Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012057.1 Corchorus olitorius cultivar O-4 contig12090, 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: 33605
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:1065 original size:16 final size:16
Alignment explanation
Indices: 1044--1077 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1034 AAATTCTTCA
*
1044 ATCCAATGTAGTTGAG
1 ATCCAATGTAGCTGAG
1060 ATCCAATGTAGCTGAG
1 ATCCAATGTAGCTGAG
1076 AT
1 AT
1078 TAGATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (16 bp):
ATCCAATGTAGCTGAG
Found at i:2781 original size:643 final size:635
Alignment explanation
Indices: 1161--3965 Score: 2478
Period size: 647 Copynumber: 4.3 Consensus size: 635
1151 AACGCGTAAT
* * ** *
1161 TACACGATTGCAGCTAGAATTTTGC-AAAAATCGACTC-GAAAGTTATT-TCCTCAATTTTTATC
1 TACACGATTTCAGCTAAAATTTTGCAAAAAAT-GAC-CAGAAAAATATTCT-CTCAATTTTTAGC
* * * * * *
1223 CACAATACTCATAAAAATTATGTAATTCAACGCCAAAAAGATTGAAGGGTTTTTCATGCTTCTAA
63 CACAATACTCATAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAA
* * *
1288 TATCGTTTTTCCTA--TTATTTTCCGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCT
128 TATCGTTTTTCCTATTTTTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAAATG--
* *
1351 TGTTTTACAAATCGTTAAATCCAATGTGGTTGAGATTTGGTTAGATGAATGTAGATATTTCAAGG
191 T-TTGT---AA-----AAA--CAA--TGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
* * *** *
1416 AGTCTCGGCGCAAAAAATCATGCAACGCT-ATACCGGGGCCCCGAAACGCGTTTTTAGCCAAAAA
243 AGTCTCGGTGCCAAAAATCAT-CAAAATTGA-ACC-GGGCCCTGAAACGCGTTTTTAGCCAAAAA
** * * * * * * * *
1480 -CTGTGATTTCGACAAACGTACATGATTTCGGCTAATATTTTGCAAAAGTTGACCAGGAATATTT
305 TC-GTGA--T-GA-TTA-TTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATAT
* * * * *
1544 TTCCTAAATTTTTGTCTAAAATACTCATAAAATATATATAATTCAACTCCAAAAAGATTGGAGGA
364 CTCCTCAA---TT-T-T----TACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGG-
* *
1609 CTTTTCTCAC-CTTTTAATATTGGTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAAC
419 C-TTT-TCACGCTTTTAATATCGATTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAAC
* * *
1673 AAGATTCATATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTGAGA---T-TTA-AT--A-
482 AAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAAT
** * * * * * *
1730 TAGATATTTTGAGGAGTTTCGACGCCAAAAATCATGGAAAAATGAGTCTGGACCCCGAAACGCGT
547 TAGATATTTCAAGGAGTTTCG-CACCAAAAACCATGCAAAACTGAGTCGGGGCCCCGAAACGCGT
**
1795 TTTTAGCAAAAAAAAAAAACAGTGATGTTAG
611 TTTTAGC-----AAAAAAACAGTGA-GACAG
* *
1826 TACACGATTTCCGCTAAAATTTTACAAAAAATGACCAGAAAAATATTCTCTCAATTTTTAGCCAC
1 TACACGATTTCAGCTAAAATTTTGCAAAAAATGACCAGAAAAATATTCTCTCAATTTTTAGCCAC
*
1891 AATACTCATAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGGTTTTCACGCTTCTAATAT
66 AATACTCATAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATAT
* * *
1956 CGTTTTTCC-ATTATTTTTTCGGAATTAATTTCTAATTAAAACGATACATGATTCAAATGTTTGT
131 CGTTTTTCCTATTTTTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAAATGTTTGT
* *
2020 AAAAACAATGGTTGGGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAATT
196 AAAAACAATGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAAT
* * *
2085 CATTCAAAATTGAACCGGGCCCTGGAAGGCATTTTTAGCCAAAAATCGTGATGATTATTACACGA
261 CA-TCAAAATTGAACCGGGCCCTGAAACGCGTTTTTAGCCAAAAATCGTGATGATTATTACACGA
2150 TTTCGGCTAAAATTTTGCAAAAAAAATTGACCCGAAAGATATCTCCTCAATTTTTACTCATAAAA
325 TTTCGGCTAAAATTTTGC---AAAAATTGACCCGAAAGATATCTCCTCAATTTTTACTCATAAAA
* *
2215 AACTATATAATTCAACGCCAAAAAGATTAAAGAGCTTTTCACGCTTTTAATATCAATTTTCATAT
387 AA-TATATAATTCAACGCCAAAAAGATTGAAG-GCTTTTCACGCTTTTAATATCGATTTTCATAT
*
2280 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAA
450 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAA
*
2345 ATGCAATGTAGCTAAGATTTTATTAGATGAATGTAGATATTTCAAGGAGTTTCAGCACCAAAAAC
515 ATGCAATGTGGCTAAGATTTTATTAGATGAAT-TAGATATTTCAAGGAGTTTC-GCACCAAAAAC
* * *
2410 CATTCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCAAAAAGACAGT-A-ACA-
578 CATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAACAGTGAGACAG
*
2465 TACACGATTTTTCAGCTAAAATTTTGCAAAAAATGACCAGAAAACTATTCTCTCAATTTTTAGCC
1 TACACGA--TTTCAGCTAAAATTTTGCAAAAAATGACCAGAAAAATATTCTCTCAATTTTTAGCC
2530 ACAATACTCATAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAAT
64 ACAATACTCATAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAAT
2595 ATCGTTTTTCCTATTTTCTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAAATGTT
129 ATCGTTTTTCCTATTTT-TTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAAATGTT
* * * *
2660 TGTAAAAACAATGGTTGAGATTTGGTTAGATGCATATAGATATTTTAAGAAGTCTCAGTGCCAAA
193 TGTAAAAACAATGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAA
2725 AATCAGTCAAAATTGAACCGGGCCCTGAAACGCGTTTTTAGCCAAAAATCGTGATGATTATTACA
258 AATCA-TCAAAATTGAACCGGGCCCTGAAACGCGTTTTTAGCCAAAAATCGTGATGATTATTACA
* * * *
2790 CGAGTTCGGCTAAACTTTTGCAAAAATTGA-TCGAAAGATATCTCCTCAATTTTTAGTCATAATA
322 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATCTCCTCAATTTTTA--C-T--CA
*
2854 CTCATAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTT
382 -T-A-AAAAATATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCACGCTTTTAATATCGATT
* *
2919 TTCATATTTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTTAGGTGCTCGTAAAAACAA
443 TTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAA
2984 ATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGA-TTGTCGGC
507 ATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAAT-TAGATATTTCAAGGAGTT-TC-GC
* * *
3048 ACCAAAAACCATGCAAAACTGAGCCGGGGCCCCGAAACATGCGTTTTTAGC-CAAAAACCGTGAT
569 ACCAAAAACCATGCAAAACTGAGTCGGGGCCCCGAAAC--GCGTTTTTAGCAAAAAAACAGTGA-
3112 GAC--
631 GACAG
* * * * * * * ** *
3115 --C-CG-----A---AAAACTTTGCAAAAAATGACCCGAAAAGT-TTTTCCCTATTTCTAGATAA
1 TACACGATTTCAGCTAAAATTTTGCAAAAAATGACCAGAAAAATATTCTCTCAATTTTTAGCCAC
* * * ** *
3168 AATACTCATAAAATATATATAATTTAATGCCAAAAAAATTGGAGAACTTTTCACGCTTTTAATAT
66 AATACTCATAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATAT
** * * * * * * **
3233 CAATTTT--TA--TATTTTTCTGAATCAATTTCTAATTAAATCGAAACAGGATTCAGATACTTGT
131 CGTTTTTCCTATTTTTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAAATGTTTGT
* * * * *
3294 AAAAACAAATTTTTCAATCCAATGTGGCTGAGATTTGATTAGATGAATATGGATATCTCAAGGAT
196 ------AAA------AA--CAA--TGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* * ** * * * * *
3359 TCTTGGCGTAAAAAATCATGCAAAACTGAGCTGGGGCC-GTAGAACGCTTTTTTAGCCAAAAA-C
245 TCTCGGTGCCAAAAATCAT-CAAAATTGAACCGGGCCCTG-A-AACGCGTTTTTAGCCAAAAATC
* * * * * *** * *
3422 TGTGATGTTTATTACATGATTTTGGCTAAAATTTTGTAAAAGTTGATTAGAAAAATATTTCCTCA
307 -GTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATCTCCTCA
* * * *
3487 ATTTTTGGCTAAAATACTCAT-AAAAATATATAATTCAATGCCATAATGATTGAAGAGCTTTTGA
371 A--TTT---T----TACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAG-GCTTTTCA
* * *
3551 CG-TTTCTAATATCGTTTTTCCAT-TTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATT
426 CGCTTT-TAATATCGATTTT-CATATTTTTCT-GAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * * * * *
3614 CAGATGCTCGAAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGATTAAACGAATTTAGAT
488 TAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAA-TTAGAT
* * * * * * * * *
3679 ATTTCAAGTAGTCTCGGAGCAAAAAATCATGCAAAATTAAGTCGGGTCCCCGAAA-GCGTTATTA
552 ATTTCAAGGAGTTTCGCA-CCAAAAACCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTA
* * **
3743 GC-CAAAAACTGTGATGGTTTGTTAG
616 GCAAAAAAACAGTGA------GACAG
* * * *
3768 TACACGATTTCAGCTAAAATTTTGCAAAAATTGACACA-AAAGAT-TTCTCTCCTGAATTCTTGG
1 TACACGATTTCAGCTAAAATTTTGCAAAAAATGAC-CAGAAAAATATTCTCT-C--AATTTTTAG
* * ** * * * *
3831 CTA-ATATACTCAT-AAAAATATATAGTTCAGCGCCAAAAAGATTGGAGGGCTTTTTACGCTTTT
62 CCACA-ATACTCATAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGCTTTTCACGCTTCT
* * **** * **
3894 AATATCGTATTT-CT-TATTTTTTAAAAAATTAATTTCTAATTAAATCGAAACAAAATTCAAATG
126 AATATCGTTTTTCCTATTTTTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAAATG
* *
3957 CTCGTAAAA
191 TTTGTAAAA
3966 GAAATTCTTA
Statistics
Matches: 1809, Mismatches: 224, Indels: 223
0.80 0.10 0.10
Matches are distributed among these distances:
631 43 0.02
632 1 0.00
634 2 0.00
636 77 0.04
637 29 0.02
638 4 0.00
639 142 0.08
640 38 0.02
641 130 0.07
642 7 0.00
643 200 0.11
644 4 0.00
645 29 0.02
646 84 0.05
647 220 0.12
648 159 0.09
649 207 0.11
650 34 0.02
651 69 0.04
652 3 0.00
653 4 0.00
654 1 0.00
655 5 0.00
656 4 0.00
658 2 0.00
660 2 0.00
661 1 0.00
662 3 0.00
663 3 0.00
664 29 0.02
665 117 0.06
666 99 0.05
667 16 0.01
668 41 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (635 bp):
TACACGATTTCAGCTAAAATTTTGCAAAAAATGACCAGAAAAATATTCTCTCAATTTTTAGCCAC
AATACTCATAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGCTTTTCACGCTTCTAATAT
CGTTTTTCCTATTTTTTTTTCCGAATTAATTTCTAATTAAAACGAAACATGATTCAAATGTTTGT
AAAAACAATGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAAT
CATCAAAATTGAACCGGGCCCTGAAACGCGTTTTTAGCCAAAAATCGTGATGATTATTACACGAT
TTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATCTCCTCAATTTTTACTCATAAAAAATA
TATAATTCAACGCCAAAAAGATTGAAGGCTTTTCACGCTTTTAATATCGATTTTCATATTTTTCT
GAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAA
TGTGGCTAAGATTTTATTAGATGAATTAGATATTTCAAGGAGTTTCGCACCAAAAACCATGCAAA
ACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAAACAGTGAGACAG
Found at i:3299 original size:318 final size:316
Alignment explanation
Indices: 2850--4006 Score: 876
Period size: 318 Copynumber: 3.5 Consensus size: 316
2840 TTTTAGTCAT
* **
2850 AATACTCATAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATC
1 AATACTCATAAAAATATATAATTCAACGCCAAAAAAATTGAAGAACTTTTCACGCTTTTAATATC
* * * * *
2915 GTTTTTCATATTTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTTAGGTGCTCGTAAAA
66 ATTTTTCATATTTTTTCAGAATCAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAA
* * * *
2980 ACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGATTGTC
131 ACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATCTCAAGGATTCTC
*
3045 GGCACCAAAAACCATGCAAAACTGAGCCGGGGCCCCG-A-AACATGCGTTTTTAGCCAAAAACCG
196 GGCACAAAAAACCATGCAAAACTGAGCCGGGG--CCGTAGAAC--GCGTTTTTAGCCAAAAACCG
3108 TGATGACCCGAAAAACTTTGCAAAAAATGACCCGAAAAGTTTTTCCCTATTTCTAGATAA
257 TGATGACCCGAAAAACTTTGCAAAAAATGACCCGAAAAGTTTTTCCCTATTTCTAGATAA
* * *
3168 AATACTCATAAAATATATATAATTTAATGCCAAAAAAATTGGAGAACTTTTCACGCTTTTAATAT
1 AATACTCATAAAA-ATATATAATTCAACGCCAAAAAAATTGAAGAACTTTTCACGCTTTTAATAT
* * *
3233 CAATTTTT-ATA-TTTTTCTGAATCAATTTCTAATTAAATCGAAACAGGATTCAGATACTTGTAA
65 C-ATTTTTCATATTTTTTCAGAATCAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAA
** * * *
3296 AAACAAATTTTTCAATCCAATGTGGCTGAGATTTGATTAGATGAATATGGATATCTCAAGGATTC
129 AAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATCTCAAGGATTC
* ** * * * *
3361 TTGGCGTAAAAAATCATGCAAAACTGAGCTGGGGCCGTAGAACGCTTTTTTAGCCAAAAACTGTG
194 TCGGCACAAAAAACCATGCAAAACTGAGCCGGGGCCGTAGAACGCGTTTTTAGCCAAAAACCGTG
** * * ** *** * * *
3426 ATGTTTATTACATGATTTTGGCTAAAATTTTGTAAAAGTTGATTAGAAAAATATTTCCTCAATTT
259 ATG------ACCCGA--------AAAACTTTGCAAAAAATGACCCGAAAAGTTTTTCC-CTATTT
* * *
3491 TTGGCTAA
309 CTAGATAA
* * ** * *
3499 AATACTCATAAAAATATATAATTCAATGCCATAATGATTGAAGAGCTTTTGACG-TTTCTAATAT
1 AATACTCATAAAAATATATAATTCAACGCCAAAAAAATTGAAGAACTTTTCACGCTTT-TAATAT
* * * * *
3563 CGTTTTTCCATTTTTTTTCA-AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGAAA
65 CATTTTT-CATATTTTTTCAGAATCAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAA
* * * * * * * *
3627 AAACAAATCCTTAAATCCAATGTGACTGAGATTTGATTAAACGAATTTAGATATTTCAAGTAGTC
129 AAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATCTCAAGGATTC
* * * * * ** * * *
3692 TCGG-AGCAAAAAATCATGCAAAATTAAGTCGGGTCC-CCGAAAGCGTTATTAGCCAAAAACTGT
194 TCGGCA-CAAAAAACCATGCAAAACTGAGCCGGGGCCGTAGAACGCGTTTTTAGCCAAAAACCGT
* * * * *
3755 GATGGTTTGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACAC-AAAAGATTTCTCTC
258 GA--------T-G-AC-C-----C-G-AAAAACTTTGCAAAAAATGACCCGAAAAG-TTTTTC-C
* * *
3819 CTGAATTCTTGGCTAA
303 CT-ATTTC-TAGATAA
* * * * * ** *
3835 TATACTCATAAAAATATATAGTTCAGCGCCAAAAAGATTGGAGGGCTTTTTACGCTTTTAATATC
1 AATACTCATAAAAATATATAATTCAACGCCAAAAAAATTGAAGAACTTTTCACGCTTTTAATATC
* * * * * * * * *
3900 GTATTTCTTATTTTTTAAAAAATTAATTTCTAATTAAATCGAAACAAAATTCAAATGCTCGT-AA
66 ATTTTTCATATTTTTT-CAGAATCAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAA
* * * * *
3964 AAGAAATTCTTAAATCCAATGTTGCTGAGATTTGGTTAGATGA
130 AACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGA
4007 TGTAAAGTGT
Statistics
Matches: 669, Mismatches: 122, Indels: 78
0.77 0.14 0.09
Matches are distributed among these distances:
316 26 0.04
317 1 0.00
318 145 0.22
319 49 0.07
320 5 0.01
322 4 0.01
329 8 0.01
330 91 0.14
331 145 0.22
332 6 0.01
333 4 0.01
334 25 0.04
335 12 0.02
336 103 0.15
337 42 0.06
338 1 0.00
339 1 0.00
341 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (316 bp):
AATACTCATAAAAATATATAATTCAACGCCAAAAAAATTGAAGAACTTTTCACGCTTTTAATATC
ATTTTTCATATTTTTTCAGAATCAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAA
ACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATCTCAAGGATTCTC
GGCACAAAAAACCATGCAAAACTGAGCCGGGGCCGTAGAACGCGTTTTTAGCCAAAAACCGTGAT
GACCCGAAAAACTTTGCAAAAAATGACCCGAAAAGTTTTTCCCTATTTCTAGATAA
Found at i:4641 original size:3 final size:3
Alignment explanation
Indices: 4633--4676 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4623 TTTTATATAG
4633 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4677 TAAGATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5463 original size:6 final size:7
Alignment explanation
Indices: 5447--5476 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5437 TCACTATAGG
*
5447 AAAAGCA
1 AAAAACA
5454 AAAAACA
1 AAAAACA
5461 AAAAACA
1 AAAAACA
5468 AAAAACA
1 AAAAACA
5475 AA
1 AA
5477 GGTGTCCCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:7515 original size:20 final size:20
Alignment explanation
Indices: 7471--7515 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
7461 ATTTTCTTCT
* *
7471 TCTCCATATTTCATTGTCTC
1 TCTCCATACTTCAATGTCTC
7491 TCTCCATACTTCAAT-TCTC
1 TCTCCATACTTCAATGTCTC
7510 TACTCC
1 T-CTCC
7516 CTTGCTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.36, G:0.02, T:0.44
Consensus pattern (20 bp):
TCTCCATACTTCAATGTCTC
Found at i:10316 original size:15 final size:14
Alignment explanation
Indices: 10296--10326 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
10286 ACCATTTAGG
10296 TTTAGAGTTTTTTTT
1 TTTAGA-TTTTTTTT
10311 TTTAGATTTTTTTT
1 TTTAGATTTTTTTT
10325 TT
1 TT
10327 GTCCACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (14 bp):
TTTAGATTTTTTTT
Found at i:13381 original size:2 final size:2
Alignment explanation
Indices: 13374--13406 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13364 AAATTGAGAC
13374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13407 TTTGGGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18095 original size:15 final size:15
Alignment explanation
Indices: 18071--18100 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18061 GCACTGAAGG
*
18071 AAAGGCAAAGAGAGC
1 AAAGGAAAAGAGAGC
18086 AAAGGAAAAGAGAGC
1 AAAGGAAAAGAGAGC
18101 TTGATGATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.10, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAGGAAAAGAGAGC
Found at i:20204 original size:13 final size:13
Alignment explanation
Indices: 20186--20211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20176 TGATTTTTAG
20186 ATTATATATGCGT
1 ATTATATATGCGT
20199 ATTATATATGCGT
1 ATTATATATGCGT
20212 TATAATTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTATATATGCGT
Found at i:28165 original size:30 final size:32
Alignment explanation
Indices: 28121--28185 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
28111 AACAACTTTA
28121 AATTAGTTCTTCAAAAATAATTTTATACT-TG
1 AATTAGTTCTTCAAAAATAATTTTATACTCTG
* * * *
28152 AATTTGTTC-TCAAAAGTCATTTTTTACTCTG
1 AATTAGTTCTTCAAAAATAATTTTATACTCTG
28183 AAT
1 AAT
28186 CTAAATTACG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (32 bp):
AATTAGTTCTTCAAAAATAATTTTATACTCTG
Found at i:28837 original size:19 final size:19
Alignment explanation
Indices: 28809--28848 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28799 TAATAATAAT
* * *
28809 ATCATTACACCTAATAGGG
1 ATCATGACACCAAATAAGG
28828 ATCATGACACCAAATAAGG
1 ATCATGACACCAAATAAGG
28847 AT
1 AT
28849 AAGTTTTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (19 bp):
ATCATGACACCAAATAAGG
Found at i:30876 original size:32 final size:32
Alignment explanation
Indices: 30832--30928 Score: 124
Period size: 32 Copynumber: 3.0 Consensus size: 32
30822 TTTTTGCAAA
* *
30832 TAGTGGCGTTTATTCAGTAAAACGCCACTAAT
1 TAGTGGCATTTATTAAGTAAAACGCCACTAAT
*
30864 TAGTGGCATTTATTGAGTAAAACGCCACTAAT
1 TAGTGGCATTTATTAAGTAAAACGCCACTAAT
* * *
30896 TAGTGGCGTTTTATGAAG-AAAACGCCCCTAAT
1 TAGTGGC-ATTTATTAAGTAAAACGCCACTAAT
30928 T
1 T
30929 TGCAATCCAG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 51 0.88
33 7 0.12
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (32 bp):
TAGTGGCATTTATTAAGTAAAACGCCACTAAT
Found at i:31681 original size:15 final size:15
Alignment explanation
Indices: 31661--31727 Score: 68
Period size: 15 Copynumber: 4.7 Consensus size: 15
31651 TGAAGTTGGT
31661 GATGATGCAAATGTA
1 GATGATGCAAATGTA
*
31676 GATGATGCAAATATA
1 GATGATGCAAATGTA
* **
31691 GGTGAT---TTTGTA
1 GATGATGCAAATGTA
31703 GATGATGCAAATGTA
1 GATGATGCAAATGTA
*
31718 GGTGATGCAA
1 GATGATGCAA
31728 GGGACGAAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
12 8 0.20
15 32 0.80
ACGTcount: A:0.36, C:0.06, G:0.28, T:0.30
Consensus pattern (15 bp):
GATGATGCAAATGTA
Found at i:31710 original size:27 final size:27
Alignment explanation
Indices: 31672--31723 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
31662 ATGATGCAAA
31672 TGTAGATGATGCAAATATAGGTGATTT
1 TGTAGATGATGCAAATATAGGTGATTT
*
31699 TGTAGATGATGCAAATGTAGGTGAT
1 TGTAGATGATGCAAATATAGGTGAT
31724 GCAAGGGACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (27 bp):
TGTAGATGATGCAAATATAGGTGATTT
Found at i:32887 original size:33 final size:33
Alignment explanation
Indices: 32770--32892 Score: 142
Period size: 33 Copynumber: 3.7 Consensus size: 33
32760 GCTTGCAAGA
*
32770 ATTGAAGAAGAAAGAAGACAA-GAGCTGGCTCGC
1 ATTGAAGAAGAAAGAAGA-AATGAGCTAGCTCGC
* * * *
32803 ATTGAAGAAGATAGACGACAGGAGCTAGCTCG-
1 ATTGAAGAAGAAAGAAGAAATGAGCTAGCTCGC
*
32835 AGTTGAAGAAGAGAGAAGAAATGAGCTAGCTCGC
1 A-TTGAAGAAGAAAGAAGAAATGAGCTAGCTCGC
* *
32869 CTTGAAGAAGACAGAAGAAATGAG
1 ATTGAAGAAGAAAGAAGAAATGAG
32893 ATTAATCGTT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.03
33 75 0.97
ACGTcount: A:0.42, C:0.13, G:0.31, T:0.14
Consensus pattern (33 bp):
ATTGAAGAAGAAAGAAGAAATGAGCTAGCTCGC
Done.