Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019134.1 Corchorus olitorius cultivar O-4 contig19167, 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: 2500
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Found at i:1319 original size:664 final size:666
Alignment explanation
Indices: 50--1795 Score: 2772
Period size: 664 Copynumber: 2.6 Consensus size: 666
40 TTGATAAGAT
*
50 GATTTCGGGTAAAATTTTGCAGAAAATGACCCAAAATGTTTTTCTTTAATTTATGGCTAAAATAC
1 GATTTCGGGTAAAATTTTGCAGAAAATGACCCAAAATATTTTTCTTTAATTTATGGCTAAAATAC
*
115 TCATGAAATATATATAATTTAACGCCAAAAAGGTTGAAGGACTTTTCGTGCTTTTCATATCCTTT
66 TCATGAAATATATATAATTTAACGCGAAAAAGGTTGAAGGACTTTTCGTGCTTTTCATATCCTTT
180 TTCATATTTTTCTAAATTAATTTCTAATTGAATCAAAACAAGATTCAAATGCTCGTAAAAACAAA
131 TTCATATTTTTCTAAATTAATTTCTAATTGAATCAAAACAAGATTCAAATGCTCGTAAAAACAAA
* *
245 TCTTTAAATTCAAATGTACCTGATATTTGATTAGATAAATATAGATATTTCAGGGAGTCTTGGTC
196 TCTTTAAATTCAAATGTA-CTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTGGTC
* * * *
310 ACGGCGCAGAAAATAATGTAAAACTAAGCCGGGGTCCCCGAAACGTGTTTTTAGCCAAAAACCGT
260 TCGGCGCAGAAAATAATGAAAAACTAAGCCGGGG-CCCGGAAACGCGTTTTTAGCCAAAAACCGT
375 GATGGTTAGTACACGATTCCAGCTTAGATTTTGCAGAAAATGACCCGAAAAATTTCTCCTCAATT
324 GATGGTTAGTACACGATTCCAGCTTAGATTTTGCAGAAAATGACCCGAAAAATTTCTCCTCAATT
*
440 TTTGGCTAAAATACCCATAAAATATATACAATTTAACTCCAAAAAGGATTGGAGGACTTTTCACG
389 TTTGGCTAAAATACCCATAAAATATATACAATTTAACTCCAAAAAAGATTGGAGGACTTTTCACG
*
505 CTTTTAATATCGTTTTTCATATTTCTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
454 CTTTTAATATCGTTTTTCATATTTCTCTGAATTAATTTCTAATTAAAACGAAACAAGATTCAGAT
* * * *
570 GCTCGTATAAACGAATCCTTGAATGCAATGTGGCTGAGATTTGATTAGATGATTATAGATATTTC
519 GCTCGTATAAACAAATCCTTAAAAGCAATGTGGCTGAGATTTGATTAGATGATTATAGATACTTC
635 AAGGAATCTCAACGCCAAAAATCATGCAAAACTGAGCCGAGCCCCAAAACGCGTTTCTAGC-AAA
584 AAGGAATCTCAACGCCAAAAATCATGCAAAACTGAGCCGAGCCCCAAAACGCGTTTCTAGCAAAA
699 AAAC-CG-TAACGTACAC
649 AAACACGATAACGTACAC
* *
715 GATTTCGGCTAAAATTTTGCAGAAAATGACCCAAAATTTTTTTCTTTAATTTATGGCTAAAATAC
1 GATTTCGGGTAAAATTTTGCAGAAAATGACCCAAAATATTTTTCTTTAATTTATGGCTAAAATAC
*
780 TCATGAAATATATATAATTTAACGCGAAACAGGTTGAAGGACTTTTCGTGCTTTTCATATCCTTT
66 TCATGAAATATATATAATTTAACGCGAAAAAGGTTGAAGGACTTTTCGTGCTTTTCATATCCTTT
845 TTCATATTTTTCT-AATTCAATTTCTAATTGAATCAAAACAAGATTCAAATGCTCGTAAAAACAA
131 TTCATATTTTTCTAAATT-AATTTCTAATTGAATCAAAACAAGATTCAAATGCTCGTAAAAACAA
* *
909 ATCTTTAAATTCAAATGTAGCTGAGATTTGATTTGATAAATATAAATATTTCAAGGAGTCTTGGT
195 ATCTTTAAATTCAAATGTA-CTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTGGT
* ** *
974 CTCGGCGCAGAAAATAATGCAAAACTAAGTTGGGGCCCGGAAACGCGTTTTTTGCCAAAAACCGT
259 CTCGGCGCAGAAAATAATGAAAAACTAAGCCGGGGCCCGGAAACGCGTTTTTAGCCAAAAACCGT
* * * *
1039 -ATTGATTAGAATACGATTCTAGCTTAGATTTTGCAGAAAATGACCCGAAAAATTTCTCCTCAAT
324 GA-TGGTTAGTACACGATTCCAGCTTAGATTTTGCAGAAAATGACCCGAAAAATTTCTCCTCAAT
* *
1103 TTTTGGCTAAAATACCCATAAAATATATATAATTTAACTCCAAAAAATATTGGAGGACTTTTCAC
388 TTTTGGCTAAAATACCCATAAAATATATACAATTTAACTCCAAAAAAGATTGGAGGACTTTTCAC
*
1168 GCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAAACGAAACAAGATTCAGA
453 GCTTTTAATATCGTTTTTCATATTTCTCTGAATTAATTTCTAATTAAAACGAAACAAGATTCAGA
*
1233 TGCTCGTATAAACAAATCCTTAAAAGCAATGTGGCTGAGATTTGATTAGGTGATTATAGATACTT
518 TGCTCGTATAAACAAATCCTTAAAAGCAATGTGGCTGAGATTTGATTAGATGATTATAGATACTT
* * *
1298 CAAGGAATCTCAACGCCAAAAATCATGCAAAACTGAGTCGAGCCCCAAAACGTGTTTTTAGCAAA
583 CAAGGAATCTCAACGCCAAAAATCATGCAAAACTGAGCCGAGCCCCAAAACGCGTTTCTAGC---
* ***
1363 AAAAAAAAACATGATGGTGTACAC
645 --AAAAAAACACGATAACGTACAC
* * **
1387 GATTTTCGGGTAAAATTTTGTA-AAAATTGCCCCGAAAA-ATTTTTCTTCCATTT-TGGCTAAAA
1 GA-TTTCGGGTAAAATTTTGCAGAAAA-TGACCC-AAAATATTTTTCTTTAATTTATGGCTAAAA
* *
1449 TACTCATGAAATATATATAATTTAACGCGAAAAAGGTTGAAAGACTTTTCGTGCTTTTCATATCG
63 TACTCATGAAATATATATAATTTAACGCGAAAAAGGTTGAAGGACTTTTCGTGCTTTTCATATCC
* * ** *
1514 TTTGTCATATTTTTCTGAATTAATTTCTAA-AAAATTCAAAACAAGATTCAAATGCTTGTAAAAA
128 TTTTTCATATTTTTCTAAATTAATTTCTAATTGAA-TCAAAACAAGATTCAAATGCTCGTAAAAA
* *
1578 CAAATCTTTAAATTCAAATGTTACTGAGATTTGATAAAATAAATATAGATATTTCAAGGAGTCTT
192 CAAATCTTTAAATTCAAATG-TACTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTT
* * * *
1643 TGTCTCGGCGCAAAAAATAATGAAAAACTAAGCCGGGGCCCGGAAACGCGTTTTTGGCCAAAATC
256 GGTCTCGGCGCAGAAAATAATGAAAAACTAAGCCGGGGCCCGGAAACGCGTTTTTAGCCAAAAAC
**
1708 CGTGATGGTTAGTACACGATTCCAGCTTAGATTTTGCAGAAAATGTGCCGAAAAAATTTCTCCTC
321 CGTGATGGTTAGTACACGATTCCAGCTTAGATTTTGCAGAAAATGACCCG-AAAAATTTCTCCTC
1773 AATTTTTGGCTAAAATACCCATA
385 AATTTTTGGCTAAAATACCCATA
1796 TTGATTTGAT
Statistics
Matches: 996, Mismatches: 67, Indels: 28
0.91 0.06 0.03
Matches are distributed among these distances:
663 1 0.00
664 333 0.33
665 276 0.28
670 7 0.01
671 3 0.00
672 294 0.30
673 78 0.08
674 4 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (666 bp):
GATTTCGGGTAAAATTTTGCAGAAAATGACCCAAAATATTTTTCTTTAATTTATGGCTAAAATAC
TCATGAAATATATATAATTTAACGCGAAAAAGGTTGAAGGACTTTTCGTGCTTTTCATATCCTTT
TTCATATTTTTCTAAATTAATTTCTAATTGAATCAAAACAAGATTCAAATGCTCGTAAAAACAAA
TCTTTAAATTCAAATGTACTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTGGTCT
CGGCGCAGAAAATAATGAAAAACTAAGCCGGGGCCCGGAAACGCGTTTTTAGCCAAAAACCGTGA
TGGTTAGTACACGATTCCAGCTTAGATTTTGCAGAAAATGACCCGAAAAATTTCTCCTCAATTTT
TGGCTAAAATACCCATAAAATATATACAATTTAACTCCAAAAAAGATTGGAGGACTTTTCACGCT
TTTAATATCGTTTTTCATATTTCTCTGAATTAATTTCTAATTAAAACGAAACAAGATTCAGATGC
TCGTATAAACAAATCCTTAAAAGCAATGTGGCTGAGATTTGATTAGATGATTATAGATACTTCAA
GGAATCTCAACGCCAAAAATCATGCAAAACTGAGCCGAGCCCCAAAACGCGTTTCTAGCAAAAAA
ACACGATAACGTACAC
Found at i:1933 original size:188 final size:186
Alignment explanation
Indices: 1616--1981 Score: 554
Period size: 188 Copynumber: 2.0 Consensus size: 186
1606 ATTTGATAAA
* *
1616 ATAAATATAGATATTTCAAGGAGTCTTTGTCTCGGCGCAAAAAATAATGAAAAACTAAGCCGGGG
1 ATAAATATAAATATTTCAAGGAGTCTTGGTCTCGGCGCAAAAAATAATGAAAAACTAAGCCGGGG
* * * * *
1681 CCCGGAAACGCGTTTTTGGCCAAAATCCGTGATGGTTAGTACACGATTCCAGCTTAGATTTTGCA
66 CCCAGAAACGCGTTTTTGGCCAAAAACCGTAATGATTAGAACACGATTCCAGCTTAGATTTTGCA
*
1746 GAAAATGTGC-CGAAAAAATTTCTCCTCAATTTTTGGCTAAAATACCCATATTGATTTG
131 GAAAATG-ACTCG-AAAAATTTCTCCTCAATTTTTGGCT-AAATACCCATATTGATTTG
* * * * * *
1804 ATAAATATAAATATTTGAAGGAGTCTTGGTCTTGGTGCAGAAAATAATGCAAAACTAAGTCGGGG
1 ATAAATATAAATATTTCAAGGAGTCTTGGTCTCGGCGCAAAAAATAATGAAAAACTAAGCCGGGG
* *
1869 CCCAGAAACGCGTTTTTGGCCAAAAACCGTAATGATTAGAATACGATTCTAGCTTAGATTTTGCA
66 CCCAGAAACGCGTTTTTGGCCAAAAACCGTAATGATTAGAACACGATTCCAGCTTAGATTTTGCA
1934 GAAAATGACTCGAAAAATTTCTCCTCAATTTTTGGCTAAATACCCATA
131 GAAAATGACTCGAAAAATTTCTCCTCAATTTTTGGCTAAATACCCATA
1982 AAATATATAT
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
186 11 0.07
187 26 0.16
188 124 0.77
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (186 bp):
ATAAATATAAATATTTCAAGGAGTCTTGGTCTCGGCGCAAAAAATAATGAAAAACTAAGCCGGGG
CCCAGAAACGCGTTTTTGGCCAAAAACCGTAATGATTAGAACACGATTCCAGCTTAGATTTTGCA
GAAAATGACTCGAAAAATTTCTCCTCAATTTTTGGCTAAATACCCATATTGATTTG
Done.