Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015201.1 Kokia drynarioides strain JFW-HI SEQ_130245, 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: 585754
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 263 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2724 original size:15 final size:16
Alignment explanation
Indices: 2706--2746 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2696 AATAAAAAAT
*
2706 ATATAAATTTATTA-A
1 ATATAAATATATTATA
2721 ATATTAAA-ATATTATA
1 ATA-TAAATATATTATA
2737 ATATAAATAT
1 ATATAAATAT
2747 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAAATATATTATA
Found at i:9599 original size:16 final size:17
Alignment explanation
Indices: 9571--9604 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9561 TAGACCGAGA
9571 TATTAGAGTTTAAAGTT
1 TATTAGAGTTTAAAGTT
*
9588 TATTAG-GTTTAAGGTT
1 TATTAGAGTTTAAAGTT
9604 T
1 T
9605 CGATTAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (17 bp):
TATTAGAGTTTAAAGTT
Found at i:9990 original size:70 final size:70
Alignment explanation
Indices: 9877--10035 Score: 300
Period size: 70 Copynumber: 2.3 Consensus size: 70
9867 GATACACGGA
9877 TCTCCAACACACCAAACATTGAACTCATAAAATCGAAAAATATCCCATAAGTGAAGCATATAGCT
1 TCTCCAACACACCAAACATTGAACTCATAAAATCGAAAAATATCCCATAAGTGAAGCATATAGCT
9942 AACAC
66 AACAC
* *
9947 TCTCCAACACACCAAACATTGAACTCATAGAATCGAAACATATCCCATAAGTGAAGCATATAGCT
1 TCTCCAACACACCAAACATTGAACTCATAAAATCGAAAAATATCCCATAAGTGAAGCATATAGCT
10012 AACAC
66 AACAC
10017 TCTCCAACACACCAAACAT
1 TCTCCAACACACCAAACAT
10036 ATCTCATTGA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 87 1.00
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.19
Consensus pattern (70 bp):
TCTCCAACACACCAAACATTGAACTCATAAAATCGAAAAATATCCCATAAGTGAAGCATATAGCT
AACAC
Found at i:12351 original size:28 final size:28
Alignment explanation
Indices: 12316--12566 Score: 146
Period size: 29 Copynumber: 8.8 Consensus size: 28
12306 CTTTTTGAAG
* *
12316 AATAGTGGCAAAATTATCAAATTTAAAA
1 AATAGTGGCAAAATTATAAAATCTAAAA
* * *
12344 AGTAGTGGCTAAATTGTAAAATCTAAAA
1 AATAGTGGCAAAATTATAAAATCTAAAA
* * * * *
12372 AAAAGTGGCAGAACTAAAAAAAT-TGGAAA
1 AATAGTGGCA-AAATTATAAAATCT-AAAA
** * * * *
12401 ACCAATGACAAAGTTATAAAACCTAGAAA
1 AATAGTGGCAAAATTATAAAATCTA-AAA
* * *
12430 AATAGTGGCAAAATTGTAAAATATGGAAA
1 AATAGTGGCAAAATTATAAAATCT-AAAA
* * * * ** * *
12459 AACAATGGTAGAGCTGTAAAATCTAGCAA
1 AATAGTGGCAAAATTATAAAATCTA-AAA
12488 AATAGTGGCAAAAATGTA-AAAATCTAAAA
1 AATAGTGGC-AAAAT-TATAAAATCTAAAA
* *
12517 AATAGTGGCAAAATTGTAAAATCTAGAA
1 AATAGTGGCAAAATTATAAAATCTAAAA
* *
12545 AATAGTGGTAAAACTATAAAAT
1 AATAGTGGCAAAATTATAAAAT
12567 ATGTAAAAAC
Statistics
Matches: 161, Mismatches: 53, Indels: 18
0.69 0.23 0.08
Matches are distributed among these distances:
27 1 0.01
28 73 0.45
29 76 0.47
30 10 0.06
31 1 0.01
ACGTcount: A:0.53, C:0.08, G:0.16, T:0.23
Consensus pattern (28 bp):
AATAGTGGCAAAATTATAAAATCTAAAA
Found at i:12441 original size:29 final size:29
Alignment explanation
Indices: 12417--12566 Score: 151
Period size: 29 Copynumber: 5.2 Consensus size: 29
12407 GACAAAGTTA
*
12417 TAAAACCTAGAAAAATAGTGGCAAAATTG
1 TAAAATCTAGAAAAATAGTGGCAAAATTG
* * * * * * **
12446 TAAAATATGGAAAAACAATGGTAGAGCTG
1 TAAAATCTAGAAAAATAGTGGCAAAATTG
* *
12475 TAAAATCTAGCAAAATAGTGGCAAAAATG
1 TAAAATCTAGAAAAATAGTGGCAAAATTG
12504 TAAAAATCTA-AAAAATAGTGGCAAAATTG
1 T-AAAATCTAGAAAAATAGTGGCAAAATTG
* * *
12533 TAAAATCTAG-AAAATAGTGGTAAAACTA
1 TAAAATCTAGAAAAATAGTGGCAAAATTG
12561 TAAAAT
1 TAAAAT
12567 ATGTAAAAAC
Statistics
Matches: 96, Mismatches: 23, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
28 29 0.30
29 59 0.61
30 8 0.08
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.23
Consensus pattern (29 bp):
TAAAATCTAGAAAAATAGTGGCAAAATTG
Found at i:12518 original size:58 final size:56
Alignment explanation
Indices: 12417--12583 Score: 158
Period size: 58 Copynumber: 2.9 Consensus size: 56
12407 GACAAAGTTA
* * * * *
12417 TAAAACCTAGAAAAATAGTGGCAAAATTGTAAAATATGGAAAAACAATGGTAGAGCTG
1 TAAAATCTAG-AAAATAGTGGCAAAAATGTAAAATAT-TAAAAACAATGGTAAAACTG
* *
12475 TAAAATCTAGCAAAATAGTGGCAAAAATGTAAAA-ATCTAAAAA-ATAGTGGCAAAATTG
1 TAAAATCTAG-AAAATAGTGGCAAAAATGTAAAATAT-TAAAAACA-A-TGGTAAAACTG
* * * *
12533 TAAAATCTAGAAAATAGTGGTAAAACTATAAAATATGTAAAAACGATGGTA
1 TAAAATCTAGAAAATAGTGGCAAAAATGTAAAATAT-TAAAAACAATGGTA
12584 CAAGATCATG
Statistics
Matches: 90, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.01
57 32 0.36
58 57 0.63
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (56 bp):
TAAAATCTAGAAAATAGTGGCAAAAATGTAAAATATTAAAAACAATGGTAAAACTG
Found at i:14350 original size:26 final size:26
Alignment explanation
Indices: 14326--14508 Score: 154
Period size: 26 Copynumber: 7.0 Consensus size: 26
14316 ACTGTTCATT
* *
14326 GGCTCGAAGTCTGCTATATAATCATC
1 GGCTCGAAGCCTGCTATATAATCACC
* *
14352 GGCTCGAAGACTGCTATTTAATCACC
1 GGCTCGAAGCCTGCTATATAATCACC
* * *
14378 GGTTC-AAGGCTTGCTATATAATCATC
1 GGCTCGAA-GCCTGCTATATAATCACC
* * ** * *
14404 AGTTCGAAGTTTGCTATTTAATCACT
1 GGCTCGAAGCCTGCTATATAATCACC
* * * *
14430 GGCTC-AAGGCCTGTTATACAATAACT
1 GGCTCGAA-GCCTGCTATATAATCACC
*
14456 GGCTCAAAGCCTGCTATATAATCACC
1 GGCTCGAAGCCTGCTATATAATCACC
* *
14482 GGCTTGAAGCCTGCTATATAATTACC
1 GGCTCGAAGCCTGCTATATAATCACC
14508 G
1 G
14509 CTTTTCTAAT
Statistics
Matches: 125, Mismatches: 28, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
25 4 0.03
26 117 0.94
27 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (26 bp):
GGCTCGAAGCCTGCTATATAATCACC
Found at i:19923 original size:17 final size:17
Alignment explanation
Indices: 19901--19934 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19891 GGTTGATATG
*
19901 GAAAATGTTATTGAAAT
1 GAAAATGCTATTGAAAT
19918 GAAAATGCTATTGAAAT
1 GAAAATGCTATTGAAAT
19935 AACGAGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (17 bp):
GAAAATGCTATTGAAAT
Found at i:30780 original size:13 final size:14
Alignment explanation
Indices: 30753--30789 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
30743 TTAAATACTT
30753 AAATTTT-AAATTA
1 AAATTTTCAAATTA
30766 AAATTTTCAAA-TA
1 AAATTTTCAAATTA
*
30779 AATTTTTCAAA
1 AAATTTTCAAA
30790 AGAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 19 0.86
14 3 0.14
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTTTCAAATTA
Found at i:31240 original size:3 final size:3
Alignment explanation
Indices: 31232--31256 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31222 TGTCTTATCC
31232 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
31257 TAGAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:32030 original size:23 final size:23
Alignment explanation
Indices: 31981--32024 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
31971 TTATCTATGT
* *
31981 TTGTGGCACGTTTTTCCTCTGTC
1 TTGTGACACGCTTTTCCTCTGTC
32004 TTGTGACACGCTTTTCCTCTG
1 TTGTGACACGCTTTTCCTCTG
32025 CATTGTCGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.07, C:0.27, G:0.20, T:0.45
Consensus pattern (23 bp):
TTGTGACACGCTTTTCCTCTGTC
Found at i:32399 original size:26 final size:27
Alignment explanation
Indices: 32348--32400 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
32338 ATATTTAGTT
* *
32348 TTTTAGTTATTTTTTTGTTTATTTTTA
1 TTTTAGTTATTTTTCTGTTTAATTTTA
32375 TTTT-GTTATTTTTCTG-TTACATTTTA
1 TTTTAGTTATTTTTCTGTTTA-ATTTTA
32401 ATTTCATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.13
26 16 0.70
27 4 0.17
ACGTcount: A:0.15, C:0.04, G:0.08, T:0.74
Consensus pattern (27 bp):
TTTTAGTTATTTTTCTGTTTAATTTTA
Found at i:33305 original size:10 final size:10
Alignment explanation
Indices: 33292--33325 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
33282 TAGATTTATC
33292 AAAATTTAAA
1 AAAATTTAAA
33302 AAAA-TTAAA
1 AAAATTTAAA
*
33311 AAAAATTAAA
1 AAAATTTAAA
33321 AAAAT
1 AAAAT
33326 CATTTGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:33324 original size:9 final size:9
Alignment explanation
Indices: 33292--33325 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
33282 TAGATTTATC
*
33292 AAAATTTAA
1 AAAAATTAA
33301 AAAAATTAAA
1 AAAAATT-AA
33311 AAAAATTAA
1 AAAAATTAA
33320 AAAAAT
1 AAAAAT
33326 CATTTGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAATTAA
Found at i:34774 original size:27 final size:27
Alignment explanation
Indices: 34737--34800 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
34727 CAGTCTTGAT
*
34737 GAACTTTCACATTAAGATAATCCCGAC
1 GAACTTCCACATTAAGATAATCCCGAC
*
34764 GAACTTCCACATTAAGATAATCCTGAC
1 GAACTTCCACATTAAGATAATCCCGAC
*
34791 GGACTTCCAC
1 GAACTTCCAC
34801 GTCATGTGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.25
Consensus pattern (27 bp):
GAACTTCCACATTAAGATAATCCCGAC
Found at i:40626 original size:79 final size:79
Alignment explanation
Indices: 40495--40656 Score: 288
Period size: 79 Copynumber: 2.1 Consensus size: 79
40485 AACTAAAATA
* *
40495 AAGAGTAATAGCTTTCCTCAATTCAACACAAAATCGTGAGATAATGAAAACACATAAAATAAAAT
1 AAGAGTAAAAGCTTCCCTCAATTCAACACAAAATCGTGAGATAATGAAAACACATAAAATAAAAT
40560 CACTAATACTAAAC
66 CACTAATACTAAAC
40574 AAGAGTAAAAGCTTCCCTCAATTCAACACAAAATCGTGAGATAATGAAAACACATAAAATAAAAT
1 AAGAGTAAAAGCTTCCCTCAATTCAACACAAAATCGTGAGATAATGAAAACACATAAAATAAAAT
**
40639 TTCTAATACTAAAC
66 CACTAATACTAAAC
40653 AAGA
1 AAGA
40657 AATCCAAACC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.22
Consensus pattern (79 bp):
AAGAGTAAAAGCTTCCCTCAATTCAACACAAAATCGTGAGATAATGAAAACACATAAAATAAAAT
CACTAATACTAAAC
Found at i:46654 original size:63 final size:65
Alignment explanation
Indices: 46550--46671 Score: 151
Period size: 63 Copynumber: 1.9 Consensus size: 65
46540 TTATATTTTA
* * *
46550 AAGTTGTAGCTATAGTTCGTCATACTTTCTTTAAGACTCTGCTTCCCTCGTTGCTACCTTGGCTT
1 AAGTTGTAGCTAAAGTTC-TCATACTTTCTTTAAGACTCTGCTTCCCTCGCTACTACCTTGGCTT
46615 C
65 C
* * *
46616 AAGTTGTAGCTAAAG-T-TCATATTTTCTTTGAG-CTTCTGCTTCTCTCGCTACTACCT
1 AAGTTGTAGCTAAAGTTCTCATACTTTCTTTAAGAC-TCTGCTTCCCTCGCTACTACCT
46672 CCGCTTTAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
62 1 0.02
63 33 0.67
65 1 0.02
66 14 0.29
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.42
Consensus pattern (65 bp):
AAGTTGTAGCTAAAGTTCTCATACTTTCTTTAAGACTCTGCTTCCCTCGCTACTACCTTGGCTTC
Found at i:47580 original size:16 final size:15
Alignment explanation
Indices: 47531--47573 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
47521 GAGGCTTATA
47531 TTTTTCTTAAAATAT
1 TTTTTCTTAAAATAT
47546 TTTTTCTTAAAATAT
1 TTTTTCTTAAAATAT
*
47561 TTTTTCTTTAAAT
1 TTTTTCTTAAAAT
47574 TACTTTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTCTTAAAATAT
Found at i:51130 original size:24 final size:24
Alignment explanation
Indices: 51101--51146 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
51091 TATCTCATTT
51101 ATAAAATATTATAATTTTTTAAAA
1 ATAAAATATTATAATTTTTTAAAA
51125 ATAAAATATTATAATTTTTTAA
1 ATAAAATATTATAATTTTTTAA
51147 CTTTATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATAAAATATTATAATTTTTTAAAA
Found at i:52476 original size:20 final size:21
Alignment explanation
Indices: 52440--52489 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
52430 ATTGACATGG
*
52440 TTTATATTAAGTGTAAATA-GA
1 TTTA-ATTAAGTGTAAAAATGA
52461 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
52482 -TTAATTAA
1 TTTAATTAA
52490 AGTTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Found at i:55278 original size:42 final size:40
Alignment explanation
Indices: 55221--55407 Score: 155
Period size: 40 Copynumber: 4.7 Consensus size: 40
55211 AGAAACGTCG
*
55221 CTATTACTTTACCTTTTGCAGCGTTTTCCCATAAATGCCA
1 CTATTACTTTACCTTTTGCGGCGTTTTCCCATAAATGCCA
* * ** *
55261 CTATTGCTCTTTACCTTTTACGGTATTTTCCCATAAATGCCG
1 CTATT--ACTTTACCTTTTGCGGCGTTTTCCCATAAATGCCA
** * * *
55303 CTATTACTTTACCTTTTGCGGCGTTTAT-AGAAAAACGACA
1 CTATTACTTTACCTTTTGCGGCGTTT-TCCCATAAATGCCA
* * ** * * *
55343 -TATTGCTTTACCTTTTGTGGCGTTTAT-AGAAAAACGCCG
1 CTATTACTTTACCTTTTGCGGCGTTT-TCCCATAAATGCCA
55382 CTATTACTTTACCTTTTGCGGCGTTT
1 CTATTACTTTACCTTTTGCGGCGTTT
55408 ATGGAAAAAC
Statistics
Matches: 121, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 35 0.29
40 51 0.42
41 1 0.01
42 34 0.28
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (40 bp):
CTATTACTTTACCTTTTGCGGCGTTTTCCCATAAATGCCA
Found at i:55408 original size:40 final size:40
Alignment explanation
Indices: 55299--55440 Score: 205
Period size: 40 Copynumber: 3.6 Consensus size: 40
55289 TCCCATAAAT
55299 GCCGCTATTACTTTACCTTTTGCGGCGTTTATAGAAAAAC
1 GCCGCTATTACTTTACCTTTTGCGGCGTTTATAGAAAAAC
* * * *
55339 GAC-ATATTGCTTTACCTTTTGTGGCGTTTATAGAAAAAC
1 GCCGCTATTACTTTACCTTTTGCGGCGTTTATAGAAAAAC
*
55378 GCCGCTATTACTTTACCTTTTGCGGCGTTTATGGAAAAAC
1 GCCGCTATTACTTTACCTTTTGCGGCGTTTATAGAAAAAC
** *
55418 GTTGCTATTGCTTTACCTTTTGC
1 GCCGCTATTACTTTACCTTTTGC
55441 AATGTTTTCG
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 35 0.39
40 54 0.61
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (40 bp):
GCCGCTATTACTTTACCTTTTGCGGCGTTTATAGAAAAAC
Found at i:58118 original size:4 final size:4
Alignment explanation
Indices: 58101--58138 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
58091 TATACTTACG
*
58101 TACA TACG TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
58139 TACATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:62819 original size:30 final size:30
Alignment explanation
Indices: 62779--63155 Score: 257
Period size: 29 Copynumber: 12.7 Consensus size: 30
62769 AAGATCCCTA
**
62779 AACTGTCCAAAAATTACCATTTTTGCCCCCG
1 AACT-TCCAAAAATTACCATTTTTAACCCCG
* *
62810 AACTTCCAAAAA-TCCCATTTTTGACCCCG
1 AACTTCCAAAAATTACCATTTTTAACCCCG
* *
62839 AACCTTCCCAAAATTACCA-TTTTACCCCCG
1 AA-CTTCCAAAAATTACCATTTTTAACCCCG
* * * *
62869 AACTTCCAAAAA-TCCCAATTTTGACCCCT
1 AACTTCCAAAAATTACCATTTTTAACCCCG
*
62898 AACCTTCCCAAAATTACCA-TTTT-ACCCTCG
1 AA-CTTCCAAAAATTACCATTTTTAACCC-CG
* *
62928 AACTTCCAAAAA-TCCCATGTTTAACCCCG
1 AACTTCCAAAAATTACCATTTTTAACCCCG
** *
62957 AACCTTTTAACAATTACCA-TTTT-ACCTCC-
1 AA-CTTCCAAAAATTACCATTTTTAACC-CCG
* *
62986 AAATTCCCAAAAA-T-CCTATTTTTAACCTCG
1 AACTT-CCAAAAATTACC-ATTTTTAACCCCG
*
63016 AAACTTCTAAAAATTACCA-TTTT-ACCCCG
1 -AACTTCCAAAAATTACCATTTTTAACCCCG
* * *
63045 AACTTCTAAAAAATT--CATTTTTGACCCCAA
1 AACTTC-CAAAAATTACCATTTTTAACCCC-G
* *
63075 AACTTCTAAAAATTACCA-TTTTACCCCCG
1 AACTTCCAAAAATTACCATTTTTAACCCCG
* * * *
63104 AACTT-CAAAAAATCCCATTTTTGACCACG
1 AACTTCCAAAAATTACCATTTTTAACCCCG
* *
63133 AAATATCCAAAAATTACTATTTT
1 AACT-TCCAAAAATTACCATTTT
63156 ACTCCCGGAT
Statistics
Matches: 272, Mismatches: 46, Indels: 56
0.73 0.12 0.15
Matches are distributed among these distances:
27 4 0.01
28 31 0.11
29 110 0.40
30 88 0.32
31 37 0.14
32 2 0.01
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (30 bp):
AACTTCCAAAAATTACCATTTTTAACCCCG
Found at i:62879 original size:59 final size:59
Alignment explanation
Indices: 62784--63162 Score: 442
Period size: 59 Copynumber: 6.4 Consensus size: 59
62774 CCCTAAACTG
*
62784 TCCAAAAATTACCATTTTTGCCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCA-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * *
62844 TCCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCCTAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * * *
62903 TCCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATGTTTAACCCCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
** * * * * * * *
62962 TTTAACAATTACCATTTTACCTCC-AAATTCCCAAAAATCCTATTTTTAACCTCGAAACT
1 TCCAAAAATTACCATTTTACCCCCGAACTT-CCAAAAATCCCATTTTTGACCCCGAACCT
* * * * *
63021 TCTAAAAATTACCATTTTA-CCCCGAACTTCTAAAAAAT-TCATTTTTGACCCCAAAACT
1 TCCAAAAATTACCATTTTACCCCCGAACTTC-CAAAAATCCCATTTTTGACCCCGAACCT
* * * *
63079 TCTAAAAATTACCATTTTACCCCCGAACTTCAAAAAATCCCATTTTTGACCACGAA-AT
1 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* *
63137 ATCCAAAAATTACTATTTTACTCCCG
1 -TCCAAAAATTACCATTTTACCCCCG
63163 GATGTCCGAA
Statistics
Matches: 276, Mismatches: 37, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
58 50 0.18
59 213 0.77
60 13 0.05
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.30
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
Found at i:63219 original size:176 final size:176
Alignment explanation
Indices: 62784--63157 Score: 430
Period size: 176 Copynumber: 2.1 Consensus size: 176
62774 CCCTAAACTG
* * * * ** * * *
62784 TCCAAAAATTACCATTTTTGCCCCCGAACTT-CCAAAAATCCCATTTTTGACCCCGAACCTTCCC
1 TCCAAAAATTACCA-TTTTACCTCC-AAATTCCCAAAAATCCTATTTTCAACCTCGAAACTTCTC
* * * *
62848 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCAATTTTGACCCCTAACCTTCCCAAAATT
64 AAAATTACCATTTTA-CCCCGAACTTCAAAAAATCCCAATTTTGACCCCAAAACTTCCAAAAATT
* * * *
62913 ACCATTTTACCCTCGAACTTCCAAAAATCCCATGTTTAACCCCGAACCT
128 ACCATTTTACCCCCGAACTTCAAAAAATCCCATGTTTAACCACGAACAT
** * * *
62962 TTTAACAATTACCATTTTACCTCCAAATTCCCAAAAATCCTATTTTTAACCTCGAAACTTCTAAA
1 TCCAAAAATTACCATTTTACCTCCAAATTCCCAAAAATCCTATTTTCAACCTCGAAACTTCTCAA
* * *
63027 AATTACCATTTTACCCCGAACTTCTAAAAAAT-TCATTTTTGACCCCAAAACTTCTAAAAATTAC
66 AATTACCATTTTACCCCGAACTTC-AAAAAATCCCAATTTTGACCCCAAAACTTCCAAAAATTAC
* *
63091 CATTTTACCCCCGAACTTCAAAAAATCCCATTTTTGACCACGAA-AT
130 CATTTTACCCCCGAACTTCAAAAAATCCCATGTTTAACCACGAACAT
*
63137 ATCCAAAAATTACTATTTTAC
1 -TCCAAAAATTACCATTTTAC
63158 TCCCGGATGT
Statistics
Matches: 164, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
175 1 0.01
176 96 0.59
177 56 0.34
178 11 0.07
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (176 bp):
TCCAAAAATTACCATTTTACCTCCAAATTCCCAAAAATCCTATTTTCAACCTCGAAACTTCTCAA
AATTACCATTTTACCCCGAACTTCAAAAAATCCCAATTTTGACCCCAAAACTTCCAAAAATTACC
ATTTTACCCCCGAACTTCAAAAAATCCCATGTTTAACCACGAACAT
Found at i:71754 original size:53 final size:53
Alignment explanation
Indices: 71691--71791 Score: 202
Period size: 53 Copynumber: 1.9 Consensus size: 53
71681 TCGCATTGGC
71691 ATGTTTTTCATGCAAATCAAAGAAATTAGAATCAAGCATGTTGTCATGTGTAA
1 ATGTTTTTCATGCAAATCAAAGAAATTAGAATCAAGCATGTTGTCATGTGTAA
71744 ATGTTTTTCATGCAAATCAAAGAAATTAGAATCAAGCATGTTGTCATG
1 ATGTTTTTCATGCAAATCAAAGAAATTAGAATCAAGCATGTTGTCATG
71792 CGATTACACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (53 bp):
ATGTTTTTCATGCAAATCAAAGAAATTAGAATCAAGCATGTTGTCATGTGTAA
Found at i:72569 original size:22 final size:23
Alignment explanation
Indices: 72527--72569 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
72517 TAGGGAGATA
**
72527 TAATAATTCAAAAATTTGATTTT
1 TAATAATTCAAAAATCGGATTTT
72550 TAATAATT-AAAAATCGGATT
1 TAATAATTCAAAAATCGGATT
72570 CAAAAGTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (23 bp):
TAATAATTCAAAAATCGGATTTT
Found at i:80875 original size:38 final size:38
Alignment explanation
Indices: 80819--80895 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
80809 TCATCATGAC
* *
80819 ATAGGATGTTCTATGTCACGATAATGGGACCAAGCCTG
1 ATAGGATGTTCTACGTCACGACAATGGGACCAAGCCTG
*
80857 ATAGGATGTTCTACGTCACGACAATGGGACCAGGCCTG
1 ATAGGATGTTCTACGTCACGACAATGGGACCAAGCCTG
80895 A
1 A
80896 AGATTTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (38 bp):
ATAGGATGTTCTACGTCACGACAATGGGACCAAGCCTG
Found at i:117253 original size:20 final size:20
Alignment explanation
Indices: 117228--117279 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
117218 TGTTATAATG
* *
117228 ATTTTGTCTTGGCTAAAATC
1 ATTTTGACTTGACTAAAATC
*
117248 ATTTTGACTTGATTAAAATC
1 ATTTTGACTTGACTAAAATC
*
117268 ATTTTAACTTGA
1 ATTTTGACTTGA
117280 TTTTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (20 bp):
ATTTTGACTTGACTAAAATC
Found at i:117280 original size:20 final size:20
Alignment explanation
Indices: 117241--117281 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
117231 TTGTCTTGGC
*
117241 TAAAATCATTTTGACTTGAT
1 TAAAATCATTTTAACTTGAT
117261 TAAAATCATTTTAACTTGAT
1 TAAAATCATTTTAACTTGAT
117281 T
1 T
117282 TTAAAATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (20 bp):
TAAAATCATTTTAACTTGAT
Found at i:128472 original size:2 final size:2
Alignment explanation
Indices: 128465--128495 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
128455 TTCTAATCAA
128465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
128496 AAAGCATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:132463 original size:24 final size:23
Alignment explanation
Indices: 132422--132466 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
132412 CCCATTCCCA
*
132422 CTCACCTCCTTATTTCTCCTTCT
1 CTCACCTCCTTATATCTCCTTCT
*
132445 CTCACCTTCTTTATATCTCCTT
1 CTCACC-TCCTTATATCTCCTT
132467 ATAGGAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.11, C:0.40, G:0.00, T:0.49
Consensus pattern (23 bp):
CTCACCTCCTTATATCTCCTTCT
Found at i:139209 original size:46 final size:45
Alignment explanation
Indices: 139132--139732 Score: 594
Period size: 46 Copynumber: 13.1 Consensus size: 45
139122 GCTTTTGTGA
* * *
139132 GATGGTAGCTTCAATCTGCCCCGCTTGATTTAGGAGTAAAAGATTT
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTTAGG-GTAAAAGATTG
* * * *
139178 GATGGTGGCTTCAGTCTGTCCCTCTTAATTTAAGGTTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTT-AGGGTAAAAGATTG
* * * * * *
139224 GATAGTCGCTTTAATTTACCCCTCTTGACTTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTTAGGGTAAAAGATTG
139270 GATGGTGGCTTCAATCTGCCCCTCTTGATTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTTA-GGGTAAAAGATTG
* * *
139316 AATGGTGGCTTTAATCTG-CCCTCTGGATTTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTT-AGGGTAAAAGATTG
* * * *
139361 GATGATGGCTTCAATATGCCCCTCTTGACTTAGGGGTAAAAGATTA
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTTA-GGGTAAAAGATTG
* * ** *
139407 GATGGTGGCTTTAGTCTATCCCTCTTGATATAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTTA-GGGTAAAAGATTG
* * *
139453 GATGGTGGCTTCAATTTGCCCCTCTTAATTTAAGGGTAAAAGATTA
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTT-AGGGTAAAAGATTG
* * *
139499 GATGGTGGCTTCAATCTGCTCCTTTTGATTTAGGGGTAAAATATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTTA-GGGTAAAAGATTG
* * ** *
139545 GATGGTGGCTTCAATCTACCCCACTTGACTTGGGGGTAAAAGATTA
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTTAGGGTAAAAGATTG
* * * *
139591 AATGGTGGCTTCAATCT-CCTCCTCTTAATTTTAGGGTAAATGTTTG
1 GATGGTGGCTTCAATCTGCC-CCTCTTGA-TTTAGGGTAAAAGATTG
* ** * * * *
139637 GATAGTAACTTCAATCTGTCCCTCTTAACTTAAGGGTAAAACATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTTAGGGTAAAAGATTG
* * * * *
139683 GATAGTGACTTCAATTTGTCCCTCTTGACTTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTTAGGGTAAAAGATTG
139729 GATG
1 GATG
139733 TGGTGAAGTA
Statistics
Matches: 456, Mismatches: 88, Indels: 22
0.81 0.16 0.04
Matches are distributed among these distances:
45 45 0.10
46 402 0.88
47 9 0.02
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (45 bp):
GATGGTGGCTTCAATCTGCCCCTCTTGATTTAGGGTAAAAGATTG
Found at i:139550 original size:138 final size:137
Alignment explanation
Indices: 139132--139732 Score: 677
Period size: 138 Copynumber: 4.4 Consensus size: 137
139122 GCTTTTGTGA
* * * * * * *
139132 GATGGTAGCTTCAATCTGCCCCGCTTGATTTAGGAGTAAAAGATTTGATGGTGGCTTCAGTCTGT
1 GATGGTGGCTTCAATCTACCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGC
* * * * *
139197 CCCTCTTAATTTAAGGTTAAAAGATTGGATAGTCGCTTTAATTTACCCCTCTTGACTTAAGGGTA
65 CCCTCTTAATTTAAGGGTAAAAGATTGGATAGTGGCTTCAATCTGCCCCTCTTGACTTAAGGGTA
139262 AAAGATTG
130 AAAGATTG
* * *
139270 GATGGTGGCTTCAATCTGCCCCTCTTGATTTAGGGGTAAAAGATTGAATGGTGGCTTTAATCTG-
1 GATGGTGGCTTCAATCTACCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGC
** * *
139334 CCCTCTGGATTTAAGGGTAAAAGATTGGAT-GATGGCTTCAATATGCCCCTCTTGACTTAGGGGT
65 CCCTCTTAATTTAAGGGTAAAAGATTGGATAG-TGGCTTCAATCTGCCCCTCTTGACTTAAGGGT
*
139398 AAAAGATTA
129 AAAAGATTG
* * * *
139407 GATGGTGGCTTTAGTCTATCCCTCTTGATATAGGGGTAAAAGATTGGATGGTGGCTTCAATTTGC
1 GATGGTGGCTTCAATCTACCCCTCTTGAT-TAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGC
* * * * * *
139472 CCCTCTTAATTTAAGGGTAAAAGATTAGATGGTGGCTTCAATCTGCTCCTTTTGATTTAGGGGTA
65 CCCTCTTAATTTAAGGGTAAAAGATTGGATAGTGGCTTCAATCTGCCCCTCTTGACTTAAGGGTA
*
139537 AAATATTG
130 AAAGATTG
* * **
139545 GATGGTGGCTTCAATCTACCCCACTTGACTTGGGGGTAAAAGATTAAATGGTGGCTTCAATCT-C
1 GATGGTGGCTTCAATCTACCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGC
* * * ** * *
139609 CTCCTCTTAATTTTAGGGTAAATGTTTGGATAGTAACTTCAATCTGTCCCTCTTAACTTAAGGGT
65 C-CCTCTTAATTTAAGGGTAAAAGATTGGATAGTGGCTTCAATCTGCCCCTCTTGACTTAAGGGT
*
139674 AAAACATTG
129 AAAAGATTG
* * * ** *
139683 GATAGTGACTTCAATTTGTCCCTCTTGACTTAAGGGTAAAAGATTGGATG
1 GATGGTGGCTTCAATCTACCCCTCTTGA-TTAGGGGTAAAAGATTGGATG
139733 TGGTGAAGTA
Statistics
Matches: 393, Mismatches: 64, Indels: 12
0.84 0.14 0.03
Matches are distributed among these distances:
136 2 0.01
137 119 0.30
138 270 0.69
139 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (137 bp):
GATGGTGGCTTCAATCTACCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
CCTCTTAATTTAAGGGTAAAAGATTGGATAGTGGCTTCAATCTGCCCCTCTTGACTTAAGGGTAA
AAGATTG
Found at i:140849 original size:10 final size:9
Alignment explanation
Indices: 140836--140874 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
140826 TCTTGACCTC
140836 TCTTGTTTTT
1 TCTT-TTTTT
140846 TCTTTTTCTT
1 TCTTTTT-TT
*
140856 TCTTTTCTT
1 TCTTTTTTT
140865 TCTTTTTTT
1 TCTTTTTTT
140874 T
1 T
140875 AGGTGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 14 0.54
10 12 0.46
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:147864 original size:15 final size:16
Alignment explanation
Indices: 147840--147872 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
147830 TAGTTATTTA
*
147840 TTTATTTATTTT-CAT
1 TTTATATATTTTACAT
147855 TTTATATATTTTACAT
1 TTTATATATTTTACAT
147871 TT
1 TT
147873 GACTCTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATATATTTTACAT
Found at i:152734 original size:15 final size:14
Alignment explanation
Indices: 152710--152739 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
152700 GAAATTCCTC
152710 ATAGCAAGGGAGTT
1 ATAGCAAGGGAGTT
152724 ATAGACAAGGGAGTT
1 ATAG-CAAGGGAGTT
152739 A
1 A
152740 CAATAATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (14 bp):
ATAGCAAGGGAGTT
Found at i:166453 original size:17 final size:19
Alignment explanation
Indices: 166431--166473 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
166421 ATAGTTTGCA
166431 TGCATTTTTATTAT-T-AT
1 TGCATTTTTATTATGTCAT
*
166448 TGCATTTTTATTTTGTCAT
1 TGCATTTTTATTATGTCAT
166467 TGCATTT
1 TGCATTT
166474 CTTTTGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 13 0.57
18 1 0.04
19 9 0.39
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.63
Consensus pattern (19 bp):
TGCATTTTTATTATGTCAT
Found at i:167020 original size:10 final size:10
Alignment explanation
Indices: 167003--167037 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
166993 TTGAAAAGGG
167003 AAAA-AAAGA
1 AAAAGAAAGA
167012 AAAAGAAAGA
1 AAAAGAAAGA
167022 AAAAGAAA-A
1 AAAAGAAAGA
167031 AAAAGAA
1 AAAAGAA
167038 GAAGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 12 0.48
10 13 0.52
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:167047 original size:15 final size:15
Alignment explanation
Indices: 167005--167048 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
166995 GAAAAGGGAA
167005 AAAAAGAAAAAGAAAG
1 AAAAAGAAAAA-AAAG
167021 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
*
167036 AAGAAGAAAAAAA
1 AAAAAGAAAAAAA
167049 TGTTTGCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:172146 original size:71 final size:71
Alignment explanation
Indices: 172056--172314 Score: 324
Period size: 71 Copynumber: 3.7 Consensus size: 71
172046 TACGATGCTA
* * * * *
172056 TAGAGAATTCACAACAAATGTAGGATCTCAGCCATTGGACCAATTTCACTTTACAATGACTCATG
1 TAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCGGACCAGTTTCACTTTACAATGACTCATG
*
172121 ATATTG
66 ATGTTG
* * * ** * *
172127 TAGAGAATCTGCAATAAATGCAAGATCTCAATCATCGAACCAGTTTCACTTTACAATGAC-CACG
1 TAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCGGACCAGTTTCACTTTACAATGACTCATG
172191 ATGTTG
66 ATGTTG
* * *
172197 TAGAGAATCCGCAACAAATGCAGAATCTCAGCCATCGGACCAGTTTCACTTTATAGTGACTCATG
1 TAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCGGACCAGTTTCACTTTACAATGACTCATG
* *
172262 ATGCTA
66 ATGTTG
*
172268 TAGAGAATCCGCAACAAAT-CTAGGATCTCAGCCATCGGACCATTTTC
1 TAGAGAATCCGCAACAAATGC-AGGATCTCAGCCATCGGACCAGTTTC
172315 TATCTTTGGC
Statistics
Matches: 159, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
70 60 0.38
71 99 0.62
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (71 bp):
TAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCGGACCAGTTTCACTTTACAATGACTCATG
ATGTTG
Found at i:172304 original size:141 final size:141
Alignment explanation
Indices: 172047--172314 Score: 340
Period size: 141 Copynumber: 1.9 Consensus size: 141
172037 TTACCAGTAT
* * * *
172047 ACGATGCTATAGAGAATTCACAACAAATGTAGGATCTCAGCCATTGGACCAATTTCACTTTACAA
1 ACGATGCTATAGAGAATCCACAACAAATGCAGAATCTCAGCCATCGGACCAATTTCACTTTACAA
* * * * *
172112 TGACTCATGATATTGTAGAGAATCTGCAATAAATGCAAGATCTCAATCATCGAACCAGTTTCACT
66 TGACTCATGATACTATAGAGAATCCGCAACAAATGCAAGATCTCAACCATCGAACCAGTTTCACT
172177 TTACAATGACC
131 TTACAATGACC
* * * * * *
172188 ACGATGTTGTAGAGAATCCGCAACAAATGCAGAATCTCAGCCATCGGACCAGTTTCACTTTATAG
1 ACGATGCTATAGAGAATCCACAACAAATGCAGAATCTCAGCCATCGGACCAATTTCACTTTACAA
* * * * *
172253 TGACTCATGATGCTATAGAGAATCCGCAACAAAT-CTAGGATCTCAGCCATCGGACCATTTTC
66 TGACTCATGATACTATAGAGAATCCGCAACAAATGC-AAGATCTCAACCATCGAACCAGTTTC
172315 TATCTTTGGC
Statistics
Matches: 106, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
140 1 0.01
141 105 0.99
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (141 bp):
ACGATGCTATAGAGAATCCACAACAAATGCAGAATCTCAGCCATCGGACCAATTTCACTTTACAA
TGACTCATGATACTATAGAGAATCCGCAACAAATGCAAGATCTCAACCATCGAACCAGTTTCACT
TTACAATGACC
Found at i:174788 original size:13 final size:13
Alignment explanation
Indices: 174766--174795 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
174756 TGTTTTATTT
*
174766 ATTTATATTTTAA
1 ATTTAAATTTTAA
174779 ATTTAAATTTTAA
1 ATTTAAATTTTAA
174792 ATTT
1 ATTT
174796 TATATTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTAAATTTTAA
Found at i:180409 original size:6 final size:6
Alignment explanation
Indices: 180398--180478 Score: 103
Period size: 6 Copynumber: 13.8 Consensus size: 6
180388 TAGTATATTT
* *
180398 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTT ATTTTC ATTTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC
* * *
180446 ATTTTT ATTTT- ATTTT- ATTTTT ATTTTT ATTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
180479 AAATTATGTA
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
5 10 0.14
6 61 0.86
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (6 bp):
ATTTTC
Found at i:180415 original size:12 final size:12
Alignment explanation
Indices: 180395--180478 Score: 118
Period size: 12 Copynumber: 7.2 Consensus size: 12
180385 AATTAGTATA
180395 TTTATTTTCATT
1 TTTATTTTCATT
*
180407 TTCATTTTCATT
1 TTTATTTTCATT
*
180419 TTCATTTTCATT
1 TTTATTTTCATT
180431 TTTATTTTCATT
1 TTTATTTTCATT
*
180443 TTTATTTTTA-T
1 TTTATTTTCATT
180454 TTTATTTT-ATT
1 TTTATTTTCATT
*
180465 TTTATTTTTATT
1 TTTATTTTCATT
180477 TT
1 TT
180479 AAATTATGTA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
10 1 0.01
11 18 0.27
12 48 0.72
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATTTTCATT
Found at i:180421 original size:18 final size:18
Alignment explanation
Indices: 180395--180478 Score: 127
Period size: 18 Copynumber: 4.8 Consensus size: 18
180385 AATTAGTATA
180395 TTTATTTTCATTTTCATT
1 TTTATTTTCATTTTCATT
*
180413 TTCATTTTCATTTTCATT
1 TTTATTTTCATTTTCATT
*
180431 TTTATTTTCATTTTTATT
1 TTTATTTTCATTTTCATT
180449 TTTATTTT-ATTTT-ATT
1 TTTATTTTCATTTTCATT
*
180465 TTTATTTTTATTTT
1 TTTATTTTCATTTT
180479 AAATTATGTA
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.18
17 10 0.16
18 41 0.66
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTCATTTTCATT
Found at i:180485 original size:22 final size:22
Alignment explanation
Indices: 180440--180499 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
180430 TTTTATTTTC
**
180440 ATTTTTATTTTTATTTTATTTT
1 ATTTTTATTTTTATTTTAAATT
180462 ATTTTTATTTTTATTTTAAATT
1 ATTTTTATTTTTATTTTAAATT
**
180484 ATGTACTATTTTTATT
1 AT-TTTTATTTTTATT
180500 CCTATGGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 22 0.67
23 11 0.33
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTTTATTTTTATTTTAAATT
Found at i:181339 original size:11 final size:10
Alignment explanation
Indices: 181322--181417 Score: 72
Period size: 11 Copynumber: 9.2 Consensus size: 10
181312 GCTTAACAGG
181322 ATTTAAATTT
1 ATTTAAATTT
181332 ATTTTAAATTT
1 A-TTTAAATTT
* *
181343 AAGTTTATATTA
1 -A-TTTAAATTT
*
181355 AGTTTAAATCT
1 A-TTTAAATTT
*
181366 ATTTAGA---
1 ATTTAAATTT
181373 ATTTAAATTT
1 ATTTAAATTT
181383 ATTATAAATTT
1 ATT-TAAATTT
181394 AAGTTTAAATTT
1 -A-TTTAAATTT
181406 ATTTAAATTT
1 ATTTAAATTT
181416 AT
1 AT
181418 AATGTCCAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
7 6 0.09
10 20 0.29
11 26 0.37
12 16 0.23
13 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:181343 original size:6 final size:6
Alignment explanation
Indices: 181322--181416 Score: 62
Period size: 6 Copynumber: 16.8 Consensus size: 6
181312 GCTTAACAGG
* * * * *
181322 ATTTAA ATTT-A TTTTAA ATTTAA GTTTAT A-TTAA GTTTAA ATCT--
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
181366 ATTTAGA ATTTAA ATTT-- ATTATAA ATTTAA GTTTAA ATTT-- ATTTAA
1 ATTTA-A ATTTAA ATTTAA ATT-TAA ATTTAA ATTTAA ATTTAA ATTTAA
181412 ATTTA
1 ATTTA
181417 TAATGTCCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
4 10 0.15
5 8 0.12
6 41 0.61
7 8 0.12
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:181344 original size:17 final size:17
Alignment explanation
Indices: 181322--181417 Score: 90
Period size: 17 Copynumber: 5.7 Consensus size: 17
181312 GCTTAACAGG
181322 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
181339 ATTTAAGTTTATATTAA
1 ATTTAAATTTATTTTAA
* *
181356 GTTTAAATCTA-TTTAGA
1 ATTTAAATTTATTTTA-A
*
181373 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
* *
181390 ATTTAAGTTTAAATTT--
1 ATTTAAATTT-ATTTTAA
181406 ATTTAAATTTAT
1 ATTTAAATTTAT
181418 AATGTCCAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
15 1 0.02
16 12 0.19
17 43 0.69
18 6 0.10
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:181378 original size:23 final size:21
Alignment explanation
Indices: 181322--181416 Score: 67
Period size: 23 Copynumber: 4.5 Consensus size: 21
181312 GCTTAACAGG
*
181322 ATTTAAATTT-ATTTTAAATTT
1 ATTTAAATTTAAGTTTAAA-TT
*
181343 AAGTTTATA-TTAAGTTTAAATCT
1 -A-TTTAAATTTAAGTTTAAAT-T
*
181366 ATTTAGAATTTAAATTT--ATT
1 ATTTA-AATTTAAGTTTAAATT
181386 A--TAAATTTAAGTTTAAATTT
1 ATTTAAATTTAAGTTTAAA-TT
181406 ATTTAAATTTA
1 ATTTAAATTTA
181417 TAATGTCCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
17 10 0.17
18 2 0.03
19 1 0.02
20 5 0.09
21 6 0.10
22 14 0.24
23 20 0.34
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTTAAATTTAAGTTTAAATT
Found at i:183334 original size:29 final size:28
Alignment explanation
Indices: 183302--183522 Score: 128
Period size: 29 Copynumber: 7.7 Consensus size: 28
183292 CTAAACTAAC
*
183302 CAAAAATCATATTTTGACCCTAAACTTTT
1 CAAAAATCACATTTTGACCCTAAAC-TTT
* * * * *
183331 CAAAAATTACATTTTAACGTCAAAACTTC
1 CAAAAATCACATTTTGAC-CCTAAACTTT
* * * * *
183360 CAAAAATTACATTTTTACCCTCGAACATC
1 CAAAAATCACATTTTGACCCT-AAACTTT
* ** *
183389 CATAAAATTACATTTTTGACATTGAACTTT
1 CA-AAAATCACA-TTTTGACCCTAAACTTT
*
183419 CAAAAAAT-ACATTTT-CCCCTAAAC-TT
1 C-AAAAATCACATTTTGACCCTAAACTTT
* * *
183445 CTAAAAATTACAATTTGACCCTGAACTTT
1 C-AAAAATCACATTTTGACCCTAAACTTT
*
183474 CCAAAAATCATATTTT-ACCCTCAAA-TTT
1 -CAAAAATCACATTTTGACCCT-AAACTTT
*
183502 CTAAAAATCACATTTTTACCC
1 C-AAAAATCACATTTTGACCC
183523 CCGAGTGACC
Statistics
Matches: 151, Mismatches: 29, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
26 9 0.06
27 12 0.08
28 33 0.22
29 63 0.42
30 26 0.17
31 8 0.05
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (28 bp):
CAAAAATCACATTTTGACCCTAAACTTT
Found at i:183376 original size:30 final size:29
Alignment explanation
Indices: 183331--183405 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
183321 CTAAACTTTT
* *
183331 CAAAAATTACA-TTTTAACGTCAAAACTTC
1 CAAAAATTACATTTTTAACCTC-AAACATC
* *
183360 CAAAAATTACATTTTTACCCTCGAACATC
1 CAAAAATTACATTTTTAACCTCAAACATC
183389 CATAAAATTACATTTTT
1 CA-AAAATTACATTTTT
183406 GACATTGAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.45
30 22 0.55
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (29 bp):
CAAAAATTACATTTTTAACCTCAAACATC
Found at i:183426 original size:30 final size:30
Alignment explanation
Indices: 183361--183433 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
183351 CAAAACTTCC
*
183361 AAAAATTACATTTTTACCCTCGAACATCCA
1 AAAAATTACATTTTTACCATCGAACATCCA
* * * *
183391 TAAAATTACATTTTTGA-CATTGAACTTTCA
1 AAAAATTACATTTTT-ACCATCGAACATCCA
183421 AAAAA-TACATTTT
1 AAAAATTACATTTT
183434 CCCCTAAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 8 0.22
30 27 0.75
31 1 0.03
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAAATTACATTTTTACCATCGAACATCCA
Found at i:183567 original size:58 final size:59
Alignment explanation
Indices: 183485--183624 Score: 162
Period size: 58 Copynumber: 2.4 Consensus size: 59
183475 CAAAAATCAT
* *
183485 ATTTTA-CCCTCAAATTTCTAAAAATCACATTTTTACCCCCGAGTGACCAAAAATTACC
1 ATTTTACCCCTAAAATTTCTAAAAATCAAATTTTTACCCCCGAGTGACCAAAAATTACC
* * * * * *
183543 ATTTTACCCCTAAAATTTC-CAAAATTAAATTTTTGCCTCCGAGTGTCCAAAAATTGCC
1 ATTTTACCCCTAAAATTTCTAAAAATCAAATTTTTACCCCCGAGTGACCAAAAATTACC
**
183601 A-TTTA-CCCTCGAATTTCTAAAAAT
1 ATTTTACCCCTAAAATTTCTAAAAAT
183625 TTCATTTTGA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
56 10 0.14
57 9 0.13
58 39 0.57
59 11 0.16
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (59 bp):
ATTTTACCCCTAAAATTTCTAAAAATCAAATTTTTACCCCCGAGTGACCAAAAATTACC
Found at i:183690 original size:28 final size:28
Alignment explanation
Indices: 183515--183691 Score: 99
Period size: 28 Copynumber: 6.1 Consensus size: 28
183505 AAAATCACAT
* *
183515 TTTTACCCCCGAGTGACCAAAAATTACCA
1 TTTTACCCCCGAATGTCCAAAAATT-CCA
** * **
183544 TTTTACCCCTAAAATTTCC-AAAATTAAA
1 TTTTACCCC-CGAATGTCCAAAAATTCCA
* * *
183572 TTTTTGCCTCCGAGTGTCCAAAAATTGCCA
1 -TTTTACCCCCGAATGTCCAAAAATT-CCA
* * * *
183602 -TTTACCCTCGAATTTCTAAAAATTTCA
1 TTTTACCCCCGAATGTCCAAAAATTCCA
* * *
183629 TTTTGA-CCCCGAACTTTTCAAAAAATCACCA
1 TTTT-ACCCCCGAA--TGTCCAAAAAT-TCCA
*
183660 TTTTACCCCCGGATGTCCAAAAATTCCA
1 TTTTACCCCCGAATGTCCAAAAATTCCA
183688 TTTT
1 TTTT
183692 TAACCCCAAA
Statistics
Matches: 108, Mismatches: 30, Indels: 21
0.68 0.19 0.13
Matches are distributed among these distances:
27 2 0.02
28 40 0.37
29 38 0.35
30 16 0.15
31 12 0.11
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (28 bp):
TTTTACCCCCGAATGTCCAAAAATTCCA
Found at i:194421 original size:209 final size:209
Alignment explanation
Indices: 194110--194943 Score: 1247
Period size: 209 Copynumber: 4.0 Consensus size: 209
194100 CCAATTCGAG
* * *
194110 GCTCAAAGTGAGCAAATCTTCGAAGCGCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCA
1 GCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCA
* * *
194175 ATAAAGCGGTTACCTTCCTAATGAGAGACAAAGAAGTGAACCAGATCCGTCTTCTTGATAAGACA
66 ATAAAGCGGTTACCTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCTTGATGAGACA
*
194240 CAGAGAAGTGTATCAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
131 CAGAGAAGTGGATCAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
*
194305 ATCAACGAAACTAA
196 ATCAACGAAACCAA
* * *
194319 GCTCAAAGCGAGCAAATCTTTGAACCCCAGCTT-CTCGATGAGATACTAAGAAGCAGGTCGAAGC
1 GCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCT-GATGAGATACTAAGAAGCAAGTCGAAGC
* * *
194383 AATAAAGCGATTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGAC
65 AATAAAGCGGTTACCTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCTTGATGAGAC
* * *
194448 ACAAAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGATCA
130 ACAGAGAAGTGGATCAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCA
*
194513 AATGAACGAAACCAA
195 AATCAACGAAACCAA
* * *
194528 GCTCAAAGTGAGCTAATCTTCGAACCCCAGTTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCA
1 GCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCA
*** * * * * *
194593 ATAAAATTGTTACCTTCCTGATGAGATATAAAGAAGTGAACTAGATTCATCTTCTTGATGACACA
66 ATAAAGCGGTTACCTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCTTGATGAGACA
* *
194658 CAGAGAAGTGGATCAAAACAAGTGATGCGGTTATCTTCCTGATGAGATACTGAGAAGTAGACCAA
131 CAGAGAAGTGGATCAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
194723 ATCAACGAAACCAA
196 ATCAACGAAACCAA
* *
194737 GCTCAAAGTGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCA
1 GCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCA
** * * * * *
194802 ATAAAATGGTTACCTTCCTGATGAGATATAGAGAAGTAAATCAGATTCGTCTTCTTGATGAGACA
66 ATAAAGCGGTTACCTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCTTGATGAGACA
* * * *
194867 TAGAAAAGTGGATCAAAACAAGTGATATGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAA
131 CAGAGAAGTGGATCAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
*
194932 ATCAATGAAACC
196 ATCAACGAAACC
194944 GGACTCAAAG
Statistics
Matches: 567, Mismatches: 56, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
208 2 0.00
209 563 0.99
210 2 0.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (209 bp):
GCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCA
ATAAAGCGGTTACCTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCTTGATGAGACA
CAGAGAAGTGGATCAAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
ATCAACGAAACCAA
Found at i:195282 original size:17 final size:17
Alignment explanation
Indices: 195260--195332 Score: 85
Period size: 17 Copynumber: 4.3 Consensus size: 17
195250 GCCCAACAGG
195260 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
195277 ATTTAAGTTTATATTAA
1 ATTTAAATTTATTTTAA
* *
195294 GTTTAAATCTA-TTTAGA
1 ATTTAAATTTATTTTA-A
*
195311 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
195328 ATTTA
1 ATTTA
195333 TAATGTCCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
16 3 0.07
17 39 0.87
18 3 0.07
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:196097 original size:3 final size:3
Alignment explanation
Indices: 196034--196081 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
196024 AATAAAATTT
* *
196034 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
196082 ATATCATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:197253 original size:30 final size:29
Alignment explanation
Indices: 197220--197416 Score: 154
Period size: 29 Copynumber: 6.7 Consensus size: 29
197210 AAGAGCTTTG
* *
197220 AACTATCTAAAAATCATATTTTGACCCTTG
1 AACT-TCTAAAAATCACATTTTGACCCTTA
* *
197250 AACTTTTCAAAAATTC-CATTTTGCCCCTTA
1 AACTTCT-AAAAA-TCACATTTTGACCCTTA
* **
197280 AACTTCCAAAAAAT-ACATTTTTGACCC-CG
1 AACTT-CTAAAAATCACA-TTTTGACCCTTA
*
197309 AACTTTCTAAAAATCACATTTTTG-CCCCTA
1 AAC-TTCTAAAAATCACA-TTTTGACCCTTA
* *
197339 AACTTCCAAAAATTACATTTTGACCC-TA
1 AACTTCTAAAAATCACATTTTGACCCTTA
* * *
197367 AACTTCCAAAAATCATATTTTTG-CCCCTA
1 AACTTCTAAAAATCACA-TTTTGACCCTTA
*
197396 AACTTCCAAAAATCACATTTT
1 AACTTCTAAAAATCACATTTT
197417 TGCCTCCGAG
Statistics
Matches: 139, Mismatches: 17, Indels: 24
0.77 0.09 0.13
Matches are distributed among these distances:
28 29 0.21
29 56 0.40
30 52 0.37
31 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
AACTTCTAAAAATCACATTTTGACCCTTA
Found at i:197396 original size:57 final size:58
Alignment explanation
Indices: 197250--197416 Score: 223
Period size: 57 Copynumber: 2.9 Consensus size: 58
197240 TTGACCCTTG
* * *
197250 AACTTTTCAAAAATTC-CA-TTTTGCCCCTTAAACTTCCAAAAAATACATTTTTGACCCCG
1 AACTTTCCAAAAA-TCACATTTTTGCCCC-TAAACTTCCAAAAATTACA-TTTTGACCCCA
* *
197309 AACTTTCTAAAAATCACATTTTTGCCCCTAAACTTCCAAAAATTACATTTTGACCCTA
1 AACTTTCCAAAAATCACATTTTTGCCCCTAAACTTCCAAAAATTACATTTTGACCCCA
* *
197367 AAC-TTCCAAAAATCATATTTTTGCCCCTAAACTTCCAAAAATCACATTTT
1 AACTTTCCAAAAATCACATTTTTGCCCCTAAACTTCCAAAAATTACATTTT
197417 TGCCTCCGAG
Statistics
Matches: 98, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
57 44 0.45
58 14 0.14
59 31 0.32
60 9 0.09
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (58 bp):
AACTTTCCAAAAATCACATTTTTGCCCCTAAACTTCCAAAAATTACATTTTGACCCCA
Found at i:197417 original size:29 final size:29
Alignment explanation
Indices: 197268--197420 Score: 204
Period size: 29 Copynumber: 5.2 Consensus size: 29
197258 AAAAATTCCA
197268 TTTTGCCCCTTAAACTTCCAAAAAAT-ACAT
1 TTTTGCCCC-TAAACTTCC-AAAAATCACAT
* *
197298 TTTTGACCCC-GAACTTTCTAAAAATCACAT
1 TTTTG-CCCCTAAAC-TTCCAAAAATCACAT
*
197328 TTTTGCCCCTAAACTTCCAAAAATTACA-
1 TTTTGCCCCTAAACTTCCAAAAATCACAT
* *
197356 TTTTGACCCTAAACTTCCAAAAATCATAT
1 TTTTGCCCCTAAACTTCCAAAAATCACAT
197385 TTTTGCCCCTAAACTTCCAAAAATCACAT
1 TTTTGCCCCTAAACTTCCAAAAATCACAT
197414 TTTTGCC
1 TTTTGCC
197421 TCCGAGTGCC
Statistics
Matches: 108, Mismatches: 10, Indels: 11
0.84 0.08 0.09
Matches are distributed among these distances:
28 25 0.23
29 59 0.55
30 20 0.19
31 4 0.04
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (29 bp):
TTTTGCCCCTAAACTTCCAAAAATCACAT
Found at i:197524 original size:58 final size:59
Alignment explanation
Indices: 197399--197530 Score: 162
Period size: 58 Copynumber: 2.3 Consensus size: 59
197389 GCCCCTAAAC
* * *
197399 TTCCAAAAATCACATTTTTGCCTCCGAGTGCCCAAAAATTACCATTTTAATCTCGAAAT
1 TTCCAAAAATTACATTTTTGCCCCCGAGTGCCCAAAAATTACCATTTTAATCCCGAAAT
* * * *
197458 TTCC-AAAATTACATTTTTGCCCCCGAGTGTGCC-AAAATTGCCATTTT-ATCCCTAGAT
1 TTCCAAAAATTACATTTTTGCCCCCGAGTG-CCCAAAAATTACCATTTTAATCCCGAAAT
*
197515 TTCCAAAAATTCCATT
1 TTCCAAAAATTACATT
197531 ATTGACCGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
57 11 0.17
58 46 0.73
59 6 0.10
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (59 bp):
TTCCAAAAATTACATTTTTGCCCCCGAGTGCCCAAAAATTACCATTTTAATCCCGAAAT
Found at i:197604 original size:84 final size:84
Alignment explanation
Indices: 197459--197614 Score: 190
Period size: 84 Copynumber: 1.9 Consensus size: 84
197449 TCTCGAAATT
* * * * * *
197459 TCCAAAATTACATTTTTGCCCCCGAGTGTGCCAAAATTGCCATTTTATCCCTAGATTTCCAAAAA
1 TCCAAAATTACATTTTTGCCCCCAAGTATGCCAAAATTACCATTTTAGCCCCAGATATCCAAAAA
197524 TTCCATTATTGACCGAACC
66 TTCCATTATTGACCGAACC
* * *
197543 TCCAAAATTAC-TATTTTGCCCCCAACGTAT-CCAAAATTACCGTTTTAGCCCCGGGTATCCAAA
1 TCCAAAATTACAT-TTTTGCCCCCAA-GTATGCCAAAATTACCATTTTAGCCCCAGATATCCAAA
*
197606 AATTGCATT
64 AATTCCATT
197615 TAATCCCGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
83 1 0.02
84 56 0.93
85 3 0.05
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (84 bp):
TCCAAAATTACATTTTTGCCCCCAAGTATGCCAAAATTACCATTTTAGCCCCAGATATCCAAAAA
TTCCATTATTGACCGAACC
Found at i:198877 original size:12 final size:12
Alignment explanation
Indices: 198844--198891 Score: 69
Period size: 13 Copynumber: 3.8 Consensus size: 12
198834 TTTAGAAAAA
*
198844 GAAAAAAAAGTT
1 GAAAAAAAAATT
198856 GAAAAGAAAAATT
1 GAAAA-AAAAATT
198869 GAAAAAAAAATT
1 GAAAAAAAAATT
198881 GAGAAAAAAAA
1 GA-AAAAAAAA
198892 AAGAGAAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 14 0.42
13 19 0.58
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (12 bp):
GAAAAAAAAATT
Found at i:198882 original size:25 final size:24
Alignment explanation
Indices: 198837--198892 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
198827 TTTATTATTT
*
198837 AGAAAAAGAAAAAAAAGTTGA-AA
1 AGAAAAAGAAAAAAAAATTGAGAA
198860 AGAAAAATTGAAAAAAAAATTGAGAA
1 AGAAAAA--GAAAAAAAAATTGAGAA
*
198886 AAAAAAA
1 AGAAAAA
198893 AGAGAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 7 0.25
25 13 0.46
26 8 0.29
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (24 bp):
AGAAAAAGAAAAAAAAATTGAGAA
Found at i:203943 original size:90 final size:89
Alignment explanation
Indices: 203849--204032 Score: 201
Period size: 90 Copynumber: 2.1 Consensus size: 89
203839 ATTTTTTCAA
* * *** *
203849 AAAAAAAAACAATTA-AGTCTATCCTTTTTTTTTCACTCAATTGAGCACTTGAACTTTCAAAGTG
1 AAAAAAAAACAATTACAGCCTA-CCTATTTTCCCCACTCAATTGAGCACTTGAACTTTCAAAAT-
* *
203913 CATAAAAAAGACCCTCAAACTTCTTC
64 CATAAAAAAGACCCTAAAAATTCTTC
* * * *
203939 -AAAAAAAGCAATTACGCGCCTACCTATTTTCCCCACTCAATTGGGTACTTGAACTTTCAAAATC
1 AAAAAAAAACAATTAC-AGCCTACCTATTTTCCCCACTCAATTGAGCACTTGAACTTTCAAAATC
* *
204003 ATCAAAAAGACCCTAAAAATTTTTC
65 ATAAAAAAGACCCTAAAAATTCTTC
204028 AAAAA
1 AAAAA
204033 CGCAATTAAG
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
89 35 0.45
90 38 0.49
91 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.29
Consensus pattern (89 bp):
AAAAAAAAACAATTACAGCCTACCTATTTTCCCCACTCAATTGAGCACTTGAACTTTCAAAATCA
TAAAAAAGACCCTAAAAATTCTTC
Found at i:204458 original size:8 final size:9
Alignment explanation
Indices: 204406--204503 Score: 72
Period size: 9 Copynumber: 10.6 Consensus size: 9
204396 CTTTTGGTAC
*
204406 TATAACTTT
1 TATAATTTT
204415 TATAAATTTT
1 TAT-AATTTT
**
204425 TACCATTTT
1 TATAATTTT
*
204434 TACAATTTT
1 TATAATTTT
*
204443 TATGATTTT
1 TATAATTTT
*
204452 TATATTTTT
1 TATAATTTT
*
204461 TCTAATTTT
1 TATAATTTT
204470 T-TATATTTT
1 TATA-ATTTT
204479 TATTAATATTT
1 TA-TAAT-TTT
* *
204490 AATAATATT
1 TATAATTTT
204499 TATAA
1 TATAA
204504 CCTTTATTGA
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
8 2 0.03
9 50 0.70
10 13 0.18
11 6 0.08
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (9 bp):
TATAATTTT
Found at i:207261 original size:25 final size:25
Alignment explanation
Indices: 207207--207261 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
207197 CAAATAGTCC
207207 TTTTATTGTGTCATATTACATTTTA
1 TTTTATTGTGTCATATTACATTTTA
* * * *
207232 ATTTATTTTGTTATATT-TATTTATA
1 TTTTATTGTGTCATATTACATTT-TA
207257 TTTTA
1 TTTTA
207262 AATTTAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.65
Consensus pattern (25 bp):
TTTTATTGTGTCATATTACATTTTA
Found at i:221281 original size:19 final size:19
Alignment explanation
Indices: 221257--221304 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
221247 TCAAAAAAAA
221257 TTTCTTTTTTCATTT-TCA-T
1 TTTCTTTTTT--TTTCTCATT
221276 TTTCTTCTTTTTTTCTCATT
1 TTTCTT-TTTTTTTCTCATT
221296 TTTCTTTTT
1 TTTCTTTTT
221305 CAAGTGACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 12 0.46
20 11 0.42
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTCTTTTTTTTTCTCATT
Found at i:238396 original size:20 final size:20
Alignment explanation
Indices: 238360--238405 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
238350 TCATTAAGTT
*
238360 TTAATTAATCATTTTTA-ATC
1 TTAATTAATCATATTTATA-C
238380 TTAATTAAATC-TATTTATAC
1 TTAATT-AATCATATTTATAC
238400 TTAATT
1 TTAATT
238406 TAAACCATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTAATCATATTTATAC
Found at i:243778 original size:20 final size:21
Alignment explanation
Indices: 243742--243780 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
243732 ACATTTGTTA
*
243742 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
243763 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
243781 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:245894 original size:52 final size:52
Alignment explanation
Indices: 245551--245893 Score: 492
Period size: 52 Copynumber: 6.6 Consensus size: 52
245541 TTCTCATTCG
* * * *
245551 ATACTCACAATGACACATAGTCATCGAACCTCATAATCTGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
245603 ATGCTCACGATGACACATAGTAATC-GAGCCTCATAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGA-CCTCATAATCCGTAAAGGATTCAT
* **
245655 ATACTCACGATGACACATAGTTATCGGACCTCATAATCCAAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
245707 ATGCTCACGATGACACATAGTAATCAGG-CCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATC-GGACCTCATAATCCGTAAAGGATTCAT
** * **
245759 ATACTCACGATGACACATAGTCATCAAACCACATAATTTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
245811 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
245863 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
245894 TTTGCATTTA
Statistics
Matches: 258, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
51 1 0.00
52 253 0.98
53 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:246905 original size:16 final size:16
Alignment explanation
Indices: 246881--246913 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
246871 TCCTTACAAA
*
246881 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
246897 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
246913 T
1 T
246914 AAAATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:249431 original size:18 final size:15
Alignment explanation
Indices: 249389--249421 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
249379 ATGACCAGTT
249389 GAAG-AAAA-AGGAA
1 GAAGAAAAAGAGGAA
249402 GAAGAAAAAGAGGAA
1 GAAGAAAAAGAGGAA
249417 GAAGA
1 GAAGA
249422 GAATGAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 4 0.22
15 10 0.56
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
GAAGAAAAAGAGGAA
Found at i:249892 original size:17 final size:18
Alignment explanation
Indices: 249870--249909 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
249860 ATAGTTTTCA
249870 TGCATTTT-TATAGTCAT
1 TGCATTTTATATAGTCAT
* *
249887 TGCATTTTATATTGTTAT
1 TGCATTTTATATAGTCAT
249905 TGCAT
1 TGCAT
249910 CCCTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.55
Consensus pattern (18 bp):
TGCATTTTATATAGTCAT
Found at i:254273 original size:17 final size:18
Alignment explanation
Indices: 254251--254291 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
254241 CTGTAATTGT
254251 ATTATCATC-ACATTTTA
1 ATTATCATCTACATTTTA
254268 ATTATC-TCTACATTTTA
1 ATTATCATCTACATTTTA
*
254285 TTTATCA
1 ATTATCA
254292 AAGCATTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATCATCTACATTTTA
Found at i:262782 original size:23 final size:24
Alignment explanation
Indices: 262756--262801 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
262746 AAATTATAAA
262756 ATATAATA-CAATAAAATAAAAAT
1 ATATAATAGCAATAAAATAAAAAT
* **
262779 ATATATTAGTGATAAAATAAAAA
1 ATATAATAGCAATAAAATAAAAA
262802 AAATTTGAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (24 bp):
ATATAATAGCAATAAAATAAAAAT
Found at i:263065 original size:20 final size:22
Alignment explanation
Indices: 263026--263065 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
263016 AACTTAACAT
*
263026 TCATATTCAACTTTAAAGTTAA
1 TCATATTCAACTTGAAAGTTAA
263048 TCAT-TTCAA-TTGAAAGTT
1 TCATATTCAACTTGAAAGTT
263066 GAACCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (22 bp):
TCATATTCAACTTGAAAGTTAA
Found at i:268247 original size:17 final size:18
Alignment explanation
Indices: 268212--268251 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
268202 AATACATAAA
268212 AAAAAATCAAGAAAATAT
1 AAAAAATCAAGAAAATAT
268230 AAAAAAT-AA-AAAATTAT
1 AAAAAATCAAGAAAA-TAT
268247 AAAAA
1 AAAAA
268252 TGGAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 10 0.48
18 7 0.33
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAAAATCAAGAAAATAT
Found at i:268378 original size:17 final size:19
Alignment explanation
Indices: 268339--268380 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
268329 GTGATTAGTT
*
268339 TTTTAATTTATATATATAT
1 TTTTAATTTATATATATAA
268358 TTTTAATTTATATA-A-AA
1 TTTTAATTTATATATATAA
268375 TTTTAA
1 TTTTAA
268381 ATAACTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 14 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAATTTATATATATAA
Found at i:274375 original size:17 final size:18
Alignment explanation
Indices: 274355--274392 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
274345 TACATCTCAA
*
274355 TTCTTTCCTTTTAT-TTT
1 TTCTTTCATTTTATGTTT
*
274372 TTCTTTTATTTTATGTTT
1 TTCTTTCATTTTATGTTT
274390 TTC
1 TTC
274393 AAAATCAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.08, C:0.13, G:0.03, T:0.76
Consensus pattern (18 bp):
TTCTTTCATTTTATGTTT
Found at i:274839 original size:12 final size:12
Alignment explanation
Indices: 274818--274847 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
274808 TTTTTATGTA
*
274818 GATGACATTTAT
1 GATGATATTTAT
274830 GATGATATTTAT
1 GATGATATTTAT
274842 GATGAT
1 GATGAT
274848 GATATCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.43
Consensus pattern (12 bp):
GATGATATTTAT
Found at i:278636 original size:23 final size:21
Alignment explanation
Indices: 278578--278636 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
278568 TAGTTTAGCC
*
278578 AAAGAAGAGAAAAATAGTGAA
1 AAAGAAAAGAAAAATAGTGAA
*
278599 AAAGAAAAAAGAAAAT-GTGTAGA
1 AAAGAAAAGA-AAAATAGTG-A-A
278622 AACAGAAAAGAAAAA
1 AA-AGAAAAGAAAAA
278637 ATCTTGAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 11 0.35
22 6 0.19
23 7 0.23
24 7 0.23
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.08
Consensus pattern (21 bp):
AAAGAAAAGAAAAATAGTGAA
Found at i:279145 original size:16 final size:16
Alignment explanation
Indices: 279124--279154 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
279114 TGTAACTTAC
279124 TGATTGAAGGACTCAA
1 TGATTGAAGGACTCAA
279140 TGATTGAAGGACTCA
1 TGATTGAAGGACTCA
279155 TACGAAAACT
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:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (16 bp):
TGATTGAAGGACTCAA
Found at i:281767 original size:12 final size:12
Alignment explanation
Indices: 281750--281784 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
281740 CAAGCTTTTC
*
281750 TTTTATTTTCTA
1 TTTTATTTTATA
*
281762 TTTTATTTTATC
1 TTTTATTTTATA
281774 TTTTATTTTAT
1 TTTTATTTTAT
281785 GCTCTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:281770 original size:17 final size:17
Alignment explanation
Indices: 281745--281784 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
281735 CATTTCAAGC
*
281745 TTTTCTTTTAT-TTTCTA
1 TTTTATTTTATCTTT-TA
281762 TTTTATTTTATCTTTTA
1 TTTTATTTTATCTTTTA
281779 TTTTAT
1 TTTTAT
281785 GCTCTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTTATCTTTTA
Found at i:284901 original size:21 final size:21
Alignment explanation
Indices: 284849--284910 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
284839 TTTGAAACAA
* *
284849 TTTCAAAATCAAGTTAAAATGAT
1 TTTC-AAA-CAAGTCAAAATAAT
284872 TTT-AAACAAGTCAAAATAAT
1 TTTCAAACAAGTCAAAATAAT
*
284892 TTTCAAACAAGTCAGAATA
1 TTTCAAACAAGTCAAAATA
284911 GCTTCAGGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 15 0.43
21 17 0.49
23 3 0.09
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (21 bp):
TTTCAAACAAGTCAAAATAAT
Found at i:289599 original size:15 final size:15
Alignment explanation
Indices: 289579--289607 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
289569 GTATTGTTGC
289579 TTGATAACACGATGA
1 TTGATAACACGATGA
289594 TTGATAACACGATG
1 TTGATAACACGATG
289608 TGTAAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (15 bp):
TTGATAACACGATGA
Found at i:305276 original size:19 final size:19
Alignment explanation
Indices: 305252--305289 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
305242 CAGATGCTAG
305252 ATAGGCTCGCTGGTAAGGC
1 ATAGGCTCGCTGGTAAGGC
* *
305271 ATAGGCTTGCTTGTAAGGC
1 ATAGGCTCGCTGGTAAGGC
305290 CTACTACTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.26
Consensus pattern (19 bp):
ATAGGCTCGCTGGTAAGGC
Found at i:316808 original size:17 final size:17
Alignment explanation
Indices: 316786--316818 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
316776 TTTGAAAGCA
316786 TAAAATA-AAAGATAAAC
1 TAAAATAGAAA-ATAAAC
316803 TAAAATAGAAAATAAA
1 TAAAATAGAAAATAAA
316819 GGAAAAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAATAGAAAATAAAC
Found at i:331773 original size:26 final size:26
Alignment explanation
Indices: 331746--331977 Score: 196
Period size: 26 Copynumber: 8.9 Consensus size: 26
331736 AGAGATTTAT
* *
331746 TCTATTTGGGCTCCAATGAGCTAAAT
1 TCTATTTGGGCTCGAATGAGCTAAAC
* * * ** * *
331772 TCTGTCTAGGCTAAAATCAACTAAAC
1 TCTATTTGGGCTCGAATGAGCTAAAC
* * * *
331798 TTTGTCTGGGCTCGTATGAGCTAAAC
1 TCTATTTGGGCTCGAATGAGCTAAAC
* *
331824 TCTATCTGGGCTCGAATAAGCTAAAC
1 TCTATTTGGGCTCGAATGAGCTAAAC
* **
331850 T-TTTTCTGGGCTCTTATGAGCTAAAC
1 TCTATT-TGGGCTCGAATGAGCTAAAC
* *
331876 TCTGTTTGGGCTCGAATAAGCTAAAC
1 TCTATTTGGGCTCGAATGAGCTAAAC
* * *
331902 TCTGTTTAGGCTCGTATGAGCTAAAC
1 TCTATTTGGGCTCGAATGAGCTAAAC
* * *
331928 TCTATCTGGGCTCGTATGAGCTATAC
1 TCTATTTGGGCTCGAATGAGCTAAAC
*
331954 TCTATTTTGGGCTCGAAAGAGCTA
1 TCTA-TTTGGGCTCGAATGAGCTA
331978 CTTTTATGTA
Statistics
Matches: 165, Mismatches: 38, Indels: 5
0.79 0.18 0.02
Matches are distributed among these distances:
25 2 0.01
26 144 0.87
27 19 0.12
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (26 bp):
TCTATTTGGGCTCGAATGAGCTAAAC
Found at i:331848 original size:52 final size:52
Alignment explanation
Indices: 331752--331950 Score: 238
Period size: 52 Copynumber: 3.8 Consensus size: 52
331742 TTATTCTATT
** * * * **
331752 TGGGCTCCAATGAGCTAAATTCTGTCTAGGCTAAAATCAA-CTAAACTTTGTC
1 TGGGCTCGTATGAGCTAAACTCTATCTGGGCTCGAAT-AAGCTAAACTTTGTC
*
331804 TGGGCTCGTATGAGCTAAACTCTATCTGGGCTCGAATAAGCTAAACTTTTTC
1 TGGGCTCGTATGAGCTAAACTCTATCTGGGCTCGAATAAGCTAAACTTTGTC
* * * * *
331856 TGGGCTCTTATGAGCTAAACTCTGTTTGGGCTCGAATAAGCTAAACTCTGTT
1 TGGGCTCGTATGAGCTAAACTCTATCTGGGCTCGAATAAGCTAAACTTTGTC
* * *
331908 TAGGCTCGTATGAGCTAAACTCTATCTGGGCTCGTATGAGCTA
1 TGGGCTCGTATGAGCTAAACTCTATCTGGGCTCGAATAAGCTA
331951 TACTCTATTT
Statistics
Matches: 126, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
51 2 0.02
52 124 0.98
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (52 bp):
TGGGCTCGTATGAGCTAAACTCTATCTGGGCTCGAATAAGCTAAACTTTGTC
Found at i:334964 original size:27 final size:26
Alignment explanation
Indices: 334897--334964 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 26
334887 CATTATCAGT
*
334897 TGGGTTGGCTAGTGTGTTTGGTGAGC
1 TGGGTTCGCTAGTGTGTTTGGTGAGC
* *
334923 TGGTGTTCACCAGTGTGTTTGGTGAGC
1 TGG-GTTCGCTAGTGTGTTTGGTGAGC
334950 TAGGGTTCGCTAGTG
1 T-GGGTTCGCTAGTG
334965 AAGTTGTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 3 0.09
27 30 0.86
28 2 0.06
ACGTcount: A:0.10, C:0.12, G:0.41, T:0.37
Consensus pattern (26 bp):
TGGGTTCGCTAGTGTGTTTGGTGAGC
Found at i:354661 original size:20 final size:21
Alignment explanation
Indices: 354636--354680 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
354626 TATATACATA
354636 TTTTTTTTTCTTCTTTTC-CT
1 TTTTTTTTTCTTCTTTTCTCT
*
354656 TTTTTTTTTCTTTTTTTCTCT
1 TTTTTTTTTCTTCTTTTCTCT
354677 TTTT
1 TTTT
354681 ATATTATGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTTTTCTTCTTTTCTCT
Found at i:355286 original size:17 final size:17
Alignment explanation
Indices: 355247--355294 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
355237 TGATATATGG
355247 AAATGCAATGACAATGA
1 AAATGCAATGACAATGA
* *
355264 AGATGCAGTGACAA-GAA
1 AAATGCAATGACAATG-A
355281 AAATGCAATGACAA
1 AAATGCAATGACAA
355295 ACGAAATGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 1 0.04
17 25 0.96
ACGTcount: A:0.52, C:0.12, G:0.21, T:0.15
Consensus pattern (17 bp):
AAATGCAATGACAATGA
Found at i:355301 original size:17 final size:16
Alignment explanation
Indices: 355246--355302 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
355236 ATGATATATG
*
355246 GAAATGCAATGACAAT
1 GAAATGCAATGACAAA
*
355262 GAAGATGCAGTGACAAGA
1 GAA-ATGCAATGACAA-A
*
355280 AAAATGCAATGACAAA
1 GAAATGCAATGACAAA
355296 CGAAATG
1 -GAAATG
355303 TGATGATAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.12
17 27 0.82
18 2 0.06
ACGTcount: A:0.51, C:0.12, G:0.23, T:0.14
Consensus pattern (16 bp):
GAAATGCAATGACAAA
Found at i:355747 original size:21 final size:22
Alignment explanation
Indices: 355707--355748 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
355697 TCAGGTCCTT
*
355707 CTCTTCTTTCTTCTTTTTCTGC
1 CTCTTCTTTCTTCCTTTTCTGC
355729 CTCTTCTTT-TTCCTTTTCTG
1 CTCTTCTTTCTTCCTTTTCTG
355749 TCTCCAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.00, C:0.31, G:0.05, T:0.64
Consensus pattern (22 bp):
CTCTTCTTTCTTCCTTTTCTGC
Found at i:366464 original size:10 final size:9
Alignment explanation
Indices: 366449--366488 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
366439 TACATATACA
366449 TTTTTTTTC
1 TTTTTTTTC
366458 TTTTTTTTC
1 TTTTTTTTC
**
366467 TTTTTATTAA
1 TTTTT-TTTC
366477 TTTTTTTTC
1 TTTTTTTTC
366486 TTT
1 TTT
366489 ATTTCTTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:367515 original size:3 final size:3
Alignment explanation
Indices: 367507--367561 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
367497 CAAGGCAACA
* *
367507 TCT TCT TCT TTT TCT TCCT TC- TCT TCT TTT TCT TCT TCT T-T TCTT
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TC-T
367552 TCT TCT TCT T
1 TCT TCT TCT T
367562 TTACCTCAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 34 0.77
4 6 0.14
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:367533 original size:18 final size:18
Alignment explanation
Indices: 367510--367559 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
367500 GGCAACATCT
367510 TCTTCTTTTTCTTCCTTC
1 TCTTCTTTTTCTTCCTTC
367528 TCTTCTTTTTCTT-CTTC
1 TCTTCTTTTTCTTCCTTC
*
367545 TTTTCTTTCTTCTTC
1 TCTTCTTT-TTCTTC
367560 TTTTACCTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TCTTCTTTTTCTTCCTTC
Found at i:367560 original size:21 final size:23
Alignment explanation
Indices: 367507--367561 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
367497 CAAGGCAACA
*
367507 TCTTCTTCTTTTTCTTCCTTCTCT
1 TCTTCTTCTTCTTCTT-CTTCTCT
*
367531 TCTTTTTCTTCTTCTT-TTCT-T
1 TCTTCTTCTTCTTCTTCTTCTCT
367552 TCTTCTTCTT
1 TCTTCTTCTT
367562 TTACCTCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.36
22 4 0.14
24 14 0.50
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (23 bp):
TCTTCTTCTTCTTCTTCTTCTCT
Found at i:367562 original size:15 final size:15
Alignment explanation
Indices: 367507--367563 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
367497 CAAGGCAACA
367507 TCTTCTTCTTTTTCTT
1 TCTTCTTC-TTTTCTT
*
367523 CCTTC-TCTTCTT-TT
1 TCTTCTTCTT-TTCTT
367537 TCTTCTTCTTTTCTT
1 TCTTCTTCTTTTCTT
367552 TCTTCTTCTTTT
1 TCTTCTTCTTTT
367564 ACCTCAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.28
15 22 0.61
16 4 0.11
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
TCTTCTTCTTTTCTT
Found at i:371343 original size:22 final size:22
Alignment explanation
Indices: 371315--371358 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
371305 TTCGATGGAG
371315 ATAGCTTTTCAATGATTTTGAC
1 ATAGCTTTTCAATGATTTTGAC
371337 ATAGCTTTTCAATGATTTTGAC
1 ATAGCTTTTCAATGATTTTGAC
371359 CTTCGCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (22 bp):
ATAGCTTTTCAATGATTTTGAC
Found at i:378385 original size:19 final size:19
Alignment explanation
Indices: 378361--378412 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
378351 ATCAAAAAAA
*
378361 AACTACTGAAACTTCATAC
1 AACTACCGAAACTTCATAC
378380 AACTACCGAAACTTCATAC
1 AACTACCGAAACTTCATAC
378399 AACTACCGAAACTT
1 AACTACCGAAACTT
378413 AGAATCAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.42, C:0.29, G:0.06, T:0.23
Consensus pattern (19 bp):
AACTACCGAAACTTCATAC
Found at i:384837 original size:17 final size:18
Alignment explanation
Indices: 384815--384852 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
384805 TTATTCTATA
*
384815 TTTTTTTTTCT-TTTTTC
1 TTTTTTTATCTATTTTTC
384832 TTTTTTTATCTATTTTTC
1 TTTTTTTATCTATTTTTC
384850 TTT
1 TTT
384853 CTTTCTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTATCTATTTTTC
Found at i:390709 original size:6 final size:6
Alignment explanation
Indices: 390686--390747 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
390676 TGGTCAAACC
* * * * *
390686 TCATCA TAATCT TCATCA TCATCA TCCTCA TCCTCA TCATCA TCCTCA
1 TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA TCATCA
* *
390734 TCTTCA TCTTCA TC
1 TCATCA TCATCA TC
390748 TTCAATATCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.24, C:0.37, G:0.00, T:0.39
Consensus pattern (6 bp):
TCATCA
Found at i:392990 original size:21 final size:21
Alignment explanation
Indices: 392966--393010 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
392956 TCAAAATGCT
392966 AAGTTAACATTTTTTTACGAA
1 AAGTTAACATTTTTTTACGAA
*
392987 AAGTTAATATTTTTTTACGAA
1 AAGTTAACATTTTTTTACGAA
393008 AAG
1 AAG
393011 CTAAGGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (21 bp):
AAGTTAACATTTTTTTACGAA
Found at i:395544 original size:84 final size:84
Alignment explanation
Indices: 395385--395545 Score: 207
Period size: 84 Copynumber: 1.9 Consensus size: 84
395375 CAGGAATTTG
* * *
395385 ATAAAAATGCCAAAGGTGTCACTGAGGACAAGGAAACTGAAGAGAATTCGAGTTTAGAGCATGAG
1 ATAAAAATGCCAAAGGTGTCACTGAGGACAAGGAAACTGAAGAGAATTCGAATTTAAAGCATGAA
*
395450 GAAGCAGAAGCAAGTTCAA
66 GAACCAGAAGCAAGTTCAA
* * * * * *
395469 ATAAAATTGCCAAAGGTGTTACTGAGGACTATGAAACTGAATG-GATTTTGAATTTAAAGCATGA
1 ATAAAAATGCCAAAGGTGTCACTGAGGACAAGGAAACTGAA-GAGAATTCGAATTTAAAGCATGA
*
395533 AGAACCCGAAGCA
65 AGAACCAGAAGCA
395546 CAATCAAATA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
84 64 0.98
85 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (84 bp):
ATAAAAATGCCAAAGGTGTCACTGAGGACAAGGAAACTGAAGAGAATTCGAATTTAAAGCATGAA
GAACCAGAAGCAAGTTCAA
Found at i:400846 original size:28 final size:28
Alignment explanation
Indices: 400814--400928 Score: 106
Period size: 28 Copynumber: 4.1 Consensus size: 28
400804 TTTATGGTTA
*
400814 ACTCTATTAAAGGAAGTCTTTGTGGCTG
1 ACTCTATTAAAGGAAGCCTTTGTGGCTG
* ** * *
400842 ACTCTATCAAAGGAAGAAATTT-TTGTTG
1 ACTCTATTAAAGGAAG-CCTTTGTGGCTG
* *
400870 ACTCTGTTAAAGGTAGCCTTTGTGGCTG
1 ACTCTATTAAAGGAAGCCTTTGTGGCTG
* * * *
400898 AATTTATTAAAGGAAGCCATTGTGGTTG
1 ACTCTATTAAAGGAAGCCTTTGTGGCTG
400926 ACT
1 ACT
400929 ATGAAAGGAC
Statistics
Matches: 66, Mismatches: 19, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
27 3 0.05
28 60 0.91
29 3 0.05
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (28 bp):
ACTCTATTAAAGGAAGCCTTTGTGGCTG
Found at i:400926 original size:56 final size:56
Alignment explanation
Indices: 400808--400928 Score: 143
Period size: 56 Copynumber: 2.2 Consensus size: 56
400798 CACACTTTTA
* * * *
400808 TGGTTAACTCTATTAAAGGAAGTCTTTGTGGCTGACTCTATCAAAGGAAGAAATTT
1 TGGTTGACTCTATTAAAGGAAGCCTTTGTGGCTGAATCTATCAAAGGAAGAAATTG
* * * * * **
400864 TTGTTGACTCTGTTAAAGGTAGCCTTTGTGGCTGAATTTATTAAAGGAAGCCATTG
1 TGGTTGACTCTATTAAAGGAAGCCTTTGTGGCTGAATCTATCAAAGGAAGAAATTG
400920 TGGTTGACT
1 TGGTTGACT
400929 ATGAAAGGAC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (56 bp):
TGGTTGACTCTATTAAAGGAAGCCTTTGTGGCTGAATCTATCAAAGGAAGAAATTG
Found at i:407212 original size:2 final size:2
Alignment explanation
Indices: 407207--407244 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
407197 TTGTCAAGCG
*
407207 CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
407245 TATATATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:407965 original size:2 final size:2
Alignment explanation
Indices: 407945--407993 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
407935 TTGTATATTT
* *
407945 TA TA CA TA TA TA CTT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
407988 TA -A TA T
1 TA TA TA T
407994 TAAAAATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.95
3 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:412287 original size:24 final size:24
Alignment explanation
Indices: 412259--412306 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
412249 GTTCACGAAC
* *
412259 AAGCTCATTTATTGCCTTGTTTAT
1 AAGCTCATTTATTGACTCGTTTAT
*
412283 AAGCTCGTTTATTGACTCGTTTAT
1 AAGCTCATTTATTGACTCGTTTAT
412307 GACTCGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.48
Consensus pattern (24 bp):
AAGCTCATTTATTGACTCGTTTAT
Found at i:412311 original size:11 final size:11
Alignment explanation
Indices: 412286--412317 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
412276 TGTTTATAAG
412286 CTCGTTTATTGA
1 CTCGTTTA-TGA
412298 CTCGTTTATGA
1 CTCGTTTATGA
412309 CTCGTTTAT
1 CTCGTTTAT
412318 TTATTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (11 bp):
CTCGTTTATGA
Found at i:412429 original size:12 final size:12
Alignment explanation
Indices: 412407--412436 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
412397 ATTATTCATT
412407 AACATTGTTCGTG
1 AACA-TGTTCGTG
412420 AACATGTTCGTG
1 AACATGTTCGTG
412432 AACAT
1 AACAT
412437 TAAACAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (12 bp):
AACATGTTCGTG
Found at i:414764 original size:29 final size:31
Alignment explanation
Indices: 414731--414797 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
414721 ACTTTTCAAT
* *
414731 TTTAAAATCAAA-TTAAAA-ATTAATTTAGC
1 TTTAAAATCAAACATAAAACACTAATTTAGC
414760 TTTAAAATCAAACATAAAACACTAATTTAGC
1 TTTAAAATCAAACATAAAACACTAATTTAGC
*
414791 TTGAAAA
1 TTTAAAA
414798 AGCCATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 12 0.36
30 5 0.15
31 16 0.48
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (31 bp):
TTTAAAATCAAACATAAAACACTAATTTAGC
Found at i:416235 original size:49 final size:49
Alignment explanation
Indices: 416171--416316 Score: 238
Period size: 49 Copynumber: 2.9 Consensus size: 49
416161 TTCGGATCAT
*
416171 AATTTATAATTATTACTCCAAACAATTCGTAACAAGAATTATTATATGTA
1 AATTT-TAATCATTACTCCAAACAATTCGTAACAAGAATTATTATATGTA
416221 AATTTTAATCATTACTCCAAACAATTCGTAACAAGAATTATTATATGTA
1 AATTTTAATCATTACTCCAAACAATTCGTAACAAGAATTATTATATGTA
* * *
416270 AATTTTAACCATTACTCCAAACAATTTGTAACAAAAAATTATTATAT
1 AATTTTAATCATTACTCCAAACAATTCGTAAC-AAGAATTATTATAT
416317 AAAACAATTA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
49 73 0.80
50 18 0.20
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.37
Consensus pattern (49 bp):
AATTTTAATCATTACTCCAAACAATTCGTAACAAGAATTATTATATGTA
Found at i:425090 original size:18 final size:19
Alignment explanation
Indices: 425056--425096 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
425046 TGGGTTTTTT
425056 ATAAATATAATATAAAA-A
1 ATAAATATAATATAAAATA
*
425074 ATAAATA-ATTATCAAAATA
1 ATAAATATAATAT-AAAATA
425093 ATAA
1 ATAA
425097 CACTTAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAAATATAATATAAAATA
Done.