Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006546.1 Corchorus capsularis cultivar CVL-1 contig06567, 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: 58758
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5641 original size:12 final size:13
Alignment explanation
Indices: 5617--5645 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5607 TTTTCTAAAT
5617 TTTATATTTTATA
1 TTTATATTTTATA
5630 TTTATA-TTTATA
1 TTTATATTTTATA
5642 TTTA
1 TTTA
5646 AATTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATATTTTATA
Found at i:7750 original size:2 final size:2
Alignment explanation
Indices: 7741--7770 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
7731 TTTCTTTTTT
7741 TA TA -A 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 T
7771 TAATATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9232 original size:2 final size:2
Alignment explanation
Indices: 9225--9253 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9215 GTATGGGATT
9225 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9254 TAGGGTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:13500 original size:20 final size:20
Alignment explanation
Indices: 13457--13493 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13447 TATATTTATA
*
13457 AATTTTCATTATTAAAATAT
1 AATTTTAATTATTAAAATAT
13477 AATTTTAATTA-TAAAAT
1 AATTTTAATTATTAAAAT
13494 TTCAATTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTTAATTATTAAAATAT
Found at i:17430 original size:2 final size:2
Alignment explanation
Indices: 17423--17447 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17413 TTTCATCACT
17423 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 T
17448 TTTTTCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17877 original size:23 final size:23
Alignment explanation
Indices: 17810--17879 Score: 122
Period size: 23 Copynumber: 3.0 Consensus size: 23
17800 CAAACAATCT
*
17810 TGAGCACTCTCGCTCGGTCTCCA
1 TGAGCACTCTCGCTCGGTCTCTA
*
17833 TGAGCTCTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
17856 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
17879 T
1 T
17880 AAACTAACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.11, C:0.36, G:0.21, T:0.31
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGGTCTCTA
Found at i:18791 original size:23 final size:23
Alignment explanation
Indices: 18759--18805 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
18749 CAAACAATCT
18759 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
*
18782 TGAGCTCTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
18805 T
1 T
18806 AAACTAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.11, C:0.34, G:0.21, T:0.34
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGGTCTCTA
Found at i:20574 original size:11 final size:11
Alignment explanation
Indices: 20531--20568 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
20521 TTCCTATATA
*
20531 AAATAAATTAT
1 AAATTAATTAT
20542 CAAA-TAATTAT
1 -AAATTAATTAT
20553 AAATTAATTAT
1 AAATTAATTAT
20564 AAATT
1 AAATT
20569 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:25433 original size:19 final size:19
Alignment explanation
Indices: 25409--25451 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
25399 ACTTACAAAG
*
25409 CAGGAGACTTTGGTGAAAC
1 CAGGAGACTTTGGGGAAAC
25428 CAGGAGACTTTGGGGAAAC
1 CAGGAGACTTTGGGGAAAC
25447 CAGGA
1 CAGGA
25452 TGGGAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.35, T:0.16
Consensus pattern (19 bp):
CAGGAGACTTTGGGGAAAC
Found at i:31574 original size:11 final size:10
Alignment explanation
Indices: 31556--31589 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
31546 AATTGTCTTC
31556 AAATCTTCAA
1 AAATCTTCAA
31566 AATATCTTCAA
1 AA-ATCTTCAA
31577 GAAATCTTCAA
1 -AAATCTTCAA
31588 AA
1 AA
31590 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:33163 original size:6 final size:6
Alignment explanation
Indices: 33152--33186 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
33142 TAATATAACA
33152 TATATC TATATC TATATC TATATC TATATC TATAT
1 TATATC TATATC TATATC TATATC TATATC TATAT
33187 GAATCGCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATC
Found at i:33733 original size:21 final size:21
Alignment explanation
Indices: 33709--33759 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
33699 GGGCGCGCGG
33709 ATGGCGCGG-CAAAGGCCGGCC
1 ATGGCGCGGAC-AAGGCCGGCC
*
33730 ATGGTGCGCGGACAAGGCCGGGC
1 AT-G-GCGCGGACAAGGCCGGCC
33753 ATGGCGC
1 ATGGCGC
33760 AGATGGATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 6 0.23
22 2 0.08
23 17 0.65
24 1 0.04
ACGTcount: A:0.18, C:0.29, G:0.45, T:0.08
Consensus pattern (21 bp):
ATGGCGCGGACAAGGCCGGCC
Found at i:33738 original size:23 final size:23
Alignment explanation
Indices: 33712--33756 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
33702 CGCGCGGATG
33712 GCGCGG-CAAAGGCCGGCCATGGT
1 GCGCGGAC-AAGGCCGGCCATGGT
*
33735 GCGCGGACAAGGCCGGGCATGG
1 GCGCGGACAAGGCCGGCCATGG
33757 CGCAGATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.18, C:0.29, G:0.47, T:0.07
Consensus pattern (23 bp):
GCGCGGACAAGGCCGGCCATGGT
Found at i:37053 original size:20 final size:20
Alignment explanation
Indices: 37028--37067 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
37018 GCAGTAACAG
*
37028 TTCTTAATCAAAAATAAAAA
1 TTCTTAAACAAAAATAAAAA
37048 TTCTTAAACAAAAATAAAAA
1 TTCTTAAACAAAAATAAAAA
37068 GAAGAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (20 bp):
TTCTTAAACAAAAATAAAAA
Found at i:39040 original size:11 final size:10
Alignment explanation
Indices: 39022--39055 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
39012 AATTGTCTTC
39022 AAATCTTCAA
1 AAATCTTCAA
39032 AATATCTTCAA
1 AA-ATCTTCAA
39043 GAAATCTTCAA
1 -AAATCTTCAA
39054 AA
1 AA
39056 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:41055 original size:16 final size:16
Alignment explanation
Indices: 41034--41064 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41024 AAAAAACTTA
41034 GTGAAGAGCAATTTAT
1 GTGAAGAGCAATTTAT
41050 GTGAAGAGCAATTTA
1 GTGAAGAGCAATTTA
41065 CCCTCAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (16 bp):
GTGAAGAGCAATTTAT
Found at i:42947 original size:21 final size:21
Alignment explanation
Indices: 42909--42968 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
42899 CCAAGATCAA
**
42909 CCTTCATTTTCCAAAAGTCCC
1 CCTTCATTTTCCTTAAGTCCC
*
42930 CCTTCATTTTCCTTAAGTCCT
1 CCTTCATTTTCCTTAAGTCCC
* * *
42951 CCTCCCTTTTCTTTAAGT
1 CCTTCATTTTCCTTAAGT
42969 TTGCCTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.17, C:0.35, G:0.05, T:0.43
Consensus pattern (21 bp):
CCTTCATTTTCCTTAAGTCCC
Found at i:46457 original size:15 final size:13
Alignment explanation
Indices: 46429--46453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46419 AGAGAACATG
46429 ATTTTTTGAAAAC
1 ATTTTTTGAAAAC
46442 ATTTTTTGAAAA
1 ATTTTTTGAAAA
46454 AACACTTTTT
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:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
ATTTTTTGAAAAC
Found at i:47874 original size:17 final size:17
Alignment explanation
Indices: 47852--47884 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47842 AATCGGCAGC
*
47852 CTTCTTCTTTTTCCTCA
1 CTTCTTCTTCTTCCTCA
47869 CTTCTTCTTCTTCCTC
1 CTTCTTCTTCTTCCTC
47885 GCTTTCCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (17 bp):
CTTCTTCTTCTTCCTCA
Found at i:49054 original size:50 final size:51
Alignment explanation
Indices: 48985--49086 Score: 170
Period size: 50 Copynumber: 2.0 Consensus size: 51
48975 TTATGCCGAC
48985 AAAATGATGTCGAATAATATTATGG-AAAAAAACAGACAAAAAAAACAAAA
1 AAAATGATGTCGAATAATATTATGGAAAAAAAACAGACAAAAAAAACAAAA
* *
49035 AAAATGATGTCGAATAATATTATGGAAAAAAAAACAGACAGAAACAACAAAA
1 AAAATGATGTCGAATAATATTATGG-AAAAAAAACAGACAAAAAAAACAAAA
49087 GCAATGTTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 25 0.52
52 23 0.48
ACGTcount: A:0.63, C:0.09, G:0.13, T:0.16
Consensus pattern (51 bp):
AAAATGATGTCGAATAATATTATGGAAAAAAAACAGACAAAAAAAACAAAA
Found at i:49835 original size:826 final size:820
Alignment explanation
Indices: 48212--49859 Score: 2426
Period size: 826 Copynumber: 2.0 Consensus size: 820
48202 TTATGCCGAC
*
48212 AAAATGATGTCGAATAATATAATGGAAAAAATAGACAGAAACAACAAAAGCAATGGTGTCTGTTA
1 AAAATGATGTCGAATAATATAATGGAAAAAACAGACAGAAACAACAAAAGCAATGGTGTCTGTTA
* * *
48277 CACGGATAGATATCATGTCAATCTATCCTATAAACATCGCTGCAGTATTATATACCCCAAATAAA
66 CACGGATAGATAGCATGCCAAACTATCCTATAAACATCGCTGCAG-ATTATATACCCCAAATAAA
* * *
48342 ATAATTCATTCTGTTGAGTATTTTAGATGCTGGACAGTTTTATGGGTAGGGGACATTATACATGT
130 ATAATTCATTCTGTTGAGTATTTTAGATGCT-GAAAGTTTTATGGGTAGAGGACATTATACAAGT
* * * * * *
48407 AAATGGGGTAGACTATGAGGTCGTGGATATATGTATCCACTTTACAGATCTTAAATCAGTATTAA
194 AAATGCGGAAGACTACGAGGTCGTGGATATACGCATCCACTTTACAAATCTTAAATCAGTATTAA
* * * * *
48472 CTAGGGAAGAAGAACCAACTCCGACATCTAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAAC
259 CAAGGGAAGAAAAACCAACTCCGACATCCAATCTTTCCAACCAGATTATCAAGATTGTTGCCAAC
*
48537 AACGATACTGACTCTACGACTACGACTGAAGAATTCACTAAAACCATAGCTAGCCCAAGCAACGA
324 AACGATACTGACTCTACGACTACGACTGAAGAATCCACTAAAACCATAGCTAGCCCAAGCAACGA
* * * * *
48602 GTCAACTGTCAAAATTACTCTATATAAGATTGCAAATTGCATAACCCTTTATTCATAGTATAAGT
389 GTCAACTGACAAAAATACTCTATATAAGAGTGCAAATTGCACAACCCTTTATTCATAGTATAAGG
* *
48667 TCTGAAAAGATCTATCTATGCCTTAGGCACATCTTTGTATAGTCCTCTGGCCAGACAGAGCAGAG
454 TCTGAAAAGATCTATCTATGCCTTAGGCACATCTTTGTATAGTCCCCTGGCCAGACAGAACAGAG
* *
48732 AAGAATACTCTGTTTCAGGTATAAAGGAAGCTTCATAGATAAGGTTGAAAGGAATTGCATTAGTT
519 AAAAATACTCTGTGTCAGGTATAAAGGAAGCTTCATAGATAAGGTTGAAAGGAATTGCATTAGTT
* * *
48797 TCTTAGGCTGTTCTGGGCTTGATGATATCTTGTTCCAATTTCATATGCACAAGACAAGCATATAT
584 TCTTAGGCTGTTCTGGGCATGATGATATCTTGTTCCAATTTCACATGCACAAGACAAACATATAT
**
48862 ATTACTTCTAGATATTGAAGCATATATATTATTTTATGATATCGGAGCCAAAATATATATTTTAA
649 ATTACTTCTAGATATTGAAGCATATATATTATTTTATGATATAAGAGCCAAAATATATATTTTAA
* *
48927 GCCATAGAAGCTTAATATAGAGATTGTCGCCTTTAAGTCATATGTTGTTTATGCCGACAAAATGA
714 GCCATAGAAGCTTAATATAGAGATTGTCACCTTTAAGTCATATATTGTTTATGCCGACAAAATGA
*
48992 TGTCGAATAATATTATGGAAAAAAACAGACAAAAAAAACAAAA
779 TATCGAATAATATTATGG-AAAAAACAGACAAAAAAAACAAAA
* *
49035 AAAATGATGTCGAATAATATTATGGAAAAAAAAACAGACAGAAACAACAAAAGCAATGTTGTCTG
1 AAAATGATGTCGAATAATATAATGG---AAAAAACAGACAGAAACAACAAAAGCAATGGTGTCTG
* * *
49100 TTACACGGATAGATAGCATGCCAAACTATTCTATGAGCATCGCTGCA-ATTATTATACCCCAAAT
63 TTACACGGATAGATAGCATGCCAAACTATCCTATAAACATCGCTGCAGATTA-TATACCCCAAAT
* *
49164 GATATAATTCATTCTGTTGAGTATTTTA-ATTGCT-AAAGCTTTTTATAGGGTAGAGGACATTAT
127 AAAATAATTCATTCTGTTGAGTATTTTAGA-TGCTGAAAG--TTTTAT-GGGTAGAGGACATTAT
* *
49227 ACAAGTAAATGCGGAAGACTACGAGGTCGTGGGTATACGCATCCACTTTACAAATTTTAAATCAG
188 ACAAGTAAATGCGGAAGACTACGAGGTCGTGGATATACGCATCCACTTTACAAATCTTAAATCAG
* * * *
49292 TATTAACAAGGGAGGAAAAAGCAGCTCTGACATCCAATCTTTCCAACCAGATTATCAAGATTGTT
253 TATTAACAAGGGAAGAAAAACCAACTCCGACATCCAATCTTTCCAACCAGATTATCAAGATTGTT
* * *
49357 GCCAACAATGATACTGACTCTACGACTACGACTGAAGAATCCGCTGAAACCATAGCTAGCCCAAG
318 GCCAACAACGATACTGACTCTACGACTACGACTGAAGAATCCACTAAAACCATAGCTAGCCCAAG
* * * *
49422 CAACGAGTCGACTGACAAAAATACTCTGTGTAAGAGTGCAAATTGCGCAACCCTTTATTCATAGT
383 CAACGAGTCAACTGACAAAAATACTCTATATAAGAGTGCAAATTGCACAACCCTTTATTCATAGT
* * * *
49487 ATAAGGTCTTACAATATCTATCTATGCCTT-GAGCACAT-TTATGTTTAGTCCCCTGGCCAGACA
448 ATAAGGTCTGAAAAGATCTATCTATGCCTTAG-GCACATCTT-TGTATAGTCCCCTGGCCAGACA
* * * **
49550 GAACAGAGAAAAATACTTTGTGTCAGGTCTAAAGGAAGCTTCATAGATAGGGTTGGCAGGAATTG
511 GAACAGAGAAAAATACTCTGTGTCAGGTATAAAGGAAGCTTCATAGATAAGGTTGAAAGGAATTG
* * *
49615 CATTAGTTTCTTTGGCTGTTCTGGGCATGATGATTTCTTGTTCCAA-TTCACATGCATAAGACAA
576 CATTAGTTTCTTAGGCTGTTCTGGGCATGATGATATCTTGTTCCAATTTCACATGCACAAGACAA
* *
49679 ACATATATATTACTTCTAGATATTGAAGCATATATATTATTTTTATTATATAAGAGCCCAAATAT
641 ACATATATATTACTTCTAGATATTGAAGCATATATATTA-TTTTATGATATAAGAGCCAAAATAT
* ** * *
49744 ATATTTTAAGCCATGGGTGCTTAGTATAGAGATTGTCACCTTTAAGTCCTATATTGTTTATGCCG
705 ATATTTTAAGCCATAGAAGCTTAATATAGAGATTGTCACCTTTAAGTCATATATTGTTTATGCCG
* * *
49809 ACAAGATGATATCGAATAATATTATGGAAAAAACAGACAGAAACAACAAAA
770 ACAAAATGATATCGAATAATATTATGGAAAAAACAGACAAAAAAAACAAAA
49860 GCAATGGTGT
Statistics
Matches: 736, Mismatches: 78, Indels: 20
0.88 0.09 0.02
Matches are distributed among these distances:
823 27 0.04
824 5 0.01
825 127 0.17
826 577 0.78
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (820 bp):
AAAATGATGTCGAATAATATAATGGAAAAAACAGACAGAAACAACAAAAGCAATGGTGTCTGTTA
CACGGATAGATAGCATGCCAAACTATCCTATAAACATCGCTGCAGATTATATACCCCAAATAAAA
TAATTCATTCTGTTGAGTATTTTAGATGCTGAAAGTTTTATGGGTAGAGGACATTATACAAGTAA
ATGCGGAAGACTACGAGGTCGTGGATATACGCATCCACTTTACAAATCTTAAATCAGTATTAACA
AGGGAAGAAAAACCAACTCCGACATCCAATCTTTCCAACCAGATTATCAAGATTGTTGCCAACAA
CGATACTGACTCTACGACTACGACTGAAGAATCCACTAAAACCATAGCTAGCCCAAGCAACGAGT
CAACTGACAAAAATACTCTATATAAGAGTGCAAATTGCACAACCCTTTATTCATAGTATAAGGTC
TGAAAAGATCTATCTATGCCTTAGGCACATCTTTGTATAGTCCCCTGGCCAGACAGAACAGAGAA
AAATACTCTGTGTCAGGTATAAAGGAAGCTTCATAGATAAGGTTGAAAGGAATTGCATTAGTTTC
TTAGGCTGTTCTGGGCATGATGATATCTTGTTCCAATTTCACATGCACAAGACAAACATATATAT
TACTTCTAGATATTGAAGCATATATATTATTTTATGATATAAGAGCCAAAATATATATTTTAAGC
CATAGAAGCTTAATATAGAGATTGTCACCTTTAAGTCATATATTGTTTATGCCGACAAAATGATA
TCGAATAATATTATGGAAAAAACAGACAAAAAAAACAAAA
Found at i:51256 original size:27 final size:28
Alignment explanation
Indices: 51218--51270 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
51208 TGCACAGGAC
51218 AAGCATATATATTACTTTTA-GATATTG
1 AAGCATATATATTACTTTTATGATATTG
*
51245 AAGCATATATATTATTTTTATGATAT
1 AAGCATATATATTACTTTTATGATAT
51271 CAGAGCCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (28 bp):
AAGCATATATATTACTTTTATGATATTG
Found at i:53048 original size:770 final size:764
Alignment explanation
Indices: 48088--52917 Score: 5459
Period size: 770 Copynumber: 6.2 Consensus size: 764
48078 AGCCGTCAGA
** *
48088 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGATATTGGAGCCAAAATATATATTTTA
1 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGATATCAGAGCCCAAATATATATTTTA
* * * *
48153 AGCCATAGATGCTTAGTATAGAGATTGTCACCTTTAAGTAATATGTTGTTTATGCCGACAAAATG
66 AGTCATGGGTGCTTAGTATAGAGATTGTCACCTTTAAGTCATATGTTGTTTATGCCGACAAAATG
* * *
48218 ATGTCGAATAATATAAT-GGAAAAAATAGACAGAAACAACAAAAGCAATGGTGTCTGTTACACGG
131 ATGTCGAATAATATCATGGGAAAAAACAGACAGAAACAACAAAAGCAATAGTGTCTGTTACACGG
* *
48282 ATAGATA-TCATGTCAATCTATCCTATAAACATCGC-TGCAG-TATTATATACCCCAAATAAAAT
196 ATAGATAGT-ATGTCAATCTATCCTATAAACATC-CTTGCAGTTA-T-TATA-CCCAAATGATAT
* * **
48344 AATTCATTCTGTTGAGTATTTTAGATGCTGGACAGTTTTATGG-GTAGGGGACATTATACATGTA
256 AATTCATTCTGTTGAGTATTTTAGTTGCTGAACCTTTTTATGGAGTA-GGGACATTATACATGTA
* * * *
48408 AATGGGGTAGACTATGAGGTCGTGGATATATGTATCCACTTTACAGATCTTAAATCAGTATTAAC
320 AATGGGGTAGACTACGAGGTCGTGGGTATACGTATCCACTTTACAAATCTTAAATCAGTATTAAC
* * * * *
48473 TAGGGAAGAAGAACCAACTCCGACATCTAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAACA
385 TAGGGAGGAAGAAGCAGCTCCAACATCCAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAACA
* * *
48538 ACGATACTGACTCTACGACTACGACTGAAGAATTCACTAAAACCATAGCTAGCCCAAGCAACGAG
450 ACGATACTGACTCTACGACTACGACTGAAGAATCCGCTGAAACCATAGCTAGCCCAAGCAACGAG
* * * * * **
48603 TCAACTGTCAAAATTACTCTATATAAGATTGCAAATTGCATAACCCTTTATTCATAGTATAAGTT
515 TCGACTGACAAAAATACTCTGTATAAGACTGCAAATTGCGCAACCCTTTATTCATAGTATAAGTT
* * * * * *
48668 CTGAAAAGATCTATCTATGCCTT-AGGCACATCTTTGTATAGTCCTCTGGCCAGACAGAGCAGAG
580 CTTACAATATCTATCTATGCCTTGA-GCACATC--TGTCTAGTCCCCTGGCCAGACAGAACAGAG
* * * * ** *
48732 AAGAATACTCTGTTTCAGGTATAAAGGAAGCTTCATAGATAAGGTTGAAAGGAATTGCATTAGTT
642 AAAAATACTTTGTGTCAGGTCTAAAGGAAGCTTCATAGATGGGGTAG-AAGG-A----ATTAGTT
* * *
48797 TCTTAGGCTGTTCTGGGCTTGATGATATCTTGTTCCAATTTCATATGCACAAGACAAGCATATAT
701 TCTTTGGCTGTTCTGGGCTTGATGATATCTTGTTCCAA-TTCACATGCACAGGACAAGCATATAT
* *
48862 ATTACTTCTAGATATTGAAGCATATATATTA-TTTTATGATATCGGAGCCAAAATATATATTTTA
1 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGATATCAGAGCCCAAATATATATTTTA
* * ** * *
48926 AGCCATAGAAGCTTAATATAGAGATTGTCGCCTTTAAGTCATATGTTGTTTATGCCGACAAAATG
66 AGTCATGGGTGCTTAGTATAGAGATTGTCACCTTTAAGTCATATGTTGTTTATGCCGACAAAATG
* * * * **
48991 ATGTCGAATAATATTATGGAAAAAAACAGACAAAAAAAACAAAAAAAAT-GATGTC-GAATAATA
131 ATGTCGAATAATATCATGGGAAAAAACAGACAGAAACAACAAAAGCAATAG-TGTCTG--T--TA
* * * * ** * * * * * * *
49054 TTATGGA-AAAAAAAACAGACAGAAAC-A-AC-A-AAAGCAAT-GTTGTCTGTTACACGGATAGA
191 -CACGGATAGATAGTA-TGTC--AATCTATCCTATAAA-C-ATCCTTG-CAGTT------AT-TA
* * * *
49113 TAGCATGCCAAACT-ATTCTATGAGCATCGCTGCAATTAT-TATACCCCAAATGATATAATTCAT
242 TA-C---CCAAA-TGA---TAT-A--AT---T-C-ATTCTGT-T------GA-G-TAT--TTTAG
* *** * * * ** * ** *
49176 TCTGTTGAGTATTTTAATTG-CTAAAG-CTTTTTATAGGGTAGAGGACATTATACAAGTAAATGC
280 T-TGCTGAACCTTTTTATGGAGTAGGGAC--ATTATA-CAT-G---------------TAAATGG
* * * *
49239 GGAAGACTACGAGGTCGTGGGTATACGCATCCACTTTACAAATTTTAAATCAGTATTAACAAGGG
325 GGTAGACTACGAGGTCGTGGGTATACGTATCCACTTTACAAATCTTAAATCAGTATTAACTAGGG
* ** * * *
49304 AGGAAAAAGCAGCTCTGACATCCAATCTTTCCAACCAGATTATCAAGATTGTTGCCAACAATGAT
390 AGGAAGAAGCAGCTCCAACATCCAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAACAACGAT
49369 ACTGACTCTACGACTACGACTGAAGAATCCGCTGAAACCATAGCTAGCCCAAGCAACGAGTCGAC
455 ACTGACTCTACGACTACGACTGAAGAATCCGCTGAAACCATAGCTAGCCCAAGCAACGAGTCGAC
* * *
49434 TGACAAAAATACTCTGTGTAAGAGTGCAAATTGCGCAACCCTTTATTCATAGTATAAGGTCTTAC
520 TGACAAAAATACTCTGTATAAGACTGCAAATTGCGCAACCCTTTATTCATAGTATAAGTTCTTAC
* *
49499 AATATCTATCTATGCCTTGAGCACATTTATGTTTAGTCCCCTGGCCAGACAGAACAGAGAAAAAT
585 AATATCTATCTATGCCTTGAGCACA--TCTGTCTAGTCCCCTGGCCAGACAGAACAGAGAAAAAT
* * *
49564 ACTTTGTGTCAGGTCTAAAGGAAGCTTCATAGATAGGGTTGGCAGGAATTGCATTAGTTTCTTTG
648 ACTTTGTGTCAGGTCTAAAGGAAGCTTCATAGAT--GG--GGTA-GAA-GGAATTAGTTTCTTTG
* * * * *
49629 GCTGTTCTGGGCATGATGATTTCTTGTTCCAATTCACATGCATAAGACAAACATATAT
707 GCTGTTCTGGGCTTGATGATATCTTGTTCCAATTCACATGCACAGGACAAGCATATAT
* *
49687 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATTATATAAGAGCCCAAATATATATTTTA
1 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGATATCAGAGCCCAAATATATATTTTA
* * * *
49752 AGCCATGGGTGCTTAGTATAGAGATTGTCACCTTTAAGTCCTATATTGTTTATGCCGACAAGATG
66 AGTCATGGGTGCTTAGTATAGAGATTGTCACCTTTAAGTCATATGTTGTTTATGCCGACAAAATG
* * * *
49817 ATATCGAATAATATTAT-GGAAAAAACAGACAGAAACAACAAAAGCAATGGTGTCTGGTACACGG
131 ATGTCGAATAATATCATGGGAAAAAACAGACAGAAACAACAAAAGCAATAGTGTCTGTTACACGG
* * **
49881 ATAGATAGCATGTCAATCTATCATATAAACATTGTTGCAGTTATTATACCCCAAATGATATAATT
196 ATAGATAGTATGTCAATCTATCCTATAAACATCCTTGCAGTTATTATA-CCCAAATGATATAATT
* * * *
49946 CATTCTATTGAGTATTTTACTTGCTGAACCTTTTGATGGAGTAAGGGAGATTATACATG-AAATG
260 CATTCTGTTGAGTATTTTAGTTGCTGAACCTTTTTATGGAGT-AGGGACATTATACATGTAAATG
* * * *
50010 GGGTAGATTACGAGGTCGTGGGTATACGTATCAACTTTACAGATTTTAAATCAGTATTAACT-GA
324 GGGTAGACTACGAGGTCGTGGGTATACGTATCCACTTTACAAATCTTAAATCAGTATTAACTAG-
* * ** *
50074 GAATGAAGAAGGGGCTCCAACATCCAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAACAATG
388 GGAGGAAGAAGCAGCTCCAACATCCAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAACAACG
**
50139 ATACTGACTCTACGACTACGACTGAAGAATCTACTGAAACCATAGCTAGCCCAAGCAACGAGTCG
453 ATACTGACTCTACGACTACGACTGAAGAATCCGCTGAAACCATAGCTAGCCCAAGCAACGAGTCG
* *
50204 ACTGACAAGAATACTTTGTATAAGACTGCAAATTGCGCAA-CCTATTATTCATAGTATAAGTTCT
518 ACTGACAAAAATACTCTGTATAAGACTGCAAATTGCGCAACCCT-TTATTCATAGTATAAGTTCT
* * * * *
50268 TACAATATCTATCTATGCCTTGAGTACATCTATGTCTACTCCCCTAGCCATACAGAACAGAGCAA
582 TACAATATCTATCTATGCCTTGAGCACATC--TGTCTAGTCCCCTGGCCAGACAGAACAGAGAAA
* * * * * *
50333 TATACTTTGTGTCAAGTCTAAAGGAAGCTTCATAAATGGATTTGGAAGGAATTGCATTAGTTTCT
645 AATACTTTGTGTCAGGTCTAAAGGAAGCTTCATAGATGG----GGTA-GAA-GGAATTAGTTTCT
*
50398 TTGGCTGTTCTAGGCTTGATGATATCTTGTTCCAATTCACATGCACAGGACAAGCATATAT
704 TTGGCTGTTCTGGGCTTGATGATATCTTGTTCCAATTCACATGCACAGGACAAGCATATAT
50459 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGAT-TACAGAGCCCAAATATATATTTT
1 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGATAT-CAGAGCCCAAATATATATTTT
*
50523 AAGTCATGGGTGCTTAGTATAGATATTGTCACCTTTAAGTCATATGTTGTTTATGCCGACAAAAT
65 AAGTCATGGGTGCTTAGTATAGAGATTGTCACCTTTAAGTCATATGTTGTTTATGCCGACAAAAT
50588 GATGTCGAATAATATCATGGTG-AAAAACAGACAGAAACAACAAAAGCAATAGTGTCTGTTACAC
130 GATGTCGAATAATATCATGG-GAAAAAACAGACAGAAACAACAAAAGCAATAGTGTCTGTTACAC
* *
50652 AGATAGATA-TCATGTCAATCTATCCTATAAACAACACTAT--AGTTATTATACCCAAATGATAT
194 GGATAGATAGT-ATGTCAATCTATCCTATAAACATC-CT-TGCAGTTATTATACCCAAATGATAT
* *
50714 AATTCATTCTGTTGAGTATTTTAGTTGCTGAACCTTTTTAT-CAGTGGGGACATTATACATGTAA
256 AATTCATTCTGTTGAGTATTTTAGTTGCTGAACCTTTTTATGGAGTAGGGACATTATACATGTAA
* * ** * * * * *
50778 ATTGGGTAGACTACGAGGTCCTAAGTATTCATATCCATTTTATAAATCTTAAATCAGTATCAACT
321 ATGGGGTAGACTACGAGGTCGTGGGTATACGTATCCACTTTACAAATCTTAAATCAGTATTAACT
* * * *
50843 AGGGAGGAAGAAGCAACTTCGAA-ATCCAATCTTCCCAACCAATTTATCAGGATTGTTGCCAACA
386 AGGGAGGAAGAAGCAGC-TCCAACATCCAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAACA
* * *
50907 ACGATACTGACTCTACGATTACGACTGAAGAATCCGCTGAAAGCATAGCTAGCCCAAGAAACGAG
450 ACGATACTGACTCTACGACTACGACTGAAGAATCCGCTGAAACCATAGCTAGCCCAAGCAACGAG
* * * * * * * * *
50972 TCAACTGTCAAAATTACTCTATATAAGACTGTAAATTGCACAATCCTTTAATCATATTATAAGTT
515 TCGACTGACAAAAATACTCTGTATAAGACTGCAAATTGCGCAACCCTTTATTCATAGTATAAGTT
* * * * * * *
51037 CTTAAAAGATCTATCAAT-CCTTAAGCACTTCTGTTCTAGTCACCTGGCCAGATAGAACAGAGAA
580 CTTACAATATCTATCTATGCCTTGAGCACATCTG-TCTAGTCCCCTGGCCAGACAGAACAGAGAA
* * * * *
51101 GAATACTCTGTGTCAGGTCTAAAGGAAACTTCATATATGGGGTTGGAAGGAATTGCATTAGTTTC
644 AAATACTTTGTGTCAGGTCTAAAGGAAGCTTCATAGATGGGG-TAGAAGG-A----ATTAGTTTC
*
51166 TTTGGCTGTTCTGGGCTTGATGATATTTTGTTCCAATTCACATGCACAGGACAAGCATATAT
703 TTTGGCTGTTCTGGGCTTGATGATATCTTGTTCCAATTCACATGCACAGGACAAGCATATAT
*
51228 ATTACTTTTAGATATTGAAGCATATATATTATTTTTATGATATCAGAGCCCAAATATATATTTTA
1 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGATATCAGAGCCCAAATATATATTTTA
* * *
51293 AGCCATGGGTGCCTAGTATAGATATTGTCACCTTTAAGTCATATGTTGTTTATGCCGACAAAATG
66 AGTCATGGGTGCTTAGTATAGAGATTGTCACCTTTAAGTCATATGTTGTTTATGCCGACAAAATG
* * *
51358 ATGTCGAATTATATCATGGTG-AAAAACATACAGAAACAACAAAAGCAATAGTGTCTGTTACACA
131 ATGTCGAATAATATCATGG-GAAAAAACAGACAGAAACAACAAAAGCAATAGTGTCTGTTACACG
51422 GATAGATA-TCATGTCAATCTATCCTATAAACATCAC-TGCAGTTATTATACCCCAAATGATATA
195 GATAGATAGT-ATGTCAATCTATCCTATAAACATC-CTTGCAGTTATTATA-CCCAAATGATATA
* *
51485 ATTCATTCTGTTGAGTATTTTAGTTGCTGAACCTCTTTATCG-GT-GGCGACATTATACATGTAA
257 ATTCATTCTGTTGAGTATTTTAGTTGCTGAACCTTTTTATGGAGTAGG-GACATTATACATGTAA
* * ** * * *
51548 ATTGGGTAGACTACGAGGTCCTAAGTATACATATCCATTTTACAAATCTTAAATCAGTATCAACT
321 ATGGGGTAGACTACGAGGTCGTGGGTATACGTATCCACTTTACAAATCTTAAATCAGTATTAACT
*
51613 AGGGATGAAGAAGCAGCTCCGAA-ATCCAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAACA
386 AGGGAGGAAGAAGCAGCTCC-AACATCCAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAACA
* *
51677 ACGATATTGACT-TCACGACTACGACT-AAGGAATCCGCTGAAACCATAGCTAGCCTAAGCAACG
450 ACGATACTGACTCT-ACGACTACGACTGAA-GAATCCGCTGAAACCATAGCTAGCCCAAGCAACG
* * * * * * * *
51740 AGTCAAGTGTCAAAATTACTCTATATAAGATTGCAAATTGCACAACCCTTTATTCATATTATAAG
513 AGTCGACTGACAAAAATACTCTGTATAAGACTGCAAATTGCGCAACCCTTTATTCATAGTATAAG
* * * * * * * * * * *
51805 TTCTTAAAAGATCTATATATCCCTTAAGCACAACCGTTTTAGTCACCTTGCCAGACAGAATAGAG
578 TTCTTACAATATCTATCTATGCCTTGAGCACATCTG-TCTAGTCCCCTGGCCAGACAGAACAGAG
* * * * * * *
51870 AAGAATACTATGTGTCAGGTTTAAAAGAAGCTTAATAGATAGGGTTGGAAGGAATTGCTTTAGTT
642 AAAAATACTTTGTGTCAGGTCTAAAGGAAGCTTCATAGAT-GGGGTAGAAGGAA-----TTAGTT
* * * *
51935 TCTTTGACTGTTCTGGGCTTGATGATATCTTGTTCCTATTCACATGCATAGGACAAGCCTATAT
701 TCTTTGGCTGTTCTGGGCTTGATGATATCTTGTTCCAATTCACATGCACAGGACAAGCATATAT
51999 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGATATCAGAGCCCAAATATATATTTTA
1 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGATATCAGAGCCCAAATATATATTTTA
* * * * * * *
52064 AGTCATTGGTGCTTAGTATAGAGATTATAACCTTTAAGT-TTATATTGTTTATGCCGAGAATATG
66 AGTCATGGGTGCTTAGTATAGAGATTGTCACCTTTAAGTCATATGTTGTTTATGCCGACAAAATG
* * * *
52128 ATTTCGAATAATATCAT-GGAAAAAATACACAGAAACAACAAAAGCAATGGTGTCTAG-TACACG
131 ATGTCGAATAATATCATGGGAAAAAACAGACAGAAACAACAAAAGCAATAGTGTCT-GTTACACG
* *
52191 GATAGATAGCATGTCAATCTATCCTATAAACATCGTTGCAGTTATTATACCCCAAATGATATAAT
195 GATAGATAGTATGTCAATCTATCCTATAAACATCCTTGCAGTTATTATA-CCCAAATGATATAAT
* * * *
52256 TCATTTTATTGAGTATTTTAGTTGTTGAACCTTTTTATGGAGTAAGGGAGATTATACATG-AAAT
259 TCATTCTGTTGAGTATTTTAGTTGCTGAACCTTTTTATGGAGT-AGGGACATTATACATGTAAAT
* * *
52320 GGGGTAGATTA-GAAGGTCGTGGGTATACGTATCCACTTTACAGATCTTAAATCAGTATTAA-TT
323 GGGGTAGACTACG-AGGTCGTGGGTATACGTATCCACTTTACAAATCTTAAATCAGTATTAACTA
** * *
52383 GGGAAGGAAGAAGTGGCTCCAACATCCATTCTTTCCAACCAGTTTATCAGGATTGTTGCGAACAA
387 GGG-AGGAAGAAGCAGCTCCAACATCCAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAACAA
* ** *
52448 CGATACTGACTCTACGACTACGACTAAAGAATCTACTAAAACCATAGCTAGCCCAAGCAACGAGT
451 CGATACTGACTCTACGACTACGACTGAAGAATCCGCTGAAACCATAGCTAGCCCAAGCAACGAGT
52513 CGACTGACAAAAATACTCTGTATAAGACTGCAAATTGCGCAACCCTTTATTCATAGTATAAGTTC
516 CGACTGACAAAAATACTCTGTATAAGACTGCAAATTGCGCAACCCTTTATTCATAGTATAAGTTC
52578 TTACAATATCTATCTATGCCTTGAGCACATCTGTCTAGTCCCCTGGCCAGACAGAA-AGAGAAAA
581 TTACAATATCTATCTATGCCTTGAGCACATCTGTCTAGTCCCCTGGCCAGACAGAACAGAGAAAA
52642 ATACTTTGTGTCAGGTCTAAAGGAAGCTTCATAGATGGGGTAGAAGGAATTAGTTTCTTTGGCTG
646 ATACTTTGTGTCAGGTCTAAAGGAAGCTTCATAGATGGGGTAGAAGGAATTAGTTTCTTTGGCTG
* *
52707 TTCTGGGCTTGATGATATCTTGTTCCATTTCACATGCACAAGACAAGCATATAT
711 TTCTGGGCTTGATGATATCTTGTTCCAATTCACATGCACAGGACAAGCATATAT
* * * * * *
52761 ATTACCTCTAGATATTGAAGTATATATATTATTTTTATGATATTAGTGCCCAAATACATATTGTA
1 ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGATATCAGAGCCCAAATATATATTTTA
* * * *
52826 AGTCGTGGGTGCTTGGTTTAGAGATTGTCACCTTTAAGTCATACGTTGTTTATGCCGACAAAATG
66 AGTCATGGGTGCTTAGTATAGAGATTGTCACCTTTAAGTCATATGTTGTTTATGCCGACAAAATG
* *
52891 ATGTCGAACAATATCTTGGGAACAAAA
131 ATGTCGAATAATATCATGGGAA-AAAA
52918 AAAACAGATA
Statistics
Matches: 3498, Mismatches: 413, Indels: 299
0.83 0.10 0.07
Matches are distributed among these distances:
762 156 0.04
763 34 0.01
764 5 0.00
765 9 0.00
766 1 0.00
767 12 0.00
768 42 0.01
769 527 0.15
770 633 0.18
771 491 0.14
772 600 0.17
773 191 0.05
774 62 0.02
775 2 0.00
776 3 0.00
777 10 0.00
778 11 0.00
779 2 0.00
780 3 0.00
784 6 0.00
785 1 0.00
787 6 0.00
788 2 0.00
789 13 0.00
790 12 0.00
791 3 0.00
792 3 0.00
793 3 0.00
794 1 0.00
796 1 0.00
797 2 0.00
798 5 0.00
800 5 0.00
801 2 0.00
802 1 0.00
804 1 0.00
805 3 0.00
806 3 0.00
807 2 0.00
808 7 0.00
809 18 0.01
810 2 0.00
811 7 0.00
814 4 0.00
815 2 0.00
819 3 0.00
820 1 0.00
821 12 0.00
822 12 0.00
823 3 0.00
825 84 0.02
826 466 0.13
827 1 0.00
828 1 0.00
830 4 0.00
831 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (764 bp):
ATTACTTCTAGATATTGAAGCATATATATTATTTTTATGATATCAGAGCCCAAATATATATTTTA
AGTCATGGGTGCTTAGTATAGAGATTGTCACCTTTAAGTCATATGTTGTTTATGCCGACAAAATG
ATGTCGAATAATATCATGGGAAAAAACAGACAGAAACAACAAAAGCAATAGTGTCTGTTACACGG
ATAGATAGTATGTCAATCTATCCTATAAACATCCTTGCAGTTATTATACCCAAATGATATAATTC
ATTCTGTTGAGTATTTTAGTTGCTGAACCTTTTTATGGAGTAGGGACATTATACATGTAAATGGG
GTAGACTACGAGGTCGTGGGTATACGTATCCACTTTACAAATCTTAAATCAGTATTAACTAGGGA
GGAAGAAGCAGCTCCAACATCCAATCTTTCCAACCAGTTTATCAGGATTGTTGCCAACAACGATA
CTGACTCTACGACTACGACTGAAGAATCCGCTGAAACCATAGCTAGCCCAAGCAACGAGTCGACT
GACAAAAATACTCTGTATAAGACTGCAAATTGCGCAACCCTTTATTCATAGTATAAGTTCTTACA
ATATCTATCTATGCCTTGAGCACATCTGTCTAGTCCCCTGGCCAGACAGAACAGAGAAAAATACT
TTGTGTCAGGTCTAAAGGAAGCTTCATAGATGGGGTAGAAGGAATTAGTTTCTTTGGCTGTTCTG
GGCTTGATGATATCTTGTTCCAATTCACATGCACAGGACAAGCATATAT
Found at i:55326 original size:44 final size:44
Alignment explanation
Indices: 55277--55403 Score: 209
Period size: 44 Copynumber: 2.9 Consensus size: 44
55267 TCCTTGGATT
* *
55277 TTCTTTGATAATAATCCTCCACATATGTAGATCTTCTTTCAGTC
1 TTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCAGTC
* *
55321 TTCTTTGATAATAATTCTCCACACACGTGGATCTTCTTTCAGTC
1 TTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCAGTC
*
55365 TTCTTTGATAATAATCTTCCACATACGTGGATCTTCTTT
1 TTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTT
55404 AATAATCCTC
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 76 1.00
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.43
Consensus pattern (44 bp):
TTCTTTGATAATAATCCTCCACATACGTGGATCTTCTTTCAGTC
Found at i:58261 original size:26 final size:27
Alignment explanation
Indices: 58208--58261 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
58198 ATATGACATA
58208 TAAATAGCAACAAAACGAGTAACAAAG
1 TAAATAGCAACAAAACGAGTAACAAAG
* *
58235 TAAATAGTAACAAAA-TAGTAACAAAG
1 TAAATAGCAACAAAACGAGTAACAAAG
58261 T
1 T
58262 TTTGGATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (27 bp):
TAAATAGCAACAAAACGAGTAACAAAG
Found at i:58480 original size:21 final size:21
Alignment explanation
Indices: 58454--58497 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
58444 TTTATCTGGA
58454 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
58475 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
58496 TT
1 TT
58498 TACGCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Done.