Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002124.1 Corchorus olitorius cultivar O-4 contig02124, 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: 2038
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:584 original size:273 final size:272
Alignment explanation
Indices: 104--614 Score: 760
Period size: 273 Copynumber: 1.9 Consensus size: 272
94 ATTTTTTTCC
104 TCAATTTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGAAGGGTTT
1 TCAATTTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGAAGGGTTT
* * *
169 TTCACGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTAAGTTCTAATTAAATCGAAACAACAT
66 TCCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTAAGTTCTAAATAAATCGAAACAACAT
* * * * * * * **
234 TTAGATGGTTGTAAAAACAAATTCTTAAATTGAATGTGGCTGGGATATGGTTCGATGAATATAGA
131 TAAGATGCTCGTAAAAACAAATCCTTAAATTGAATGTGACTGAGATATGATTAAATGAATATAGA
*
299 TATTTCAAGGAGTCTTTAC-GCCGAAAATCATGCAAAACTGAGCTGAGGCTAAAAACTGACCCGA
196 TATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTGAGCTGAGGCTAAAAACTGACCCGA
363 AAATTTTTTTGTA
260 AAATTTTTTTGTA
376 TCAA-TTTTTTGCCACAAATACTCAT-AAAAATATATAATTCAACG-TCAAAAAGATTGAAGGGT
1 TCAATTTTTTTGCCAC-AATACTCATAAAAAATATATAATTCAACGCT-AAAAAGATTGAAGGGT
*
438 ATTTCCACGCTTCCAATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAAATAAATCGAAACA
64 -TTTCCACGCTTCCAATATCGTTTTTCCATTTTTTTC-GAATTAAGTTCTAAATAAATCGAAACA
* * * *
503 ATATTAAGATGCTCGTAAAAATAAATCCTTAAATTTAATGTGACTGAGATTTGATTAAATGAATA
127 ACATTAAGATGCTCGTAAAAACAAATCCTTAAATTGAATGTGACTGAGATATGATTAAATGAATA
* * *
568 TAGATATTTTAAGGAGTCTTTCTGTCAAAAATCATGCAAAATTGAGC
192 TAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGC
615 CGGGGACCCG
Statistics
Matches: 213, Mismatches: 21, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
270 1 0.00
271 46 0.22
272 48 0.23
273 118 0.55
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (272 bp):
TCAATTTTTTTGCCACAATACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGAAGGGTTT
TCCACGCTTCCAATATCGTTTTTCCATTTTTTTCGAATTAAGTTCTAAATAAATCGAAACAACAT
TAAGATGCTCGTAAAAACAAATCCTTAAATTGAATGTGACTGAGATATGATTAAATGAATATAGA
TATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCTGAGGCTAAAAACTGACCCGAA
AATTTTTTTGTA
Found at i:1514 original size:323 final size:326
Alignment explanation
Indices: 360--2037 Score: 1510
Period size: 323 Copynumber: 5.1 Consensus size: 326
350 AAAACTGACC
* * * *
360 CGAAAATTTTTTTGTATCAATTTTTTGCCACAAATACTCA-TAAAAATATATAATTCAACGTCAA
1 CGAAAATTTTTTT-TCTCAATTTTTTGCCAC-AATACTCAGAAAAAACATATAATTCAACGCCAA
* *
424 AAAGATTGAAGGG-TATTTCCACGCTTCCAATATCGTTTTTCCATTTTTTTCTGAATTAATTTCT
64 AAAAATTGAAGGGCT-TTT-CACGCTTCTAATATCGTTTTTCCATTTTTTTCTGAATTAATTTCT
* * * * ** *
488 AAATAAATCGAAACAATATTAAGATGCTCGTAAAAATAAATCCTTAAATTTAATGTGACTGAGAT
127 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGCCTGAGAT
* * * * *
553 TTGATTAAATGAATATAGATATTTTAAGGAGTCTTTCTGTC-AAAAATCATGCAAAATTGAGCCG
192 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATG-CAAAAAATCATGCAAAACTGAGCCG
617 GGGACC-CGAAACACATTTTTAGCCCAAAAACCT-TGATGGCGTA-C-GA-GATTTC-AGCTAAA
256 GGG-CCTCGAAACACATTTTTAGCCCAAAAA-CTGTGATGG-GTAGCAGACGATTTCGA-CTAAA
*
676 AAC-TGA-CT
317 AACTTAATCT
* * *
684 CGAAAAGTTTTTTTTCTCAATTTTTTGTCACAATACTCA-AAAAAACATATAATTTAACGTCAAA
1 CGAAAA-TTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAACATATAATTCAACGCCAAA
* * * * * *
748 AAGATTGACA-GTCTTTTCCCGCTTCTAATATCGTTTTTCAATTTTTTTTCCGAATCAATTTCTA
65 AAAATTGA-AGGGCTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTTCTGAATTAATTTCTA
* * *
812 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATCCTTAAATCGAATGTGGCT-AGAAT
128 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGCCTGAG-AT
* * *
876 TTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCAAAAAATCATGCAAAACTGAGCCAG
192 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCAAAAAATCATGCAAAACTGAGCCGG
* * * * * * * * **
941 GGCCCCGAAACACGTTTTTAGTCCAAAAACAGTGATGGTTAGCACACAATTTCGGCTAAAATTTT
257 GGCCTCGAAACACATTTTTAGCCCAAAAACTGTGATGGGTAGCAGACGATTTCGACTAAAAACTT
*
1006 GGAAAAACT
322 ----AATCT
* * *
1015 GACCAAAATTTTTTTTTCTCAATTCTTTGCCATC-ATACTCAGAAAAAATATATAATTCAACGCA
1 --CGAAAA-TTTTTTTTCTCAATTTTTTGCCA-CAATACTCAGAAAAAACATATAATTCAACGC-
* * * ** * * *
1079 AAAAAAAAAATTGAAGGGTTTTTCACCCTTCTAATATTATTTTT-CTTTTTTTTCCCCGAATTTA
61 --CAAAAAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTT--CTGAATTAA
* * * * *
1143 TTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATCCTTTAATCTAATGTTCCA
122 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGCCT
* * * * *
1208 GAGATTTGGTTAGATGAATATAAATATTTCAAGGAATTTTTATGCAAAAAATCTTACAAAACTGA
187 GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCAAAAAATCATGCAAAACTGA
*** * *
1273 TTGGGGGCCTCGAAACACGTTTTTAGCCCGAAAACTGTGATGGGTAGCAGACGATTTCGACTAAA
252 GCCGGGGCCTCGAAACACATTTTTAGCCCAAAAACTGTGATGGGTAGCAGACGATTTCGACTAAA
1338 AACTT-ATCT
317 AACTTAATCT
* * * * * *
1347 -GAAAA-TTTTTTTCTGAATTTTTTGCCACAATAGTAAGAAAAAATACATAATGCAACAG-CAAA
1 CGAAAATTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAACATATAATTCAAC-GCCAAA
** * * * * * *
1409 ATGATCGACGGGCTTTTCAAGTTTCTAATATCGTTTTTCCATTTTTTTCTAAATTAATTTCTCAT
65 AAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAAT
*
1474 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC-TAATATCCAATGTGGCTGAGATTT
130 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA-ATCCAATGTGCCTGAGATTT
* * * ** * * *
1538 GGTTCGATGAATATAGATATTTAAAGGATTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGG
194 GGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCAAAAAATCATGCAAAACTGAGCCGGGG
* * * *** * **
1603 -CTCTGGAACGCATTTTTAG-CCAAAAACTGTGATGGTTAGTTTACGATTTCGCCTAAAATTTTG
259 CCTC-GAAACACATTTTTAGCCCAAAAACTGTGATGGGTAGCAGACGATTTCGACTAAAAACTT-
1666 CAAAAACTAACT
322 ----AA-T--CT
** * * * * * * *
1678 C-AAAAAGTTTTTCCTCAATTTTTTTACCATAATATTTAGAAAAAACATAGAATTCAATGCCAAA
1 CGAAAATTTTTTTTCTCAA-TTTTTTGCCACAATACTCAGAAAAAACATATAATTCAACGCCAAA
* * * * * *
1742 AAAATTGAAGGGTTTTTTACGCTTCTAATATCGTTTTTCTAATTTTTTTTTTCAAATTTATTTCT
65 AAAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTC-CA-TTTTTTTCT-GAATTAATTTCT
**
1807 AATTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATCCAATGTGGTTGAGAT
127 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGCCTGAGAT
** * * **
1871 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCTTAAAACCATGCAAAACTGAGTCTA
192 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCAAAAAATCATGCAAAACTGAGCCGG
* * * * * * * ** *
1936 TGCCTTGAAACGCGTTTTTAG-CCAAAAACCGTGAT-GGTTGTACTCGATTTCGGCTAAAAA-TT
257 GGCCTCGAAACACATTTTTAGCCCAAAAACTGTGATGGGTAGCAGACGATTTCGACTAAAAACTT
*
1998 AA-CC
322 AATCT
* * *
2002 CGAAAA--TTTTTTCTCAATCTTTTGCCAGAGTACTCA
1 CGAAAATTTTTTTTCTCAATTTTTTGCCACAATACTCA
2038 T
Statistics
Matches: 1107, Mismatches: 194, Indels: 108
0.79 0.14 0.08
Matches are distributed among these distances:
322 82 0.07
323 343 0.31
324 57 0.05
325 30 0.03
326 2 0.00
327 43 0.04
328 4 0.00
329 5 0.00
330 1 0.00
331 8 0.01
332 13 0.01
333 100 0.09
334 38 0.03
335 124 0.11
336 47 0.04
337 208 0.19
338 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (326 bp):
CGAAAATTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAACATATAATTCAACGCCAAAA
AAATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATT
AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGCCTGAGATTTGG
TTAGATGAATATAGATATTTCAAGGAGTCTTTATGCAAAAAATCATGCAAAACTGAGCCGGGGCC
TCGAAACACATTTTTAGCCCAAAAACTGTGATGGGTAGCAGACGATTTCGACTAAAAACTTAATC
T
Found at i:1721 original size:660 final size:652
Alignment explanation
Indices: 392--2028 Score: 1825
Period size: 660 Copynumber: 2.5 Consensus size: 652
382 TTTTGCCACA
* * * *
392 AATACTCA-TAAAAATATATAATTCAACGTCAAAAAGATTGAAGGGTATTTCCACGCTTCCAATA
1 AATACTCAGAAAAAATATATAATTCAACG-CAAAAAAATTGAAGGGT-TTTTCACGCTTCTAATA
* * * * * *
456 TCGTTTTTCCATTTTTTTCTGAATTAATTTCTAAATAAATCGAAACAATATTAAGATGCTCGTAA
64 TCGTTTTT-CTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * * *
521 AAATAAATCCTTAAATTTAATGTGACTGAGATTTGATTAAATGAATATAGATATTTTAAGGAGTC
128 AAACAAATCCTTAAATCTAATGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * *
586 TTTCTGTCAAAAATCATGCAAAATTGAGCCGGGGACCCGAAACACATTTTTAGCCCAAAAACCTT
193 TTTATG-CAAAAATCATACAAAACTGAGCCGGGGACCCGAAACACATTTTTAGCCCAAAAACCTT
*
651 GATGGCGTACGAGATTTCAGCTAAAAACTGACTCGAAAAGTTTTTTTTCTCAATTTTTTGTCACA
257 GATGGCGTACGAGATTTCAGCTAAAAACTGACTCGAAAAG-TTTTTTTCTCAATTTTTTGCCACA
* * ** * * **
716 ATACTCAAAAAAACATATAATTTAACGTCAAAAAGATTGACAGTCTTTTCCCGCTTCTAATATCG
321 ATACTAAAAAAAACACATAATGCAACGTCAAAAAGATCGACAGGCTTTTCAAGCTTCTAATATCG
*
781 TTTTTCAATTTTTTTTCCGAATCAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
386 TTTTTCAATTTTTTTTCCAAATCAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * *
846 GCAAATCCTTAAATCGAATGTGGCTAGAATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTT
451 ACAAATCCTTAAATCCAATGTGGCTAGAATTTGGTTCGATGAATATAGATATTTAAAGGAGTCTT
*
911 TACGCAAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACACGTTTTTAGTCCAAAAACAGTGA
516 TACGCAAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACACATTTTTAGTCCAAAAACAGTGA
* * * ** *
976 TGGTTAGCACACAATTTCGGCTAAAATTTTGGAAAAACTGACCAAAATTTTTTTTTCTCAATTCT
581 TGGTTAGCACACAATTTCGCCTAAAATTTTGCAAAAACTAACCAAAATAGTTTTTCCTCAATTCT
*
1041 TTGCCAT
646 TTACCAT
* *
1048 CATACTCAGAAAAAATATATAATTCAACGCAAAAAAAAAAATTGAAGGGTTTTTCACCCTTCTAA
1 AATACTCAGAAAAAATATATAATTCAACGC----AAAAAAATTGAAGGGTTTTTCACGCTTCTAA
** *
1113 TATTATTTTTCTTTTTTTTCCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTTG
62 TATCGTTTTTCTTTTTTTT--CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* ** * *
1178 TAAAAACAAATCCTTTAATCTAATGTTCCAGAGATTTGGTTAGATGAATATAAATATTTCAAGGA
125 TAAAAACAAATCCTTAAATCTAATGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA
* * * ** * * *
1243 ATTTTTATGCAAAAAATCTTACAAAACTGA-TTGGGGGCCTCGAAACACGTTTTTAGCCCGAAAA
190 GTCTTTATGC-AAAAATCATACAAAACTGAGCCGGGGACC-CGAAACACATTTTTAGCCCAAAAA
* *
1307 -CTGTGATGG-GTAGCAGACGATTTC-GACTAAAAACTTA-TCTGAAAA-TTTTTTTCTGAATTT
253 CCT-TGATGGCGTA-C-GA-GATTTCAG-CTAAAAACTGACTC-GAAAAGTTTTTTTCTCAATTT
* * * * *
1367 TTTGCCACAATAGTAAGAAAAAATACATAATGCAACAG-CAAAATGATCGACGGGCTTTTCAAGT
312 TTTGCCACAATACTAA-AAAAAACACATAATGCAAC-GTCAAAAAGATCGACAGGCTTTTCAAGC
* * * *
1431 TTCTAATATCGTTTTTCCA-TTTTTTTCTAAATTAATTTCTCATTAAATCGAAACAAGATTCAGA
375 TTCTAATATCGTTTTTCAATTTTTTTTCCAAATCAATTTCTAATTAAATCGAAACAAGATTCAGA
1495 TGCTCGTAAAAACAAATCC-TAATATCCAATGTGGCT-GAGATTTGGTTCGATGAATATAGATAT
440 TGCTCGTAAAAACAAATCCTTAA-ATCCAATGTGGCTAGA-ATTTGGTTCGATGAATATAGATAT
* * * * * * * * * *
1558 TTAAAGGATTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCTGGAACGCATTTTTAG-
503 TTAAAGGAGTCTTTACGCAAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACACATTTTTAGT
* *** *
1622 CCAAAAACTGTGATGGTTAGTTTACGATTTCGCCTAAAATTTTGCAAAAACTAACTCAAAA-AGT
568 CCAAAAACAGTGATGGTTAGCACACAATTTCGCCTAAAATTTTGCAAAAACTAAC-CAAAATAGT
*
1686 TTTTCCTCAATTTTTTTACCAT
632 TTTTCCTCAA-TTCTTTACCAT
* * * * * *
1708 AATATTTAGAAAAAACATAGAATTCAATGCCAAAAAAATTGAAGGGTTTTTTACGCTTCTAATAT
1 AATACTCAGAAAAAATATATAATTCAACG-CAAAAAAATTGAAGGGTTTTTCACGCTTCTAATAT
* *
1773 CGTTTTTCTAATTTTTTTTTTCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
65 CGTTTTTC----TTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* **
1838 -AAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
126 AAAAACAAATCCTTAAATCTAATGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* * * * *** * * *
1902 TCTTTATGCTTAAAACCATGCAAAACTGAGTCTATG-CCTTGAAACGCGTTTTTAG-CCAAAAAC
191 TCTTTATGC-AAAAATCATACAAAACTGAGCCGGGGACC-CGAAACACATTTTTAGCCCAAAAAC
* * ** * * * * *
1965 CGTGATGGTTGTACTCGATTTCGGCTAAAAATTAACCCGAAAA--TTTTTTCTCAATCTTTTGCC
254 CTTGATGG-CGTACGAGATTTCAGCTAAAAACTGACTCGAAAAGTTTTTTTCTCAATTTTTTGCC
2028 A
318 A
2029 GAGTACTCAT
Statistics
Matches: 823, Mismatches: 126, Indels: 65
0.81 0.12 0.06
Matches are distributed among these distances:
655 19 0.02
656 28 0.03
657 71 0.09
658 106 0.13
659 141 0.17
660 370 0.45
661 66 0.08
662 22 0.03
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (652 bp):
AATACTCAGAAAAAATATATAATTCAACGCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATC
GTTTTTCTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
CAAATCCTTAAATCTAATGTGACTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT
ATGCAAAAATCATACAAAACTGAGCCGGGGACCCGAAACACATTTTTAGCCCAAAAACCTTGATG
GCGTACGAGATTTCAGCTAAAAACTGACTCGAAAAGTTTTTTTCTCAATTTTTTGCCACAATACT
AAAAAAAACACATAATGCAACGTCAAAAAGATCGACAGGCTTTTCAAGCTTCTAATATCGTTTTT
CAATTTTTTTTCCAAATCAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
TCCTTAAATCCAATGTGGCTAGAATTTGGTTCGATGAATATAGATATTTAAAGGAGTCTTTACGC
AAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACACATTTTTAGTCCAAAAACAGTGATGGTT
AGCACACAATTTCGCCTAAAATTTTGCAAAAACTAACCAAAATAGTTTTTCCTCAATTCTTTACC
AT
Done.