Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021187.1 Corchorus olitorius cultivar O-4 contig21220, 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: 30334
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1318 original size:35 final size:35
Alignment explanation
Indices: 1266--1853 Score: 844
Period size: 35 Copynumber: 16.9 Consensus size: 35
1256 GCAGTCGTTC
* *
1266 CAAGAAGTATTCGATGATCAAAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
1301 CAAGAAGTTTTCAATGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
1336 CCAGGAAGTTTTCGATGATCAGAGTTGATCTCATTT
1 -CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
1372 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
1407 CAAGAAGTTTT--ATGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
1440 CAAAAAGTTTTCGATGATCAGAGTTGATCTCA-TT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
** * *
1474 CTAAGAAGTTTTTTATGAACAGAGTTGATTTCATTT
1 C-AAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
1510 CAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* *
1545 CAAGAGGTTTTCGATGATCAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* * *
1580 CAAGAAGTTTTCGATTATTAGAGTTGATCTCATTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
1615 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATGT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* **
1650 CAAAAAGTTTTTTATGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* * *
1685 CAAGAAGTTTTCGATGTTTAGAGTTGATCTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
1720 CAAGAAGTTTT--ATGATTAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* * *
1753 CAAAAAGTTTTCGATGATCAGAGTTGATTTCGTTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
1788 CAAGAAGTTTTCGATGATCAGAGTTGATCTTATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* * *
1823 CAAGAAGTTTACGAGGATCAAAGTTGATCTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTC
1854 CAAGTTGACC
Statistics
Matches: 493, Mismatches: 53, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
33 61 0.12
34 3 0.01
35 393 0.80
36 36 0.07
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (35 bp):
CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
Found at i:9120 original size:437 final size:437
Alignment explanation
Indices: 8493--9358 Score: 1249
Period size: 437 Copynumber: 2.0 Consensus size: 437
8483 AGGCGGCATT
* *
8493 AATTGGGATTTTAACTCCAATCATGGGCTTATATGGGCTGAGTATTATCCCATATAAAATATCCA
1 AATTGGGATTTTAACTCCAATCATGGGCTCATATGGGCTGAATATTATCCCATATAAAATATCCA
* * * ** ** * * * *
8558 AAATTCCTTAGCTTCTGGGCTTGTTCATGGCTTGTCTTCAATCCTTCGCGATTTAAGCTCCAATC
66 AAAGTCCATAGCTCCAAGGCTTGGACAAGCCTTATCTTCAATCCTTCGCAATTTAAGCTCCAATC
* * *
8623 TTCAATTCTTGCCTCTTGAGATAATTCTTTAATAATCTTCAAATCTTCAAATTATCTTCAATAAG
131 TTCAATTCTTGCCTCTTGAAATAATTCTTCAATAATCTTCAAATCTTCAAATTATCTTCAATAAA
*
8688 TCTTCAATCACGAACTTCGAATCTCCAAATCCAT-ACTCAAAATTGCTAAGTCCATATTTGTG-C
196 TCTTCAATCACGAACTTCGAATCTCCAAAT-CATCACTCAAAATTACTAAGTCCATATTTGTGAC
* * * ** *
8751 AAAAAGTCATCAATTTAGCTCCAAAAATAGTTAAAAACTATTAGTTT-TAAATTTTCTTGTCTTC
260 -AAAAGTCATCAAATTAGCTCCAAAAATAGTGAAAAACAACAAGTTTCT-AATTTTCTTCTCTTC
* *
8815 AAGACCTAAAAACACAAATACTTACAAAATAGGGTTAAATCACACATAAAAATACCAAAAAGCAT
323 AAGACCTAAAAACACAAATACTTACAAAATAGAGTTAAATCACACATAAAAATACAAAAAAGCAT
8880 AGGAAAATGATCATAAAAATAAGGTTAATTTTAGCTCGATCAGCGGCACC
388 AGGAAAATGATCATAAAAATAAGGTTAATTTTAGCTCGATCAGCGGCACC
** *
8930 AATTGGGATTTTAACTCCAATTGTGGGCTCATATGGGCTGAATATTATCCCATATAAAATATTCA
1 AATTGGGATTTTAACTCCAATCATGGGCTCATATGGGCTGAATATTATCCCATATAAAATATCCA
* *
8995 AAAGTGCAT-GTCTCCAAGGCTATGGAGAAGCCTTATCTTCAATCCTTCGCAATTTAAGCT-CAA
66 AAAGTCCATAG-CTCCAAGGCT-TGGACAAGCCTTATCTTCAATCCTTCGCAATTTAAGCTCCAA
* ** *
9058 TCCTT-AATTCTTGCTTCTTGAAATAATTCTTCAATGGTCTTCATATCTTCAAATTATCTTCAAT
129 T-CTTCAATTCTTGCCTCTTGAAATAATTCTTCAATAATCTTCAAATCTTCAAATTATCTTCAAT
*
9122 AAATCTTCAATCACGAACTTCGAATCTCCAAATCTTCACTCAAAATTACTAAGTCCATATTTGTG
193 AAATCTTCAATCACGAACTTCGAATCTCCAAATCATCACTCAAAATTACTAAGTCCATATTTGTG
* *
9187 ACAAAAGTCATCAAATTAGCTCCAAAAATAGTGAAAAGCAACAAGTTTCTACTTTTCTTCTCTTC
258 ACAAAAGTCATCAAATTAGCTCCAAAAATAGTGAAAAACAACAAGTTTCTAATTTTCTTCTCTTC
*
9252 AAGATCTAAAAACACAAATACTTACAAAATAGAGTTAAATCACACATAAAAATACAAAAAAGCAT
323 AAGACCTAAAAACACAAATACTTACAAAATAGAGTTAAATCACACATAAAAATACAAAAAAGCAT
* * * * *
9317 AGGGAATTGATCATAAAATTATGGTTAATTTTGGCTCGATCA
388 AGGAAAATGATCATAAAAATAAGGTTAATTTTAGCTCGATCA
9359 TTTAGTTAGT
Statistics
Matches: 380, Mismatches: 43, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
436 3 0.01
437 341 0.90
438 36 0.09
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (437 bp):
AATTGGGATTTTAACTCCAATCATGGGCTCATATGGGCTGAATATTATCCCATATAAAATATCCA
AAAGTCCATAGCTCCAAGGCTTGGACAAGCCTTATCTTCAATCCTTCGCAATTTAAGCTCCAATC
TTCAATTCTTGCCTCTTGAAATAATTCTTCAATAATCTTCAAATCTTCAAATTATCTTCAATAAA
TCTTCAATCACGAACTTCGAATCTCCAAATCATCACTCAAAATTACTAAGTCCATATTTGTGACA
AAAGTCATCAAATTAGCTCCAAAAATAGTGAAAAACAACAAGTTTCTAATTTTCTTCTCTTCAAG
ACCTAAAAACACAAATACTTACAAAATAGAGTTAAATCACACATAAAAATACAAAAAAGCATAGG
AAAATGATCATAAAAATAAGGTTAATTTTAGCTCGATCAGCGGCACC
Found at i:9706 original size:30 final size:30
Alignment explanation
Indices: 9672--9728 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
9662 AGTTCATGAT
*
9672 TGAAGGTTAATTGAAGATA-ATTTCAAGTCA
1 TGAAGG-TAATTGAAGAAATATTTCAAGTCA
*
9702 TGAAGGTCATTGAAGAAATATTTCAAG
1 TGAAGGTAATTGAAGAAATATTTCAAG
9729 GAGAAAGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (30 bp):
TGAAGGTAATTGAAGAAATATTTCAAGTCA
Found at i:10919 original size:18 final size:19
Alignment explanation
Indices: 10893--10932 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
10883 ATTCTCTTCA
* *
10893 TTTATTTTTC-TTCTAGTT
1 TTTAGTTTTCTTTATAGTT
10911 TTTAGTTTTCTTTATAGTT
1 TTTAGTTTTCTTTATAGTT
10930 TTT
1 TTT
10933 GAAGGGGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTAGTTTTCTTTATAGTT
Found at i:19258 original size:29 final size:29
Alignment explanation
Indices: 19225--19281 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
19215 TGGAGATTCG
* *
19225 AATTTCATGA-TTGAAGATTAATTGAAGAT
1 AATTTCAAGATTTGAAGACT-ATTGAAGAT
*
19254 AATTTGAAGATTTGAAGACTATTGAAGA
1 AATTTCAAGATTTGAAGACTATTGAAGA
19282 ATTATCTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (29 bp):
AATTTCAAGATTTGAAGACTATTGAAGAT
Found at i:20584 original size:21 final size:21
Alignment explanation
Indices: 20554--20608 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
20544 ATTGCCATAG
* *
20554 TTTAGATTTAATTTACTT-TGC
1 TTTATATTTAATTTAATTGT-C
* *
20575 TTTATTTTTAGTTTAATTGTC
1 TTTATATTTAATTTAATTGTC
20596 TTTATATTTAATT
1 TTTATATTTAATT
20609 GTTTTAATCC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTATATTTAATTTAATTGTC
Found at i:27261 original size:36 final size:36
Alignment explanation
Indices: 27220--27289 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
27210 ATTTTCTCTA
*
27220 ATTTATTTCATCAACGTCTAAAGACATTGGCTAATC
1 ATTTATTTCATCAACATCTAAAGACATTGGCTAATC
* *
27256 ATTTATTTCATCAATATCTCAAGACATTGGCTAA
1 ATTTATTTCATCAACATCTAAAGACATTGGCTAA
27290 ATCTCCATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (36 bp):
ATTTATTTCATCAACATCTAAAGACATTGGCTAATC
Found at i:29843 original size:15 final size:15
Alignment explanation
Indices: 29815--29863 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
29805 TGGTATGGAG
29815 GAAATGGGAAGGAAA
1 GAAATGGGAAGGAAA
* *
29830 GAAGTGGGACGGAAA
1 GAAATGGGAAGGAAA
* *
29845 GAAATGGGGAGGAAG
1 GAAATGGGAAGGAAA
29860 GAAA
1 GAAA
29864 AAGCTTCCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.47, C:0.02, G:0.45, T:0.06
Consensus pattern (15 bp):
GAAATGGGAAGGAAA
Done.