACGGATTTGTTTTTACGAGCAC
255 AATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
*
13985 CTAAATC
320 CTGAATC
*
13992 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCGTGAAAA
1 TTGTTTCGATTTAATTAGAAATAAATTC-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * *
14057 ATCCTTCAATTTTTTTTTGCATTGAGTTATGTATTTTTTCTGAGTATTGTGGCAAAAAATTGAGG
65 ACCCTTCAA-TCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-G
* ** * *
14122 AAAAATTTTTCGGGTCAGTTTTTCG-AAATTCTAATCGAAATCGTGCACTAATCATCACCGTTTC
128 -AAAATTTTTCGGGTCAGTTTTTTGCAAATT-TAGCCGAAATCGTGTACT-A-CATCA-CG-GT-
* * * ** *
14186 TTTTGGCTAAAAACGCGTT-TCGG-GACACCGGCTTAGTTTTGCATGATTTAAGGTAG-AAAGAC
186 TTTTGGCTAAAAACGCGTTCT-GGAGTCA-CGGCTCAATTTTGCATGATTTTTGG-CGCAAAGAC
* ** *
14248 TCCTTGAAATATCTATATTCATCTAATTAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTA
248 TCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
14313 CGAGCATCTGAATC
313 CGAGCATCTGAATC
* * *
14327 ATGTTTTGATTTAATTAGAAATAAATTCGAAAAAAA-GGAAAAACGATATTAAAAGCGTGAAAAA
1 TTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAA
* * * *
14391 CCCTTCAATGTTTTTGGCGTTGAATTATATATTTTTTTTGAGTATTCTGGCAAAAAATTGAGGAA
66 CCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-G-A
*
14456 AAACTTTTCGGGTCA-TTTTTTGCAAAATTTTAGCCGAAATCGTGTACGT---T-ACGGTTTTTG
129 AAATTTTTCGGGTCAGTTTTTTGC-AAA-TTTAGCCGAAATCGTGTAC-TACATCACGGTTTTTG
** * *
14516 GCTAAAAACGCGTT-TCGGAGTGGCGGCTCAATTTTGCAAGATTTTTGGCACAAAGACTCCTT-A
191 GCTAAAAACGCGTTCT-GGAGTCACGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGA
* * *
14579 AATTATCTATATTCATCGAACCAAATGTCAGCCACATTGGATATATATAAGGATTTGTATTCACG
255 AA-TATCTATATTCATCGAACCAAATCTCAGCCACATTGG--AT-T-TAAGGATTTGTTTTTACG
* *
14644 AGCATCTCATTC
315 AGCATCTGAATC
* * *
14656 TTGTTTTGATTTAATAAGAAATTAATTCGAAAACAAATGGAAAAACGATATTAGAAGCGTG-AAA
1 TTGTTTCGATTTAATTAGAAATAAATTCGAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAAA
* * * * *
14720 AGCCTGTCAATCTTTTTGGCATTAAATTATATATTTTTTCTAAATATT-TCGCAAAAAAATTGAG
65 ACCCT-TCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGAG
** *
14784 AAAAAAATTTCGGGTAAGTTTTT
128 -AAAATTTTTCGGGTCAGTTTTT
14807 AGCCGAAATC
Statistics
Matches: 1219, Mismatches: 181, Indels: 122
0.80 0.12 0.08
Matches are distributed among these distances:
318 1 0.00
319 148 0.12
320 140 0.11
321 78 0.06
322 4 0.00
323 24 0.02
324 3 0.00
325 91 0.07
326 2 0.00
327 4 0.00
328 2 0.00
329 67 0.05
330 62 0.05
331 189 0.16
332 127 0.10
333 115 0.09
334 18 0.01
335 144 0.12
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (326 bp):
TTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAA
CCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAA
ATTTTTCGGGTCAGTTTTTTGCAAATTTAGCCGAAATCGTGTACTACATCACGGTTTTTGGCTAA
AAACGCGTTCTGGAGTCACGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
TATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAAT
C
Found at i:16206 original size:31 final size:31
Alignment explanation
Indices: 16164--16227 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
16154 AACAGCCAAT
16164 AAAGCCCAATACTAA-CTAAAATAAGAAAATA
1 AAAGCCCAATACTAATCT-AAATAAGAAAATA
*
16195 AAAGCCTAATACTAATCTAAATAAGAAAATA
1 AAAGCCCAATACTAATCTAAATAAGAAAATA
16226 AA
1 AA
16228 GACAAACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.61, C:0.14, G:0.06, T:0.19
Consensus pattern (31 bp):
AAAGCCCAATACTAATCTAAATAAGAAAATA
Found at i:16402 original size:21 final size:20
Alignment explanation
Indices: 16356--16402 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
16346 TCCTCTTGCC
*
16356 TTTCCATCGAGTCCTTGTCT
1 TTTCCATCGAGTCCTTGTAT
16376 TCTTCCATCGAGTCCTTGTAT
1 T-TTCCATCGAGTCCTTGTAT
16397 ATTTCC
1 -TTTCC
16403 TGTAAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.13, C:0.30, G:0.13, T:0.45
Consensus pattern (20 bp):
TTTCCATCGAGTCCTTGTAT
Done.