Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012377.1 Corchorus olitorius cultivar O-4 contig12410, 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: 7065
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:898 original size:324 final size:325
Alignment explanation
Indices: 138--951 Score: 873
Period size: 332 Copynumber: 2.5 Consensus size: 325
128 TGAAATATCT
* * * *
138 AAATCATGCACTAACCATCACAGTTGTTTTTGGCTAAAAACGCATTTCAGGG-CACCGGCTTAGT
1 AAATCGTGTACTAACCATCACAG--GTTTTCGGCTAAAAACGCGTTT-AGGGTCACCGGCTTAGT
* * * *
202 TTTGCATGATTTTAGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAATTC-AATTTAAGCC
63 TTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAA-CCAAATCTAAGCC
* * *
266 ACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCAAGTTTCGATTTAATTAGAAATAAA
127 ACATTGGATTTAAGGATTTGTTTTTACGAGAATCTCAATCAAGTTTCGATTTAATTAGAAATAAA
* *
331 TTCGGGAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAAACCCTTCAATATTTTCGACGTTGA
192 TTC-GGAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAAACCCGTCAATATTTTCGACATTGA
* * * ** *
396 ATTATATATTTTTTATGAGTATTCTGGCAAAATTTGAGGAAAAATTTTTTCGGTCAATTTTTGAA
256 ATTATATATTTTTTATAAATATTCTCGCAAAATTTGAGGAAAAAACTCTTCGGTCAA----TG--
461 AAATTTTAGCCG
315 -AATTTTAGCCG
* * ** * *
473 AAATCGTGTACTAACCATCACGGGTTTTC-ACTAAAAACGCGTTCCGGTGT-GCCGGCTCAGTTT
1 AAATCGTGTACTAACCATCACAGGTTTTCGGCTAAAAACGCGTTTAGG-GTCACCGGCTTAGTTT
* * * * * * *
536 TGCAAGAATTTTGGCACAAAGGCTCCTT-AAATTATCTATATTCAT-TGAACCAAATGTCAGCCG
65 TGCATGATTTTTGGCAGAAAGACTCCTTGAAA-TATCTATATTCATCT-AACCAAATCTAAGCCA
* * ** * *
599 CATTGGATATAAGGATTTGTATTTACGAGAATCTCAATCTTGTTTTGATTTAATTAGAAATTAAT
128 CATTGGATTTAAGGATTTGTTTTTACGAGAATCTCAATCAAGTTTCGATTTAATTAGAAATAAAT
* * * * * *
664 TC-GAAAACAAATGGAAAAACGATATTAGAAGGGTG-AAAAGCCCGTCAATCTTTTTGGCATTGA
193 TCGGAAAA-AAA-AGAAAAACGATATTAGAAGCGTGAAAAAACCCGTCAATATTTTCGACATTGA
*
727 ATTATATATTTTTTCTAAATATT-TCGCAAAAAAAATTTGA-GAAAAAACTCTTCGGGTC-A-G-
256 ATTATATATTTTTTATAAATATTCTCGC----AAAATTTGAGGAAAAAACTCTTC-GGTCAATGA
*
787 TTTTTAGCCG
316 ATTTTAGCCG
* * **
797 AAATCGTGTACTAACCATCAC-GGTTTTCGGCTAAAAACGCGTTTTGGGTCCCCGATTTAGTTTT
1 AAATCGTGTACTAACCATCACAGGTTTTCGGCTAAAAACGCGTTTAGGGTCACCGGCTTAGTTTT
*
861 GCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTAAGCCACAA
66 GCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTAAGCCACAT
926 TGGATTTAAGGATTTGTTTTTACGAG
131 TGGATTTAAGGATTTGTTTTTACGAG
952 CATTTGAAAA
Statistics
Matches: 401, Mismatches: 62, Indels: 43
0.79 0.12 0.08
Matches are distributed among these distances:
323 9 0.02
324 130 0.32
325 4 0.01
328 1 0.00
330 8 0.02
331 52 0.13
332 148 0.37
333 16 0.04
334 13 0.03
335 20 0.05
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (325 bp):
AAATCGTGTACTAACCATCACAGGTTTTCGGCTAAAAACGCGTTTAGGGTCACCGGCTTAGTTTT
GCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTAAGCCACAT
TGGATTTAAGGATTTGTTTTTACGAGAATCTCAATCAAGTTTCGATTTAATTAGAAATAAATTCG
GAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAAACCCGTCAATATTTTCGACATTGAATTAT
ATATTTTTTATAAATATTCTCGCAAAATTTGAGGAAAAAACTCTTCGGTCAATGAATTTTAGCCG
Found at i:2022 original size:863 final size:863
Alignment explanation
Indices: 138--3345 Score: 5202
Period size: 864 Copynumber: 3.7 Consensus size: 863
128 TGAAATATCT
*
138 AAATCATGCACTAACCATCACAGTTGTTTTTGGCTAAAAACGCATTTCAGGGCACCGGCTTAGTT
1 AAATCGTGCACTAACCATCACAGTTGTTTTTGGCTAAAAACGCATTTCAGGGCACCGGCTTAGTT
203 TTGCATGATTTTAGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAATTCAATTTAAGCCAC
66 TTGCATGATTTTAGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAATTCAATTTAAGCCAC
268 ATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCAAGTTTCGATTTAATTAGAAATAAATT
131 ATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCAAGTTTCGATTTAATTAGAAATAAATT
* *
333 C-GGGAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAAACCCTTCAATATTTTCGACGTTGAA
196 CGGGGAAAAAAAAGAAAAACGATATTAGAAGCGTG-AAAAACCCTTCAATATTTTTGGCGTTGAA
* *
397 TTATATATTTTTTATGAGTATTCTGGC-AAAATTTGAGGAAA-AATTTTTTCGGTCAATTTTTGA
260 TTATATATTTTTTATGAGTATTCTGGCAAAAAATTGAGGAAATACTTTTTTCGGTCAATTTTTGA
**
460 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTCACTAAAAACGCGTTCCGGTGTGC
325 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTCCGGTGTGC
* * *
525 CGGCTCAGTTTTGCAAGAATTTTGGCACAAAGGCTCCTTAAATTATCTATATTCATTGAACCAAA
390 CGGCTCAATTTTGCAAGATTTTTGGCACAAAGGCTCCTTAAATTATCTATATTCATCGAACCAAA
*
590 TGTCAGCCGCATTGGATATAAGGATTTGTATTTACGAGAATCTCAATCTTGTTTTGATTTAATTA
455 TGTCAGCCACATTGGATATAAGGATTTGTATTTACGAGAATCTCAATCTTGTTTTGATTTAATTA
*
655 GAAATTAATTCGAAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAGCCCGTCAATCTTTTTG
520 GAAATTAATTCGAAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAACCCGTCAATCTTTTTG
720 GCATTGAATTATATATTTTTTCTAAATATTTCGCAAAAAAAATTTGAGAAAAAACTCTTCGGGTC
585 GCATTGAATTATATATTTTTTCTAAATATTTCGCAAAAAAAATTTGAGAAAAAACTCTTC-GGTC
785 AGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAAACGCGTTTTGGGTCCCC
649 AGTTTTTAGCCGAAATCGTG---T-ACCATCACGGTTTTCGGCTAAAAACGCGTTTTGGGTCCCC
850 GATTTAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
710 GATTTAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
915 CTAAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAAAATTGAGGAAAATTTTTCGG
775 CTAAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAAAATTGAGGAAAATTTTTCGG
980 GTCAGTTTTTCGAAATTTTAATCG
840 GTCAGTTTTTCGAAATTTTAATCG
*
1004 AAATCGTGCACTAACCATCACAGTTGTTTTTGGCTAAAAACTCATTTCAGGGCACCGGCTTAGTT
1 AAATCGTGCACTAACCATCACAGTTGTTTTTGGCTAAAAACGCATTTCAGGGCACCGGCTTAGTT
1069 TTGCATGATTTTAGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAATTCAATTTAAGCCAC
66 TTGCATGATTTTAGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAATTCAATTTAAGCCAC
*
1134 ATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCAAGTTTCGATTTGATTAGAAATAAATT
131 ATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCAAGTTTCGATTTAATTAGAAATAAATT
* * *
1199 CGGGGTAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCATTCAATGTTTTTGGCGTTGAA
196 CGGGG-AAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGAA
* * * *
1264 ATATATATTTTTTATGATTATTCTGGCAAAAAATTGAGGAAATACTATTTT-GGTCAATTTTTGC
260 TTATATATTTTTTATGAGTATTCTGGCAAAAAATTGAGGAAATACTTTTTTCGGTCAATTTTTGA
*
1328 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTCCGGAGTGC
325 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTCCGGTGTGC
* *
1393 CGGCTCAATTTTGCAAGATTTTCGGCACAAAGGCTCCTTAAAGTATCTATATTCATCGAACCAAA
390 CGGCTCAATTTTGCAAGATTTTTGGCACAAAGGCTCCTTAAATTATCTATATTCATCGAACCAAA
*
1458 TGTCAGCCACATTGGATATAAGGATTTGTATTTACAAGAATCTCAATCTTGTTTTGATTTAATTA
455 TGTCAGCCACATTGGATATAAGGATTTGTATTTACGAGAATCTCAATCTTGTTTTGATTTAATTA
*
1523 GAAATTAATTCGAAAATAAATGGAAAAACGATATTAGAAGGGTGAAAAACCCGTCAATCTTTTTG
520 GAAATTAATTCGAAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAACCCGTCAATCTTTTTG
* *
1588 GCATTTAATTATATATTTTTTCTAAATATTTCACAAAAAAAATTTG-GAAAAAACTCTTCAGGTC
585 GCATTGAATTATATATTTTTTCTAAATATTTCGCAAAAAAAATTTGAGAAAAAACTCTTC-GGTC
* * *
1652 AGTTTTTAGCCGAAACCGTGTACCATCACGATTTTCGGTTAAAAACGCGTTTTGGGTCCCCGATT
649 AGTTTTTAGCCGAAATCGTGTACCATCACGGTTTTCGGCTAAAAACGCGTTTTGGGTCCCCGATT
1717 TAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTAA
714 TAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTAA
1782 GCCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAAAATTGAGGAAAATTTTTCGGGTCA
779 GCCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAAAATTGAGGAAAATTTTTCGGGTCA
1847 GTTTTTCGAAATTTTAATCG
844 GTTTTTCGAAATTTTAATCG
* *
1867 AAATCGTGCACTAACCATCACAGTTTTTTTTGGCTAAAAACGCGTTTCAGGGCACCGGCTTAGTT
1 AAATCGTGCACTAACCATCACAGTTGTTTTTGGCTAAAAACGCATTTCAGGGCACCGGCTTAGTT
1932 TTGCATGATTTTAGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAATTCAATTTAAGCCAC
66 TTGCATGATTTTAGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAATTCAATTTAAGCCAC
1997 ATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCAAGTTTCGATTTAATTAGAAATAAATT
131 ATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCAAGTTTCGATTTAATTAGAAATAAATT
*
2062 CGGGAAAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGAA
196 CGGGGAAAAAAAA-GAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGAA
* **
2127 TTATTTATTTTTTATGAGTATTCTGGCAAAAAAATTGAGGAAA-AAGTTTTTCGGTCAATTTTTG
260 TTATATATTTTTTATGAGTATTCTGGC-AAAAAATTGAGGAAATACTTTTTTCGGTCAATTTTTG
*
2191 AAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCATTCCGGTGTG
324 AAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTCCGGTGTG
2256 CCGGCTCAATTTTGCAAGATTTTTGGCACAAAGGCTCCTTAAATTATCTATATTCATCGAACCAA
389 CCGGCTCAATTTTGCAAGATTTTTGGCACAAAGGCTCCTTAAATTATCTATATTCATCGAACCAA
* *
2321 ATGTCAGTCACATTGGATATAAGGATTTGTATTTACGAGAATCCCAATCTTGTTTTGATTTAATT
454 ATGTCAGCCACATTGGATATAAGGATTTGTATTTACGAGAATCTCAATCTTGTTTTGATTTAATT
* * *
2386 AGAAATTAATTCGAAAACAAATGGAAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTA
519 AGAAATTAATTCGAAAACAAATGG-AAAAACGATATTAGAAGGGTGAAAAACCCGTCAATCTTTT
* *
2451 TGGCATTGAATTATATATTTTTTCTAAATATTTCGC--AAAAAATTTGAGAAAAAAAATTTTCGG
583 TGGCATTGAATTATATATTTTTTCTAAATATTTCGCAAAAAAAATTTGAG-AAAAAACTCTTCGG
* * * *
2514 ATCAGTTTTTAACCGAAATCGTGTACCATCACGGTTTTCGGGTAAAAACGCATTTCGGGTCCCCG
647 -TCAGTTTTTAGCCGAAATCGTGTACCATCACGGTTTTCGGCTAAAAACGCGTTTTGGGTCCCCG
2579 ATTTAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATC
711 ATTTAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATC
*
2644 TAAGCCACAATGAATTTAAGGATTTGTTTTTACGAGCATTTGAAAATTGAGGAAAATTTTTCGGG
776 TAAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAAAATTGAGGAAAATTTTTCGGG
*
2709 TCAGTTTTTCGAAATTTTAACCG
841 TCAGTTTTTCGAAATTTTAATCG
* * * * * * *
2732 AAATTGTGCACTAACCATCACGGTT-TTTTTGGCTAAAAAC-TAGTTTCGGGGCCCCGACTTTGT
1 AAATCGTGCACTAACCATCACAGTTGTTTTTGGCTAAAAACGCA-TTTCAGGGCACCGGCTTAGT
* * *
2795 TTTGCATGATTTTAGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAATTAAATTTCAGGCA
65 TTTGCATGATTTTAGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAATTCAATTTAAGCCA
* * *
2860 CATTGAATTTAAGAATTTGTTTTTACGAGCATCGGAATCAAGTTTCGATTTGATTAGAAATAAAT
130 CATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCAAGTTTCGATTTAATTAGAAATAAAT
* * *
2925 TCGGGGGAAAAAAAAAAGAAAACGATATTAGAAACGTGAAAAACCCTTCAATGTTTTTGGCGTTG
195 TC-GGGGAAAAAAAAGA-AAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTG
*
2990 AATTGTATATTTTTTATGAGTATTCTGGCAAAAAATTGAGGAAATACTTTTTT-GGTCAATTTTT
258 AATTATATATTTTTTATGAGTATTCTGGCAAAAAATTGAGGAAATACTTTTTTCGGTCAATTTTT
* * *
3054 GCAAAATTTTAGCCGAAATCGTGTACTAACCATCA-TGGTTTTCGGCTAAAAACGCGTTTCAGGT
323 GAAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTT-GGCTAAAAACGCG-TTCCGGT
** ** * * * * * *
3118 -CCCCGATTTAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA-TATCTATATTCATCTAA
386 GTGCCGGCTCAATTTTGCAAGATTTTTGGCACAAAGGCTCCTT-AAATTATCTATATTCATCGAA
* * * * * * * * *
3181 CCAAATCTAAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTT
450 CCAAATGTCAGCCACATTGGATATAAGGATTTGTATTTACGAGAATCTCAATCTTGTTTTGATTT
* * * *
3246 AATTAACTAGAAATAAATTCGGAAAAGAAAAAAGGAAAAACGATATTAGAAGTGTGAAAAACCCG
515 AA-T---TAGAAATTAATTC-G-AAA-ACAAATGGAAAAACGATATTAGAAGGGTGAAAAACCCG
* * * *
3311 TGAATTTTTTTGCCGTTGAATTATATATTTTTTCT
573 TCAATCTTTTTGGCATTGAATTATATATTTTTTCT
3346 GAGTATTGTG
Statistics
Matches: 2190, Mismatches: 127, Indels: 46
0.93 0.05 0.02
Matches are distributed among these distances:
862 7 0.00
863 481 0.22
864 576 0.26
865 412 0.19
866 193 0.09
867 89 0.04
868 358 0.16
869 7 0.00
870 61 0.03
871 6 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (863 bp):
AAATCGTGCACTAACCATCACAGTTGTTTTTGGCTAAAAACGCATTTCAGGGCACCGGCTTAGTT
TTGCATGATTTTAGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAATTCAATTTAAGCCAC
ATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCAAGTTTCGATTTAATTAGAAATAAATT
CGGGGAAAAAAAAGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGAAT
TATATATTTTTTATGAGTATTCTGGCAAAAAATTGAGGAAATACTTTTTTCGGTCAATTTTTGAA
AAATTTTAGCCGAAATCGTGTACTAACCATCACGGGTTTTGGCTAAAAACGCGTTCCGGTGTGCC
GGCTCAATTTTGCAAGATTTTTGGCACAAAGGCTCCTTAAATTATCTATATTCATCGAACCAAAT
GTCAGCCACATTGGATATAAGGATTTGTATTTACGAGAATCTCAATCTTGTTTTGATTTAATTAG
AAATTAATTCGAAAACAAATGGAAAAACGATATTAGAAGGGTGAAAAACCCGTCAATCTTTTTGG
CATTGAATTATATATTTTTTCTAAATATTTCGCAAAAAAAATTTGAGAAAAAACTCTTCGGTCAG
TTTTTAGCCGAAATCGTGTACCATCACGGTTTTCGGCTAAAAACGCGTTTTGGGTCCCCGATTTA
GTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTAAGC
CACAATGGATTTAAGGATTTGTTTTTACGAGCATTTGAAAATTGAGGAAAATTTTTCGGGTCAGT
TTTTCGAAATTTTAATCG
Done.