Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019700.1 Corchorus olitorius cultivar O-4 contig19733, 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: 4236
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--38 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 CTAG
5 TA TA 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 TA TA
39 AAAATTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3174 original size:334 final size:334
Alignment explanation
Indices: 2559--4202 Score: 2527
Period size: 334 Copynumber: 4.9 Consensus size: 334
2549 AAAAATCGTG
* *
2559 ATTTTG-AAAAATTGACCCGAAAGATATTTCTTCAATTTTTAGCTGAAATACTCATAAAGATATA
1 ATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATA
*
2623 TATAATTCAACGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCATTTTTCATACTTTTT
66 TATAATTCAACGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTT
* *
2688 CCGAATTAATTTCTAATTGAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGC
131 CCGAATAAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGC
* *
2753 AATGTGGCTGAGATTTGATTCGATGAATATGGATATTTGAAGGAGTCTCGACGCCGAAAATCATG
196 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATG
2818 CAGAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAGTACACGATT
261 CAGAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAGTACACGATT
2883 TCGGCTAAA
326 TCGGCTAAA
*
2892 ATTTTGCAAAAATTGACCCGAAAGATATTTCCACAATTTTTAGCTGAAATACTCATAGAGATATA
1 ATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATA
* * *
2957 TATAATTCAACGCCAAAAATATTGAAGGTTTTTTTACGATTCTAATATCATTTTTCGTACTTTTT
66 TATAATTCAACGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTT
*
3022 CCGAATAAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGGAAAAACAAATCCTTAAATGC
131 CCGAATAAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGC
* * * *
3087 AATGTGGCTAAGATTTGAGTAGATGAATATAGATATTTGAAGGAGTCCCGACGCCGAAAATCTTG
196 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATG
** *
3152 CAGAACTGAGTCGGAACCCCGAAACGTGTTTTTAGC-AAAAAATCGTGATGGTTAGTACACGATT
261 CAGAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAGTACACGATT
3216 TCGGCTAAA
326 TCGGCTAAA
* * * * * *
3225 ATTCTT-CAAAAAATGATCCGAAAAATTTTTCTTCAATTTTT-GCCT-AATATACTCGT-GTA-A
1 ATT-TTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAG-CTGAA-ATACTCATAG-AGA
* * * ** * * * * *
3285 TATTTATAATTTC-ACACC-AAAATGATTGGAGGACTTTTCACACTTTTCATATCATTTTTCATT
62 TATATATAA-TTCAACGCCAAAAAT-ATTGAAGGGTTTTTTACGCTTCTAATATCATTTTTC-CT
* * * * * *
3348 AATTTTTCCGAA-ATAATTTCTAATTAAATCGAAATAACATTCAGATGCTCGTAAAAACAAATAC
124 ACTTTTTCCGAATA-AATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCC
* * * * * **
3412 TTAAATGAAATTTGACTGAGATTTGACTAGATGAATATAGATATTTTAAGGAGTCTCGACGTTGA
188 TTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGA
3477 AAATCATGCAGAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAAATCGTGATGGTTAG
253 AAATCATGCAGAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGC-AAAAAAATCGTGATGGTTAG
3542 TACACGATTTCGGCTAAA
317 TACACGATTTCGGCTAAA
* *
3560 ATTTTGTAAAAATTGACCCGAAAGATATTTCCACAATTTTTAGCTGAAATACTCATAGAGATATA
1 ATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATA
* *
3625 TATAATTCAACGCGAAAAATATTGAA-GGTTTTTTACGCTTCTAATATCGTTTTTCCTACTTTTT
66 TATAATTCAACGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTT
* *
3689 CCGAATTAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAAAAATATCCTTAAATG
131 CCGAATAAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAA-ATCCTTAAATG
3754 CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCAT
195 CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCAT
* * *
3819 GCAGAATTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAGAAATCGTGATTGTTAGTACACGAT
260 GCAGAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAGTACACGAT
3884 TTCGGCTAAA
325 TTCGGCTAAA
* * *
3894 ATTTAGCAAAAATTGATCCGAAAGATATTTCCTCAATTTTTAACTGAAATACTCATAGAGATATA
1 ATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATA
*
3959 TATATTTCAACGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTT
66 TATAATTCAACGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTT
* * *
4024 CCGAATAAATTTCTAATTAAATTGAATCAAGACTTAGATGCTCGTAAAAACAAATTCTTAAATGC
131 CCGAATAAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGC
*
4089 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTAAAGGAGTCTCGACGCCGAAAATCATG
196 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATG
*
4154 CAGAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAATTCGTGA
261 CAGAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAATCGTGA
4203 ACGATTTCGG
Statistics
Matches: 1179, Mismatches: 111, Indels: 41
0.89 0.08 0.03
Matches are distributed among these distances:
331 5 0.00
332 46 0.04
333 240 0.20
334 569 0.48
335 293 0.25
336 21 0.02
337 5 0.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (334 bp):
ATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCTGAAATACTCATAGAGATATA
TATAATTCAACGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTT
CCGAATAAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGC
AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCGAAAATCATG
CAGAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAGTACACGATT
TCGGCTAAA
Found at i:3858 original size:668 final size:668
Alignment explanation
Indices: 2565--4195 Score: 2492
Period size: 667 Copynumber: 2.4 Consensus size: 668
2555 CGTGATTTTG
* * * * * * *
2565 AAAAATTGACCCGAAAGATATTTCTTCAATTTTTAGCTGAAATACTCATAAAGATATATATAATT
1 AAAAAATGATCCGAAAAATATTTCCTCAATTTTTAACTGAAATACTCATAGAGATATATATATTT
* ** * * *
2630 CAACGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCATTTTTCATACTTTTTCCGAATT
66 CAACACCAAAAATATTGAAGGACTTTTCACACTTCTAATATCATTTTTCATACTTTTTCCGAAAT
* * *
2695 AATTTCTAATTGAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGG
131 AATTTCTAATTAAATTGAAATAAGA-TTAGATGCTCGTAAAAACAAATACTTAAATGCAATGTGG
* * *
2760 CTGAGATTTGATTCGATGAATATGGATATTTGAAGGAGTCTCGACGCCGAAAATCATGCAGAACT
195 CTGAGATTTGATTAGATGAATATAGATATTTAAAGGAGTCTCGACGCCGAAAATCATGCAGAACT
2825 GAGTCGGGGCCCCGAAACGCGTTTTTAGC-AAAAAAATCGTGATGGTTAGTACACGATTTCGGCT
260 GAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAAATCGTGATGGTTAGTACACGATTTCGGCT
2889 AAAATTTTGCAAAAATTGACCCGAAAGATATTTCCACAATTTTTAGCTGAAATACTCATAGAGAT
325 AAAATTTTGCAAAAATTGACCCGAAAGATATTTCCACAATTTTTAGCTGAAATACTCATAGAGAT
*
2954 ATATATAATTCAACGCCAAAAATATTGAAGGTTTTTTTACGATTCTAATATCATTTTTCGTACTT
390 ATATATAATTCAACGCCAAAAATATTGAAGGTTTTTTTACGATTCTAATATCATTTTTCCTACTT
*
3019 TTTCCGAATAAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGGAAAAACAAATCCTTAAA
455 TTTCCGAATAAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGGAAAAAAAAATCCTTAAA
3084 TGCAATGTGGCTAAGATTTGAGTAGATGAATATAGATATTTGAAGGAGTCCCGACGCCGAAAATC
520 TGCAATGTGGCTAAGATTTGAGTAGATGAATATAGATATTTGAAGGAGTCCCGACGCCGAAAATC
* *
3149 TTGCAGAACTGAGTCGGAACCCCGAAACGTGTTTTTAGCAAA-AAATCGTGATGGTTAGTACACG
585 ATGCAGAACTGAGTCGGAACCCCGAAACGCGTTTTTAGCAAAGAAATCGTGATGGTTAGTACACG
*
3213 ATTTCGGCTAAAATTCT-TC
650 ATTTCGGCTAAAATT-TAGC
* * ** * *
3232 AAAAAATGATCCGAAAAATTTTTCTTCAATTTTTGCCT-AATATACTCGT-GTA-ATATTTATAA
1 AAAAAATGATCCGAAAAATATTTCCTCAATTTTTAACTGAA-ATACTCATAG-AGATATATAT-A
* * * *
3294 TTTC-ACACC-AAAATGATTGGAGGACTTTTCACACTTTTCATATCATTTTTCATTAATTTTTCC
63 TTTCAACACCAAAAAT-ATTGAAGGACTTTTCACACTTCTAATATCATTTTTCA-TACTTTTTCC
* * *
3357 GAAATAATTTCTAATTAAATCGAAATAACATTCAGATGCTCGTAAAAACAAATACTTAAATGAAA
126 GAAATAATTTCTAATTAAATTGAAATAAGATT-AGATGCTCGTAAAAACAAATACTTAAATGCAA
* * * * **
3422 TTTGACTGAGATTTGACTAGATGAATATAGATATTTTAAGGAGTCTCGACGTTGAAAATCATGCA
190 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTAAAGGAGTCTCGACGCCGAAAATCATGCA
3487 GAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAAATCGTGATGGTTAGTACACGATTT
255 GAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAAATCGTGATGGTTAGTACACGATTT
*
3552 CGGCTAAAATTTTGTAAAAATTGACCCGAAAGATATTTCCACAATTTTTAGCTGAAATACTCATA
320 CGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCACAATTTTTAGCTGAAATACTCATA
* * *
3617 GAGATATATATAATTCAACGCGAAAAATATTGAAGG-TTTTTTACGCTTCTAATATCGTTTTTCC
385 GAGATATATATAATTCAACGCCAAAAATATTGAAGGTTTTTTTACGATTCTAATATCATTTTTCC
* *
3681 TACTTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAAAAATATC
450 TACTTTTTCCGAATAAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGGAAAAAAAA-ATC
* * *
3746 CTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTGAAGGAGTCTCGACGCCG
514 CTTAAATGCAATGTGGCTAAGATTTGAGTAGATGAATATAGATATTTGAAGGAGTCCCGACGCCG
* ** *
3811 AAAATCATGCAGAATTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAGAAATCGTGATTGTTAG
579 AAAATCATGCAGAACTGAGTCGGAACCCCGAAACGCGTTTTTAGCAAAGAAATCGTGATGGTTAG
3876 TACACGATTTCGGCTAAAATTTAGC
644 TACACGATTTCGGCTAAAATTTAGC
* *
3901 AAAAATTGATCCGAAAGATATTTCCTCAATTTTTAACTGAAATACTCATAGAGATATATATATTT
1 AAAAAATGATCCGAAAAATATTTCCTCAATTTTTAACTGAAATACTCATAGAGATATATATATTT
* ** * * *
3966 CAACGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCATTTTTCCTACTTTTTCCG-AAT
66 CAACACCAAAAATATTGAAGGACTTTTCACACTTCTAATATCATTTTTCATACTTTTTCCGAAAT
*
4030 AAATTTCTAATTAAATTG-AATCAAGACTTAGATGCTCGTAAAAACAAATTCTTAAATGCAATGT
131 -AATTTCTAATTAAATTGAAAT-AAGA-TTAGATGCTCGTAAAAACAAATACTTAAATGCAATGT
4094 GGCTGAGATTTGATTAGATGAATATAGATATTTAAAGGAGTCTCGACGCCGAAAATCATGCAGAA
193 GGCTGAGATTTGATTAGATGAATATAGATATTTAAAGGAGTCTCGACGCCGAAAATCATGCAGAA
4159 CTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAA
258 CTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAA
4196 TTCGTGAACG
Statistics
Matches: 866, Mismatches: 80, Indels: 34
0.88 0.08 0.03
Matches are distributed among these distances:
665 5 0.01
666 45 0.05
667 282 0.33
668 244 0.28
669 240 0.28
670 45 0.05
671 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (668 bp):
AAAAAATGATCCGAAAAATATTTCCTCAATTTTTAACTGAAATACTCATAGAGATATATATATTT
CAACACCAAAAATATTGAAGGACTTTTCACACTTCTAATATCATTTTTCATACTTTTTCCGAAAT
AATTTCTAATTAAATTGAAATAAGATTAGATGCTCGTAAAAACAAATACTTAAATGCAATGTGGC
TGAGATTTGATTAGATGAATATAGATATTTAAAGGAGTCTCGACGCCGAAAATCATGCAGAACTG
AGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAAATCGTGATGGTTAGTACACGATTTCGGCTA
AAATTTTGCAAAAATTGACCCGAAAGATATTTCCACAATTTTTAGCTGAAATACTCATAGAGATA
TATATAATTCAACGCCAAAAATATTGAAGGTTTTTTTACGATTCTAATATCATTTTTCCTACTTT
TTCCGAATAAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGGAAAAAAAAATCCTTAAAT
GCAATGTGGCTAAGATTTGAGTAGATGAATATAGATATTTGAAGGAGTCCCGACGCCGAAAATCA
TGCAGAACTGAGTCGGAACCCCGAAACGCGTTTTTAGCAAAGAAATCGTGATGGTTAGTACACGA
TTTCGGCTAAAATTTAGC
Done.