Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017764.1 Corchorus olitorius cultivar O-4 contig17797, 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: 53480
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:399 original size:13 final size:13
Alignment explanation
Indices: 381--405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
371 CGAAATAAGT
381 AACCAATCACTTG
1 AACCAATCACTTG
394 AACCAATCACTT
1 AACCAATCACTT
406 ATTGAAAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.32, G:0.04, T:0.24
Consensus pattern (13 bp):
AACCAATCACTTG
Found at i:6606 original size:31 final size:31
Alignment explanation
Indices: 6569--6756 Score: 193
Period size: 31 Copynumber: 6.1 Consensus size: 31
6559 ACGGTGTCCA
* *
6569 ACGTGGCATGCCACGTGTATCAAAAAGCGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
*
6600 ATGTGGCACGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
*
6631 ACGTGGCACACCA-GATGTACCAAAAAGCGAC
1 ACGTGGCACGCCACG-TGTACCAAAAAGCGAC
* * * *
6662 ATGTGGCACACCACATGTACCAAAAAGTGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAA--GCGAC
* * *
6695 ACGTGTCACGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
* * * *
6726 ACGTGACATGCCTCGTGCA-CAAAAAG-GAC
1 ACGTGGCACGCCACGTGTACCAAAAAGCGAC
6755 AC
1 AC
6757 CTGCCATGTG
Statistics
Matches: 135, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
29 5 0.04
30 8 0.06
31 97 0.72
33 25 0.19
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGCGAC
Found at i:7377 original size:25 final size:27
Alignment explanation
Indices: 7346--7404 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
7336 TTTCTTTTAT
*
7346 TTTTTTTTGTCACCAAATTACGAAATTA
1 TTTTTGTTG-CACCAAATTACGAAATTA
*
7374 TTTTTGTTGGCATCAAATTACGAAATTA
1 TTTTTGTT-GCACCAAATTACGAAATTA
7402 TTT
1 TTT
7405 ATGTGCTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (27 bp):
TTTTTGTTGCACCAAATTACGAAATTA
Found at i:17818 original size:21 final size:19
Alignment explanation
Indices: 17775--17828 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
17765 GTTTAGCAAT
17775 TGTACAGATGAGATTACAC
1 TGTACAGATGAGATTACAC
* *
17794 TGTACAGATTAGATTAGGTAC
1 TGTACAGATGAGATTA--CAC
17815 TGTACAGATGAGAT
1 TGTACAGATGAGAT
17829 CATTAGAGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (19 bp):
TGTACAGATGAGATTACAC
Found at i:29964 original size:17 final size:17
Alignment explanation
Indices: 29942--29977 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29932 ACCGCCGGTG
29942 TATTGTATAATTTGCCC
1 TATTGTATAATTTGCCC
29959 TATTGTATAATTTGCCC
1 TATTGTATAATTTGCCC
29976 TA
1 TA
29978 AATAAGTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (17 bp):
TATTGTATAATTTGCCC
Found at i:30762 original size:60 final size:60
Alignment explanation
Indices: 30691--30828 Score: 231
Period size: 60 Copynumber: 2.3 Consensus size: 60
30681 AACGTTTGTC
*
30691 AAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGCCAAATAAGGGCCCAACGTTATCG
1 AAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGCCAAATAAGGGCCCAACGTTATCA
* * *
30751 AAAATGGTCAAATAAGGGTCCGATTTTTTAATTTGGCCAAATAAGGGCCTAACGTTATCA
1 AAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGCCAAATAAGGGCCCAACGTTATCA
*
30811 AAAATACTCAAATAAGGG
1 AAAATGCTCAAATAAGGG
30829 CATGACGTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGCCAAATAAGGGCCCAACGTTATCA
Found at i:30766 original size:31 final size:31
Alignment explanation
Indices: 30728--30829 Score: 82
Period size: 31 Copynumber: 3.4 Consensus size: 31
30718 TTAATTTGGC
*
30728 CAAATAAGGGCCCAACGTTATCGAAAATGGT
1 CAAATAAGGGCCCAACGTTATCAAAAATGGT
* * * ** ** *
30759 CAAATAAGGGTCCGA--TTTTTTAATTTGGC
1 CAAATAAGGGCCCAACGTTATCAAAAATGGT
* **
30788 CAAATAAGGGCCTAACGTTATCAAAAATACT
1 CAAATAAGGGCCCAACGTTATCAAAAATGGT
30819 CAAATAAGGGC
1 CAAATAAGGGC
30830 ATGACGTCAG
Statistics
Matches: 50, Mismatches: 19, Indels: 4
0.68 0.26 0.05
Matches are distributed among these distances:
29 20 0.40
31 30 0.60
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCCAACGTTATCAAAAATGGT
Found at i:30797 original size:29 final size:29
Alignment explanation
Indices: 30699--30797 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
30689 TCAAAATGCT
*
30699 CAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGTCCGATTTTTTAATTTGGC
* * * ** ** *
30728 CAAATAAGGGCCCAACGTTATCGAAAATGGT
1 CAAATAAGGGTCCGA--TTTTTTAATTTGGC
30759 CAAATAAGGGTCCGATTTTTTAATTTGGC
1 CAAATAAGGGTCCGATTTTTTAATTTGGC
30788 CAAATAAGGG
1 CAAATAAGGG
30798 CCTAACGTTA
Statistics
Matches: 51, Mismatches: 17, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
29 31 0.61
31 20 0.39
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGTCCGATTTTTTAATTTGGC
Found at i:30969 original size:60 final size:60
Alignment explanation
Indices: 30876--31006 Score: 208
Period size: 60 Copynumber: 2.2 Consensus size: 60
30866 CGCCAGACCC
* * ** *
30876 TTATTTAAGCATTTTGGCAAACGTTAGGTCCTTATTTGGCCAAATTAAAAGATCGGGCCA
1 TTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGGCCAAATTAAAAGATCAGGCCA
*
30936 TTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGGCCAAATTAAAAGATCAGGCCC
1 TTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGGCCAAATTAAAAGATCAGGCCA
30996 TTATTTGAGCA
1 TTATTTGAGCA
31007 AATTAGCCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (60 bp):
TTATTTGAGCATTTTGGCAAACATTAGACCCTTATTTGGCCAAATTAAAAGATCAGGCCA
Found at i:30999 original size:29 final size:29
Alignment explanation
Indices: 30905--31011 Score: 92
Period size: 29 Copynumber: 3.6 Consensus size: 29
30895 AACGTTAGGT
*
30905 CCTTATTTG-GCCAAATTAAAAGATCGGGC
1 CCTTATTTGAG-CAAATTAAAAGATCAGGC
* ** * * * *
30934 CATTATTTGAGCATTTTGGCAAACATTAGAC
1 CCTTATTTGAGCAAATT--AAAAGATCAGGC
30965 CCTTATTTG-GCCAAATTAAAAGATCAGGC
1 CCTTATTTGAG-CAAATTAAAAGATCAGGC
30994 CCTTATTTGAGCAAATTA
1 CCTTATTTGAGCAAATTA
31012 GCCTTGATTA
Statistics
Matches: 58, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
29 36 0.62
30 3 0.05
31 19 0.33
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (29 bp):
CCTTATTTGAGCAAATTAAAAGATCAGGC
Found at i:32195 original size:17 final size:17
Alignment explanation
Indices: 32173--32209 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
32163 ATTTGAGTAG
32173 CTTGCGAATAGTCATCA
1 CTTGCGAATAGTCATCA
32190 CTTGCGAATAGTCATCA
1 CTTGCGAATAGTCATCA
32207 CTT
1 CTT
32210 ACACCACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (17 bp):
CTTGCGAATAGTCATCA
Found at i:40234 original size:12 final size:13
Alignment explanation
Indices: 40214--40246 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
40204 GGCTAGCCTG
40214 TATTAGTTGCCAA
1 TATTAGTTGCCAA
40227 TA-TAGTTGCCAA
1 TATTAGTTGCCAA
40239 TATTAGTT
1 TATTAGTT
40247 AGAGTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (13 bp):
TATTAGTTGCCAA
Found at i:47624 original size:650 final size:658
Alignment explanation
Indices: 44915--48842 Score: 3121
Period size: 650 Copynumber: 6.0 Consensus size: 658
44905 AGAGTTTCCA
* * * * * * * *
44915 AATGTGGCTGAGATTTGGTTAGATAAATAAAGATATTTCAACGAGTTTTCG-TGCGAAAAATCAA
1 AATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAG-TCTCGCT-CCAAAAATCAT
* * ** ** * * * *
44979 ACAAAACTGAGCTAGGAG-CCCAAAACGCGTTTTTAGCCAAACATCATGATAGTTAGTAAACGAT
64 GCAAAACTGAGC-CGG-GCCCCGGAACGAATTTTTAGCCAAAAATCGTGATGGTTAGTACACGAT
* * * * * * * **
45043 TTCGGGTAAAATTTTACAAAAGTTAACCCGAATTTTTTTTCCTCAATTCCTGGCCAAAATACTCA
127 TTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCA
* * *
45108 TAAACAA-CATATAATTCAACGCCAAAAACGATTGGAGGGCTTTTCACGCATCAAATATCA-TTT
192 TAAA-AAGTATATAATTTAACGCCAAAAA-GATTGGAGGGCTTTTCACGCTTCAAATATCATTTT
* * * * * *
45171 TCCTTATTTTTTTCTGAATTAATTTCTAATTAAA-GGAAGCCGATTTCAGATG-GTTGTAAAAAC
255 TCC-TATTTTTTTCAGAATTAATTTCTAATTAAATCGAAGCAGGTTTCAGATGCCTAGTAAAAAC
* * *
45234 ATATCCTTAAATCCAATGTGGCTGAGATATAATTAGATGAATATAGATATTTCAAGCAATCTCGG
319 ATATCCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTCAAGGAGTCTCGG
* * * * * ** * * *
45299 CTCCAAAAATCTTGCAAAACTGATCAACCGGGGTCCGGAACGCATTTTTAGCCCAAAACCGTGAT
384 CGCTAAAAATCATGCAAAACTGAGCTA---GGCCCCGAAACGCGTTTTTAG-CCATAA-CGTGA-
* * * * *
45364 GGTAAGTACACAATTTCAGCTAAAATTTTGCAAAAATTAACCTGGAAT-TTTTTTCTCAATTTTT
443 -GT-AG-ACACTATTTCAGCTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTTAATTTTT
** * * * * * *
45428 AACCAAAATACTCATAAAAATTATATATTTCAACGTCAGAAAA-ATTGGAGGGCTTTTCATGCTT
505 GGCCAAAATACTCATAAAAAGTATATAATTCAATGCCA-AAAAGATTGGAGGGCTTTTCACGATT
* * * ** *
45492 CAAATATCAT-TTTCCCTATTTTTTTTCTGAATTAA-TTACAAATTAAATCGAAGGCAGTTTCAG
569 CTAATAT-ATGTTTCCCT-TTTTTTTTCCGAATTAATTTTC-AATTAAATCGAAACCGGTTTCAG
*
45555 ATGCTCGTAAAAA-AAATCCTTAAATCC
631 ATGCTCGTAAAAACATATCCTTAAATCC
* * * ** *
45582 AATGTGGTTGAGATTTGATTAGATGAATATACATATTTCAAATAGTCTCGGTGCCAAAAATCATG
1 AATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGCT-CCAAAAATCATG
* * * * *
45647 CAAAATTGAGCCGGGTCCTGGAAC-AATTTTTTAGCCAAAAA--GT-AT-G--ATTACACGGTTT
65 CAAAACTGAGCCGGGCCCCGGAACGAA-TTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTT
* * *
45705 CGGCTAAAATTTTGCAAAAATTGACCCGAAATATTATTT-CTCAATTTTTGACTAAAATACTCAT
129 CGGCTAAAATTTTGCAAAAATTGACCCGAAATATT-TTTCCTTAATTTTTGGCCAAAATACTCAT
* * ** *
45769 AAAAAATATAT-ATTTCACGTAAAAAAGATTGGAGGGCTTTTCACGCTTCAAGTAT--TGTTTTC
193 AAAAAGTATATAATTTAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCAAATATCAT-TTTTC
* * ** * *
45831 CTTATGTTTTTT--GAATTAATTTTTAATGAGTTCGAAGCTGGTTTCAGATG-CTCGTAAAAACA
257 C-TAT-TTTTTTCAGAATTAATTTCTAATTAAATCGAAGCAGGTTTCAGATGCCTAGTAAAAACA
* * * *
45893 TATCCTTAAATCCAATGTGACTAAGATTTAATTAGATGAGTATAGATATTTAAAGGAGTCTCGGC
320 TATCCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTCAAGGAGTCTCGGC
* * * * * * * *
45958 -CCAAAAATCATGCAAAGCTAAGTTGGGGCCCCGAAACGCATTTTCAGCCAAATACCGTGA-T-G
385 GCTAAAAATCATGCAAAACTGAGCT-AGGCCCCGAAACGCGTTTTTAGCC--ATAACGTGAGTAG
*** * * * * *
46020 --A-T-TTCTGCAAAAAAAATGTTGCAAAAATTGACCGGAAATAATTTTT-CTCAATTTTTGACG
447 ACACTATT-T-CAGCTAAAATTTTGCAAAAATTGACCTGAAAT-ATTTTTCCTTAATTTTTGGCC
* * * *
46080 AAAATACTCATAAAAAATATATATTTCAATGCCAAAAAGATTGGAGGGATTTTCACGATTCAAAT
509 AAAATACTCATAAAAAGTATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACGATTCTAAT
* * * **
46145 ATCAT-TTTTCC-TATTTTTTCTGAATTAA-TTTCTAATTAAATCGAAGTCGGTTTCAGATGCTC
574 AT-ATGTTTCCCTTTTTTTTTCCGAATTAATTTTC-AATTAAATCGAAACCGGTTTCAGATGCTC
*
46207 GT--AAACATATCCTTAAATTC
637 GTAAAAACATATCCTTAAATCC
* *
46227 AATGTGGCTAAGATTT-AGTTAGA-G--TAT--ATATAT-AA--A---T---ACCAAAAATCATG
1 AATGTGGCTAAGATTTGA-TTAGATGAATATAGATATTTCAAGGAGTCTCGCTCCAAAAATCATG
* * * *
46277 CAAAACTGAGCCGAAGTCCCGGAACG-GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT
65 CAAAACTGAGCCG-GGCCCCGGAACGAATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTT
** * * * * * *
46341 TAGCTAAAATTTTGCAAAAATTGA-CC-AATTTTTTTTCATGAATTTTTGGTCATAATACTCATA
129 CGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATA
* * ** * * * * **
46404 AAAAGTATATAATTGAACGCCAGAAAGATTAAAGGGCTTTTTATGCTTCTAATAACATTTTTTAT
194 AAAAGTATATAATTTAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCAAATATCATTTTTCCT
* * * * * *
46469 ATTTTTTCCA-AATTAATTTCTGATTAAA-CAAAACAAGATACATAT-ATATG-CTCA-TAAAAA
259 ATTTTTTTCAGAATTAATTTCTAATTAAATCGAAGC-AGGT---T-TCAGATGCCT-AGTAAAAA
* * * * * *
46529 TATATCCTTAAATCCAATATGGCTGAGATTTGATTCGATGAATATAAATATTTCAAGAAGTCTCG
318 CATATCCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTCAAGGAGTCTCG
** * * *
46594 GCGCTAAAAATCATGCAAAACT-A-AAACGGACCTCGGAACGCGTTTTTAGGCAATAACCGTGAT
383 GCGCTAAAAATCATGCAAAACTGAGCTA-GG-CCCCGAAACGCGTTTTTA-GCCATAA-CGTGA-
* * * * *
46657 GATTAGTACA-TGATTTCGGCTAAAATTTTGCAAAAATTTAACTAAAATA-TTTTCCCTAATTTT
443 G--TAG-ACACT-ATTTCAGCTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTTAATTTT
** * ** *
46720 TGGAAAAAATACTCATAAAAAGTATATAATTCAATGTCAAAACTATTGGAGGGCTTTTCACGCTT
504 TGGCCAAAATACTCATAAAAAGTATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACGATT
* * *** * * *
46785 CTAATAT-CGTTTTTCCTAAATATTTCTC-AGTAAATTTTCAGATTAAATCGAAACCGGTTTCAG
569 CTAATATATG-TTTCCCTTTTTTTTTC-CGAATTAATTTTCA-ATTAAATCGAAACCGGTTTCAG
* *
46848 ATGCTCGTAAAAACATATACTTTAATCC
631 ATGCTCGTAAAAACATATCCTTAAATCC
* * * * * *
46876 AACGGGGC-AGATATTTGATTAGATGAATTTAGATATTTCAAGGAGTCTCGGCGCCAAAAATTAT
1 AATGTGGCTA-AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-GCTCCAAAAATCAT
* * * ** *
46940 ACAAAACT-ATGCCGGGCCTCGGAATGCGTTTTTAGCAAAAAATCGTGATGGTTAGTACACGATT
64 GCAAAACTGA-GCCGGGCCCCGGAACGAATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATT
* *
47004 TCGGCTAAAATTTTGCAGAAATTGACCCGAAATATTTTTCCTTAAGTTTTGGCCAAAATACTCAT
128 TCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCAT
*
47069 AAAAAGTATATAATTTAATGCCAAAAAGATTGGA-GGCTTTTCACGCTTCAAATATCATTTTTCC
193 AAAAAGTATATAATTTAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCAAATATCATTTTT-C
** * * * *
47133 CT-TTTTTTTCAGAATTAAAAATCTAATGAAATCGAAGTC-GGCTTCATATGCCT-GTAAATA-A
257 CTATTTTTTTCAGAATT-AATTTCTAATTAAATCGAAG-CAGGTTTCAGATGCCTAGTAAAAACA
* * **
47194 TATCCTTAAATCCAATGTGGCTGAGATTTAATTAGATTAATATATATATTTCCTGGAGTCTCGGC
320 TATCCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTCAAGGAGTCTCGGC
*
47259 GCTAAAAATCATGCAAAACTGAGCTAGGCCCCGGAACGCGTTTTTAG-C-TAA-GTGA-TA-ACA
385 GCTAAAAATCATGCAAAACTGAGCTAGGCCCCGAAACGCGTTTTTAGCCATAACGTGAGTAGACA
* * *
47319 -TACTTCAGCAAAAATTTTGTAAAAATTGACCTGAAATATTTTTCCTTAATTTTTGGCCAAAATA
450 CTATTTCAGCTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTTAATTTTTGGCCAAAATA
* * * *
47383 CTCATAAAAAGTAAATAATT-AAGTGCCAAAAAGGTTGGAGGGCTTTTCACGCTTTTAATAT-TG
515 CTCATAAAAAGTATATAATTCAA-TGCCAAAAAGATTGGAGGGCTTTTCACGATTCTAATATATG
* * * *
47446 TTTCCCTTTTTTTTTCCGAATTACTTTTTAATTAAATCAAAACCGGTTTCAGATGCTTGTAAAAA
579 TTTCCCTTTTTTTTTCCGAATTAATTTTCAATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAA
* * *
47511 CATATCCTTTACTGC
644 CATATCCTTAAATCC
* * * *
47526 AATGTGGCTAAGAGTTGATTAGATGAATATAAATATTTCAAGGAGTCTTGCCTCCATAAATCATG
1 AATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCG-CTCCAAAAATCATG
* ** *
47591 CAAAAGTGAGCCGGGCCCCATAACGAATTTTTAGCCAAAAATCGTGATGGTTTGTACACGATTTC
65 CAAAACTGAGCCGGGCCCCGGAACGAATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTC
* *
47656 GGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCATGA
130 GGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATAA
* * *
47721 AAAGTATATAATTTAATGCGAAAAAGATTGGAGGGCTTTTCACGCTTCGAATATCATTTTTCCTA
195 AAAGTATATAATTTAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCAAATATCATTTTTCCTA
* * * * * *
47786 -TTTTTTCTA-AATTAATTTTTAATTTAATCGAAGCTGGTTTCGGATG-CTTGTAAAAACTTATC
260 TTTTTTTC-AGAATTAATTTCTAATTAAATCGAAGCAGGTTTCAGATGCCTAGTAAAAACATATC
* * * *
47848 CTTAAATCCAATATGGATGAGATTTAATTAGATGAATATATATATATCTCAAGGAGTCTCGGTGC
324 CTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATAT-T-TCAAGGAGTCTCGGCGC
* * * * * * *
47913 TAAAAATCTTGCAAAATTGAGCTGGGGCCACGAAACGCGTTTTTAGCTAAAAACCGTG-TTAGTA
387 TAAAAATCATGCAAAACTGAGCT-AGGCCCCGAAACGCGTTTTTAGC-CATAA-CGTGAGTAG-A
* ** ** *** * * * * *
47977 CACGATTTTGGCTAATTTTTTGCAAAAATTGACAAAAAAAAAATTTTCCTAAATTTTTGTCCACA
448 CACTATTTCAGCTAAAATTTTGCAAAAATTGAC-CTGAAATATTTTTCCTTAATTTTTGGCCAAA
* * *
48042 ATAAC-CAT-AAAAGATATATAGTTCATTCAATGCCAAAAAAATTGAAGGGCTTTTCAAGATTCT
512 AT-ACTCATAAAAAG-TATATA----ATTCAATGCCAAAAAGATTGGAGGGCTTTTCACGATTCT
* * * *
48105 AATATCATTTTTCCTATTTTTTTTTCC------A-----AATTAAA-C--AA---GATTCAGATT
571 AATAT-ATGTTTCC-CTTTTTTTTTCCGAATTAATTTTCAATTAAATCGAAACCGGTTTCAGATG
*
48153 CTCGTAAAAACA-CTCCTTAAATCC
634 CTCGTAAAAACATATCCTTAAATCC
* * * * * *
48177 AATGTGGTTGAGATTTGATTAGATAAATATAGATATTCCAATGAGTCTCGGCTCTAAAAA-CAAT
1 AATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-GCTCCAAAAATC-AT
** * *
48241 GCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTTAGCCAAAAATCGTGTTGGTTGGTACACGATT
64 GCAAAACTGAGCCGGGCCCCGGAACG-AATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATT
* * **
48306 TCGGTTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTTAATTTTTGGAAAAAATACTCAT
128 TCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCAT
* * * * * * * ** * *
48371 -AAAAGTATATAATTCAATGTCAAAAAGGTTGAAGGGCTATTCACACTTTTACTATCATTTTCCC
193 AAAAAGTATATAATTTAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCAAATATCATTTTTCC
* * * * * * * **
48435 TGTTTTTTCCAAAATTAATTTCTAATTAAACCAAAAG-TGGTTTCAAATGCTCATAAAAAAAATC
258 TATTTTTTTCAGAATTAATTTCTAATTAAATC-GAAGCAGGTTTCAGATGC-C-TAGTAAAAA--
* * * * *
48499 CCATTATCCTTTAATCCAATGTGACTAAGATTTGATTAGATGAATATAGATATTTCAGGGAGTCT
318 -CA-TATCCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTCAAGGAGTCT
* ** * * * *
48564 CGGCGCTAAAAATCATGCAAAGCTGAGCCGGGCCCTGAAACACGGTTTTAGCCAAAAACCGTGAT
381 CGGCGCTAAAAATCATGCAAAACTGAGCTAGGCCCCGAAACGCGTTTTTAGCC-ATAA-CGTGA-
* * * *
48629 GGTGAGGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCTTTAGTTTT
443 -GT-A-G-ACACTATTTCAGCTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTTAATTTT
* * * * * *
48694 TGGCAAAAATACTCA-AAAAAGTATATAATTAAATACCAAATAGGTTGGAGGGCTTTTCACTATT
504 TGGCCAAAATACTCATAAAAAGTATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACGATT
* * * * *
48758 TTAATAT-TGTTTTCTCTATTTTTTTTTTTCAGAATT-AGTTTCATATTAAATCGAAACCAGTTT
569 CTAATATATG-TTTC-C---CTTTTTTTTTCCGAATTAATTTTCA-ATTAAATCGAAACCGGTTT
48821 CAGATGCTCGTAAAAACATATC
628 CAGATGCTCGTAAAAACATATC
48843 ACTCGATATA
Statistics
Matches: 2630, Mismatches: 459, Indels: 336
0.77 0.13 0.10
Matches are distributed among these distances:
630 38 0.01
631 9 0.00
632 2 0.00
633 5 0.00
634 45 0.02
635 52 0.02
636 36 0.01
637 7 0.00
638 90 0.03
639 22 0.01
640 5 0.00
642 4 0.00
643 1 0.00
644 9 0.00
645 108 0.04
646 85 0.03
647 63 0.02
648 82 0.03
649 66 0.03
650 306 0.12
651 218 0.08
652 264 0.10
653 23 0.01
654 14 0.01
655 68 0.03
656 32 0.01
657 80 0.03
658 138 0.05
659 70 0.03
660 103 0.04
661 62 0.02
662 36 0.01
663 109 0.04
664 93 0.04
665 38 0.01
666 122 0.05
667 73 0.03
668 15 0.01
669 13 0.00
671 2 0.00
674 20 0.01
675 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (658 bp):
AATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGCTCCAAAAATCATGC
AAAACTGAGCCGGGCCCCGGAACGAATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCG
GCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATAAA
AAGTATATAATTTAACGCCAAAAAGATTGGAGGGCTTTTCACGCTTCAAATATCATTTTTCCTAT
TTTTTTCAGAATTAATTTCTAATTAAATCGAAGCAGGTTTCAGATGCCTAGTAAAAACATATCCT
TAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCTAAA
AATCATGCAAAACTGAGCTAGGCCCCGAAACGCGTTTTTAGCCATAACGTGAGTAGACACTATTT
CAGCTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATA
AAAAGTATATAATTCAATGCCAAAAAGATTGGAGGGCTTTTCACGATTCTAATATATGTTTCCCT
TTTTTTTTCCGAATTAATTTTCAATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCC
TTAAATCC
Found at i:47754 original size:331 final size:331
Alignment explanation
Indices: 44915--48842 Score: 3096
Period size: 331 Copynumber: 12.0 Consensus size: 331
44905 AGAGTTTCCA
* * * * * *
44915 AATGTGGCTGAGATTTGGTTAGATAAATAAAGATATTTCAACGAGTTTTC-G-TGCGAAAAATCA
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG-TCTCGGCT-CCAAAAATCA
** * ** * * * * *
44978 AACAAAACTGAGCTAGGAG-CCCAAAACGCGTTTTTAGCCAAACATCATGATAGTTAGTAAACGA
64 TGCAAAACTGAGC-CGG-GCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
* * * * * * **
45042 TTTCGGGTAAAATTTTACAAAAGTTAACCCG-AATTTTTTTTCCTCAATTCCTGGCCAAAATACT
127 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTT-CTTAATTTTTGGCCAAAATACT
* * * * *
45106 CATAAACAA-CATATAATTCAACGCCAAAAACGATTGGAGGGCTTTTCACGCATCAAATATCATT
191 CATAAA-AAGTATATAATTTAATGCCAAAAA-GATTGGAGGGCTTTTCACGCTTCTAATAT-ATT
* * * * * *
45170 TT-CCTTATTTTTTTCTGAATTAATTTCTAATTAAA-GGAAGCCGATTTCAGATGGTTGTAAAAA
253 TTCCCTT-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAA
45233 CATATCCTTAAATCC
317 CATATCCTTAAATCC
* * * * *
45248 AATGTGGCTGAGATATAATTAGATGAATATAGATATTTCAAGCAATCTCGGCTCCAAAAATCTTG
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCTCCAAAAATCATG
* ** * * * *
45313 CAAAACTGATCAACCGGGGTCCGGAACGCATTTTTAGCCCAAAACCGTGATGGTAAGTACACAAT
66 CAAAACTG---AGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAT
* * * * * **
45378 TTCAGCTAAAATTTTGCAAAAATTAACCTGGAAT-TTTTTTCTCAATTTTTAACCAAAATACTCA
128 TTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCA
* * * * *
45442 TAAAAATTATAT-ATTTCAACGTCAGAAAA-ATTGGAGGGCTTTTCATGCTTCAAATATCATTTT
193 TAAAAAGTATATAATTT-AATGCCA-AAAAGATTGGAGGGCTTTTCACGCTTCTAATAT-ATTTT
* * * ** *
45505 CCCTATTTTTTTTCTGAATTAATTACAAATTAAATCGAAGGCAGTTTCAGATGCTCGTAAAAA-A
255 CCCT-TTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACA
*
45569 AATCCTTAAATCC
319 TATCCTTAAATCC
* * **
45582 AATGTGGTTGAGATTTGATTAGATGAATATACATATTTCAAATAGTCTCGG-TGCCAAAAATCAT
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCT-CCAAAAATCAT
* * * *** * *
45646 GCAAAATTGAGCCGGGTCCTGGAACAATTTTTTAGCCAAAAA--GT-AT-G--ATTACACGGTTT
65 GCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT
* * * *
45705 CGGCTAAAATTTTGCAAAAATTGACCCGAAATATTATTTCTCAATTTTTGACTAAAATACTCATA
130 CGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCATA
* * * ** *
45770 AAAAATATAT-ATTTCACGTAAAAAAGATTGGAGGGCTTTTCACGCTTC-AAGTAT-TGTTTTCC
195 AAAAGTATATAATTTAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAA-TATAT-TTTCCC
* * ** * *
45832 TTATGTTTTTT--GAATTAATTTTTAATGAGTTCGAAGCTGGTTTCAGATGCTCGTAAAAACATA
258 TT-T-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATA
45895 TCCTTAAATCC
321 TCCTTAAATCC
* * * * *
45906 AATGTGACTAAGATTTAATTAGATGAGTATAGATATTTAAAGGAGTCTCGGC-CCAAAAATCATG
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCTCCAAAAATCATG
* * ** * * * * * *
45970 CAAAGCTAAGTTGGGGCCCCGAAACGCATTTTCAGCCAAATACCGTGATGATT--T---C---TG
66 CAAAACTGAG-CCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT
**** * * * * * *
46027 CAAAAAAAATGTTGCAAAAATTGACCGGAAATAATTTTTCTCAATTTTTGACGAAAATACTCATA
130 CGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCATA
* * * * *
46092 AAAAATATAT-ATTTCAATGCCAAAAAGATTGGAGGGATTTTCACGATTCAAATATCATTTTTCC
195 AAAAGTATATAATTT-AATGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATAT-ATTTTCCC
* * **
46156 -TATTTTTTCTGAATTAATTTCTAATTAAATCGAAGTCGGTTTCAGATGCTCGT--AAACATATC
258 TTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATC
*
46218 CTTAAATTC
323 CTTAAATCC
* * *
46227 AATGTGGCTAAGATTT-AGTTAGA-G--TAT--ATATAT-AA--A---T----ACCAAAAATCAT
1 AATGTGGCTGAGATTTGA-TTAGATGAATATAGATATTTCAAGGAGTCTCGGCTCCAAAAATCAT
* *
46276 GCAAAACTGAGCCGAAGTCCCGGAACG-GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATT
65 GCAAAACTGAGCCG-GGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATT
** * * * *
46340 TTAGCTAAAATTTTGCAAAAATTGA-CC--AATTTTTTTTCATGAATTTTTGGTCATAATACTCA
129 TCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTC-TTAATTTTTGGCCAAAATACTCA
* * * ** * * *
46402 TAAAAAGTATATAATTGAACGCCAGAAAGATTAAAGGGCTTTTTATGCTTCTAATAACATTTT--
193 TAAAAAGTATATAATTTAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAAT-ATATTTTCC
* * * * * * *
46465 -TTATATTTTTTCCAAATTAATTTCTGATTAAA-CAAAACAAGATACATAT-ATATGCTCATAAA
257 CTT-T-TTTTTTCCGAATTAATTTCTAATTAAATCGAAAC-CGGT---T-TCAGATGCTCGTAAA
*
46527 AATATATCCTTAAATCC
315 AACATATCCTTAAATCC
* * * * * *
46544 AATATGGCTGAGATTTGATTCGATGAATATAAATATTTCAAGAAGTCTCGGCGCTAAAAATCATG
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCTCCAAAAATCATG
* ** * * * * * *
46609 CAAAACTAAAACGGACCTCGGAACGCGTTTTTAGGCAATAACCGTGATGATTAGTACATGATTTC
66 CAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC
* * ** * * **
46674 GGCTAAAATTTTGCAAAAATTTAACTAAAATA-TTTTCCCTAATTTTTGGAAAAAATACTCATAA
131 GGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCATAA
* * ** * * *
46738 AAAGTATATAATTCAATGTCAAAACTATTGGAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTA
196 AAAGTATATAATTTAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATAT-ATTTTCCCTT
** * * *
46803 AATATTTCTC-AGTAAATTT-TCAGATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATAT
260 TTTTTTTC-CGAATTAATTTCT-A-ATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATAT
* *
46866 ACTTTAATCC
322 CCTTAAATCC
* * * * * * * *
46876 AACGGGGCAGATATTTGATTAGATGAATTTAGATATTTCAAGGAGTCTCGGCGCCAAAAATTATA
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCTCCAAAAATCATG
* * * *
46941 CAAAACT-ATGCCGGGCCTCGGAATGCGTTTTTAGCAAAAAATCGTGATGGTTAGTACACGATTT
66 CAAAACTGA-GCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT
* * *
47005 CGGCTAAAATTTTGCAGAAATTGACCCGAAATATTTTTCCTTAAGTTTTGGCCAAAATACTCATA
130 CGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCATA
*
47070 AAAAGTATATAATTTAATGCCAAAAAGATTGGA-GGCTTTTCACGCTTCAAATATCATTTTTCCC
195 AAAAGTATATAATTTAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATAT-A-TTTTCCC
* ** * ** * * *
47134 -TTTTTTTTCAGAATTAAAAATCTAATGAAATCGAAGTCGGCTTCATATGC-CTGTAAATA-ATA
258 TTTTTTTTTCCGAATT-AATTTCTAATTAAATCGAAACCGGTTTCAGATGCTC-GTAAAAACATA
47196 TCCTTAAATCC
321 TCCTTAAATCC
* * * ** * *
47207 AATGTGGCTGAGATTTAATTAGATTAATATATATATTTCCTGGAGTCTCGGCGCTAAAAATCATG
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCTCCAAAAATCATG
** * * *
47272 CAAAACTGAGCTAGGCCCCGGAACGCGTTTTTAG-C--TAA--GTGA----TA--ACA-TACTTC
66 CAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC
* * * * *
47325 AGCAAAAATTTTGTAAAAATTGACCTGAAATATTTTTCCTTAATTTTTGGCCAAAATACTCATAA
131 GGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCATAA
* * *
47390 AAAGTAAATAA-TTAAGTGCCAAAAAGGTTGGAGGGCTTTTCACGCTTTTAATAT-TGTTTCCCT
196 AAAGTATATAATTTAA-TGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATAT-TTTCCCT
* * * *
47453 TTTTTTTTCCGAATTACTTTTTAATTAAATCAAAACCGGTTTCAGATGCTTGTAAAAACATATCC
259 TTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCC
* * *
47518 TTTACTGC
324 TTAAATCC
* * * * * *
47526 AATGTGGCTAAGAGTTGATTAGATGAATATAAATATTTCAAGGAGTCTTGCCTCCATAAATCATG
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCTCCAAAAATCATG
* ** ** * *
47591 CAAAAGTGAGCCGGGCCCCATAACGAATTTTTAGCCAAAAATCGTGATGGTTTGTACACGATTTC
66 CAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC
*
47656 GGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCATGA
131 GGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCATAA
* * *
47721 AAAGTATATAATTTAATGCGAAAAAGATTGGAGGGCTTTTCACGCTTCGAATATCATTTTTCC-T
196 AAAGTATATAATTTAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATAT-ATTTTCCCTT
* ** * * * * * * *
47785 ATTTTTTCTAAATTAATTTTTAATTTAATCGAAGCTGGTTTCGGATGCTTGTAAAAACTTATCCT
260 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCT
47850 TAAATCC
325 TAAATCC
* * * * *
47857 AATATGGATGAGATTTAATTAGATGAATATATATATATCTCAAGGAGTCTCGG-TGCTAAAAATC
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATAT-T-TCAAGGAGTCTCGGCT-CCAAAAATC
* * * * * *
47921 TTGCAAAATTGAGCTGGGGCCACGAAACGCGTTTTTAGCTAAAAACC--G-T-GTTAGTACACGA
63 ATGCAAAACTGAGC-CGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
* ** *** * * * * * *
47982 TTTTGGCTAATTTTTTGCAAAAATTGACAAAAAAAAAATTTTCCTAAATTTTTGTCCACAATAAC
127 TTTCGGCTAAAATTTTGCAAAAATTGAC-CCGAAATATTTTTTCTTAATTTTTGGCCAAAAT-AC
* * * * *
48047 -CAT-AAAAGATATATAGTTCATTCAATGCCAAAAAAATTGAAGGGCTTTTCAAGATTCTAATAT
190 TCATAAAAAG-TATATA----ATTTAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATAT
* * * * * *
48110 CATTTTTCC--TATTTTT-----TT--TTCCAAATTAAA-C--AA---GATTCAGATTCTCGTAA
250 -ATTTTCCCTTTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGTTTCAGATGCTCGTAA
*
48160 AAACA-CTCCTTAAATCC
314 AAACATATCCTTAAATCC
* * * * *
48177 AATGTGGTTGAGATTTGATTAGATAAATATAGATATTCCAATGAGTCTCGGCTCTAAAAA-CAAT
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCTCCAAAAATC-AT
* * *
48241 GCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTTAGCCAAAAATCGTGTTGGTTGGTACACGATT
65 GCAAAACTGAGCCGGGCCCCGGAACGCG-TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATT
* * * **
48306 TCGGTTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTTAATTTTTGGAAAAAATACTCAT
129 TCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCAT
* * * * * * * *
48371 -AAAAGTATATAATTCAATGTCAAAAAGGTTGAAGGGCTATTCACACTTTTACTATCATTTTCCC
194 AAAAAGTATATAATTTAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATAT-ATTTTCCC
* * * * ** * *
48435 -TGTTTTTTCCAAAATTAATTTCTAATTAAACCAAAAGTGGTTTCAAATGCTCATAAAAAAAATC
258 TTTTTTTTTCC-GAATTAATTTCTAATTAAATCGAAACCGGTTTCAGATGCTCGT---AAAAA--
*
48499 CCATTATCCTTTAATCC
317 -CA-TATCCTTAAATCC
* * * * *
48516 AATGTGACTAAGATTTGATTAGATGAATATAGATATTTCAGGGAGTCTCGGCGCTAAAAATCATG
1 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCTCCAAAAATCATG
* * * * * *
48581 CAAAGCTGAGCCGGGCCCTGAAACACGGTTTTAGCCAAAAACCGTGATGGTGAGGTACACGATTT
66 CAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA-GTACACGATTT
* * *
48646 CAGCTAAAATTTTGCAAAAATTGACCCGAAATA-TTTTTCTTTAGTTTTTGGCAAAAATACTCA-
130 CGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTC-TTAATTTTTGGCCAAAATACTCAT
* * * * ** * *
48709 AAAAAGTATATAATTAAATACCAAATAGGTTGGAGGGCTTTTCACTATTTTAATATTGTTTTCTC
194 AAAAAGTATATAATTTAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATA-TATTTTC-C
* * * *
48774 TATTTTTTTTTTTCAGAATTAGTTTC-ATATTAAATCGAAACCAGTTTCAGATGCTCGTAAAAAC
257 ---CTTTTTTTTTCCGAATTAATTTCTA-ATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAAC
48838 ATATC
318 ATATC
48843 ACTCGATATA
Statistics
Matches: 2883, Mismatches: 542, Indels: 337
0.77 0.14 0.09
Matches are distributed among these distances:
306 23 0.01
307 29 0.01
308 1 0.00
310 2 0.00
311 13 0.00
312 89 0.03
313 6 0.00
314 20 0.01
315 11 0.00
316 49 0.02
317 54 0.02
318 90 0.03
319 195 0.07
320 79 0.03
321 93 0.03
322 115 0.04
323 133 0.05
324 102 0.04
325 85 0.03
326 50 0.02
327 11 0.00
328 9 0.00
329 4 0.00
330 44 0.02
331 370 0.13
332 309 0.11
333 259 0.09
334 192 0.07
335 152 0.05
336 15 0.01
337 4 0.00
338 26 0.01
339 200 0.07
340 8 0.00
342 1 0.00
343 32 0.01
344 8 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (331 bp):
AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCTCCAAAAATCATG
CAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC
GGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTTCTTAATTTTTGGCCAAAATACTCATAA
AAAGTATATAATTTAATGCCAAAAAGATTGGAGGGCTTTTCACGCTTCTAATATATTTTCCCTTT
TTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGTTTCAGATGCTCGTAAAAACATATCCTT
AAATCC
Found at i:48860 original size:12 final size:12
Alignment explanation
Indices: 48845--48888 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
48835 AACATATCAC
*
48845 TCGATATATCCG
1 TCGATATATCCT
48857 TCGATATATCCAT
1 TCGATATATCC-T
*
48870 TCAATATATCCT
1 TCGATATATCCT
48882 TCGATAT
1 TCGATAT
48889 CTGGATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (12 bp):
TCGATATATCCT
Found at i:52744 original size:27 final size:27
Alignment explanation
Indices: 52714--52768 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
52704 TGAAATATTT
52714 TTCTTTAATTTTTGGCAAAAATTCTCA
1 TTCTTTAATTTTTGGCAAAAATTCTCA
52741 TTCTTTAATTTTTGGCAAAAATTCTCA
1 TTCTTTAATTTTTGGCAAAAATTCTCA
52768 T
1 T
52769 AAAAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (27 bp):
TTCTTTAATTTTTGGCAAAAATTCTCA
Done.