Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021106.1 Corchorus olitorius cultivar O-4 contig21139, 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: 7322
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:4825 original size:31 final size:31
Alignment explanation
Indices: 4787--4855 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
4777 CATAGAACAT
*
4787 TAATAAATAATAATCTCATAATAATAGGTAG
1 TAATAAATAATAATCCCATAATAATAGGTAG
4818 TAATAAATAATAATCCCATAATAATAGGTAG
1 TAATAAATAATAATCCCATAATAATAGGTAG
4849 TAATAAA
1 TAATAAA
4856 ATTGGGGCAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (31 bp):
TAATAAATAATAATCCCATAATAATAGGTAG
Found at i:6078 original size:324 final size:322
Alignment explanation
Indices: 5483--7318 Score: 1360
Period size: 324 Copynumber: 5.6 Consensus size: 322
5473 AGAATTTTAA
* * * * **
5483 TCAATTTTTGGCAAAAATACTCATAAAATATATATAATTCAACGCCAAAAAAATT-ACAGAACTT
1 TCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGAC-GGGCTT
* * *
5547 TTCATGCTGT-TAATATCGTTTTTCATATTTTTT-TATGAATTAATTTCTAATTAAATCGAAACA
65 TTCACGCT-TCTAATATCGTTTTCCAT-TTTTTTCCA--AATTAATTTCTAATTAAATCGAAACA
* * *
5610 AAATTCAGATGCAT-GTAAAAGCAAATCCTTAAATCCAATGTGGCTGTGATTTGATTAGATGAAT
126 AGATTCAGATGC-TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
* * *** * * ** *
5674 AAAGATATTTTAAGGAGTCTCGGCGCCAAAAATCATGCAAAACAGAGCCGTGGCCCCGGAACACG
190 ATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCATCGGAACGCG
* *
5739 TTTTTAGTCAAAAACCGTGATGGTTGTTAGTACAC-AGTTTCAGCTAAAAACTGACCCGAAATGT
255 TTTTTAGTCAAAAACCGTGATGG-TGTTAGTACACGA-TTTCGGCTAAAAACTGACCCGAAAAGT
5803 TTATTC
318 TT-TTC
* * * *
5809 TCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATATTGACGGCCTTT
1 TCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGGGCTTT
* * *
5874 TCACGCTTCTAATATCGTTTTCCATGTTTTTCCAAATTTATTTATAATTAAATCGAAACAAGATT
66 TCACGCTTCTAATATCGTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * *
5939 CAGATGCTCGTAAAACCAAATCCTTATATCCAATGTGGTTAACATTTGATTCA-ATGAATAT-GA
131 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATT-AGATGAATATAG-
* * *
6002 ATATTTCAATGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGGCTTCGGAACGCGTTTT
194 ATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCATCGGAACGCGTTTT
*
6067 TAGTAAAAAACCGTGATGGT-TTA-TACACCGATTTCGGTCAAAATTTTGCAAAAACTGACCCGA
259 TAGTCAAAAACCGTGATGGTGTTAGTACA-CGATTTCGG-C-------T--AAAAACTGACCCGA
6130 AAAGTTTTTCC
313 AAAGTTTTT-C
* * * * * * *
6141 TCAATTTTTTCGCCACAATACTTAGAAAAAATATATAATTTAAC-ACAAAAAAAATGAAGGGTTT
1 TCAATTTTTT-GCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGGGCTT
* ** * *
6205 TTCACGCTTCTAATATCATTTTTCTTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAA
65 TTCACGCTTCTAATATC-GTTTTC-CATTTTTTTCCAAATTAATTTCTAATTAAATCGAAAC-AA
* * *
6270 GATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTG-TTAGATGAATA
127 GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA-TTTGATTAGATGAATA
** * ** * *
6334 TAGATATTTCAAGGAGTCAATGCGCCAAAAATCATTTAAAACTGAGCC-AGG-ATCTGAAACGCG
191 TAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCATC-GGAACGCG
* * ** *
6397 TTTTTAGCCAAAAATCGTGAT-G-GTTAGTACACGATTTCGGCTGGAAACTAACCCGAAAAGTTT
255 TTTTTAGTCAAAAACCGTGATGGTGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAG-TT
6460 TTTC
319 TTTC
* * * *
6464 TCAATTTTTCG-CAAAATATTTAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTT
1 TCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGGGCTTT
* *
6528 TCACGCTTCTAAATTTTAATATTGTTTTTCCATTTTTTTTCCGAATTAATTTCTAATTAAATCGA
66 TCACGCTTC-------TAATATCG-TTTTCCA-TTTTTTTCCAAATTAATTTCTAATTAAATCGA
* * * * * * *
6593 AACAAGACTCGGATGCTCGTAAAAACAAATCCATATATACAATTTGGCTGAGATTTGGTTCA-AT
122 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATT-AGAT
* * *
6657 GAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGAC-TCCGAA
186 GAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCAT-CGGA
* * * *
6721 ACGTAC-TTTTT-GCCAAAAACCGTGAT--AGTTAGTACACGATTTCGTTGGTAGAAAAAAAATA
250 ACG--CGTTTTTAGTCAAAAACCGTGATGGTGTTAGTACACGATTTCG--GCT----AAAAACT-
* *
6782 CACAACTTCGGCTAAAATTTTGCAAAAATTGAC
306 GAC--C--C-G--AAAAGTTT-------TT--C
* * * ** ** ***** *
6815 CCGAAAAGTTTTTCCTCAATTTTGTTTTTCCAAAATACTCAGAAAAAATATAAAATTCAACGCCA
1 TC---AATTTTTTGC-CAA-AATACTCAGAAAAAATA-T-----ATAAT-------TCAACGCCA
* * * * * *
6880 AAAAAATTGAAGGGGTTTTCACACTTCCAATATCGTTTT-C--------CCGAATTTATTTCTAA
48 AAAAAATTGACGGGCTTTTCACGCTTCTAATATCGTTTTCCATTTTTTTCCAAATTAATTTCTAA
* * * * * *
6936 TTAAATCGAAACAAAATTCAAATACTCGTAAAAACAAATCCTTATAT-CAATATGGTTGAGATTT
113 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * * *
7000 GGTTAGATGAATGTAGATATTTGAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACAGAGTCGGG
178 GATTAGATGAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATCATGCAAAACTGAGCCGGG
** * ** * * *
7064 GCCCCGAAACGCGTTTTTAACCAAAAA-C---A--GTGATAGTACACGATTTCGGCTAAAACCTT
242 GCATCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTGTTAGTACACGATTTCGGCTAAAAACTG
*
7123 ACACGAAAAGTTTTTTC
307 ACCCGAAAAG-TTTTTC
* * * *
7140 TCAATTTTTTG-CAAAATATTCAGAAAAACTATATAATTCAACG-CAAAAAATATTGATGGCCTT
1 TCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAA-ATTGACGGGCTT
* * *
7203 TTCACGCTTCTAATATCGTTTTCCATTATTTTTTTCGAATTAATTTTTAATTAAATCGAAACAAG
65 TTCACGCTTCTAATATCGTTTTCCA-T-TTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAG
*
7268 ATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTG
128 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
7319 GTTT
Statistics
Matches: 1217, Mismatches: 183, Indels: 228
0.75 0.11 0.14
Matches are distributed among these distances:
305 7 0.01
306 35 0.03
307 1 0.00
313 4 0.00
317 57 0.05
318 17 0.01
319 8 0.01
320 3 0.00
321 32 0.03
322 42 0.03
323 30 0.02
324 155 0.13
325 10 0.01
326 75 0.06
327 8 0.01
328 92 0.08
329 85 0.07
330 7 0.01
331 5 0.00
332 63 0.05
333 54 0.04
334 67 0.06
335 95 0.08
336 8 0.01
338 1 0.00
340 3 0.00
341 6 0.00
342 3 0.00
343 4 0.00
345 2 0.00
347 17 0.01
349 3 0.00
350 8 0.01
351 87 0.07
352 56 0.05
354 6 0.00
356 3 0.00
357 10 0.01
358 1 0.00
361 1 0.00
362 4 0.00
363 10 0.01
370 32 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (322 bp):
TCAATTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGGGCTTT
TCACGCTTCTAATATCGTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATT
CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGAT
ATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCATCGGAACGCGTTTTTA
GTCAAAAACCGTGATGGTGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTC
Found at i:6744 original size:663 final size:655
Alignment explanation
Indices: 5496--7321 Score: 1979
Period size: 663 Copynumber: 2.7 Consensus size: 655
5486 ATTTTTGGCA
* * * * * *** **
5496 AAAATACTCATAAAATATATATAATTCAACG-CCAAAAAAATTACAGAACTTTTCATGCTGT-TA
1 AAAATACTCAGAAAAAATATAAAATTCAACGACAAAAAAAATGA-AGGGGTTTTCACACT-TCTA
** *
5559 ATATCGTTTTTCATATTTTTTTATGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCAT
64 ATATC-TTTTTC-T-TTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGC-T
* * * *
5624 -GTAAAAGCAAATCCTTAAATCCAATGTGGCTGTGA-TTTGATTAGATGAATAAAGATATTTTAA
125 CGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTG-TTAGATGAATATAGATATTTCAA
* * * *
5687 GGAGTC-TCGGCGCCAAAAATCATGCAAAACAGAGCCGTGGCCCCGGAACACGTTTTTAGTCAAA
189 GGAGTCAT--GCGCCAAAAATCATGCAAAACAGAGCC-AGGCCCCGAAACGCGTTTTTAGCCAAA
* * * *
5751 AACCGTGATGGTTGTTAGTACAC-AGTTTCAGCTAAAAACTGACCCGAAATGTTTATTCTCAATT
251 AA-CGTGAT-G--GTTAGTACACGA-TTTCGGCT-AAAACTAACCCGAAAAGTTTTTTCTCAATT
* * *
5815 TTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATATTGACGGCCTTTTCACGC
310 TTTTG-CAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAATATTGACGGCCTTTTCACGC
* * *
5880 TTCTAATATCGTTTTCCA-TGTTTTTCCAAATTTATTTATAATTAAATCGAAACAAGATTCAGAT
374 TTCTAATATCGTTTTCCATTTTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGAT
* * * * *
5944 GCTCGTAAAACCAAATCCTTATATCCAATGTGGTTAACATTTGATTCAATGAATATGAATATTTC
439 GCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCAATGAATATGAATATTTC
* * * * *
6009 AATGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGGCTTCGGAACGCGTTTTTAGTAAA
504 AAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGAAACGCGTTTTTAGCAAA
*
6074 AAACCGTGATGGTTTA-TACACCGATTTC-G-G-T-C-AAAATTTTGCAAAAACTGACCCGAAAA
569 AAACCGTGATAG-TTAGTACA-CGATTTCGGAGATGCTAAAATTTTGCAAAAACTGACCCGAAAA
6133 GTTTTTCCTCAA-TTT-TTTCGCC
632 GTTTTTCCTCAATTTTGTTTCGCC
* * * * * *
6155 ACAATACTTAGAAAAAATATATAATTTAAC-ACAAAAAAAATGAAGGGTTTTTCACGCTTCTAAT
1 AAAATACTCAGAAAAAATATAAAATTCAACGACAAAAAAAATGAAGGGGTTTTCACACTTCTAAT
*
6219 ATCATTTTTCTTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAGATTGAGATGCTCG
66 ATC-TTTTTC--TTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAA-ATTCAGATGCTCG
* *
6284 TAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGA
127 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGA
** * ** *
6349 GTCAATGCGCCAAAAATCATTTAAAACTGAGCCAGGATCTGAAACGCGTTTTTAGCCAAAAATCG
192 GTC-ATGCGCCAAAAATCATGCAAAACAGAGCCAGGCCCCGAAACGCGTTTTTAGCCAAAAA-CG
* *
6414 TGATGGTTAGTACACGATTTCGGCTGGAAACTAACCCGAAAAGTTTTTTCTCAATTTTTCGCAAA
255 TGATGGTTAGTACACGATTTCGGCT-AAAACTAACCCGAAAAGTTTTTTCTCAATTTTTTGCAAA
* * *
6479 ATATTTAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAAATTT
319 ATATTCAGAAAAAATATATAATTCAACGCCAAAAATATTGACGGCCTTTTCACGCTTC-------
* * * *
6544 TAATATTGTTTTTCCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGACTCGGATGC
377 TAATATCG-TTTTCCATTTTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATGC
* * *
6609 TCGTAAAAACAAATCCATATATACAATTTGGCTGAGATTTGGTTCAATGAATAT-AGATATTTCA
441 TCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCAATGAATATGA-ATATTTCA
*
6673 AGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGAAACGTAC-TTTTT-GCCA
505 AGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGAAACG--CGTTTTTAGCAA
6736 AAAACCGTGATAGTTAGTACACGATTTCGTTGGTAGAAAAAAAATACACAACTTCGGCTAAAATT
568 AAAACCGTGATAGTTAGTACACGATTTC---GG-AG--------------A--T--GCTAAAATT
* **
6801 TTGCAAAAATTGACCCGAAAAGTTTTTCCTCAATTTTGTTTTTCC
611 TTGCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTGTTTCGCC
* * *
6846 AAAATACTCAGAAAAAATATAAAATTCAACGCCAAAAAAATTGAAGGGGTTTTCACACTTCCAAT
1 AAAATACTCAGAAAAAATATAAAATTCAACGACAAAAAAAATGAAGGGGTTTTCACACTTCTAAT
* * *
6911 ATCGTTTTC--------CCGAATTTATTTCTAATTAAATCGAAACAAAATTCAAATACTCGTAAA
66 ATCTTTTTCTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAA
* * * * * * *
6968 AACAAATCCTTATAT-CAATATGGTTGAGATTTGGTTAGATGAATGTAGATATTTGAAGGAGTCT
131 AACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCA
* ** *
7032 TTCTGCCAAAAATCATGCAAAACAGAGTCGGGGCCCCGAAACGCGTTTTTAACCAAAAACAGTGA
196 TGC-GCCAAAAATCATGCAAAACAGAG-CCAGGCCCCGAAACGCGTTTTTAGCCAAAAAC-GTGA
* *
7097 ----TAGTACACGATTTCGGCTAAAACCTTACACGAAAAGTTTTTTCTCAATTTTTTGCAAAATA
258 TGGTTAGTACACGATTTCGGCTAAAA-CTAACCCGAAAAGTTTTTTCTCAATTTTTTGCAAAATA
* * *
7158 TTCAGAAAAACTATATAATTCAACGCAAAAAATATTGATGGCCTTTTCACGCTTCTAATATCGTT
322 TTCAGAAAAAATATATAATTCAACGCCAAAAATATTGACGGCCTTTTCACGCTTCTAATATCGTT
* *
7223 TTCCATTATTTTTTTCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
387 TTCCATT-TTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
7288 AAATCCTTATATCCAATGTGGCTGAGATTTGGTT
451 AAATCCTTATATCCAATGTGGCTGAGATTTGGTT
7322 T
Statistics
Matches: 988, Mismatches: 122, Indels: 104
0.81 0.10 0.09
Matches are distributed among these distances:
654 56 0.06
655 47 0.05
656 1 0.00
657 2 0.00
658 88 0.09
659 127 0.13
660 4 0.00
661 8 0.01
662 18 0.02
663 161 0.16
664 5 0.01
665 1 0.00
666 1 0.00
668 10 0.01
669 91 0.09
675 3 0.00
676 102 0.10
678 2 0.00
679 63 0.06
680 56 0.06
681 31 0.03
685 1 0.00
688 1 0.00
689 38 0.04
690 3 0.00
691 36 0.04
692 32 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (655 bp):
AAAATACTCAGAAAAAATATAAAATTCAACGACAAAAAAAATGAAGGGGTTTTCACACTTCTAAT
ATCTTTTTCTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAA
AACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCA
TGCGCCAAAAATCATGCAAAACAGAGCCAGGCCCCGAAACGCGTTTTTAGCCAAAAACGTGATGG
TTAGTACACGATTTCGGCTAAAACTAACCCGAAAAGTTTTTTCTCAATTTTTTGCAAAATATTCA
GAAAAAATATATAATTCAACGCCAAAAATATTGACGGCCTTTTCACGCTTCTAATATCGTTTTCC
ATTTTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
CTTATATCCAATGTGGCTGAGATTTGGTTCAATGAATATGAATATTTCAAGGAGTCTTTACGCCA
AAAATCATGCAAAATTGAGCCGGGACTCCGAAACGCGTTTTTAGCAAAAAACCGTGATAGTTAGT
ACACGATTTCGGAGATGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTGTT
TCGCC
Done.