Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019660.1 Corchorus olitorius cultivar O-4 contig19693, 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: 3069
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:852 original size:334 final size:331
Alignment explanation
Indices: 69--1073 Score: 1305
Period size: 334 Copynumber: 3.0 Consensus size: 331
59 ACCTCGGAAT
* *
69 GCGTTTTTAGTC--AAAAAACCGTGATGG---TACATGATTTCGGCTAAAATTTTGCAAAAATAG
1 GCGTTTTTAGCCAAAAAAAACCGTGATGGTTATACACGATTTCGGCTAAAATTTTGCAAAAAT-G
* * * * * *
129 ACCCGAAATATTTTTCCTCAATTTTTAGCCACAATACTCACAAAATATATATAATTGAACTCCAA
65 ACCCGAAA-AATTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCCAA
* *
194 AAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTCCATATTTTTCTGAATTAATTTTTAAT
129 AAAGATTGGAGGACTTTTCAGGCTTTTAATATCGTTTT-CATATTTTTCTGAATTAATTTCTAAT
* *
259 TAAATAAAAACAAAATTCAGATGCTCGTAAAAACAAATCATTAAATTCAAATGTGGCTGAGATTT
193 TAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATTCAAATGTGGCTGAGATTT
* * *
324 TAATAGATGAGTATAGATATTTCAAGGAGTCTCGGTGACAAAAATCATGCAAAACTAAGTCGGGG
258 GATTAGATGAGTATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAGTCGGGG
389 CCCCGAAAC
323 CCCCGAAAC
* ** * ** *
398 GCGATTTTAGCCAAAACCAA---TGATGGTTAGTACACGATTCCAACTTAAATTTTGCAGAAAAT
1 GCGTTTTTAGCCAAAAAAAACCGTGATGGTTA-TACACGATTTCGGCTAAAATTTTGCA-AAAAT
* *
460 GACCCGATAAATTTGTCCTCAATTTTTAGCTAAAATATTCATAAAATATATTTATAATTTAACGC
64 GACCCGAAAAATTT-TCCTCAATTTTTAGCTAAAATACTCATAAAATATA--TATAATTTAACGC
* * *
525 CAAAAATATTGGAGGACTTTTCAGGCTTTTAATACCGTTGTTCATATTTTTTTGAATTAATTTCT
126 CAAAAAGATTGGAGGACTTTTCAGGCTTTTAATATCGTT-TTCATATTTTTCTGAATTAATTTCT
* * * * * *
590 AATTAAATCGAAACAAGATTCAAATGCTCGTATAAACAAATCCTT-ATTTGC-AATGTGACTGAG
190 AATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATT-CAAATGTGGCTGAG
* * * *
653 ATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGATGCCAAAAATCATGCAAAACTGAGTC
254 ATTTGATTAGATGAGTATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAGTC
* * * *
718 TGAGCCCTGAAAT
319 GGGGCCCCGAAAC
*
731 GCGTTTTTA-CCAAAAAAAAACCGTGATGGTTACTACACGATTTTGGCTAAAATTTTGCACAAAA
1 GCGTTTTTAGCC-AAAAAAAACCGTGATGGTTA-TACACGATTTCGGCTAAAATTTTGCA-AAAA
* * *
795 TGACCCGAAAAATCTTTCTTCAATTTTTGGCTAAAATACTCATGAAATATATATAATTTAACGCC
63 TGACCCGAAAAAT-TTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCC
* * *
860 AAAAAGGTTGAAGGACTTTTC-GAGCTTTTAATATCATTTTTCATATTTTTCTGAATTAATTTCT
127 AAAAAGATTGGAGGACTTTTCAG-GCTTTTAATATC-GTTTTCATATTTTTCTGAATTAATTTCT
* *
924 AATTAAATCAAAACAAGATTCAGATGTTGGTAAAAACAAATCATTAAATTCAAATGTGGCTGAGA
190 AATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATTCAAATGTGGCTGAGA
* * *
989 TTTGATTAGATGAGTATAGATATTTCACGGAGTCTCGGCGCTAAAAATCATGCAAAACTAAGTCG
255 TTTGATTAGATGAGTATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAGTCG
1054 GGGCCCCGAAAC
320 GGGCCCCGAAAC
1066 GCGTTTTT
1 GCGTTTTT
1074 TGCAGAAAAT
Statistics
Matches: 574, Mismatches: 81, Indels: 36
0.83 0.12 0.05
Matches are distributed among these distances:
328 6 0.01
329 10 0.02
331 8 0.01
332 62 0.11
333 101 0.18
334 215 0.37
335 93 0.16
336 77 0.13
337 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (331 bp):
GCGTTTTTAGCCAAAAAAAACCGTGATGGTTATACACGATTTCGGCTAAAATTTTGCAAAAATGA
CCCGAAAAATTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTTAACGCCAAAA
AGATTGGAGGACTTTTCAGGCTTTTAATATCGTTTTCATATTTTTCTGAATTAATTTCTAATTAA
ATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATTCAAATGTGGCTGAGATTTGAT
TAGATGAGTATAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTAAGTCGGGGCCC
CGAAAC
Found at i:2131 original size:337 final size:331
Alignment explanation
Indices: 1414--3065 Score: 1487
Period size: 337 Copynumber: 4.9 Consensus size: 331
1404 AATTTTGCAA
* * * *
1414 ATTTGATTAGATGAGTATAGATATTTCACGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGTC
1 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCG-CAAAAATCATGCAAAACTGAGCC
* * * *
1479 GGGGCCCCGAAACGCGTTTTTTGCCAAAAACC-TGATGGTTAGTACACGATTCCGGCTTAAATTT
65 GAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTT
* * * *
1543 TGC-AGAAAATG-CCTCGAAAA-ATTTCTCCTCAATTTTTGGCTAAAATAGTCATAAAATATATA
130 TGCAAAAAAATGACCTCGAAAATTTTTCT-CTCAAATTTTGGCTAAAATACTCATAAAATATATA
* * * *
1605 TAATTTAACTCCAAAAAGATTGGA-GATTTTTTTCACGCTTTTAATATCGTTTTTCTTATTTTTC
194 TAATTTAACACCAAAAAGATTGAAGGA--CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTC
* * *
1669 TGAATTAATTTTTAATTAAATCTAAACAAGATTCAGATGCTCTTATAAACAAATCCTTAAATGCA
257 TGAATTAATTTCTAATTAAATC-AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCA
1734 ATGTGGCTGAG
321 ATGTGGCTGAG
**
1745 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAACGCCAAAAATCATGCAAAACTGAGCC
1 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCG-CAAAAATCATGCAAAACTGAGCC
* * *
1810 GAAGCCCCGAAACGCGTTTTTAGCAAAAAAAAAACCGTGATGGTTAGTTCACGATTTCGGCTAAA
65 GAGGCCCCGAAACGCGTTTTTAGC----CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * *
1875 ATTTTGCAAAAAAATGACGTGGAAAATTTTTCTC-CAAATTTTGGCTAAAATACTCATGAAATAT
126 ATTTTGCAAAAAAATGACCTCGAAAATTTTTCTCTCAAATTTTGGCTAAAATACTCATAAAATAT
* * *
1939 ATATTATTTAACACCAAAAAGGTTGAAGGACTTTTCGA-GCTTTTCATATCGTTTTTCATATTTT
191 ATATAATTTAACACCAAAAAGATTGAAGGACTTTTC-ACGCTTTTAATATCGTTTTTCATATTTT
*
2003 TCTGAATTAATTTCTAATTAAATCAAATCAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATT
255 TCTGAATTAATTTCTAATTAAATCAAA-CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATG
2068 CAAATGTGGCTGAG
319 C-AATGTGGCTGAG
* *
2082 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCTAAAAATCATGCAAAACTAAGCC
1 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGC-AAAAATCATGCAAAACTGAGCC
* * *
2147 AAGGCCCCGAAACGCGTTTTTAGCCAAAAA-C----T-G-T-G-ACACGATTTCAGCTTAAATTT
65 GAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTT
* * * **
2203 TGC-AGAAAATGACC-AGAAAATTTTCCCCTCGATTTTTGGCGAATTATTTTTCCTCAATATTTA
130 TGCAAAAAAATGACCTCGAAAATTTT----TC----TCT--C-AA--ATTTTGGCT-AA-A---A
* * * * * *
2266 GTCACAATTCTCATAAAAAAAATTATAATTCAACGCCAAAAAGATTGAAGGGCCTTTCACGCTTT
177 -T----A--CTCATAAAATATA-TATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTT
* * * * *
2331 TAATATCGTTTTTCTTATTTTTTCCGAACTAATTTCTAATTAAATCAAAACATGACTCAGATGCT
234 TAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATC-AAACAAGATTCAGATGCT
* *
2396 TGT---AA-AAA----T-AAT---A----GCTGTG
297 CGTAAAAACAAATCCTTAAATGCAATGTGGCTGAG
* * * *
2415 ATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTCGGTGACAAAAATCATGCAAAACTGAACC
1 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCG-CAAAAATCATGCAAAACTGAGCC
* * * * * *
2480 G-GGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTATACGATTTC--CTCAGATTG
65 GAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATT-
* *** * * * *
2542 TAG-ATTATTATACGTTTTTACC-C-AAAATATATTTC-CTCAAATTTTAGCCACAATACTCATC
129 TTGCA--A--A-A--AAATGACCTCGAAAAT-T-TTTCTCTCAAATTTTGGCTAAAATACTCAT-
* * *
2603 AAAAATATATATAATTTTACACCAAAATGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTC
184 -AAAATATATATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTC
* * * * *
2668 AAATTTTTTCAGAATTAATTTATAATTTAAATTAAAACAAGATTCAGATGCTCATAAAAACAAAT
248 ATA-TTTTTCTGAATTAATTTCTAA-TTAAA-TCAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * *
2733 CCTTAAATGCAACGTGGTTAAG
310 CCTTAAATGCAATGTGGCTGAG
* *
2755 ATTTTATTAGATGAATATGGATATTTCAAGGAGTCT-----CAAAAATCATGCAAAACTGAGCCG
1 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAATCATGCAAAACTGAGCCG
* **
2815 AGGCCCCGAAACGCGTTTTTAGCCAAAAAAAGAAAACTGTGATGGTTAGTACACGATTTTTGCTA
66 AGGCCCCGAAACGCGTTTTTAGCC------A-AAAACCGTGATGGTTAGTACACGATTTCGGCTA
* * * *
2880 AAATTTTG-AAGAAAAATGGCC-CGAAAAATTTTTC-CTCAATTTTTGGATAAAATACTCATAAT
124 AAATTTTGCAA-AAAAATGACCTCG-AAAATTTTTCTCTCAAATTTTGGCTAAAATACTCATAAA
*
2942 ATATATATAATTTAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTTCATA
187 ATATATATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCG-TTTTTCATA
*
3007 TTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAAT
251 TTTTTCTGAATTAATTTCTAATTAAATC-AAACAAGATTCAGATGCTCGTAAAAACAAAT
3066 TTTA
Statistics
Matches: 1078, Mismatches: 145, Indels: 194
0.76 0.10 0.14
Matches are distributed among these distances:
322 14 0.01
323 80 0.07
324 50 0.05
325 2 0.00
326 3 0.00
327 3 0.00
328 5 0.00
329 1 0.00
330 1 0.00
331 80 0.07
332 30 0.03
333 78 0.07
334 62 0.06
335 103 0.10
336 138 0.13
337 184 0.17
338 12 0.01
339 19 0.02
340 38 0.04
341 15 0.01
342 26 0.02
343 3 0.00
344 8 0.01
345 1 0.00
346 9 0.01
347 7 0.01
348 13 0.01
349 49 0.05
350 41 0.04
351 3 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (331 bp):
ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAATCATGCAAAACTGAGCCG
AGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTT
GCAAAAAAATGACCTCGAAAATTTTTCTCTCAAATTTTGGCTAAAATACTCATAAAATATATATA
ATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAA
TTAATTTCTAATTAAATCAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTG
GCTGAG
Done.