Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010447.1 Corchorus olitorius cultivar O-4 contig10479, 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: 3116
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:589 original size:319 final size:323
Alignment explanation
Indices: 5--614 Score: 1002
Period size: 319 Copynumber: 1.9 Consensus size: 323
1 TTTG
5 GGTTAGATAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGC
1 GGTTAGATAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGC
* * * *
70 ACCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAATATTAACCG
66 ACCGGAACGCGTTTTTAACCAAAAAACGTGATGG-TAGTACACGATTTCGGCTAAAAATGAACCG
* *
135 AAATTTTTTTTTCTCAATTTTTTTGCAACAATGCTCAGAAAAAATATATAATTCAACGCCAAAAA
130 AAATATTTTTTTCTCAATTTTTTTGCAACAATACTCAGAAAAAATATATAATTCAACGCCAAAAA
*
200 GATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTTCCGATTTAATTTCTAAT
195 GATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTTCCGAATTAATTTCTAAT
*
265 TAAATTGAAACAA-ATTTTAGATACTCGTAAAAACATATCCTTATATCGAATGTGGCTGAGATTT
260 TAAATTGAAACAAGA-TTCAGATACTCGTAAAAACATATCCTTATATCGAATGTGGCTGAGATTT
*
329 GGTTAGATAAATATAGAAACTTTTAGGAGTCTTTGTGCCCAAAATCATGCAAAATTGAGCCGGGC
1 GGTTAGATAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGC
* *
394 TCCGGAACGCGTTTTTAACCAAAAAAC-TG-T-G-ACGTACACGATTTCGGCTAAAAACTGACCC
66 ACCGGAACGCGTTTTTAACCAAAAAACGTGATGGTA-GTACACGATTTCGGCTAAAAA-TGAACC
455 GAAA-ATTTTTTTCTCAA-TTTTTTGCAACAATACT-AGGAAAAAATATATAATTCAACGCCAAA
129 GAAATATTTTTTTCTCAATTTTTTTGCAACAATACTCA-GAAAAAATATATAATTCAACGCCAAA
* *
517 AAGATTGACGGGATTTTCACGCTTCTGAATATCGTTTTCGCATTTTTTTTCTGAATTAATTTCTA
193 AAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTTCCGAATTAATTTCTA
582 ATTAAATTGAAACAAGATTCAGATACTCGTAAA
258 ATTAAATTGAAACAAGATTCAGATACTCGTAAA
615 GGAGCCGGGC
Statistics
Matches: 269, Mismatches: 13, Indels: 13
0.91 0.04 0.04
Matches are distributed among these distances:
318 1 0.00
319 135 0.50
320 33 0.12
321 9 0.03
322 1 0.00
323 2 0.01
324 88 0.33
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (323 bp):
GGTTAGATAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATTGAGCCGGGC
ACCGGAACGCGTTTTTAACCAAAAAACGTGATGGTAGTACACGATTTCGGCTAAAAATGAACCGA
AATATTTTTTTCTCAATTTTTTTGCAACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAG
ATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTTCCGAATTAATTTCTAATT
AAATTGAAACAAGATTCAGATACTCGTAAAAACATATCCTTATATCGAATGTGGCTGAGATTT
Found at i:792 original size:235 final size:230
Alignment explanation
Indices: 385--848 Score: 709
Period size: 235 Copynumber: 2.0 Consensus size: 230
375 ATGCAAAATT
385 GAGCCGGGCTCCGGAACGCGTTTTTAACCAAAAAACTGTGACGTACACGATTTCGGCTAAAAACT
1 GAGCCGGGCTCCGGAACGCGTTTTTAACCAAAAAACTGTGACGTACACGATTTCGGCTAAAAACT
* * *
450 GACCCGAAAATTTTTTTCTCAATTTTTTGCAACAATACTAGGAAAAAATATATAATTCAACGCCA
66 GACCAGAAAATTTGTTTCTCAATTTTTTGCAACAATACTAGCAAAAAATATATAATTCAACGCCA
* * * *
515 AAAAGATTGACGGGATTTTCACGCTTCTGAATATCGTTTTCGCATTTTTTTTCTGAATTAATTTC
131 AAAAGATTGACAGCATTTTCACGCTTCTAAATATCGTTTTCGCA-TTTTTTTCCGAATTAATTTC
*
580 TAATTAAATTGAAACAAGA-TTCAGATACTCGTAAAG
195 TAATTAAATTGAAA-AAAATTTCAGATACTCGTAAAG
* * *
616 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA-GTACACGATTTCTGCTAA
1 GAGCCGGGCTCCGGAACGCGTTTTTAACCAAAAAAC-TG-T-G--ACGTACACGATTTCGGCTAA
* *
680 AAACTGACCAGAAAATTTGTTTCTCAATTTTTTGCAACAATACTTA-CAAAAGATATATTATTCA
61 AAACTGACCAGAAAATTTGTTTCTCAATTTTTTGCAACAATAC-TAGCAAAAAATATATAATTCA
744 ACGCCAAAAAGATTGACAGCATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCGAATTA
125 ACGCCAAAAAGATTGACAGCATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCGAATTA
*
809 ATTTCTAATTAAATTGAAAAAAATTTTAGATACTCGTAAA
190 ATTTCTAATTAAATTGAAAAAAATTTCAGATACTCGTAAA
849 AACAAATCCT
Statistics
Matches: 212, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
231 34 0.16
232 2 0.01
233 4 0.02
234 49 0.23
235 120 0.57
236 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (230 bp):
GAGCCGGGCTCCGGAACGCGTTTTTAACCAAAAAACTGTGACGTACACGATTTCGGCTAAAAACT
GACCAGAAAATTTGTTTCTCAATTTTTTGCAACAATACTAGCAAAAAATATATAATTCAACGCCA
AAAAGATTGACAGCATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCGAATTAATTTCT
AATTAAATTGAAAAAAATTTCAGATACTCGTAAAG
Found at i:1067 original size:322 final size:321
Alignment explanation
Indices: 616--3116 Score: 3811
Period size: 321 Copynumber: 7.8 Consensus size: 321
606 ACTCGTAAAG
*
616 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCTGCTAAA
1 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * * * * *
681 AACTGACCAGAAAATTTGTTTCTCAATTTTTTGCAACAATACTTACAAAAGATATATTATTCAAC
66 AACTGACCCGAAAATTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAAC
* *
746 GCCAAAAAGATTGACAGCATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCCGAATTAAT
131 GCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCA-TTTTTTCCGAATTAAT
* *
811 TTCTAATTAAATTGAAAAAAATTTTAGATACTCGTAAAAACAAATCCTTATATCGAATGTGGCTG
195 TTCTAATTAAATTGAAACAAATTTCAGATACTCGTAAAAACAAATCCTTATATCGAATGTGGCTG
* *
876 AGATTTGGTTAGATTATATATAGAAACTTTTA-GACTCTTTGCGCCCAAAATCATGCAAAATT
260 AGATTTGGTTAGA-TAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATT
*
938 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAA
1 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
*
1003 AACTGACCCGAAAATTTTTTTCTCAAATTTTTGCAACAATACTCAGAAAAAATATATAATTCAAC
66 AACTGACCCGAAAATTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAAC
*
1068 GCCAAAAAGATTGACGGGATTTTCACGCTTCTAAACATCGTTTTCGCATTTTTTCCGAATTAATT
131 GCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTCCGAATTAATT
* * * *
1133 TCTAATTAAATTGAGACAAGA-TTCAGATACTTGTAAAGACAAATTCTTATATCGAATGTGGCTG
196 TCTAATTAAATTGAAACAA-ATTTCAGATACTCGTAAAAACAAATCCTTATATCGAATGTGGCTG
* * * * * *
1197 AGATTTGGTTAGATAAATATAGAAACATTTAGGAGTCTTTGTGCGCAAAATAATGCGAATTT
260 AGATTTGGTTAGATAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATT
* *
1259 TAGCCGGGCTCCGTAACGCGTTTTTAG-CAAAAACCCGTGATGGTTAGTACACGATTTCGGCTAA
1 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAA-CCGTGATGGTTAGTACACGATTTCGGCTAA
* *
1323 AAACTGACCCGAAAATTCTTTTCTTC-ATTTTTTGCAACAATACTCATAAAAAATATATAATTCA
65 AAACTGACCCGAAAATTTTTTTC-TCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCA
* * * *
1387 ACGCC-AAAATATTGACGAGATTTTCACGCTTCTAAATATCGTCTTCACATTTTTTTCCGAATTA
129 ACGCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCA-TTTTTTCCGAATTA
** *
1451 ATTTCTAATTAAATTGAAACAAGCTTCAGATACTCGTATAAACAAATCCTTATATCGAATGTGGC
193 ATTTCTAATTAAATTGAAACAAATTTCAGATACTCGTAAAAACAAATCCTTATATCGAATGTGGC
* * **
1516 TGAGATTTGGTTAGATAAATGTAGAAACTTTTAGGAGTCTTTGTGTGCAAAATCATGCAAAATT
258 TGAGATTTGGTTAGATAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATT
* *
1580 GAGCTGGGCTCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
1 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * * **
1645 AACTGACTC-AGAAATTTTTTTCTCAATTTTTTGCAACAATACTTAGAAAAGATATATTTTTCAA
66 AACTGACCCGA-AAATTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAA
*
1709 CGCCAAAAAGATTGACGGCATTTTCACGCTTCTAAATATCGTTTTCGCA-TTTTTCCGAATTAAT
130 CGCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTCCGAATTAAT
* * *
1773 TTCTAATTAATTTGAAACAAATTTTAGATACTCGTAAAAACATATCCTTATATCGAATGTGGCTG
195 TTCTAATTAAATTGAAACAAATTTCAGATACTCGTAAAAACAAATCCTTATATCGAATGTGGCTG
* *
1838 AGATTTAGTTAGATAAATATAGAAACTTTTAGCAGTCTTTGCGCCCAAAATCATGCAAAATT
260 AGATTTGGTTAGATAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATT
* *
1900 GAGCCGGGCTCCGGAACGC-ATTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
1 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
*
1964 AACTGACCCGAAGAA-TTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATAAAATTCAA
66 AACTGACCCGAA-AATTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAA
* * *
2028 CGGCAAAAAGATTTACGGGATTTTCACGATTCTAAATATCGTTTTCGCATTTTTTTCCGAATTAA
130 CGCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCA-TTTTTTCCGAATTAA
* * *
2093 GTTCTAATTAAATTGAAACAAGTTTCAGATACTCGTATAAACAAATCCTTATATCGAATGTGGCT
194 TTTCTAATTAAATTGAAACAAATTTCAGATACTCGTAAAAACAAATCCTTATATCGAATGTGGCT
*
2158 GAGATTTGGTTAGATTATATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATT
259 GAGATTTGGTTAGA-TAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATT
*
2222 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAG
1 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
** ** *
2287 AACTGACCCGAAAAAGTTTTTCTCAATTTTTTGCAACAATACTCAGAAATGATATATAATTCAAA
66 AACTGACCCGAAAATTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAAC
*
2352 GCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTCCAAATTAATT
131 GCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTCCGAATTAATT
*
2417 TCTATTTAAATTGAAACAAGA-TTCAGATACTCGTAAAAACAAATCCTTATATCGAATGTGGCTG
196 TCTAATTAAATTGAAACAA-ATTTCAGATACTCGTAAAAACAAATCCTTATATCGAATGTGGCTG
* * *
2481 AAATTTGGTTAGAAAAATATAGAAA-TTTTAGGAGTCTTTGAGCCCAAAATCATGCAAAATT
260 AGATTTGGTTAGATAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATT
* * * * *
2542 GAGCCGAGCTCCGGAATGCGTTTTTAGCCAAAAACCGTGATGGGTAGTACAAGATTTCGGGTAAA
1 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
** * * * *
2607 AACTTTCCCGAAAAATTTTTTCTTAATTTTTTGCAACAATACTCAGAAAAATTATATAATTTAAC
66 AACTGACCCGAAAATTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAAC
* *
2672 ACCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATTGTTTTCGCATTTTTTCCGAATTAATT
131 GCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTCCGAATTAATT
* * * * *
2737 TCTATTTAAATTGAAACAAATTTTAAATACTCGTAAAGACAGATCCTTATATCGAATGTGGCTGA
196 TCTAATTAAATTGAAACAAATTTCAGATACTCGTAAAAACAAATCCTTATATCGAATGTGGCTGA
* *
2802 GATTTGGTTAGATTATATATAAAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATT
261 GATTTGGTTAGA-TAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATT
* * *
2864 GAGCCGGGCTCCGAAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAA
1 GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * * * *
2929 AACTGACCCGAAAATTTTTTTCTCAAATTTTTGCAACAATACTTACAAAAGATATATTATTCAAC
66 AACTGACCCGAAAATTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAAC
* *
2994 GCCAAAAAGATTGACGGCATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTTCTGAATTAAT
131 GCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCA-TTTTTTCCGAATTAAT
* * * *
3059 TTTTAATTAAATTG-AACTAAATTTTAGATACTCGTAGAAACAAATCCATATATCGAAT
195 TTCTAATTAAATTGAAAC-AAATTTCAGATACTCGTAAAAACAAATCCTTATATCGAAT
Statistics
Matches: 1979, Mismatches: 177, Indels: 45
0.90 0.08 0.02
Matches are distributed among these distances:
319 141 0.07
320 497 0.25
321 573 0.29
322 562 0.28
323 206 0.10
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (321 bp):
GAGCCGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
AACTGACCCGAAAATTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAATTCAAC
GCCAAAAAGATTGACGGGATTTTCACGCTTCTAAATATCGTTTTCGCATTTTTTCCGAATTAATT
TCTAATTAAATTGAAACAAATTTCAGATACTCGTAAAAACAAATCCTTATATCGAATGTGGCTGA
GATTTGGTTAGATAAATATAGAAACTTTTAGGAGTCTTTGCGCCCAAAATCATGCAAAATT
Done.