Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021482.1 Corchorus olitorius cultivar O-4 contig21515, 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: 4058
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Found at i:1770 original size:647 final size:644
Alignment explanation
Indices: 470--2268 Score: 1617
Period size: 647 Copynumber: 2.7 Consensus size: 644
460 AGTTGACCTG
* * *
470 AAATATTTTTTTTCTCAATTTTTAG-CCACAATACTCATAAAATATATATAATTGAA-TGCCAAA
1 AAAT-TTTTTTTTCTCAATTTTTAGTCAAAAATACTCATAAAATATATATAATTCAACT-CCAAA
* *
533 AAAATTGGAGGACTTTTCACACTTTTAATATCATTCTTTCATA-TTTTCTGAATTAATTTCTAAT
64 AATATTGGAGGACTTTTCACACTTTTAATATCGTT-TTTCATATTTTTCTGAATTAATTTCTAAT
* * *
597 TAAATCGAAACAAGATTCAGATACTCATAAAAACAAATTCTTAAATCCAATGTAGCTAAGATTTG
128 TAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATACTTAAATCCAATGTGGCTAAGATTTG
* * * * *
662 ATTAGATGAATGTAGATATCTCAA-AGAGTCTTGACGCCGAAAATCATGGAAAACTTAGCAGGGG
193 ATTAGATGAATATAGATATTTCAAGA-AGTCTTGACGCCAAAAATCATGCAAAACTGAGCAGGGG
* * * *
726 CCACAAGATGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAATATTTTGCA
257 CCACAAGATGCGTTTTTAGCAAAAAACCGTGACGATTAGTACACGATTTCGGCTAAAATTTTGCA
** * *
791 AAATTTTCCCGAAAGTTATTTCCTCAATTTATAGCCACAATAATCATAAAAATTATATAATTGAA
322 AAATTGACCCAAAAATTATTTCCTCAATTTATAGCCACAATAATCATAAAAATTATATAATTGAA
* ** *
856 CGCCAAAAACATTGAAAGGTTTTTCATGCTTCTAATATCGTTTTTCCTATTATTTTCCGAATTAA
387 CGCCAAAAACATTGAAAGGCTTTTCACACTTCTAATATCGTTTTTCATATTATTTTCCGAATTAA
** * * * *
921 TTTATAATTAAACCAAAACGTGATTCAGATGATTGTTTTACAAATCCTTAAATCCAATGTAGCTG
452 TTTATAATTAAACCAAAACAAGATTCAGATGATCGTATAACAAATCCTTAAATCCAATGTAGATG
** * *
986 AGTTTTGGTTAGATAAATATAGATAGTTCAAGGAGTCTCGCCACCAAAAATCATATAACACTGAA
517 AAATTTGATTAGATAAATATAGATAGTTCAAGGAGTCTCGCCACCAAAAATCATACAACACTGAA
** * * *
1051 CTGGGGTCCCGGAACGCTCTTTTAGCCAAAAACCGTGATTTCGGCTAATATTTTGCAAAAATTGA
582 CCAGGGTCCCGGAACACTCTTTTAGCCAAAAACCGTGA-TTC-G--AATATATTACAAAAATTGA
1116 CC
643 CC
1118 AAATTTTTTTTTCTCAATTTTT-GTCAAAAATACTCATAAAATATATATAATTCAACTCCAAAAA
1 AAATTTTTTTTTCTCAATTTTTAGTCAAAAATACTCATAAAATATATATAATTCAACTCCAAAAA
*
1182 TATTGGAGGACTTTTCACACTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTTTAATTAA
66 TATTGGAGGACTTTTCACACTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAA
* **
1247 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATGTAATGTGGCTAAGATTTGATT
131 ATCGAAACAAGATTCAGATGCTCATAAAAACAAATACTTAAATCCAATGTGGCTAAGATTTGATT
* ** * * *
1312 AAATGAATATAGATATTTCAAGAAGTCTCAACGCCAAAAATCATGCAAAACTGAGCCGTGGCCTC
196 AGATGAATATAGATATTTCAAGAAGTCTTGACGCCAAAAATCATGCAAAACTGAGCAGGGGCCAC
* * * *
1377 GAA-ATGCGTTTTTAGCAAAATAACCGTGACGTTTAGTACGCTATTTTGG-TAAAAATTTTGCAA
261 -AAGATGCGTTTTTAGCAAAA-AACCGTGACGATTAGTACACGATTTCGGCT-AAAATTTTGCAA
* * * *
1440 CAATTGACCCAAAAATT-TTTCCCTCAATTTTTGGCTA-AATTAATCAT-GAAATATATATAATT
323 -AATTGACCCAAAAATTATTT-CCTCAATTTATAGCCACAA-TAATCATAAAAAT-TATATAA--
* ** ** * *
1502 TTTTTAGTGCCAAAAGGATTG-GAGGACTTTTCACACATT-TCATATCGTTTTTCATATT-TTTT
382 --TTGAACGCCAAAAACATTGAAAGG-CTTTTCACAC-TTCTAATATCGTTTTTCATATTATTTT
* * * * * *
1564 CTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAATAACAAATCCTTAAATGC
443 CCGAATTAATTTATAATTAAACCAAAACAAGATTCAGATGATCGT-ATAACAAATCCTTAAATCC
* * * * * **
1629 AATGTGGATGAAATTTGATTAGATAAATATGGATA-TCTCAAGGATTCTTGGCGTCAAAAATCAT
507 AATGTAGATGAAATTTGATTAGATAAATATAGATAGT-TCAAGGAGTCTCGCCACCAAAAATCAT
* * * *
1693 GCAA-AGCTGACCCAGGGTCCTGGAACACGT-TTTTAGGCAAAAACCGTGA-T-G-AT-TATTAC
571 ACAACA-CTGAACCAGGGTCCCGGAACAC-TCTTTTAGCCAAAAACCGTGATTCGAATATATTAC
** * *
1752 ATGATTTCGGCTC
634 AAAAATT-GAC-C
* ** *
1765 AAATTTTGCAAAAATTGGCCCGAAAGATATTTCCTCAAGTCTTGGATAAAATACTCAATAAAAAA
1 AAATTTT------TTTTTCTC---A-AT-TTT--T--AGTC----A-AAAATACTC-AT--AAAA
* * * ** * * * *
1830 TTATATATAATTCAACGCTAAAAATATTGAAGGGTTTTTTTACGCTTCTAGTATCGATTTTTC-T
43 -TATATATAATTCAACTCCAAAAATATTGGA-GGACTTTTCACACTTTTAATATCG-TTTTTCAT
* * *
1894 ACTTTTT-TCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCATAAAAAGAAATCC
105 A-TTTTTCT-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATAC
* * * * * *
1958 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGAGTCTTGTCACCAA
168 TTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTTGACGCCAA
* * * * * **** *
2023 AAATCATGCAAAACTGACCCGGGACGCAGAACA--CGTTTTTAGCAAAAAA-AAAAAC-CTTAGT
233 AAATCATGCAAAACTGAGCAGGGGC-CACAAGATGCGTTTTTAGCAAAAAACCGTGACGATTAGT
** * * * *
2084 ACACGATTTCATCTTATATTTTGCAAATATTGACCCGAAATATT-TTTCCTCAATAT-TAGCCAC
297 ACACGATTTCGGCTAAAATTTTGCAAA-ATTGACCC-AAAAATTATTTCCTCAATTTATAGCCAC
* * * * * *
2147 GATACTCAT-AAAATATATATAATTCAACGGCAAAAGA-ATTGAAGGGCTTTTCACGCTTCTAAT
360 AATAATCATAAAAAT-TATATAATTGAACGCCAAAA-ACATTGAAAGGCTTTTCACACTTCTAAT
* * * * * *
2210 ATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGA-TCAGATG
423 ATCGTTTTTCATATTATTTTCCGAATTAATTTATAATTAAACCAAAACAAGATTCAGATG
2269 CTTGTAAAAA
Statistics
Matches: 938, Mismatches: 151, Indels: 107
0.78 0.13 0.09
Matches are distributed among these distances:
645 8 0.01
646 12 0.01
647 243 0.26
648 50 0.05
649 40 0.04
651 1 0.00
652 46 0.05
653 146 0.16
654 3 0.00
656 1 0.00
657 2 0.00
658 3 0.00
660 1 0.00
663 3 0.00
664 2 0.00
665 46 0.05
666 36 0.04
667 1 0.00
668 9 0.01
669 25 0.03
670 39 0.04
671 16 0.02
672 29 0.03
673 35 0.04
674 139 0.15
675 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (644 bp):
AAATTTTTTTTTCTCAATTTTTAGTCAAAAATACTCATAAAATATATATAATTCAACTCCAAAAA
TATTGGAGGACTTTTCACACTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAA
ATCGAAACAAGATTCAGATGCTCATAAAAACAAATACTTAAATCCAATGTGGCTAAGATTTGATT
AGATGAATATAGATATTTCAAGAAGTCTTGACGCCAAAAATCATGCAAAACTGAGCAGGGGCCAC
AAGATGCGTTTTTAGCAAAAAACCGTGACGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAT
TGACCCAAAAATTATTTCCTCAATTTATAGCCACAATAATCATAAAAATTATATAATTGAACGCC
AAAAACATTGAAAGGCTTTTCACACTTCTAATATCGTTTTTCATATTATTTTCCGAATTAATTTA
TAATTAAACCAAAACAAGATTCAGATGATCGTATAACAAATCCTTAAATCCAATGTAGATGAAAT
TTGATTAGATAAATATAGATAGTTCAAGGAGTCTCGCCACCAAAAATCATACAACACTGAACCAG
GGTCCCGGAACACTCTTTTAGCCAAAAACCGTGATTCGAATATATTACAAAAATTGACC
Found at i:1909 original size:337 final size:328
Alignment explanation
Indices: 431--2614 Score: 1723
Period size: 337 Copynumber: 6.7 Consensus size: 328
421 CACAGTGATG
* * ** * * * * *
431 GTACACGATTTCGGCTAAAAGTTTATAAAAGTTGACCTGAAATATTTTTTTTCTCAATTTTTAGC
1 GTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA--TATTTCCTCAATTTTTAGC
* * * * * * *
496 CACAATACTCAT-AAAATATATATAATTGAATGCCAAAAAAATTGGAGGACTTTTCACACTTTTA
64 CAAAATACTCATAAAAATATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACACTTCTA
* * * *
560 ATATCATTCTTTC-ATATTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCA
129 ATATCGTT-TTTCTATTTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * * * *
624 TAAAAACAAATTCTTAAATCCAATGTAGCT-AAGATTTGATTAGATGAATGTAGATATCTCAAAG
192 TAAAAACAAATCCTTAAATGCAATGTGGCTGAA-ATTTGATTAGATGAATATAGATATTTCAAGG
* * * * ** ** *
688 AGTCTTGACGCCGAAAATCATGGAAAACTTAGCAGGGGCC-ACAAGATGCGTTTTTAGCCAAAAA
256 AGTCTCGACGCCAAAAATCATGCAAAACTGA-CCCGGGCCTGGAACA--CGTTTTTAG-CAAAAA
752 CCGTGATGATTA
317 CCGTGATGATTA
* * * ** * *
764 TTACACGATTTCGGCTAATATTTTGC-AAAATTTTCCCGAAAGTTATTTCCTCAATTTATAGCCA
1 GTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCA
* * * * * * **
828 CAATAATCATAAAAAT-TATATAATTGAACGCCAAAAACATTGAAAGGTTTTTCATGCTTCTAAT
66 AAATACTCATAAAAATATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACACTTCTAAT
* * * ** * *
892 ATCGTTTTTCCTATTATTTTCCGAATTAATTTATAATTAAACCAAAACGTGATTCAGATGATTGT
131 ATCGTTTTT-CTATT-TTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
*** * * ** * * *
957 -TTTACAAATCCTTAAATCCAATGTAGCTGAGTTTTGGTTAGATAAATATAGATAGTTCAAGGAG
193 AAAAACAAATCCTTAAATGCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAG
* * ** * ** * *
1021 TCTCGCCACCAAAAATCATATAACACTGAACTGGGGTCCCGGAACGC-TCTTTTAGCCAAAAACC
258 TCTCGACGCCAAAAATCATGCAAAACTG-ACCCGGG-CCTGGAACACGT-TTTTAG-CAAAAACC
1085 ----------
319 GTGATGATTA
* ** * *
1085 G----TGATTTCGGCTAATATTTTGCAAAAATTGA-CC-AAATTTTTTTTTCTCAATTTTT-GTC
1 GTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-GATATTTCCTCAATTTTTAG-C
* * * * *
1143 AAAAATACTCAT-AAAATATATATAATTCAACTCCAAAAATATTGGAGGACTTTTCACACTTTTA
64 CAAAATACTCATAAAAATATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACACTTCTA
*
1207 ATATCGTTTTTC-ATATTTTTCTGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCG
129 ATATCGTTTTTCTAT-TTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * *
1271 TAAAAACAAATACTTAAATGTAATGTGGCT-AAGATTTGATTAAATGAATATAGATATTTCAAGA
192 TAAAAACAAATCCTTAAATGCAATGTGGCTGAA-ATTTGATTAGATGAATATAGATATTTCAAGG
* * *
1335 AGTCTCAACGCCAAAAATCATGCAAAACTGAGCCGTGGCCTCGAA-ATGCGTTTTTAGCAAAATA
256 AGTCTCGACGCCAAAAATCATGCAAAACTGACCCG-GGCCTGGAACA--CGTTTTTAGC-AAA-A
* *
1399 ACCGTGACGTTTA
316 ACCGTGATGATTA
* * * * * *
1412 GTACGCT-ATTTTGG-TAAAAATTTTGCAACAATTGACCC-AAAAATTTTTCCCTCAATTTTTGG
1 GTAC-ATGATTTCGGCT-AAAATTTTGCAAAAATTGACCCGAAAGATATTT-CCTCAATTTTTAG
* * * * * ** ** * *
1474 CTAAATTAATCAT-GAAATATATATAATTTTTTTAGTGCCAAAAGGATTGGAGGACTTTTCACAC
63 CCAAAATACTCATAAAAATATATATAA----TTCAACGCCAAAAATATTGAAGGGCTTTTCACAC
*
1538 ATT-TCATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
124 -TTCTAATATCGTTTTTC-TATTTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * * * *
1602 TGCTCGTAATAACAAATCCTTAAATGCAATGTGGATGAAATTTGATTAGATAAATATGGATATCT
186 TGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTT
* * * * *
1667 CAAGGATTCTTGGCGTCAAAAATCATGCAAAGCTGACCCAGGGTCCTGGAACACGTTTTTAGGCA
251 CAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGACCC-GGG-CCTGGAACACGTTTTTA-GCA
1732 AAAACCGTGATGATTA
313 AAAACCGTGATGATTA
* * * * * * **
1748 TTACATGATTTCGGCTCAAATTTTGCAAAAATTGGCCCGAAAGATATTTCCTCAAGTCTTGGATA
1 GTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCA
* * * *
1813 AAATACTCAATAAAAAATTATATATAATTCAACGCTAAAAATATTGAAGGGTTTTTTTACGCTTC
66 AAATACTC-AT-AAAAA-TATATATAATTCAACGCCAAAAATATTGAAGGG-CTTTTCACACTTC
* *
1878 TAGTATCGATTTTTCTACTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCT
127 TAATATCG-TTTTTCTA-TTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
* * * * * *
1943 CATAAAAAGAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAG
190 CGTAAAAACAAATCCTTAAATGCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAG
* * * *
2008 GAGTCTTGTCACCAAAAATCATGCAAAACTGACCCGGGACGC-AGAACACGTTTTTAGCAAAAA-
255 GAGTCTCGACGCCAAAAATCATGCAAAACTGACCCGGG-C-CTGGAACACGTTTTTAGCAAAAAC
**** ***
2071 AAAAAACCTTA
318 CGTGATGATTA
* ** * * * * * *
2082 GTACACGATTTCATCTTATATTTTGCAAATATTGACCCGAAATATTTTTCCTCAA-TATTAGCCA
1 GTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCA
** * *
2146 CGATACTCAT-AAAATATATATAATTCAACGGCAAAAGA-ATTGAAGGGCTTTTCACGCTTCTAA
66 AAATACTCATAAAAATATATATAATTCAACGCCAAAA-ATATTGAAGGGCTTTTCACACTTCTAA
* *
2209 TATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACATGA-TCAGATGCTTG
130 TATCGTTTTT-CTA-TTTTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * * **
2273 T---AA-AAA--C---AATG----GT--TTGGAA-TTGGTTAGATGAATATATATATTTTGA-GA
192 TAAAAACAAATCCTTAAATGCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGA
* * * * * *
2321 -TCTCGAAGCAAAAAAACATGCAAAACTGAACCGGGCCCTGGAACGCGTTTTTAGCCAAAAATCG
257 GTCTCGACGCCAAAAATCATGCAAAACTGACCCGGG-CCTGGAACACGTTTTTAG-CAAAAACCG
*
2385 TTATGATTA
320 TGATGATTA
* * * *
2394 TTACAGGATTTCGGTTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTGAATTTTTAGCCA
1 GTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCA
* *
2459 CAATACTCATAAAAA-ATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACACTTTTAAT
66 AAATACTCATAAAAATATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACACTTCTAAT
* *
2523 ATCGTTTTTCATATTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTA
131 ATCGTTTTTC-TA-TTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* *
2588 AAAACAAATCCTTAAATTCTATGTGGC
194 AAAACAAATCCTTAAATGCAATGTGGC
2615 GTTGAATTAA
Statistics
Matches: 1481, Mismatches: 277, Indels: 191
0.76 0.14 0.10
Matches are distributed among these distances:
309 1 0.00
310 42 0.03
311 8 0.01
312 102 0.07
313 92 0.06
314 5 0.00
315 53 0.04
316 95 0.06
317 101 0.07
318 6 0.00
319 4 0.00
322 4 0.00
324 3 0.00
325 2 0.00
326 2 0.00
327 6 0.00
328 36 0.02
329 62 0.04
330 79 0.05
331 126 0.09
332 93 0.06
333 36 0.02
334 49 0.03
335 8 0.01
336 135 0.09
337 292 0.20
338 26 0.02
339 4 0.00
340 9 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (328 bp):
GTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCA
AAATACTCATAAAAATATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACACTTCTAAT
ATCGTTTTTCTATTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
AACAAATCCTTAAATGCAATGTGGCTGAAATTTGATTAGATGAATATAGATATTTCAAGGAGTCT
CGACGCCAAAAATCATGCAAAACTGACCCGGGCCTGGAACACGTTTTTAGCAAAAACCGTGATGA
TTA
Found at i:3725 original size:13 final size:13
Alignment explanation
Indices: 3692--3744 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
3682 GCACCCAAAA
*
3692 CATTTAT-TAAAA
1 CATTTATATAAAG
3704 CATTT-TATAAAG
1 CATTTATATAAAG
3716 CATTTATATAAAG
1 CATTTATATAAAG
*
3729 CAGTTATA-AAA-
1 CATTTATATAAAG
3740 CATTT
1 CATTT
3745 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Done.