Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold479
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: 168536
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 12792 characters in sequence are not A, C, G, or T
Found at i:5962 original size:9 final size:9
Alignment explanation
Indices: 5950--5983 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
5940 ATTTAAGCCA
5950 TTTAAAATT
1 TTTAAAATT
*
5959 TTTAAGATT
1 TTTAAAATT
5968 TTTAAAA-T
1 TTTAAAATT
5976 TTTAAAAT
1 TTTAAAAT
5984 GATAAAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
TTTAAAATT
Found at i:17385 original size:6 final size:6
Alignment explanation
Indices: 17374--17404 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
17364 TTAAATTTTA
17374 TAATTT TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT TAATTT T
17405 TAAACAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:20580 original size:28 final size:30
Alignment explanation
Indices: 20549--20612 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
20539 ATTTAAGAAA
*
20549 TAAATAT-AATATATATAAATTAA-AATAT
1 TAAATATAAATATAAATAAATTAACAATAT
*
20577 TAAA-ATAAATTTAAATAAATTAACAATAT
1 TAAATATAAATATAAATAAATTAACAATAT
20606 TGAAATA
1 T-AAATA
20613 AGTTGAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 2 0.07
28 18 0.60
29 6 0.20
30 3 0.10
31 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (30 bp):
TAAATATAAATATAAATAAATTAACAATAT
Found at i:20604 original size:29 final size:28
Alignment explanation
Indices: 20563--20641 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
20553 TATAATATAT
*
20563 ATAAATTAAAATATTAAAATAAATTTAA
1 ATAAATTAAAATATTAAAATAAATTGAA
* *
20591 ATAAATTAACAATATTGAAATAAGTTGAA
1 ATAAATTAA-AATATTAAAATAAATTGAA
* *
20620 ACAAATTAAAGATGTTAAAATA
1 ATAAATTAAA-ATATTAAAATA
20642 TTTGAAAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
28 10 0.23
29 33 0.77
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (28 bp):
ATAAATTAAAATATTAAAATAAATTGAA
Found at i:23367 original size:89 final size:89
Alignment explanation
Indices: 23177--23672 Score: 468
Period size: 88 Copynumber: 5.6 Consensus size: 89
23167 GATAAGACTG
* * * * *
23177 GTGTCTTCGATTTGCTTCGCTG-CTAGTACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCA
1 GTGTCTTCGATCTGCTTCGCTGTC-AGTACAGGAAGGCAAGATCTGCTATCTTCAATCTACTCCA
* *
23241 CT--ATTACTCAGGGAGATAAGGCTA
65 CTGCA-AACTCAGGGAGACAAGGCTA
* ** * * * *
23265 GTGTCTTCGATCTGCTTCGTTGTCAGTTTAGGAAGTCAAGATCTGCTATCTTCATTCTGCTCCGC
1 GTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTACTCCAC
*
23330 TGCAAACTCAGGGAGGCAAGGCTA
66 TGCAAACTCAGGGAGACAAGGCTA
* * * * *
23354 GTGTCTTCAATCTGCTTCGCTGCCAGTACATGAAGGCAAGATTTGCTATCTTCAACCTACTCCAC
1 GTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTACTCCAC
** *
23419 TGC-TGCTCAGGGAGATAAGGCTGA
66 TGCAAACTCAGGGAGACAAGGCT-A
* * * * * * *
23443 G-GTCTTCGATTTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCAC
1 GTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTACTCCAC
** *
23507 T--ATTGCTCAAGGAGACAAGGCTGA
66 TGCA-AACTCAGGGAGACAAGGCT-A
** * * * * *
23531 G-GTCTTCGATCTATTTCACTGTTAGTATAGGAAGGCAAGATCTGCTATCTTCAATCTACTCTAT
1 GTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTACTCCAC
* * * *
23595 TGCAAACCCAGGGAGGCAAGACTG
66 TGCAAACTCAGGGAGACAAGGCTA
* * *
23619 GTGTCTTCGATCTGCTTCGCGGTCAGCACAGGGAGGCAAGATCTGCTATCTTCA
1 GTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCA
23673 TTGATCTATT
Statistics
Matches: 332, Mismatches: 67, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
88 197 0.59
89 133 0.40
90 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (89 bp):
GTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTACTCCAC
TGCAAACTCAGGGAGACAAGGCTA
Found at i:23484 original size:177 final size:177
Alignment explanation
Indices: 23177--23674 Score: 455
Period size: 177 Copynumber: 2.8 Consensus size: 177
23167 GATAAGACTG
* * * *
23177 GTGTCTTCGATTTGCTTCGCTGCTAGTACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCAC
1 GTGTCTTCAATCTGCTTCGCTGCCAGTACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCAC
* * * * * ** *
23242 TATTACTCAGGGAGATAAGGCTAGTGTCTTCGATCTGCTTCGTTGTCAGTTTAGGAAGTCAAGAT
66 TACTACTCAGGGAGATAAGGCTAGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGAT
23307 CTGCTATCTTCATTCTGCTCCGCTGCAAACTCAGGGAGGCAAGGCTA
131 CTGCTATCTTCATTCTGCTCCGCTGCAAACTCAGGGAGGCAAGGCTA
* * *
23354 GTGTCTTCAATCTGCTTCGCTGCCAGTACATGAAGGCAAGATTTGCTATCTTCAACCTACTCCAC
1 GTGTCTTCAATCTGCTTCGCTGCCAGTACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCAC
* * *
23419 TGCTGCTCAGGGAGATAAGGCTGAG-GTCTTCGATTTACTTCGCTGCCAATACAGGAAGACAAGA
66 TACTACTCAGGGAGATAAGGCT-AGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGA
* ** * * ** * *
23483 TCTGCTATTTTCAACCTACTCCACT--ATTGCTCAAGGAGACAAGGCTGA
130 TCTGCTATCTTCATTCTGCTCCGCTGCA-AACTCAGGGAGGCAAGGCT-A
* ** * ** * * * * * *
23531 G-GTCTTCGATCTATTTCACTGTTAGTATAGGAAGGCAAGATCTGCTATCTTCAATCTACTCTAT
1 GTGTCTTCAATCTGCTTCGCTGCCAGTACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCAC
* * * ** * * * * * ** * *
23595 TGCAAACCCAGGGAGGCAAGACTGGTGTCTTCGATCTGCTTCGCGGTCAGCACAGGGAGGCAAGA
66 TAC-TACTCAGGGAGATAAGGCTAGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGA
23660 TCTGCTATCTTCATT
130 TCTGCTATCTTCATT
23675 GATCTATTCT
Statistics
Matches: 259, Mismatches: 57, Indels: 10
0.79 0.17 0.03
Matches are distributed among these distances:
175 1 0.00
176 70 0.27
177 186 0.72
178 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (177 bp):
GTGTCTTCAATCTGCTTCGCTGCCAGTACAAGAAGACAAGATCTGCTATCTTCAACCTACTCCAC
TACTACTCAGGGAGATAAGGCTAGTGTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGAT
CTGCTATCTTCATTCTGCTCCGCTGCAAACTCAGGGAGGCAAGGCTA
Found at i:23658 original size:265 final size:265
Alignment explanation
Indices: 23179--23672 Score: 711
Period size: 265 Copynumber: 1.9 Consensus size: 265
23169 TAAGACTGGT
* * *
23179 GTCTTCGATTTGCTTCGCTGCTAGTACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
1 GTCTTCGATTTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
* * * ** * *
23244 TTACTCAGGGAGATAAGGCTAGTGTCTTCGATCTGCTTCGTTGTCAGTTTAGGAAGTCAAGATCT
66 TTACTCAAGGAGACAAGGCTAGTGTCTTCGATCTACTTCACTGTCAGTATAGGAAGGCAAGATCT
* * * * *
23309 GCTATCTTCATTCTGCTCCGCTGCAAACTCAGGGAGGCAAGGCTAGTGTCTTCAATCTGCTTCGC
131 GCTATCTTCAATCTACTCCACTGCAAACCCAGGGAGGCAAGACTAGTGTCTTCAATCTGCTTCGC
* * * *
23374 TGCCAGTACATGAAGGCAAGATTTGCTATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGG
196 GGCCAGCACAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGG
23439 CTGAG
261 CTGAG
*
23444 GTCTTCGATTTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
1 GTCTTCGATTTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
* * *
23509 TTGCTCAAGGAGACAAGGCTGAG-GTCTTCGATCTATTTCACTGTTAGTATAGGAAGGCAAGATC
66 TTACTCAAGGAGACAAGGCT-AGTGTCTTCGATCTACTTCACTGTCAGTATAGGAAGGCAAGATC
* * * *
23573 TGCTATCTTCAATCTACTCTATTGCAAACCCAGGGAGGCAAGACTGGTGTCTTCGATCTGCTTCG
130 TGCTATCTTCAATCTACTCCACTGCAAACCCAGGGAGGCAAGACTAGTGTCTTCAATCTGCTTCG
* *
23638 CGGTCAGCACAGGGAGGCAAGATCTGCTATCTTCA
195 CGGCCAGCACAGGAAGGCAAGATCTGCTATCTTCA
23673 TTGATCTATT
Statistics
Matches: 199, Mismatches: 29, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
265 197 0.99
266 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (265 bp):
GTCTTCGATTTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
TTACTCAAGGAGACAAGGCTAGTGTCTTCGATCTACTTCACTGTCAGTATAGGAAGGCAAGATCT
GCTATCTTCAATCTACTCCACTGCAAACCCAGGGAGGCAAGACTAGTGTCTTCAATCTGCTTCGC
GGCCAGCACAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGG
CTGAG
Found at i:25979 original size:25 final size:25
Alignment explanation
Indices: 25926--25985 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
25916 AAGAAAATCC
* *
25926 AAAAGAATGAAAGAATAATTATTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
25951 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
25976 AAAA-AATGAA
1 AAAAGAATGAA
25986 TACAAAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.29
25 22 0.71
ACGTcount: A:0.58, C:0.05, G:0.17, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:29685 original size:29 final size:28
Alignment explanation
Indices: 29644--29722 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
29634 TATAATATTT
*
29644 ATAAATTAAAATATTAAAATAAATTTAA
1 ATAAATTAAAATATTAAAATAAATTGAA
* *
29672 ATAAATTAACAATATTGAAATAAGTTGAA
1 ATAAATTAA-AATATTAAAATAAATTGAA
* *
29701 ACAAATTAAAGATGTTAAAATA
1 ATAAATTAAA-ATATTAAAATA
29723 TTTGAAAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
28 10 0.23
29 33 0.77
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (28 bp):
ATAAATTAAAATATTAAAATAAATTGAA
Found at i:29898 original size:16 final size:16
Alignment explanation
Indices: 29879--29927 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29869 TATAAATACG
29879 TATATAAATTGTATAA
1 TATATAAATTGTATAA
* * *
29895 TATAAAAAATGTATGTA
1 TATATAAATTGTAT-AA
*
29912 TATATAAATTATATAA
1 TATATAAATTGTATAA
29928 AAAATATGTA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
TATATAAATTGTATAA
Found at i:29943 original size:28 final size:31
Alignment explanation
Indices: 29875--29944 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
29865 TATATATAAA
29875 TACGTATATAAATTGTATAATATAAAAAATG
1 TACGTATATAAATTGTATAATATAAAAAATG
* *
29906 TATGTATATATAAAT-TAT-ATA-AAAAATATG
1 TACGTATATA-AATTGTATAATATAAAAA-ATG
29936 TACGTATAT
1 TACGTATAT
29945 TTTAAAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 5 0.15
30 14 0.41
31 12 0.35
32 3 0.09
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.39
Consensus pattern (31 bp):
TACGTATATAAATTGTATAATATAAAAAATG
Found at i:33955 original size:28 final size:28
Alignment explanation
Indices: 33903--33956 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
33893 CTCACCATTC
* *
33903 TTTCTTTTGTTTTTCTTTATGCTTTCTT
1 TTTCTTTTCTTTTTCTTTATCCTTTCTT
33931 TTTCTTTTCTTTTTCTGTTA-CCTTTC
1 TTTCTTTTCTTTTTCT-TTATCCTTTC
33957 AAATCACGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.04, C:0.19, G:0.06, T:0.72
Consensus pattern (28 bp):
TTTCTTTTCTTTTTCTTTATCCTTTCTT
Found at i:34713 original size:7 final size:7
Alignment explanation
Indices: 34701--34729 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
34691 TTCTATAAAG
34701 ATTTTGA
1 ATTTTGA
34708 ATTTTGA
1 ATTTTGA
34715 ATTTTGA
1 ATTTTGA
34722 ATTTTGA
1 ATTTTGA
34729 A
1 A
34730 GCAAATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (7 bp):
ATTTTGA
Found at i:36084 original size:20 final size:20
Alignment explanation
Indices: 36031--36084 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
36021 GTTGTTGCAA
36031 GTAAATTTTAAAAAAAATTAG
1 GTAAATTTT-AAAAAAATTAG
****
36052 GTAAAAAGAAAAAAAATTAG
1 GTAAATTTTAAAAAAATTAG
36072 GTAAATTTTAAAA
1 GTAAATTTTAAAA
36085 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (20 bp):
GTAAATTTTAAAAAAATTAG
Found at i:36394 original size:28 final size:28
Alignment explanation
Indices: 36342--36395 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
36332 CTCACCATTC
* *
36342 TTTCTTTTGTTTTTCTTTATGCTTTCTT
1 TTTCTTTTCTTTTTCTTTATCCTTTCTT
36370 TTTCTTTTCTTTTTCTGTTA-CCTTTC
1 TTTCTTTTCTTTTTCT-TTATCCTTTC
36396 AAGTCACGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.04, C:0.19, G:0.06, T:0.72
Consensus pattern (28 bp):
TTTCTTTTCTTTTTCTTTATCCTTTCTT
Found at i:47961 original size:13 final size:12
Alignment explanation
Indices: 47938--47994 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 12
47928 AAAATTAGTG
47938 ATATATTTTAATT
1 ATAT-TTTTAATT
47951 ATATTTATTAATT
1 ATATTT-TTAATT
47964 ATTATTTTTAATAAT
1 A-TATTTTTAAT--T
* *
47979 GTTTTTTTAATT
1 ATATTTTTAATT
47991 ATAT
1 ATAT
47995 AAAGTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
12 5 0.14
13 16 0.44
14 14 0.39
15 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
ATATTTTTAATT
Found at i:50106 original size:10 final size:10
Alignment explanation
Indices: 50069--50113 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
50059 AGTTTCTAAT
50069 AATTTTT-AC
1 AATTTTTAAC
* *
50078 AATATTTAGC
1 AATTTTTAAC
50088 AATTTTTAAC
1 AATTTTTAAC
*
50098 AATTTTTAAT
1 AATTTTTAAC
50108 AATTTT
1 AATTTT
50114 CTAAAGTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 6 0.20
10 24 0.80
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (10 bp):
AATTTTTAAC
Found at i:50111 original size:20 final size:19
Alignment explanation
Indices: 50065--50113 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
50055 TTATAGTTTC
50065 TAATAATTTTTACAATATT
1 TAATAATTTTTACAATATT
** *
50084 TAGCAATTTTTAACAATTTT
1 TAATAATTTTT-ACAATATT
50104 TAATAATTTT
1 TAATAATTTT
50114 CTAAAGTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (19 bp):
TAATAATTTTTACAATATT
Found at i:59307 original size:28 final size:30
Alignment explanation
Indices: 59270--59326 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
59260 AATTCATCTA
*
59270 CATTTGCAAATGA-ATCATTTCT-CATTTT
1 CATTTCCAAATGATATCATTTCTCCATTTT
*
59298 CATTTCCAAATGATTTCATTTCTCCATTT
1 CATTTCCAAATGATATCATTTCTCCATTT
59327 CGAAGAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.48
29 8 0.32
30 5 0.20
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (30 bp):
CATTTCCAAATGATATCATTTCTCCATTTT
Found at i:64720 original size:35 final size:35
Alignment explanation
Indices: 64674--64741 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
64664 ATAACACATT
64674 TTCTACTCTGCTCT-ATTTTGTTATGCTCT-CTTCGG
1 TTCTACTCTGCT-TGA-TTTGTTATGCTCTGCTTCGG
* *
64709 TTCTATTCTGCTTGATTTGTTATGTTCTGCTTC
1 TTCTACTCTGCTTGATTTGTTATGCTCTGCTTC
64742 ATTCTGTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 13 0.45
35 16 0.55
ACGTcount: A:0.09, C:0.22, G:0.15, T:0.54
Consensus pattern (35 bp):
TTCTACTCTGCTTGATTTGTTATGCTCTGCTTCGG
Found at i:64738 original size:19 final size:20
Alignment explanation
Indices: 64714--64754 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
64704 TTCGGTTCTA
*
64714 TTCTGCTTGATT-TGTTATG
1 TTCTGCTTCATTCTGTTATG
*
64733 TTCTGCTTCATTCTGTTGTG
1 TTCTGCTTCATTCTGTTATG
64753 TT
1 TT
64755 TGGTTCTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.07, C:0.15, G:0.20, T:0.59
Consensus pattern (20 bp):
TTCTGCTTCATTCTGTTATG
Found at i:66378 original size:20 final size:20
Alignment explanation
Indices: 66353--66398 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
66343 GTACTGGATC
*
66353 ACACTTTGGTGCCTCTCTTT
1 ACACTTTGGTCCCTCTCTTT
66373 ACACTTTGGTCCCTCTCTTT
1 ACACTTTGGTCCCTCTCTTT
*
66393 GCACTT
1 ACACTT
66399 CAGTGCCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.11, C:0.33, G:0.13, T:0.43
Consensus pattern (20 bp):
ACACTTTGGTCCCTCTCTTT
Found at i:69064 original size:17 final size:16
Alignment explanation
Indices: 69026--69068 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
69016 TAAATAGTGG
69026 AAGATGGA-ATGAATA
1 AAGATGGATATGAATA
69041 AACGATGGATATGACATA
1 AA-GATGGATATGA-ATA
*
69059 TAGATGGATA
1 AAGATGGATA
69069 AGTGTTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 6 0.25
17 12 0.50
18 4 0.17
ACGTcount: A:0.47, C:0.05, G:0.26, T:0.23
Consensus pattern (16 bp):
AAGATGGATATGAATA
Found at i:74909 original size:38 final size:38
Alignment explanation
Indices: 74867--74941 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
74857 ATGCTTCCAC
74867 TAATGAGATATACTAAAGAAAAGAGTAACTTTCTTTTA
1 TAATGAGATATACTAAAGAAAAGAGTAACTTTCTTTTA
*
74905 TAATGAGATATACTCAAGAAAAGAGTAACTTTCTTTT
1 TAATGAGATATACTAAAGAAAAGAGTAACTTTCTTTT
74942 TAGGATAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (38 bp):
TAATGAGATATACTAAAGAAAAGAGTAACTTTCTTTTA
Found at i:81438 original size:15 final size:15
Alignment explanation
Indices: 81415--81445 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
81405 CTAATATTTA
*
81415 AAACTTATTAAAAAT
1 AAACATATTAAAAAT
81430 AAACATATTAAAAAT
1 AAACATATTAAAAAT
81445 A
1 A
81446 CTAAGCTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACATATTAAAAAT
Found at i:82464 original size:22 final size:19
Alignment explanation
Indices: 82439--82487 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
82429 TATGGAGGCA
*
82439 GAGGCTGGCGTGGAGCGGCTCG
1 GAGGCTGGC-TGCAGC-GCT-G
82461 GAGGCGTGGCTGCAGCGCTG
1 GAGGC-TGGCTGCAGCGCTG
82481 GAGGCTG
1 GAGGCTG
82488 AATGCTGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 6 0.24
21 3 0.12
22 10 0.40
23 4 0.16
ACGTcount: A:0.10, C:0.22, G:0.53, T:0.14
Consensus pattern (19 bp):
GAGGCTGGCTGCAGCGCTG
Found at i:83488 original size:16 final size:16
Alignment explanation
Indices: 83459--83528 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
83449 TTTGGTTCGC
* *
83459 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
83475 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
83491 TGTAATGGATTAGAGG
1 TGTAATGGAATAGAGG
83507 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
83523 TGTAAT
1 TGTAAT
83529 AGCAAATCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:83500 original size:32 final size:32
Alignment explanation
Indices: 83459--83528 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
83449 TTTGGTTCGC
*
83459 TGTATTGGATTAGAGGCGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATGGAATAGAGG
*
83491 TGTAATGGATTAGAGGTGTAATGGAATAGAGG
1 TGTAATGGATTAGAGGCGTAATGGAATAGAGG
83523 TGTAAT
1 TGTAAT
83529 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.30
Consensus pattern (32 bp):
TGTAATGGATTAGAGGCGTAATGGAATAGAGG
Found at i:83612 original size:39 final size:43
Alignment explanation
Indices: 83507--83616 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
83497 GGATTAGAGG
83507 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTAAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
83552 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
83592 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
83617 TAATGGGAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:83783 original size:18 final size:17
Alignment explanation
Indices: 83762--83796 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
83752 TTATTATTAA
*
83762 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
83780 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
83797 TCTNNNNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:87592 original size:32 final size:32
Alignment explanation
Indices: 87551--87673 Score: 131
Period size: 32 Copynumber: 3.5 Consensus size: 32
87541 CTAATTTCAA
87551 AATAAATAAAATGAAGAATGAAGATTTGGTTT
1 AATAAATAAAATGAAGAATGAAGATTTGGTTT
87583 AATAAATAAAATGAAGAATGAAGATTTGGTTTTCT
1 AATAAATAAAATGAAGAATGAAGATTTGG--TT-T
87618 AATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTT
1 AA--T------AAATAAAATGAAGAATGAAGATTTGGTTT
87658 AAT-AATGAAAATGAAG
1 AATAAAT-AAAATGAAG
87674 TTTTAAAACT
Statistics
Matches: 79, Mismatches: 0, Indels: 24
0.77 0.00 0.23
Matches are distributed among these distances:
31 3 0.04
32 38 0.48
34 2 0.03
35 3 0.04
37 1 0.01
38 1 0.01
40 3 0.04
41 2 0.03
43 26 0.33
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (32 bp):
AATAAATAAAATGAAGAATGAAGATTTGGTTT
Found at i:87658 original size:75 final size:75
Alignment explanation
Indices: 87535--87673 Score: 262
Period size: 75 Copynumber: 1.9 Consensus size: 75
87525 ATTTAATTAA
87535 GGTTTTCTAATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAATAAAT-AAAATGAAG
1 GGTTTTCTAATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAAT-AATGAAAATGAAG
87599 AATGAAGATTT
65 AATGAAGATTT
87610 GGTTTTCTAATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAATAATGAAAATGAAG
1 GGTTTTCTAATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAATAATGAAAATGAAG
87674 TTTTAAAACT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 3 0.05
75 60 0.95
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (75 bp):
GGTTTTCTAATTTCAAAATAAATAAAATGAAGAATGAAGATTTGGTTTAATAATGAAAATGAAGA
ATGAAGATTT
Found at i:87985 original size:13 final size:13
Alignment explanation
Indices: 87967--87991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
87957 ATCAAATTTG
87967 TATGTACTCTTTA
1 TATGTACTCTTTA
87980 TATGTACTCTTT
1 TATGTACTCTTT
87992 CACTAATAAT
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:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:91683 original size:86 final size:86
Alignment explanation
Indices: 91511--92109 Score: 1164
Period size: 86 Copynumber: 7.0 Consensus size: 86
91501 CAAATGTTGT
* * *
91511 ATATCAGGTTATGTGTTTTACTCTAAACATATCAGTATTTAC-TATTTTTTCTACAAATTGGGTT
1 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
91575 GAAGTGCATGGAAAATCTTTA
66 GAAGTGCATGGAAAATCTTTA
91596 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
1 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
91661 GAAGTGCATGGAAAATCTTTA
66 GAAGTGCATGGAAAATCTTTA
91682 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
1 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
91747 GAAGTGCATGGAAAATCTTTA
66 GAAGTGCATGGAAAATCTTTA
91768 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
1 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
91833 GAAGTGCATGGAAAATCTTTA
66 GAAGTGCATGGAAAATCTTTA
91854 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
1 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
91919 GAAGTGCATGGAAAATCTTTA
66 GAAGTGCATGGAAAATCTTTA
91940 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
1 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
92005 GAAGTGCATGGAAAATCTTTA
66 GAAGTGCATGGAAAATCTTTA
92026 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
1 ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
92091 GAAGTGCATGGAAAATCTT
66 GAAGTGCATGGAAAATCTT
92110 CAATTTTAAC
Statistics
Matches: 510, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
85 39 0.08
86 471 0.92
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (86 bp):
ATATCAAGTTATGTATTTTACTCTAAACATATCAGCATTTACTTATTTTTTCTACAAATTGGGTT
GAAGTGCATGGAAAATCTTTA
Found at i:102610 original size:11 final size:11
Alignment explanation
Indices: 102594--102634 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
102584 AATTTCTAAT
102594 ATTTTTTTATA
1 ATTTTTTTATA
*
102605 ATTTTTTTACA
1 ATTTTTTTATA
* *
102616 ATATTTATATA
1 ATTTTTTTATA
102627 ATTTTTTT
1 ATTTTTTT
102635 TGAAATTTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTTTTTATA
Found at i:111233 original size:21 final size:21
Alignment explanation
Indices: 111178--111237 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
111168 GAAAAGGGCG
111178 GCTCAAACATTGATCAGAATA
1 GCTCAAACATTGATCAGAATA
** * *
111199 GGGCATAAGA-TGATCAGAGTA
1 GCTCA-AACATTGATCAGAATA
*
111220 GCTCAAATATTGATCAGA
1 GCTCAAACATTGATCAGA
111238 CTGGGGCATG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 3 0.10
21 24 0.80
22 3 0.10
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (21 bp):
GCTCAAACATTGATCAGAATA
Found at i:112573 original size:45 final size:45
Alignment explanation
Indices: 112469--112827 Score: 194
Period size: 44 Copynumber: 8.2 Consensus size: 45
112459 TTGCATCAGG
* ** * * * **
112469 TCTTATCTCCCTGAATTTATAGCGGAGCAGACTGAATA-AGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
* * *
112513 TCTTATC-CCTTTGAAGTTGCAGTGGGGCAGACTGAAGATGGAAAA
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
* ** * *
112558 TCTTATCTCCCTGAAGTTGTAGTAAAGCAGA-TTAA-A-GCCAATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGC-A-AA
* * * * * *
112602 TCCTATCTCTCTGAAGTTGCAGCGGAGCGGA-TTAAAAT-G---A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
* * * * **
112642 TCTTATCTCTCTAAAGTTGCAGTAGAGTAGA-TG--GCAT--CAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-ATGGCAAA
* * * **
112683 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAATA-AGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
* * * *
112727 TCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAGGATGGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
* *
112772 TCTTATACT-TCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAA
1 TCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
*
112817 TCCTATCTCCC
1 TCTTATCTCCC
112828 CGACATTGCG
Statistics
Matches: 241, Mismatches: 55, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
39 2 0.01
40 27 0.11
41 26 0.11
42 3 0.01
43 5 0.02
44 100 0.41
45 75 0.31
46 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCAAA
Found at i:112652 original size:214 final size:214
Alignment explanation
Indices: 112283--112792 Score: 806
Period size: 214 Copynumber: 2.4 Consensus size: 214
112273 TTAAGTTCAT
*
112283 AGACTGAATAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTT
1 AGACTGAATAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTT
* ** *
112348 TTCTCCCTGAAGTTGCACTGGAGTAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGCAG
66 ATCTCCCTGAAGTTGCACTAAAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGCAG
* * *
112413 AGCGGATTAAAATGATCTTATCTCTCTGAAGTTACAGTAGGGTAGATTGCATCAGGTCTTATCTC
131 AGCGGATTAAAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATGGCATCAGGTCTTATCTC
* *
112478 CCTGAATTTATAGCGGAGC
196 CCTGAAGTTACAGCGGAGC
** *
112497 AGACTGAATAAGCAGGTCTTATCCCTTTGAAGTTGCAGTGGGGCAGACTGAAGATGGAAAATCTT
1 AGACTGAATAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTT
* * * *
112562 ATCTCCCTGAAGTTGTAGTAAAGCAGATTAAAGCCAATAATCCTATCTCTCTGAAGTTGCAGCGG
66 ATCTCCCTGAAGTTGCACTAAAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGCAG
*
112627 AGCGGATTAAAATGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATGGCATCAGGTCTTATCTC
131 AGCGGATTAAAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATGGCATCAGGTCTTATCTC
*
112692 CCTGAAGTTGCAGCGGAGC
196 CCTGAAGTTACAGCGGAGC
* *
112711 AGACTGAATAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAGGATGGCAAGTCTT
1 AGACTGAATAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTT
*
112776 ATACT-TCTGAAGTTGCA
66 AT-CTCCCTGAAGTTGCA
112793 GTGGGGCAGA
Statistics
Matches: 269, Mismatches: 26, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
214 267 0.99
215 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (214 bp):
AGACTGAATAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAATCTT
ATCTCCCTGAAGTTGCACTAAAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGCAG
AGCGGATTAAAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATGGCATCAGGTCTTATCTC
CCTGAAGTTACAGCGGAGC
Found at i:112732 original size:44 final size:44
Alignment explanation
Indices: 112283--112807 Score: 172
Period size: 44 Copynumber: 12.2 Consensus size: 44
112273 TTAAGTTCAT
* * *
112283 AGACTGAATAAGCAGGTCTTATCCCCCTGAAGTTGCAG-TGAGGC
1 AGACTGAATAAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGA-GC
* * * * *
112327 AGACTGAAGATGGCAAATCTTTTCTCCCTGAAGTTGCA-CTGGAGT
1 AGACTGAATA-AGCAAGTCTTATCTCCCTGAAGTTGCAGC-GGAGC
* * * *
112372 AGA-T-TA-AAGCCAATAATCCTATCTCCCTGAAGTTGCAGCAGAGC
1 AGACTGAATAAG-C-A-AGTCTTATCTCCCTGAAGTTGCAGCGGAGC
* * * * * *
112416 GGA-TTAA-AATG--A-TCTTATCTCTCTGAAGTTACAGTAGG-GT
1 AGACTGAATAA-GCAAGTCTTATCTCCCTGAAGTTGCAG-CGGAGC
* * * * **
112456 AGATTGCAT---CAGGTCTTATCTCCCTGAATTTATAGCGGAGC
1 AGACTGAATAAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGC
* * * *
112497 AGACTGAATAAGCAGGTCTTATC-CCTTTGAAGTTGCAGTGGGGC
1 AGACTGAATAAGCAAGTCTTATCTCC-CTGAAGTTGCAGCGGAGC
* * * * * ***
112541 AGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGTAGTAAAGC
1 AGACTGAATA-AGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGC
* * * *
112586 AGA-T-TA-AAGCCAATAATCCTATCTCTCTGAAGTTGCAGCGGAGC
1 AGACTGAATAAG-C-A-AGTCTTATCTCCCTGAAGTTGCAGCGGAGC
* * * * ** *
112630 GGA-TTAA-AATG--A-TCTTATCTCTCTAAAGTTGCAGTAGAGT
1 AGACTGAATAA-GCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGC
* *
112670 AGA-TGGCAT---CAGGTCTTATCTCCCTGAAGTTGCAGCGGAGC
1 AGACT-GAATAAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGC
* * * *
112711 AGACTGAATAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGC
1 AGACTGAATAAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGC
* * * *
112755 AGACTGAGGAT-GGCAAGTCTTATACT-TCTGAAGTTGCAGTGGGGC
1 AGACTGA--ATAAGCAAGTCTTAT-CTCCCTGAAGTTGCAGCGGAGC
112800 AGACTGAA
1 AGACTGAA
112808 GATGGCAAAT
Statistics
Matches: 360, Mismatches: 82, Indels: 79
0.69 0.16 0.15
Matches are distributed among these distances:
40 50 0.14
41 64 0.18
42 4 0.01
43 7 0.02
44 133 0.37
45 93 0.26
46 9 0.03
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (44 bp):
AGACTGAATAAGCAAGTCTTATCTCCCTGAAGTTGCAGCGGAGC
Found at i:115836 original size:30 final size:30
Alignment explanation
Indices: 115800--115859 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
115790 CACAAACCAA
115800 TATTTAGGTTATACTTCAGTGCTTGACAAG
1 TATTTAGGTTATACTTCAGTGCTTGACAAG
115830 TATTTAGGTTATACTTCAGTGCTTGACAAG
1 TATTTAGGTTATACTTCAGTGCTTGACAAG
115860 CACTTTCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (30 bp):
TATTTAGGTTATACTTCAGTGCTTGACAAG
Found at i:117241 original size:16 final size:15
Alignment explanation
Indices: 117205--117249 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
117195 ATGAAAAATT
117205 TAATAATA-ATATGAA
1 TAATAATATATAT-AA
*
117220 TGATAATATATATACA
1 TAATAATATATATA-A
117236 TAATAATATATATA
1 TAATAATATATATA
117250 TATATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (15 bp):
TAATAATATATATAA
Found at i:125077 original size:17 final size:18
Alignment explanation
Indices: 125042--125076 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
125032 GGAAAATGAG
*
125042 CAAAAAATGAGTGAAAAA
1 CAAAAAATGAGGGAAAAA
*
125060 CAAAAAATGGGGGAAAA
1 CAAAAAATGAGGGAAAA
125077 CTATAGGACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.23, T:0.09
Consensus pattern (18 bp):
CAAAAAATGAGGGAAAAA
Found at i:126088 original size:20 final size:18
Alignment explanation
Indices: 126044--126092 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
126034 GATTTTGATG
*
126044 ATTTAAAAATTAAATACT
1 ATTTAAAAATTAAAAACT
126062 -TTATAAAATATTTAAAAACT
1 ATT-TAAAA-A-TTAAAAACT
126082 ATTTAAAAATT
1 ATTTAAAAATT
126093 GTAAGCCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 2 0.08
18 7 0.27
19 2 0.08
20 13 0.50
21 2 0.08
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTAAAAATTAAAAACT
Found at i:126477 original size:61 final size:61
Alignment explanation
Indices: 126382--126504 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
126372 AAGTGACCTA
126382 AACCGACTTATGGAATAATCAAAAGTATTATTTTAGTCTTTGTCTTAGGTATGAATGATAT
1 AACCGACTTATGGAATAATCAAAAGTATTATTTTAGTCTTTGTCTTAGGTATGAATGATAT
126443 AACCGACTTATGGAATAATCAAAAGTATTATTTTAGTCTTTGTCTTAGGTATGAATGATAT
1 AACCGACTTATGGAATAATCAAAAGTATTATTTTAGTCTTTGTCTTAGGTATGAATGATAT
126504 A
1 A
126505 TTCTAGATTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (61 bp):
AACCGACTTATGGAATAATCAAAAGTATTATTTTAGTCTTTGTCTTAGGTATGAATGATAT
Found at i:139286 original size:601 final size:593
Alignment explanation
Indices: 137743--139360 Score: 2398
Period size: 597 Copynumber: 2.7 Consensus size: 593
137733 ATTTTGCCTT
* * * *
137743 AAATGAAATAAAATGCTCTTACTTTTGTTATCTATTACAAATCAAACTCTTTTATGAAAAAAATA
1 AAATGAAATAAAAAGTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTAT-AAAAAAATA
* * * * * * * * ** * *
137808 TTTTAAATTAAAGAAA-CAAAGAAAATTCAATATCTTCTAAGTTATTCCACTCCACA-TAATTTT
65 CTTTAAATTCAAGAAATC-AAGGAAATTGATTACCTT-AAAATTATTAAACTCCAAATTAATTCT
* * ** *
137871 TTGAGTCGTGTCAGATTTCCAATACTTCTTGGAATGATCCCTGTAAATTGATTCA-AGGACAATG
128 TGGAGTCGTGTTAGATTTCCAATACTTCTTGGAATGATCCCCATAAATTGATT-ATAGGACAACG
* * * *** * ***
137935 ATAAATTTTTAAGGTTGTTGCATATGCCCATACTTGATGGAATGTTACCAAATAATTCATTTTTA
192 ACAAATTTTTAAGGTTGTTGCATTTGCCCATGCCAAATGGAATGTTACCAGATAATTCATTCCAA
* *
138000 TTCAAGTAAAGCCCTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAATCTACCTGATAA
257 CTCAGGTAAAGCCCTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAATCTACCTGATAA
*
138065 GCTATTGTTGGAGAGAACAATGGTTTTCAGAGAAGAAATGTTGAAGATCGAAGTCGGAATCTGAC
322 GCTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAATGTTGAAGATCGAAGTCGGAATCTGAC
* *
138130 CTGTAAGACCTTTAATTGCTTGAATATTAAGCAAGTCAAAACGAAGAAGATTACCGATTTGCTCA
387 CTGTAAGGCCTTTAATTGCTTGAATATTAAGC-AGTCAAAACCAAGAAGATTACCGATTTGCTCA
* *
138195 GGAATTTGACCTGCACACATAGTCGAAAAATCAAGGTGTCAAACTACCTATTTTGTTAGCATAAG
451 GGAATTTGACCTACACACATAGTCGAAAAATCAAGGTGTCAAACTACCTATTTTGTTAACATAAG
*
138260 TCAAAGAGGTTTTCGTTTCTATTCTACAGTAATTTGGAGATGTTAGATTTTAATATATTTCAGCT
516 TCAAAGAAGTTTTCGTTTCTATTCTACAGTAATTTGGAGATGTTAGATTTTAATATATTTCAGCT
*
138325 TATGTTTTTCATT
581 TATGTTTTTCATC
**
138338 AAATGAAATGAAAAAGTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATAAAAAAGCA
1 AAATGAAAT-AAAAAGTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATAAAAAAATA
* *
138403 CTTTAAATTCAAGAAATCAAGGAAATTGATTACCTTCTAGATTATTAAACTCCAAATATAATTCT
65 CTTTAAATTCAAGAAATCAAGGAAATTGATTACCTT-AAAATTATTAAACTCCAAAT-TAATTCT
* *
138468 TGGAGTCGTGTTAGATTTCCAATACTTCTTGGAATGATCCCCATAAATTAATTATAGGACAACAA
128 TGGAGTCGTGTTAGATTTCCAATACTTCTTGGAATGATCCCCATAAATTGATTATAGGACAACGA
** * * *
138533 CAAACATTTAAAGTTGCTGCATTTGCCTATGCCAAATGGAATGTTACCAGATAATTCATTCCAAC
193 CAAATTTTTAAGGTTGTTGCATTTGCCCATGCCAAATGGAATGTTACCAGATAATTCATTCCAAC
* *
138598 TCAGATAAAGCCCTTCAAGCTTGGGAATATGTTGACACATATCATTAGGCAATCTACCTGATAAG
258 TCAGGTAAAGCCCTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAATCTACCTGATAAG
138663 CTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAATGTTGAAGATC-AGAGTCGGAATCTGAC
323 CTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAATGTTGAAGATCGA-AGTCGGAATCTGAC
*
138727 CTGTAAGGCCTTTAATTGCTTGAATATTAAGCAGTTCCAAACCAAGAAGATTACCGATTTGCTCA
387 CTGTAAGGCCTTTAATTGCTTGAATATTAAGCAG-TCAAAACCAAGAAGATTACCGATTTGCTCA
138792 GGAATTTGACCTACACACATAGTCGAAAAATCAAGGTGTCAAACTACCTATTTTGTTAACATAAG
451 GGAATTTGACCTACACACATAGTCGAAAAATCAAGGTGTCAAACTACCTATTTTGTTAACATAAG
* *
138857 TCAAAGAAGTTTTCTTTTCTGTTCTACAGTAATTTGGAGATGTTAGATTTTAATATATTTCAGCA
516 TCAAAGAAGTTTTCGTTTCTATTCTACAGTAATTTGGAGATGTTAGATTTTAATATATTTCAGC-
*
138922 TATATATGTTTTTTATC
580 --T-TATGTTTTTCATC
138939 AAATGAAATAAAAAGTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATAAAAAAAATA
1 AAATGAAATAAAAAGTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTAT-AAAAAAATA
*
139004 CTTTAAATTCAAGAAATCAAGGAAATTGATTACCTTAAATATTATTAAACCCCAAATGTAATTCT
65 CTTTAAATTCAAGAAATCAAGGAAATTGATTACCTTAAA-ATTATTAAACTCCAAAT-TAATTCT
* * * *
139069 TGGAGTCGTGTTACATTTCCAATACTTTTTGGAATGATCCCCATAAATTGATTATAGGGCAAGGA
128 TGGAGTCGTGTTAGATTTCCAATACTTCTTGGAATGATCCCCATAAATTGATTATAGGACAACGA
139134 CAAATTTTTAAGGTTGTTGCATTTGCCCATGCCAAATGGAATGTTACCAGATAATTCATTCCAAC
193 CAAATTTTTAAGGTTGTTGCATTTGCCCATGCCAAATGGAATGTTACCAGATAATTCATTCCAAC
* * * *
139199 TCAGGTAAAGCCCTTCAAGCTTAGGAAGATGTTGACGCATATCATTAGGCAAACTACCTGATAGG
258 TCAGGTAAAGCCCTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAATCTACCTGATAAG
* * * *
139264 CTATTGTTGGAGAGATCAATGGTCTTCAGTGAAGGAATGTTGAAGATCGAAGTTGGAATCTGACC
323 CTATTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAATGTTGAAGATCGAAGTCGGAATCTGACC
* * *
139329 TGTAAAGCCTTTAATTTCTTTAATATTAAGCA
388 TGTAAGGCCTTTAATTGCTTGAATATTAAGCA
139361 TTTCTAAATT
Statistics
Matches: 924, Mismatches: 85, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
595 59 0.06
596 47 0.05
597 417 0.45
600 48 0.05
601 352 0.38
602 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (593 bp):
AAATGAAATAAAAAGTTTTTCCTTTTGTTATCTATTACAAATCAAACTCTTTTATAAAAAAATAC
TTTAAATTCAAGAAATCAAGGAAATTGATTACCTTAAAATTATTAAACTCCAAATTAATTCTTGG
AGTCGTGTTAGATTTCCAATACTTCTTGGAATGATCCCCATAAATTGATTATAGGACAACGACAA
ATTTTTAAGGTTGTTGCATTTGCCCATGCCAAATGGAATGTTACCAGATAATTCATTCCAACTCA
GGTAAAGCCCTTCAAGCTTGGGAAGATGTTGACACATATCATTAGGCAATCTACCTGATAAGCTA
TTGTTGGAGAGAACAATGGTCTTCAGAGAAGAAATGTTGAAGATCGAAGTCGGAATCTGACCTGT
AAGGCCTTTAATTGCTTGAATATTAAGCAGTCAAAACCAAGAAGATTACCGATTTGCTCAGGAAT
TTGACCTACACACATAGTCGAAAAATCAAGGTGTCAAACTACCTATTTTGTTAACATAAGTCAAA
GAAGTTTTCGTTTCTATTCTACAGTAATTTGGAGATGTTAGATTTTAATATATTTCAGCTTATGT
TTTTCATC
Found at i:145622 original size:11 final size:11
Alignment explanation
Indices: 145606--145650 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
145596 NNTTTTTTAA
145606 AATTTATAATT
1 AATTTATAATT
145617 AATTTATAATT
1 AATTTATAATT
145628 --TTT-TAA--
1 AATTTATAATT
145634 AATTTATAATT
1 AATTTATAATT
145645 AATTTA
1 AATTTA
145651 ATTAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.21
9 6 0.21
11 17 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTATAATT
Found at i:145863 original size:40 final size:41
Alignment explanation
Indices: 145790--145887 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 41
145780 GAAAGTGCTT
* *
145790 CCTCAAGGAACCG-CTT-TGTCCACGTGGACACAAAGCGCAC
1 CCTCAAGGAAGCGTTTTCTGTCCACGTGGA-ACAAAGCGCAC
**
145830 CCTCAAGGAAGCGTTTTCTGTCCACGTGG-ACAAAGCGCTT
1 CCTCAAGGAAGCGTTTTCTGTCCACGTGGAACAAAGCGCAC
**
145870 CCTTGAGGAAGCGTTTTC
1 CCTCAAGGAAGCGTTTTC
145888 CTGCTTTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 37 0.74
41 2 0.04
42 11 0.22
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.22
Consensus pattern (41 bp):
CCTCAAGGAAGCGTTTTCTGTCCACGTGGAACAAAGCGCAC
Found at i:146617 original size:13 final size:12
Alignment explanation
Indices: 146590--146645 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 12
146580 AAAATTAGTG
146590 ATATATTTTAATT
1 ATAT-TTTTAATT
*
146603 ATATTTATTATTT
1 ATATTT-TTAATT
*
146616 ATTATTTTTAATA
1 A-TATTTTTAATT
146629 ATATTTTTTAATT
1 ATA-TTTTTAATT
146642 ATAT
1 ATAT
146646 GAAGTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
12 5 0.14
13 26 0.72
14 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTTTTAATT
Found at i:150391 original size:23 final size:23
Alignment explanation
Indices: 150358--150405 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
150348 ATTTTTTTGT
* *
150358 TTTGAGATGCTAAGATTAAAAAA
1 TTTGAGATGCTAAAACTAAAAAA
*
150381 TTTGAGTTGCTAAAACTAAAAAA
1 TTTGAGATGCTAAAACTAAAAAA
150404 TT
1 TT
150406 GTATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (23 bp):
TTTGAGATGCTAAAACTAAAAAA
Found at i:153065 original size:3 final size:3
Alignment explanation
Indices: 153057--153119 Score: 94
Period size: 3 Copynumber: 21.3 Consensus size: 3
153047 TATTTGTTCG
153057 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
153105 TGA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA T
153120 AGTTATCGGA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 3 0.05
3 51 0.93
4 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:153397 original size:35 final size:34
Alignment explanation
Indices: 153350--153421 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 34
153340 ATTTATTATC
*
153350 AAAATAGTAATCCA-TCTAAGGA-TTAAATTAACAA
1 AAAATAGCAATCCAGTCTAA--ACTTAAATTAACAA
153384 AAAACTAGCAATCCATGTCTAAACTTAAATTAACAA
1 AAAA-TAGCAATCCA-GTCTAAACTTAAATTAACAA
153420 AA
1 AA
153422 TTTGTCACGC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 4 0.12
35 10 0.30
36 14 0.42
37 5 0.15
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (34 bp):
AAAATAGCAATCCAGTCTAAACTTAAATTAACAA
Found at i:154917 original size:3 final size:3
Alignment explanation
Indices: 154909--155129 Score: 426
Period size: 3 Copynumber: 73.7 Consensus size: 3
154899 TATTTGTTCG
154909 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
154957 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
155005 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
155053 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
155101 TTA TTA TTA TTA TTA TTA TTGA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TT
155130 GTCAGTGCAA
Statistics
Matches: 216, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
2 1 0.00
3 214 0.99
4 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:155971 original size:19 final size:19
Alignment explanation
Indices: 155944--156004 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
155934 AAAAAAACTA
*
155944 AAATGAGAAATTTAAGAAT
1 AAATAAGAAATTTAAGAAT
*
155963 AAATAAGAAATATTAAAAAT
1 AAATAAGAAAT-TTAAGAAT
155983 -AATAAAGAAA-TTATAGAAT
1 AAAT-AAGAAATTTA-AGAAT
156002 AAA
1 AAA
156005 AAGTGGCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 3 0.09
19 17 0.49
20 15 0.43
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.25
Consensus pattern (19 bp):
AAATAAGAAATTTAAGAAT
Found at i:156044 original size:17 final size:17
Alignment explanation
Indices: 156022--156054 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
156012 AAATGGAATG
*
156022 AATAAATGATGGATATA
1 AATAAAAGATGGATATA
156039 AATAAAAGATGGATAT
1 AATAAAAGATGGATAT
156055 GACATATAGA
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:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (17 bp):
AATAAAAGATGGATATA
Found at i:158225 original size:19 final size:19
Alignment explanation
Indices: 158201--158239 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
158191 ATAGTTGAAG
* *
158201 AATTTATTATAATTTATTC
1 AATTTATGACAATTTATTC
158220 AATTTATGACAATTTATTC
1 AATTTATGACAATTTATTC
158239 A
1 A
158240 GACCTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (19 bp):
AATTTATGACAATTTATTC
Found at i:159283 original size:11 final size:11
Alignment explanation
Indices: 159267--159294 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
159257 GGAATTGATA
159267 TGTTTTAAATG
1 TGTTTTAAATG
159278 TGTTTTAAATG
1 TGTTTTAAATG
159289 TGTTTT
1 TGTTTT
159295 GATTATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (11 bp):
TGTTTTAAATG
Found at i:160763 original size:20 final size:21
Alignment explanation
Indices: 160718--160763 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
160708 AACTAAAATG
*
160718 AGAAAT-TTAAGAATAAATAA
1 AGAAATATTAAAAATAAATAA
*
160738 TG-AATATTAAAAAT-AATAA
1 AGAAATATTAAAAATAAATAA
160757 AGAAATA
1 AGAAATA
160764 AAGAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (21 bp):
AGAAATATTAAAAATAAATAA
Found at i:167236 original size:45 final size:46
Alignment explanation
Indices: 167175--167265 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
167165 GCTTACACTA
* * *
167175 TTCATACGAAATAAATGATGA-CCTCCTAAGCATGAATTTAAATTG
1 TTCATACGAAATAAATGATGATACTCCTAAACATGAACTTAAATTG
*
167220 TTCATAC-ATAATAAATGATGATACTCCTAAACATGAGCTTAAATTG
1 TTCATACGA-AATAAATGATGATACTCCTAAACATGAACTTAAATTG
167266 CAGTCCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 1 0.03
45 19 0.47
46 20 0.50
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (46 bp):
TTCATACGAAATAAATGATGATACTCCTAAACATGAACTTAAATTG
Done.