Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010854.1 Corchorus capsularis cultivar CVL-1 contig10875, 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: 16131
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:633 original size:322 final size:323
Alignment explanation
Indices: 1--3293 Score: 3451
Period size: 322 Copynumber: 10.1 Consensus size: 323
* *
1 AGTCTTTCTGCCAAAAATCATACAAAACTGAG-CCGGGCACCGAAACACGTTTTTAGCCCGAAAA
1 AGTCTTTCTGCCAAAAATCATACAAAACTGAGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAAA
* * * *
65 CTGTGATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAGATAATTTCTTTGAATTTTTCAC
66 CTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATAATTTTTTTGAATTTTTCAC
* *
130 CACAATACTCAGCAAAAATATATAATTCATTGCCAAAAAGATTGACGGTCTTTTTACGCTTCTAA
131 CACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTTACGCTTCTAA
*
195 TATCATTTTTCCATTTTTTTCCGAATTTAAATCTAATTAAATCGAAACAAGATTCAGATGCTCGT
196 TATCATTTTTCCATTTTTTTCCGAATTTAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * *
260 AAAAACAAATGCTTATATCCAACGTGGCTGAGATTTTACTAGATAAATATAGATATTTGAAGG
261 AAAAACAAATCCTTATATCCAACGTGGCTGAGATTTTGCTAGATAAATATAGATATTTCAAGG
** *
323 AGT-TTTCTGTTAAAAATCATACAAAACTGAGTCGGGGCATCGAAACGCGTTTTTAGCCCGAAAA
1 AGTCTTTCTGCCAAAAATCATACAAAACTGAGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAAA
*
387 CTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCTGAAATAATTTTTTTGAATTTTTCAC
66 CTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATAATTTTTTTGAATTTTTCAC
*
452 CAGAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTTACGCTTCTAA
131 CACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTTACGCTTCTAA
*
517 TATCATTTTTCCATTTTTTTCCGAATTTAAATCTAATTAAATCGAAACAAGATTCAGATGCTCGT
196 TATCATTTTTCCATTTTTTTCCGAATTTAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * *
582 AAAAACAAATGCTTATATCCAACATGGATGAGATTTTACTAGATAAATATAGATATTTCAAGG
261 AAAAACAAATCCTTATATCCAACGTGGCTGAGATTTTGCTAGATAAATATAGATATTTCAAGG
* * *
645 AGTCTTTCTGCCAAAAATCATACAAAGCTGGGTCGGGGCACCGAAACGTGTTTTTAGCCCGAAAA
1 AGTCTTTCTGCCAAAAATCATACAAAACTGAGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAAA
* * * **
710 CTTTGATGGTTAGTACACGATTTCGTCTAAAAACTAACTAGAAATAATTTTTTTTGAATTTTTCA
66 CTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATAA-TTTTTTTGAATTTTTCA
*
775 CCATAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTTACGCTTCTA
130 CCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTTACGCTTCTA
840 ATATCATTTTTCCATTTCTTTTCCGAA-TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
195 ATATCATTTTTCCATTT-TTTTCCGAATTTAA-TTCTAATTAAATCGAAACAAGATTCAGATGCT
* * * * * *
904 TGT-AAAACAAATCCTTATATCCAATGTGGTTGA-AATTTGCTTGGATGAATATAGATATTTCAA
258 CGTAAAAACAAATCCTTATATCCAACGTGGCTGAGATTTTGC-TAGATAAATATAGATATTTCAA
967 GG
322 GG
* * * * * *
969 AGTCTTTGC-GTCAAAAATCATGA-AAAATTGAG-CAGGGGCTCC-ATAACACGTGTTTAG-CCA
1 AGTCTTT-CTGCCAAAAATCAT-ACAAAACTGAGTC-GGGGCACCGA-AACGCGTTTTTAGCCCG
* * * * *
1029 AAAACTCTGATGATTTGTAAACGATTTCGGCAAAAATTTTGCAAAAACTGATCC-AAA-AAGTTT
62 AAAACTGTGATGGTTAGTACACGATTTCGGC--------T--AAAAACTGACCCGAAATAA-TTT
* ** * *
1092 TGCTCAAATTTTT-TCCACAATACTCAGAATAAAAAAATATAATTCAATGCCAAAACA-ATTGAA
116 T-TTTGAATTTTTCACCACAATACTCAG-A-AAAAATATATAATTCAATGCCAAAA-AGATTG-A
* * * * * * **
1155 GGGT-TTTTCACGTTTTTAATATTATTTTCCCATTTTTTTCCGAATTTAAAACTAATTAAATCGA
176 CGGTCTTTTTACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTTAATTCTAATTAAATCGA
*
1219 AACAAGATTCAGATGCTCGTAAAAACAAATGCTTATATCCAACGTGGCTGAGATTTTGCTAGATA
241 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAACGTGGCTGAGATTTTGCTAGATA
1284 AATATAGATATTTCAAGG
306 AATATAGATATTTCAAGG
* *
1302 AGTCTTTCTGCCAAAAATCATACAAAACTGAG-CCGGGCACCGAAACACGTTTTTAGCCCGAAAA
1 AGTCTTTCTGCCAAAAATCATACAAAACTGAGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAAA
* *
1366 CTGTGATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAATAATTTTTTTGAATTTTTCAC
66 CTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATAATTTTTTTGAATTTTTCAC
* *
1431 CACAATACTCAGCAAAAATATATAATTAAATGCCAAAAAGATTGACGGTCTTTTTACGCTTCTAA
131 CACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTTACGCTTCTAA
*
1496 TATCATTTTTCCATTTTTTTCCGAATTTAAATCTAATTAAATCGAAACAAGATTCAGATGCTCGT
196 TATCATTTTTCCATTTTTTTCCGAATTTAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* *
1561 AAAAACAAATGCC-TATATCCAACGTGGCTAAGATTTTGCTAGATAAATATAGATATTTTAAGG
261 AAAAACAAAT-CCTTATATCCAACGTGGCTGAGATTTTGCTAGATAAATATAGATATTTCAAGG
* *
1624 AGTCTTTTTGCAAAAAATCATAC--AA---AGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAAA
1 AGTCTTTCTGCCAAAAATCATACAAAACTGAGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAAA
* * * * *
1684 TTGTGATGGTTAGTACACGATTTCTG-TTAAAACTGACCCGAAATCATTTTTCTGAATTTTTCAC
66 CTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATAATTTTTTTGAATTTTTCAC
* *
1748 CATAATACTCA-AAAAATATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTTACACTTCTA
131 CACAATACTCAGAAAAA-ATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTTACGCTTCTA
* *
1812 ATATCATTTTCCCA-TTTTTTCC-AA-TTAATTTCTAATTAAATCGAAACAAGATTCGCGATGCT
195 ATATCATTTTTCCATTTTTTTCCGAATTTAA-TTCTAATTAAATCGAAACAAGATTC-AGATGCT
* * * * *
1874 TGTAAAAACAAATCATTATTTCCAATCCTTGTATCCAATGTGGTTGAGA-TTTGCTTCGATAAAT
258 CGT---AA-AAA-C---A-----AATCCTTATATCCAACGTGGCTGAGATTTTGC-TAGATAAAT
* *
1938 ATAGATTTTTTAAGG
309 ATAGATATTTCAAGG
* * * * *
1953 AGTCTTTGC-GCCAAAAATCATGCAACATTGAGCCGGGGCTCCGAAACGCGTTTTTAG-CC-AAA
1 AGTCTTT-CTGCCAAAAATCATACAAAACTGAGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAA
* * * * *
2015 ATCTGTGATGATTAGTAAACGATTTCGGCCAAAATTTTGTAAAAACTTATCCGAAAT-GTTTTTC
65 A-CTGTGATGGTTAGTACACGATTTCGG-C---------TAAAAACTGACCCGAAATAATTTTT-
* * * *
2079 ATCAATTTTT--CCACAATACTCAGAAAAAAATATATAATTCAATGCTAAAACA-ATTGAAAGGT
118 TTGAATTTTTCACCACAATACTCAG-AAAAAATATATAATTCAATGCCAAAA-AGATTG-ACGGT
* * * * *
2141 -TTTTCACGCTTCCAAATATCA-TTTTCC-TATTTTTTCGGAATTCATTTCTAATTAAATCGAAA
180 CTTTTTACGCTT-CTAATATCATTTTTCCAT-TTTTTTCCGAATTTAATTCTAATTAAATCGAAA
* * * ** **
2203 CACGATTCAGATCCTCGTAAAAACAAATCCTTATGTCCATTGTGGCTGAGATTAGGCTAGATAAA
243 CAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAACGTGGCTGAGATTTTGCTAGATAAA
*
2268 TATAGATATTTAAAGG
308 TATAGATATTTCAAGG
* * * *
2284 AGTCTTTCTGCCAAAAATCATACAAAATTAAGCCGGGGCACCGAAACGCGTTTTTAGCCTGAAAA
1 AGTCTTTCTGCCAAAAATCATACAAAACTGAGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAAA
* * *
2349 CTGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCCGAAATAATTTTTCTGAAATTTTCAC
66 CTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATAATTTTTTTGAATTTTTCAC
* * * * *
2414 CATAATACTCAGAAAAAATATATAATTTAATGCGAAAAAAATTGACCGG-CTTTTTACGCTTATA
131 CACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGA-CGGTCTTTTTACGCTTCTA
* *
2478 ATATCATTTTTCCATTTTTTT-CGAA-TTAATTTCTAATTAAATCGAAACAAGATTCGGATGCTT
195 ATATCATTTTTCCATTTTTTTCCGAATTTAA-TTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * * *
2541 GTAAACCAAATCTTTATATCCAATCCTTATATCCAATGTGGTTGGGA-TTTGTTTCGATTAATAT
259 GT-AA--AAA-C-----A---AATCCTTATATCCAACGTGGCTGAGATTTTG-CTAGATAAATAT
2605 AGATATTTCAAGG
311 AGATATTTCAAGG
* * * * * * ** * *
2618 AGTCTTTGC-GTCAAAAATCATGCAAAATTGAGCCGGGGCTCCG-GACATGTTTTTAG-ACAAAA
1 AGTCTTT-CTGCCAAAAATCATACAAAACTGAGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAA
** * * *
2680 ACCATGAT-G-T-GTACACGATTTCGGCTAAAATTTTACAAAAACTGATCCGAAA-AGTTTTTCC
65 ACTGTGATGGTTAGTACACGATTTCGGC--------T--AAAAACTGACCCGAAATAATTTTT-T
* * * *
2741 TCAATTTTT-ACCACAATACTTAGAAAAAAATATATAATTCAACGCCAAAACA-ATTGAAGGGT-
119 TGAATTTTTCACCACAATACTCAG-AAAAAATATATAATTCAATGCCAAAA-AGATTG-ACGGTC
* * * * * * * * *
2803 TTTTCACGCTTCTAGTATCGTCTTTCCA-TTTTTTCCGAATTTATTTCTCATAAAATCAAAATAA
181 TTTTTACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTTAATTCTAATTAAATCGAAACAA
* * **
2867 GATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTAAGATTAGGCTAGATAAATAT
246 GATTCAGATGCTCGTAAAAACAAATCCTTATATCCAACGTGGCTGAGATTTTGCTAGATAAATAT
2932 AGATATTTCAAGG
311 AGATATTTCAAGG
* * * * *
2945 TGTATTTCTGCCAAAAATTATGCAAAACTGAGTCGGGGCACCGAAACGAGTTTTTAGCCC-AAAA
1 AGTCTTTCTGCCAAAAATCATACAAAACTGAGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAAA
* * *
3009 AT-TG-T-G--ACGTACACGATTTCGACTAAAAACTGACCAGAAAT-ATTTTTTCTGAACTTTTT
66 CTGTGATGGTTA-GTACACGATTTCGGCTAAAAACTGACCCGAAATAATTTTTT-TGAA-TTTTT
* * * * * * *
3068 GC-CCTAGAAT--TAAGAAAAAATATATAATTCAACGTCAAAAAGATTGGCGGGCTTTTCACGCT
128 -CACC-ACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTTACGCT
* * * * * *
3130 TTTAATATCGTTTTTCCA-TTTTTTCTGAA-TTAATTTCTAATTAAATAGAAACAACATTCAAAT
191 TCTAATATCATTTTTCCATTTTTTTCCGAATTTAA-TTCTAATTAAATCGAAACAAGATTCAGAT
* * * * * * *
3193 GCTTGTAAAAACAAATACTTATATCCAATGTGGCTGAGATTTGGTTCA-ATGAATGTAGATATTT
255 GCTCGTAAAAACAAATCCTTATATCCAACGTGGCTGAGATTTTGCT-AGATAAATATAGATATTT
*
3257 TAAGG
319 CAAGG
* * *
3262 AGTCTTTATGCCAAAAATCATGCAAAATTGAG
1 AGTCTTTCTGCCAAAAATCATACAAAACTGAG
3294 CCGGAACTCC
Statistics
Matches: 2524, Mismatches: 302, Indels: 295
0.81 0.10 0.09
Matches are distributed among these distances:
314 4 0.00
315 26 0.01
316 26 0.01
317 298 0.12
318 63 0.02
319 5 0.00
320 9 0.00
321 34 0.01
322 528 0.21
323 210 0.08
324 225 0.09
325 50 0.02
326 4 0.00
327 95 0.04
328 23 0.01
329 75 0.03
330 3 0.00
331 116 0.05
332 114 0.05
333 211 0.08
334 116 0.05
335 2 0.00
336 4 0.00
337 1 0.00
338 26 0.01
339 109 0.04
340 8 0.00
341 2 0.00
342 11 0.00
343 43 0.02
344 55 0.02
345 26 0.01
346 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (323 bp):
AGTCTTTCTGCCAAAAATCATACAAAACTGAGTCGGGGCACCGAAACGCGTTTTTAGCCCGAAAA
CTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAATAATTTTTTTGAATTTTTCAC
CACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTTACGCTTCTAA
TATCATTTTTCCATTTTTTTCCGAATTTAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
AAAAACAAATCCTTATATCCAACGTGGCTGAGATTTTGCTAGATAAATATAGATATTTCAAGG
Done.