Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005576.1 Hibiscus syriacus cultivar Beakdansim tig00012937_pilon, 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: 113624
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8520 original size:13 final size:13
Alignment explanation
Indices: 8502--8528 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8492 TGCGTCATAA
8502 ATTTATGACGCAC
1 ATTTATGACGCAC
8515 ATTTATGACGCAC
1 ATTTATGACGCAC
8528 A
1 A
8529 ATTTTTACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:12372 original size:17 final size:17
Alignment explanation
Indices: 12350--12386 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12340 TCCACCAACA
*
12350 GAAGTATAGATTAATGT
1 GAAGTATAGATTAATAT
12367 GAAGTATAGATTAATAT
1 GAAGTATAGATTAATAT
12384 GAA
1 GAA
12387 AGATAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (17 bp):
GAAGTATAGATTAATAT
Found at i:14518 original size:21 final size:21
Alignment explanation
Indices: 14489--14542 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
14479 GGGTGTTCAA
*
14489 TTCCGGGTACCCTACCCGAAG
1 TTCCAGGTACCCTACCCGAAG
14510 TTCCAGGTACCCTACCCGAAG
1 TTCCAGGTACCCTACCCGAAG
14531 TTCCAGGTACCC
1 TTCCAGGTACCC
14543 GGGTCTTCGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.20
Consensus pattern (21 bp):
TTCCAGGTACCCTACCCGAAG
Found at i:14710 original size:18 final size:18
Alignment explanation
Indices: 14669--14714 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
14659 TTTTTTTAAC
* *
14669 TATTATTTTTTTAAAAAA
1 TATTATATTATTAAAAAA
14687 -ACTTATATTATTAAAAAA
1 TA-TTATATTATTAAAAAA
14705 TATTATATTA
1 TATTATATTA
14715 ATTATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTATATTATTAAAAAA
Found at i:14784 original size:24 final size:23
Alignment explanation
Indices: 14757--14822 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
14747 TTTATTAGTT
*
14757 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTA-TAA
* *
14781 TAATTAAATATGTAATATTATAA
1 TAATTAAATATATAAAATTATAA
* *
14804 TATATAAAATA-ATTAAATT
1 TA-ATTAAATATATAAAATT
14823 TGAACACAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 10 0.29
24 24 0.71
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATTAAATATATAAAATTATAA
Found at i:18290 original size:12 final size:12
Alignment explanation
Indices: 18267--18297 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
18257 TTAATTACGA
18267 AAATTGAAAATTT
1 AAATT-AAAATTT
18280 AAATTAAAATTT
1 AAATTAAAATTT
18292 AAATTA
1 AAATTA
18298 CCTGATTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:18425 original size:23 final size:23
Alignment explanation
Indices: 18392--18458 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
18382 TAAAAGTAAT
* *
18392 AAAAATAATAAACTAATACATAA
1 AAAAATAATAAAATAATAAATAA
*
18415 AAAAATGATAAAATAATAAATAA
1 AAAAATAATAAAATAATAAATAA
* *
18438 ATAAATAAAAAGAATAATAAA
1 AAAAATAATAA-AATAATAAA
18459 GAATAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 28 0.76
24 9 0.24
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (23 bp):
AAAAATAATAAAATAATAAATAA
Found at i:18427 original size:8 final size:8
Alignment explanation
Indices: 18382--18469 Score: 56
Period size: 8 Copynumber: 10.6 Consensus size: 8
18372 TGAAGTTAGG
18382 TAAAAGTAA
1 TAAAA-TAA
18391 TAAAAATAA
1 T-AAAATAA
*
18400 TAAACTAA
1 TAAAATAA
*
18408 T-ACATAA
1 TAAAATAA
* *
18415 AAAAATGA
1 TAAAATAA
18423 TAAAATAA
1 TAAAATAA
18431 T-AAATAA
1 TAAAATAA
18438 -ATAAATAA
1 TA-AAATAA
*
18446 AAAGAATAA
1 TAA-AATAA
18455 TAAAGAATAA
1 T-AA-AATAA
18465 TAAAA
1 TAAAA
18470 AGGGTAAAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
7 10 0.16
8 27 0.43
9 13 0.21
10 13 0.21
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (8 bp):
TAAAATAA
Found at i:18429 original size:31 final size:33
Alignment explanation
Indices: 18388--18468 Score: 105
Period size: 31 Copynumber: 2.5 Consensus size: 33
18378 TAGGTAAAAG
*
18388 TAATAAAAATAATAAACT-AATACATAAAAA-AA
1 TAATAAAAATAATAAA-TAAATAAATAAAAAGAA
*
18420 TGAT-AAAATAATAAATAAATAAATAAAAAGAA
1 TAATAAAAATAATAAATAAATAAATAAAAAGAA
18452 TAATAAAGAATAATAAA
1 TAATAAA-AATAATAAA
18469 AAGGGTAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 1 0.02
31 22 0.52
32 8 0.19
33 2 0.05
34 9 0.21
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (33 bp):
TAATAAAAATAATAAATAAATAAATAAAAAGAA
Found at i:20057 original size:3 final size:3
Alignment explanation
Indices: 20022--20101 Score: 85
Period size: 3 Copynumber: 26.7 Consensus size: 3
20012 ACCTGAAAAA
* *
20022 AAT AA- AAT AA- AAT AAGT AAT ATAT AA- AAA AAT AAT AGT AAT AAAT
1 AAT AAT AAT AAT AAT AA-T AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
*
20067 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20102 ATAAATAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
2 6 0.09
3 51 0.77
4 9 0.14
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:20261 original size:29 final size:30
Alignment explanation
Indices: 20166--20262 Score: 124
Period size: 30 Copynumber: 3.2 Consensus size: 30
20156 CTATATATCA
*
20166 TATATAATTTTTTAAAAATGATTTTAGAAAAC
1 TATATAA-TTTTAAAAAATGATTTTA-AAAAC
*
20198 TATATAATTTTAAAAAATGTTTTTAAAAAC
1 TATATAATTTTAAAAAATGATTTTAAAAAC
* * *
20228 CATATAATTTTCAAAAATG-TTTTAAAAAT
1 TATATAATTTTAAAAAATGATTTTAAAAAC
20257 TATATA
1 TATATA
20263 TTATATATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
29 14 0.24
30 22 0.37
31 16 0.27
32 7 0.12
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (30 bp):
TATATAATTTTAAAAAATGATTTTAAAAAC
Found at i:20293 original size:38 final size:36
Alignment explanation
Indices: 20229--20491 Score: 296
Period size: 38 Copynumber: 7.1 Consensus size: 36
20219 TTTAAAAACC
*
20229 ATATA-ATTTTCAAAAATGTTTTAAAAATTATATATT
1 ATATATATTTTC-AAAATGTTTTAAAAACTATATATT
*
20265 ATATATATTTTCAAAATGTTTTTCAAAAACTATATGTT
1 ATATATATTTTCAAAATG-TTTT-AAAAACTATATATT
* * *
20303 ATATTTATTTTCAAAACGTTTT-AAAACTATATAACAT
1 ATATATATTTTCAAAATGTTTTAAAAACTATAT-A-TT
* *
20340 ATAAATGTTTTCAAAATGTTTTAAAAACTATATATT
1 ATATATATTTTCAAAATGTTTTAAAAACTATATATT
*
20376 ATATATATATATTCAAAATGTTTTAAAAACTATATAAT
1 ATATATAT-T-TTCAAAATGTTTTAAAAACTATATATT
* * *
20414 ATATATGTTTTAAAAAATGTTTTAAAAACTATATATC
1 ATATATATTTT-CAAAATGTTTTAAAAACTATATATT
* * * * *
20451 ATATATATTTTTAAAATGTTTTCACAATTATATAAT
1 ATATATATTTTCAAAATGTTTTAAAAACTATATATT
20487 ATATA
1 ATATA
20492 AAAAAATAAA
Statistics
Matches: 193, Mismatches: 25, Indels: 18
0.82 0.11 0.08
Matches are distributed among these distances:
35 10 0.05
36 44 0.23
37 68 0.35
38 71 0.37
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
ATATATATTTTCAAAATGTTTTAAAAACTATATATT
Found at i:20351 original size:75 final size:73
Alignment explanation
Indices: 20234--20493 Score: 292
Period size: 75 Copynumber: 3.5 Consensus size: 73
20224 AAACCATATA
* * * *
20234 ATTTTCAAAAATGTTTTAAAAATTATAT-ATTATATATATTTTCAAAATGTTTTTCAAAAACTAT
1 ATTTTC-AAAATGTTTTAAAAACTATATAAATATAAATGTTTTCAAAATG-TTTT-AAAAACTAT
*
20298 ATGTTATATTT
63 ATATTATATTT
*
20309 ATTTTCAAAACGTTTT-AAAACTATATAACATATAAATGTTTTCAAAATGTTTTAAAAACTATAT
1 ATTTTCAAAATGTTTTAAAAACTATATAA-ATATAAATGTTTTCAAAATGTTTTAAAAACTATAT
20373 ATTATATATAT
65 ATTATAT-T-T
* * *
20384 ATATTCAAAATGTTTTAAAAACTATAT-AATATATATGTTTTAAAAAATGTTTTAAAAACTATAT
1 ATTTTCAAAATGTTTTAAAAACTATATAAATATAAATGTTTT-CAAAATGTTTTAAAAACTATAT
* *
20448 ATCATATAT
65 ATTATATTT
* * * *
20457 ATTTTTAAAATGTTTTCACAATTATATAATATATAAA
1 ATTTTCAAAATGTTTTAAAAACTATATAA-ATATAAA
20494 AAAATAAAGT
Statistics
Matches: 159, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
73 49 0.31
74 28 0.18
75 72 0.45
76 10 0.06
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (73 bp):
ATTTTCAAAATGTTTTAAAAACTATATAAATATAAATGTTTTCAAAATGTTTTAAAAACTATATA
TTATATTT
Found at i:20365 original size:111 final size:112
Alignment explanation
Indices: 20228--20491 Score: 335
Period size: 111 Copynumber: 2.4 Consensus size: 112
20218 TTTTAAAAAC
20228 CATAT-AA-TTTTCAAAAATGTTTTAAAAATTATATATTATATATAT-T-TTCAAAATGTTTTTC
1 CATATAAATTTTTC-AAAATGTTTTAAAAATTATATATTATATATATATATTCAAAATG-TTTT-
** * *
20289 AAAAACTATATGTTATATTTATTTT-CAAAACGTTTT-AAAACTATATAA
63 AAAAACTATATAATATATATATTTTAAAAAACGTTTTAAAAACTATATAA
*
20337 CATATAAATGTTTTCAAAATGTTTTAAAAACTATATATTATATATATATATTCAAAATGTTTTAA
1 CATATAAAT-TTTTCAAAATGTTTTAAAAATTATATATTATATATATATATTCAAAATGTTTTAA
* * *
20402 AAACTATATAATATATATGTTTTAAAAAATGTTTTAAAAACTATATAT
65 AAACTATATAATATATATATTTTAAAAAACGTTTTAAAAACTATATAA
* * * *
20450 CATATATATTTTT-AAAATGTTTTCACAATTATATAATATATA
1 CATATAAATTTTTCAAAATGTTTTAAAAATTATATATTATATA
20492 AAAAAATAAA
Statistics
Matches: 135, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
109 5 0.04
110 2 0.01
111 77 0.57
112 23 0.17
113 28 0.21
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (112 bp):
CATATAAATTTTTCAAAATGTTTTAAAAATTATATATTATATATATATATTCAAAATGTTTTAAA
AACTATATAATATATATATTTTAAAAAACGTTTTAAAAACTATATAA
Found at i:21264 original size:84 final size:83
Alignment explanation
Indices: 21083--22078 Score: 1048
Period size: 84 Copynumber: 12.0 Consensus size: 83
21073 GTTGTATATA
* * * * *
21083 ATGTGCTTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCT
1 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGACT
*
21148 TGAGTTATGCTGTAAATG
66 TAAGTTATGCTGTAAATG
* *
21166 ATGTG-CTGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGA
1 ATGTGCCT-TGGAGCTGAGCGTAGTCGAACTCAAAGG-TCTTTGTTGGCAGATAACCCTTCTAGA
* *
21230 CTTAAGTTGTGCTGCAAATG
64 CTTAAGTTATGCTGTAAATG
* * * * * *
21250 ATATGCCTTGGAGCTGAGCGTAGTCGGACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCT
1 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGACT
*
21315 TGAGTTATGCTGTAAATG
66 TAAGTTATGCTGTAAATG
* * * * * * *
21333 ATGTGCCCTCGAAGATGAGCGTAGTCGAACTCGAGGGTC--T-TTGGCAGATAGCCCTTCTCGAC
1 ATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGAC
* *
21395 TTAAGCTATGCTGCAAATG
65 TTAAGTTATGCTGTAAATG
* * * * *
21414 ATGTATCGTT-GAGCTGAGCGTAGTCAAACTCAAAGGTTCTTTGTTGACAGATAACCCTTCTAGC
1 ATGT-GCCTTGGAGCTGAGCGTAGTCGAACTCAAAGG-TCTTTGTTGGCAGATAACCCTTCTAGA
* *
21478 CTTGAGTTATGCTATAAATG
64 CTTAAGTTATGCTGTAAATG
* * * * * *
21498 ATGTGTCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTC--T-TTGGCAGATAGCCCTTCTCGAC
1 ATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGAC
**
21560 TTAAGTTATGCTACAAATG
65 TTAAGTTATGCTGTAAATG
*
21579 ATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGA
1 ATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGG-TCTTTGTTGGCAGATAACCCTTCTAGA
*
21643 CTTAAGTTGTGCTGTAAATG
64 CTTAAGTTATGCTGTAAATG
* * * * * *
21663 ATATGCCTTGGAGCTTAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCT
1 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGACT
* *
21728 TGAGTTATGTTGTAAATG
66 TAAGTTATGCTGTAAATG
* * * *
21746 ATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTC--T-TTGGCAGATAACCCTTCTAGAC
1 ATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGAC
* **
21808 TTAAGCTATGCTACAAATG
65 TTAAGTTATGCTGTAAATG
* * * *
21827 ATGTG-ATGTTGAGCTGAGCGTAGTCAAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGA
1 ATGTGCCT-TGGAGCTGAGCGTAGTCGAACTCAAAGG-TCTTTGTTGGCAGATAACCCTTCTAGA
* *
21891 CTTAAGTTGTGCTGCAAATG
64 CTTAAGTTATGCTGTAAATG
* * * * * * *
21911 ATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGAAAATAACCCTTCTCGAT
1 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT-GTTGGCAGATAACCCTTCTAGAC
* *
21976 TTAAGTTATACTATAAATG
65 TTAAGTTATGCTGTAAATG
* * * * *
21995 ATATGCCTTGAAGCTGAGCGTAGTCGAACT-AGAAGGTCTTTTGGTGACAGATAACCCTTCTAGC
1 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCA-AAGGTC-TTTGTTGGCAGATAACCCTTCTAGA
* *
22059 CTTGAGTTATACTGTAAATG
64 CTTAAGTTATGCTGTAAATG
22079 TTGTCTTAAA
Statistics
Matches: 751, Mismatches: 135, Indels: 53
0.80 0.14 0.06
Matches are distributed among these distances:
79 1 0.00
80 68 0.09
81 124 0.17
82 4 0.01
83 129 0.17
84 397 0.53
85 28 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (83 bp):
ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTAGACT
TAAGTTATGCTGTAAATG
Found at i:21772 original size:248 final size:248
Alignment explanation
Indices: 21093--22068 Score: 1155
Period size: 248 Copynumber: 3.9 Consensus size: 248
21083 ATGTGCTTTG
* * * * * *
21093 GAGCTGAGCGTAGTCGAACTCGAAGG-TCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
* * * * * *
21157 CTGTAAATGATGTG-CTGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAAC
66 CTGCAAATGATATGCCT-TGGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGGTGACAGATAAC
* ** * * *
21221 CCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGGACTCGAAGG
130 CCTTCTAGACTTAAGTTATGCTATAAATGATATGCCTCGAAGCTGAGCGTAGTCGAACTCGAAGG
* * ** * *
21286 TCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTC
195 TCTTT-G-G-CAGATAACCCTTCTAGACTTAAGTTATGCTACAAATGATGTGCCGTT
* * * * * * *
21343 GAAGATGAGCGTAGTCGAACTC-GAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 G-AGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTAT
* * *
21404 GCTGCAAATGATGTAT-CGTT-GAGCTGAGCGTAGTCAAACTCAAAGGTTCTTTGTTGACAGATA
65 GCTGCAAATGA--TATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGGTGACAGATA
* * *
21467 ACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGTCCTCGAAGCTGAGCGTAGTCGAACTCGA
128 ACCCTTCTAGACTTAAGTTATGCTATAAATGATATG-CCTCGAAGCTGAGCGTAGTCGAACTCGA
* * *
21532 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCGTT
192 AGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTACAAATGATGTGCCGTT
*
21589 GAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 GAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
* * *
21654 CTGTAAATGATATGCCTTGGAGCTTAGCGTAGTCGAACTCGAAGG-TCTTTGGTGACAGATAACC
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGGTGACAGATAACC
* * * * * *
21718 CTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGG
131 CTTCTAGACTTAAGTTATGCTATAAATGATATG-CCTCGAAGCTGAGCGTAGTCGAACTCGAAGG
* **
21783 TCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTACAAATGATGTGATGTT
195 TCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTACAAATGATGTGCCGTT
* *
21837 GAGCTGAGCGTAGTCAAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 GAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
* * *
21902 CTGCAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGG-TCTTTGGTTGGA-AAATAA
66 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGG-T-GACAGATAA
* * * * *
21965 CCCTTCTCGATTTAAGTTATACTATAAATGATATGCCTTGAAGCTGAGCGTAGTCGAACTAGAAG
129 CCCTTCTAGACTTAAGTTATGCTATAAATGATATGCCTCGAAGCTGAGCGTAGTCGAACTCGAAG
* *
22030 GTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
194 GTC-TTT-G-G-CAGATAACCCTTCTAGACTTAAGTTAT
22069 ACTGTAAATG
Statistics
Matches: 634, Mismatches: 74, Indels: 34
0.85 0.10 0.05
Matches are distributed among these distances:
245 19 0.03
246 45 0.07
247 4 0.01
248 381 0.60
249 129 0.20
250 10 0.02
251 22 0.03
252 24 0.04
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (248 bp):
GAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGGTGACAGATAACC
CTTCTAGACTTAAGTTATGCTATAAATGATATGCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGT
CTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTACAAATGATGTGCCGTT
Found at i:21778 original size:413 final size:412
Alignment explanation
Indices: 21094--22078 Score: 1483
Period size: 413 Copynumber: 2.4 Consensus size: 412
21084 TGTGCTTTGG
* * *
21094 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCT
* *
21159 GTAAATGATGTGCTGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCT
63 ATAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCT
* *
21224 TCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGGACTCGAAGGTCT
128 TCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
21289 TTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGATGAGCG
193 TTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGATGAGCG
* * *
21354 TAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT-
258 TAGTCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTACAAATGATGTG
* * *
21418 ATCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTTCTTTGTTGACAGATAACCCTTCTAGCCTTGA
323 AT-GTTGAGCTGAGCGTAGTCAAACTCAAAGGTTCTTTGTTGACAGACAACCCTTCTAGACTTAA
* *
21483 GTTATGCTATAAATGATGTGTCCTCGA
387 GTTATGCTACAAATGATATG-CCTCGA
* * *
21510 AGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTACA
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTATA
21575 AATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCT
66 AATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCT
*
21640 AGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTTAGCGTAGTCGAACTCGAAGGTCTTTG
131 AGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
* *
21705 GTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGCGTAG
196 GTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGATGAGCGTAG
21770 TCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTACAAATGATGTGATG
261 TCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTACAAATGATGTGATG
* *
21835 TTGAGCTGAGCGTAGTCAAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTG
326 TTGAGCTGAGCGTAGTCAAACTCAAAGGTTCTTTGTTGACAGACAACCCTTCTAGACTTAAGTTA
* * *
21900 TGCTGCAAATGATATGCCTTGG
391 TGCTACAAATGATATGCCTCGA
* * * * *
21922 AGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGAAAATAACCCTTCTCGATTTAAGTTATAC
1 AGCTGAGCGTAGTCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* * * *
21987 TATAAATGATATGCC-TTGAAGCTGAGCGTAGTCGAACT-AGAAGG-TCTTTTGGTGACAGATAA
62 TATAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCA-AAGGTTC-TTTGTTGGCAGACAA
* * * *
22049 CCCTTCTAGCCTTGAGTTATACTGTAAATG
124 CCCTTCTAGACTTAAGTTGTGCTGTAAATG
22079 TTGTCTTAAA
Statistics
Matches: 519, Mismatches: 42, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
412 29 0.06
413 348 0.67
414 4 0.01
415 7 0.01
416 131 0.25
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (412 bp):
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTATA
AATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTTCTTTGTTGGCAGACAACCCTTCT
AGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
GTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGATGAGCGTAG
TCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTACAAATGATGTGATG
TTGAGCTGAGCGTAGTCAAACTCAAAGGTTCTTTGTTGACAGACAACCCTTCTAGACTTAAGTTA
TGCTACAAATGATATGCCTCGA
Found at i:27097 original size:12 final size:13
Alignment explanation
Indices: 27073--27102 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
27063 TTAATTGCAA
27073 AAATTGAAAATTT
1 AAATTGAAAATTT
27086 AAATTG-AAATTT
1 AAATTGAAAATTT
27098 AAATT
1 AAATT
27103 ACCCGATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (13 bp):
AAATTGAAAATTT
Found at i:27244 original size:4 final size:4
Alignment explanation
Indices: 27231--27286 Score: 66
Period size: 4 Copynumber: 14.8 Consensus size: 4
27221 AAAAATGATA
*
27231 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAA AGAAT -AAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT
27277 AAAT -AAT AAA
1 AAAT AAAT AAA
27287 AAAGGTAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 12 0.27
4 31 0.69
5 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:27957 original size:22 final size:22
Alignment explanation
Indices: 27931--27972 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
27921 TCCTGAGGCT
*
27931 CTTTGTT-TGTTGTTTTGCTTGG
1 CTTTGTTGTGTT-TATTGCTTGG
27953 CTTTGTTGTGTTTATTGCTT
1 CTTTGTTGTGTTTATTGCTT
27973 TGAGGTTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.02, C:0.10, G:0.24, T:0.64
Consensus pattern (22 bp):
CTTTGTTGTGTTTATTGCTTGG
Found at i:28535 original size:21 final size:20
Alignment explanation
Indices: 28509--28599 Score: 68
Period size: 21 Copynumber: 4.5 Consensus size: 20
28499 CATGAAAAAA
28509 ATAAAATAAAATAATTAATAT
1 ATAAAATAAAATAA-TAATAT
28530 AT--AA-AAAATAATAATAGT
1 ATAAAATAAAATAATAATA-T
*
28548 ATAGTAAT-AAATAATAATA-
1 ATA-AAATAAAATAATAATAT
28567 ATAATAATAACAATAATAA-AT
1 ATAA-AATAA-AATAATAATAT
*
28588 AAATAAATAAAA
1 ATA-AAATAAAA
28600 ACTATATAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
17 5 0.09
18 10 0.17
19 8 0.14
20 4 0.07
21 30 0.52
22 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAAAATAAAATAATAATAT
Found at i:28539 original size:18 final size:17
Alignment explanation
Indices: 28516--28608 Score: 71
Period size: 18 Copynumber: 5.0 Consensus size: 17
28506 AAAATAAAAT
28516 AAAATAATTAATATATAA
1 AAAATAA-TAATATATAA
28534 AAAATAATAATAGTATAGTA
1 AAAATAATAATA-TATA--A
28554 ATAAATAATAATA-ATAA
1 A-AAATAATAATATATAA
* *
28571 TAATAACAATAATAAATAA
1 -AA-AATAATAATATATAA
*
28590 ATAAATAAAAACTATATAA
1 A-AAATAATAA-TATATAA
28609 TATACATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
17 7 0.11
18 28 0.45
19 14 0.23
20 2 0.03
21 11 0.18
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAATAATAATATATAA
Found at i:28544 original size:3 final size:3
Alignment explanation
Indices: 28508--28585 Score: 67
Period size: 3 Copynumber: 26.7 Consensus size: 3
28498 ACATGAAAAA
*
28508 AAT AA- AAT AA- AAT AATT AAT ATAT AA- AA- AAT AAT AAT AGT -AT
1 AAT AAT AAT AAT AAT AA-T AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* *
28550 AGT AAT AAAT AAT AAT AAT AAT AAT AAC AAT AAT AA
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28586 ATAAATAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
2 9 0.15
3 44 0.71
4 9 0.15
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:28696 original size:31 final size:29
Alignment explanation
Indices: 28648--28744 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 29
28638 CTATATATCA
*
28648 TATATAAATTTTTAAAAATGATTTTAGAAAAC
1 TATAT-AATTTTAAAAAATG-TTTTA-AAAAC
28680 TATATAATTTTAAAAAATGTTTTTAAAAAC
1 TATATAATTTTAAAAAATG-TTTTAAAAAC
* *
28710 TATATAATTTTCAAAAATGTTTTAAAAAT
1 TATATAATTTTAAAAAATGTTTTAAAAAC
28739 TATATA
1 TATATA
28745 TTATATATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
29 15 0.25
30 23 0.38
31 18 0.30
32 5 0.08
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (29 bp):
TATATAATTTTAAAAAATGTTTTAAAAAC
Found at i:28775 original size:38 final size:36
Alignment explanation
Indices: 28710--28976 Score: 268
Period size: 38 Copynumber: 7.2 Consensus size: 36
28700 TTTTAAAAAC
*
28710 TATATA-ATTTTCAAAAATGTTTTAAAAATTATATAT
1 TATATATATTTTC-AAAATGTTTTAAAAACTATATAT
*
28746 TATATATATTTTCAAAATGTTTTTCAAAAACTATATCT
1 TATATATATTTTCAAAATG-TTTT-AAAAACTATATAT
* * *
28784 TATATTTATTTTCAAAAACGTTTT-AAAACTATATAACA
1 TATATATATTTTC-AAAATGTTTTAAAAACTATAT-A-T
* *
28822 TATAAATGTTTTCAAAATGTTTTAAAAACTATATATT
1 TATATATATTTTCAAAATGTTTTAAAAACTATATA-T
* *
28859 ATATATATATATATTCAAAACGTTTTAAAAACTATATAA
1 -TATATATAT-T-TTCAAAATGTTTTAAAAACTATATAT
* *
28898 TATATATGTTTTAAAAAATGTTTTAAAAACTATATAT
1 TATATATATTTT-CAAAATGTTTTAAAAACTATATAT
* * * * * *
28935 CATATATATTTTTAAAATGTTTTCACAATTATATAA
1 TATATATATTTTCAAAATGTTTTAAAAACTATATAT
28971 TATATA
1 TATATA
28977 AAAAAATAAA
Statistics
Matches: 192, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
36 48 0.25
37 52 0.27
38 62 0.32
39 6 0.03
40 24 0.12
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
TATATATATTTTCAAAATGTTTTAAAAACTATATAT
Found at i:28901 original size:76 final size:76
Alignment explanation
Indices: 28710--28976 Score: 295
Period size: 77 Copynumber: 3.6 Consensus size: 76
28700 TTTTAAAAAC
* * * *
28710 TATATA-AT-TTTCAAAAATGTTTTAAAAATTATATATTATATATATTTTCAAAATGTTTTTCAA
1 TATATATATATTTCAAAAACGTTTTAAAAACTATATAATATATATGTTTTCAAAATG-TTTT-AA
*
28773 AAACTATATCTTA
64 AAACTATATATTA
*
28786 TAT-T-TAT-TTTCAAAAACGTTTT-AAAACTATATAACATATAAATGTTTTCAAAATGTTTTAA
1 TATATATATATTTCAAAAACGTTTTAAAAACTATAT-A-ATATATATGTTTTCAAAATGTTTTAA
28847 AAACTATATATTA
64 AAACTATATATTA
*
28860 TATATATATATATTC-AAAACGTTTTAAAAACTATATAATATATATGTTTTAAAAAATGTTTTAA
1 TATATATATAT-TTCAAAAACGTTTTAAAAACTATATAATATATATGTTTT-CAAAATGTTTTAA
*
28924 AAACTATATATCA
64 AAACTATATATTA
* * * *
28937 TATATAT-T-TTT--AAAATGTTTTCACAATTATATAATATATA
1 TATATATATATTTCAAAAACGTTTTAAAAACTATATAATATATA
28977 AAAAAATAAA
Statistics
Matches: 169, Mismatches: 13, Indels: 21
0.83 0.06 0.10
Matches are distributed among these distances:
73 25 0.15
74 28 0.17
75 24 0.14
76 36 0.21
77 43 0.25
78 13 0.08
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (76 bp):
TATATATATATTTCAAAAACGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAA
ACTATATATTA
Found at i:28993 original size:6 final size:6
Alignment explanation
Indices: 28978--29014 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
28968 TAATATATAA
28978 AAAAAT -AAAAT AAAAAT AAAAAT -AAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
29015 TATGGACGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:28994 original size:11 final size:11
Alignment explanation
Indices: 28979--29014 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
28969 AATATATAAA
28979 AAAAT-AAAAT
1 AAAATAAAAAT
28989 AAAAATAAAAAT
1 -AAAATAAAAAT
29001 AAAATAAAAAT
1 AAAATAAAAAT
29012 AAA
1 AAA
29015 TATGGACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:28998 original size:17 final size:17
Alignment explanation
Indices: 28978--29014 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
28968 TAATATATAA
28978 AAAAATAAAATAAAAAT
1 AAAAATAAAATAAAAAT
28995 AAAAATAAAATAAAAAT
1 AAAAATAAAATAAAAAT
29012 AAA
1 AAA
29015 TATGGACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:29800 original size:21 final size:20
Alignment explanation
Indices: 29763--29801 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29753 TATGATTTAG
**
29763 AAAAATAAAACTAAATAACA
1 AAAAATAAAAAAAAATAACA
29783 AAAAATAAAAAAAGAATAA
1 AAAAATAAAAAAA-AATAA
29802 GTAAGTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.13
Consensus pattern (20 bp):
AAAAATAAAAAAAAATAACA
Found at i:30140 original size:36 final size:36
Alignment explanation
Indices: 30089--30171 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 36
30079 GGTAACCAAC
30089 TTTGAAAAAATAG-TTTTCAAAGTTTGGTAAATATTT
1 TTTG-AAAAATAGTTTTTCAAAGTTTGGTAAATATTT
* *
30125 ATTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 -TTTGAAAAATAGTTTTTCAAAGTTTGGTAAATATTT
*
30162 GTTGAAAAAT
1 TTTGAAAAAT
30172 GATAATGGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 17 0.40
37 25 0.60
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.43
Consensus pattern (36 bp):
TTTGAAAAATAGTTTTTCAAAGTTTGGTAAATATTT
Found at i:34687 original size:35 final size:34
Alignment explanation
Indices: 34629--34737 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 34
34619 TGAAATTATT
34629 AAAATGGTTTTC-AAGTTTGGTAAATGTTTATTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTT-TTTG
34663 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTT-TTTG
* * *
34698 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTTGTTG
1 -AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTTTTG
34734 AAAA
1 AAAA
34738 ATGATAATGG
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
34 12 0.18
35 25 0.37
36 8 0.12
37 23 0.34
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.44
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTTTTG
Found at i:34720 original size:37 final size:35
Alignment explanation
Indices: 34629--34740 Score: 156
Period size: 37 Copynumber: 3.2 Consensus size: 35
34619 TGAAATTATT
34629 AAAATGGTTTTC-AAGTTTGGTAAATGTTTATTTG-
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTT-TTTGA
34663 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTT-TTTGA
* * *
34699 AAAATAGTTTTTCAAAGTTTGGTAGATGTTTGTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTTTTGA
34735 AAAATG
1 AAAATG
34741 ATAATGGGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
34 12 0.17
35 22 0.31
36 14 0.20
37 23 0.32
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.44
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTTTTGA
Found at i:35178 original size:10 final size:10
Alignment explanation
Indices: 35165--35189 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35155 GCTTTTCCCT
35165 GCTTGCGTAA
1 GCTTGCGTAA
35175 GCTTGCGTAA
1 GCTTGCGTAA
35185 GCTTG
1 GCTTG
35190 GGGGCATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (10 bp):
GCTTGCGTAA
Found at i:38172 original size:3 final size:3
Alignment explanation
Indices: 38164--38249 Score: 118
Period size: 3 Copynumber: 27.0 Consensus size: 3
38154 CGGGTCTTTT
38164 TTA TTA TTA TTTA TATA TATA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA T-TA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
38213 TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
38250 CATTTTACAT
Statistics
Matches: 77, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
3 62 0.81
4 14 0.18
5 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:41963 original size:27 final size:30
Alignment explanation
Indices: 41933--41995 Score: 69
Period size: 31 Copynumber: 2.1 Consensus size: 30
41923 GTATCAATTA
41933 TTTTAC-ATG-TACTAACTTATTT-TTCTC
1 TTTTACTATGATACTAACTTATTTCTTCTC
* *
41960 TTTTGCTTGTGTATACTAACTTATTTCTTCTC
1 TTTTAC-TATG-ATACTAACTTATTTCTTCTC
41992 TTTT
1 TTTT
41996 GTTTGTGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 5 0.17
29 2 0.07
31 13 0.45
32 9 0.31
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.59
Consensus pattern (30 bp):
TTTTACTATGATACTAACTTATTTCTTCTC
Found at i:41978 original size:31 final size:32
Alignment explanation
Indices: 41942--42003 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
41932 ATTTTACATG
41942 TACTAACTTATTT-TTCTCTTTTGCTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGCTTGTGTA
*
41973 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGCTTGTGT
42004 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.15, C:0.16, G:0.10, T:0.60
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGCTTGTGTA
Found at i:45162 original size:11 final size:11
Alignment explanation
Indices: 45134--45171 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
45124 AAGAGCAAAG
45134 AGAAAAATCAA
1 AGAAAAATCAA
45145 AGCAAAAATCAA
1 AG-AAAAATCAA
*
45157 AGAAAAAGCAA
1 AGAAAAATCAA
45168 AGAA
1 AGAA
45172 CAAAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:46366 original size:14 final size:14
Alignment explanation
Indices: 46347--46374 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46337 CAGATTGAGA
46347 ACACATACATACAT
1 ACACATACATACAT
46361 ACACATACATACAT
1 ACACATACATACAT
46375 GATACATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
ACACATACATACAT
Found at i:46967 original size:36 final size:36
Alignment explanation
Indices: 46917--47034 Score: 141
Period size: 36 Copynumber: 3.3 Consensus size: 36
46907 TGAGAATTTT
* * *
46917 AAAACAATTTTTTGTCTCGCTTGAGACAATTTCTTTC
1 AAAACAA-ATTTTGTCTCGATTGAGACAATTTCTTTA
* *
46954 AAAGCAAATTTTGTCTCGATTGAGACAGCTTTC--TA
1 AAAACAAATTTTGTCTCGATTGAGACA-ATTTCTTTA
* *
46989 AAAACAAATTTTGTCTCGTTTGAGACAATTTCTTGA
1 AAAACAAATTTTGTCTCGATTGAGACAATTTCTTTA
47025 AAAACAAATT
1 AAAACAAATT
47035 CCGCCTCACT
Statistics
Matches: 69, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
34 4 0.06
35 26 0.38
36 29 0.42
37 10 0.14
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGATTGAGACAATTTCTTTA
Found at i:47050 original size:71 final size:72
Alignment explanation
Indices: 46917--47051 Score: 166
Period size: 71 Copynumber: 1.9 Consensus size: 72
46907 TGAGAATTTT
* ** * ** * *
46917 AAAACAATTTTTTGTCTCGCTTGAGACAATTTCTTTCAAAGCAAATTTTGTCTCGATTGAGACAG
1 AAAACAATATTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACAG
46982 CTTTCTA
66 CTTTCTA
*
46989 AAAACAA-ATTTTGTCTCGTTTGAGACAATTTCTTGAAAAACAAATTCCGCCTC-ACTGGAGACA
1 AAAACAATATTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGA-TGGAGACA
47052 TTTTTCGTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
70 1 0.02
71 45 0.85
72 7 0.13
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (72 bp):
AAAACAATATTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACAG
CTTTCTA
Found at i:47218 original size:36 final size:36
Alignment explanation
Indices: 47137--47218 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 36
47127 ATTTTGTTTT
* * *
47137 GCTTGAGACAATTTCTTTAAAAACAAAGTTTGTATC
1 GCTTGAGACAAATTCTTTAAAAACAAACTTCGTATC
* * * *
47173 ACCTAAGACAAATTCTCTT-AAAACAAACTTCGTCTC
1 GCTTGAGACAAATTCT-TTAAAAACAAACTTCGTATC
47209 GCTTGAGACA
1 GCTTGAGACA
47219 TTTTTCCTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (36 bp):
GCTTGAGACAAATTCTTTAAAAACAAACTTCGTATC
Found at i:47318 original size:105 final size:102
Alignment explanation
Indices: 47192--47430 Score: 279
Period size: 105 Copynumber: 2.3 Consensus size: 102
47182 AAATTCTCTT
* * *
47192 AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* *
47256 TAAAAACAAAATTAATCTCACCTT-ATATTGTTGTTTCTTTC-
66 T-AAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * *
47297 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* * *
47362 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
*
47399 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
47431 TCTAAAAACA
Statistics
Matches: 117, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 26 0.22
103 7 0.06
104 4 0.03
105 77 0.66
106 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:47421 original size:36 final size:36
Alignment explanation
Indices: 47376--47495 Score: 106
Period size: 36 Copynumber: 3.4 Consensus size: 36
47366 ACAAAGTTGA
**
47376 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
47412 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * *
47448 TCTCA-TTCGAGACTATATCT-T-AAAGCAAA-TTTCG
1 TCTCACTT-GAGACAATTTCTCTAAAAACAAACTTT-G
*
47482 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
47496 TCATTTTCTC
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
33 3 0.04
34 17 0.24
35 12 0.17
36 38 0.54
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:47785 original size:29 final size:29
Alignment explanation
Indices: 47735--47808 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
47725 AAGACAATTT
* *
47735 CTTTTGGA-AAAAATCTTTGAGTTTGTTC
1 CTTTTGAATAAAAATCTTGGAGTTTGTTC
47763 CTTTTGAATAAAAATCTTGGAGTTTGTTC
1 CTTTTGAATAAAAATCTTGGAGTTTGTTC
*
47792 CTTTGGAATAAAAATCT
1 CTTTTGAATAAAAATCT
47809 GTGAGTTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 7 0.17
29 35 0.83
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (29 bp):
CTTTTGAATAAAAATCTTGGAGTTTGTTC
Found at i:47908 original size:30 final size:30
Alignment explanation
Indices: 47872--48136 Score: 163
Period size: 30 Copynumber: 8.1 Consensus size: 30
47862 AATTTTGTGA
47872 AAAAATCTTTGAGATTGTTTCCTTT-GAAAC
1 AAAAATCTTTGAGATTGTTT-CTTTGGAAAC
*
47902 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * ** *
47932 AAAATTTTGTCTCTTTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATC-TTTGAGATTGTTTCTTTGGAAAC
*
47969 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * ** *
47999 AAAATTTTGTCTCTTTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATC-TTTGAGATTGTTTCTTTGGAAAC
*
48036 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * * *
48066 AAAATTTTGTCTCTCTAAAGATAGTTTCTTTTGAAAC
1 AAAA----ATCT-T-T-GAGATTGTTTCTTTGGAAAC
*
48103 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
48133 AAAA
1 AAAA
48137 TTTTGTCTCT
Statistics
Matches: 178, Mismatches: 35, Indels: 44
0.69 0.14 0.17
Matches are distributed among these distances:
29 4 0.02
30 92 0.52
31 5 0.03
32 1 0.01
33 3 0.02
34 3 0.02
35 1 0.01
36 5 0.03
37 64 0.36
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:47968 original size:67 final size:67
Alignment explanation
Indices: 47889--48247 Score: 630
Period size: 67 Copynumber: 5.4 Consensus size: 67
47879 TTTGAGATTG
* *
47889 TTTCCTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
47954 AA
66 AA
*
47956 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
48021 AA
66 AA
*
48023 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTAAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
*
48088 AG
66 AA
48090 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
48155 AA
66 AA
* * * *
48157 ATTCTTTTGAAACGAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAAAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
48222 AA
66 AA
48224 TTTCTTTTGAAA-AAAAATCTTTGA
1 TTTCTTTTGAAACAAAAATCTTTGA
48248 ACATGTTTCT
Statistics
Matches: 280, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
66 11 0.04
67 269 0.96
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:48595 original size:59 final size:63
Alignment explanation
Indices: 48478--48598 Score: 160
Period size: 59 Copynumber: 2.0 Consensus size: 63
48468 GATGTGATTC
* * *
48478 ATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTATTAAAGACAATTTCTTTTGAAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTACTAAAGACAACTTCTTTTGAAAAA
* **
48541 ATCTTTGAGT-TG-TTCCTTTGAAACAAAA-TTTGTCT-CTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTACTAAAGACAACTTCTTTTGAAAA
48599 TACCAACCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 19 0.37
60 6 0.12
61 15 0.29
62 2 0.04
63 10 0.19
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (63 bp):
ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTACTAAAGACAACTTCTTTTGAAAAA
Found at i:48778 original size:15 final size:15
Alignment explanation
Indices: 48755--48798 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
48745 TTTTGAGTCG
*
48755 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
48770 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
48785 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
48799 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:49345 original size:28 final size:28
Alignment explanation
Indices: 49295--49348 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
49285 TCAAAATCCA
* *
49295 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
49323 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
49349 CATTATCCCT
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:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:49512 original size:43 final size:43
Alignment explanation
Indices: 49361--49525 Score: 133
Period size: 40 Copynumber: 3.8 Consensus size: 43
49351 TTATCCCTAG
* *
49361 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATAACCAGACC-TCCTCATCACGTAGGAACCGTGTCA--ACC-AT
** * * * * * **
49407 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
1 AGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACCAT
* *
49450 AG---ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
1 AGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACCAT
49490 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGT
1 AGATAACCAGACC-TCCTCATCACGTAGGAACCGTGT
49526 TATCACCTTA
Statistics
Matches: 95, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
40 33 0.35
42 1 0.01
43 29 0.31
44 2 0.02
46 29 0.31
47 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (43 bp):
AGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACCAT
Found at i:49593 original size:129 final size:129
Alignment explanation
Indices: 49361--49613 Score: 420
Period size: 129 Copynumber: 2.0 Consensus size: 129
49351 TTATCCCTAG
*
49361 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAGAACTCTTCA
* * * *
49426 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCATGTCAACCCCAGACCAGATCTCCTCATCACGTAGGAACCATGTCAACCAT
49490 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTC
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCC-AGAACTCTTC
*
49555 ATCACGTATGAG-CATGTCAACCCTC-GACCAGATTTCCTCATCACGTAGGAACCATGTCA
65 ATCACGTATGAGCCATGTCAACCC-CAGACCAGATCTCCTCATCACGTAGGAACCATGTCA
49614 CCCTTAGACG
Statistics
Matches: 116, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
129 93 0.80
130 23 0.20
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAGAACTCTTCA
TCACGTATGAGCCATGTCAACCCCAGACCAGATCTCCTCATCACGTAGGAACCATGTCAACCAT
Found at i:49640 original size:43 final size:43
Alignment explanation
Indices: 49374--49640 Score: 158
Period size: 43 Copynumber: 6.2 Consensus size: 43
49364 TAACCAGCCG
* *
49374 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 TCCTCATCACGTAGGAACCGTG---TCACCCTTAGATGACCAGAAC
* * * * *
49420 TCTTCATCACGTATGAGCCGTGTCATCCC---CA-GACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCA-CCCTTAGATGACCAGAAC
* * * * *
49460 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCACCCTTAGATGACCAGAAC
* *
49502 GTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCA-C-CCTT-AGATGACC-AGAAC
* * * * * **
49550 TCTTCATCACGTATG-AGCATGTCAACCC-T---CGACCAGATT
1 TCCTCATCACGTAGGAACCGTGTC-ACCCTTAGATGACCAGAAC
* *
49589 TCCTCATCACGTAGGAACCATGTCACCCTTAGACGACCAGAAC
1 TCCTCATCACGTAGGAACCGTGTCACCCTTAGATGACCAGAAC
*
49632 TCTTCATCA
1 TCCTCATCA
49641 TGTATGAGCA
Statistics
Matches: 169, Mismatches: 35, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
39 22 0.13
40 41 0.24
41 1 0.01
42 2 0.01
43 47 0.28
44 3 0.02
45 5 0.03
46 31 0.18
47 16 0.09
48 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (43 bp):
TCCTCATCACGTAGGAACCGTGTCACCCTTAGATGACCAGAAC
Found at i:49814 original size:3 final size:3
Alignment explanation
Indices: 49806--49874 Score: 86
Period size: 3 Copynumber: 22.0 Consensus size: 3
49796 CCGGGTCTTT
49806 TTA TTA TTA TTTA TATA TTTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA T-TA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
49855 TTA TTA -TA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA
49875 CATTTTACAT
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.03
3 46 0.77
4 11 0.18
5 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:53725 original size:30 final size:30
Alignment explanation
Indices: 53689--53756 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
53679 AAATTCCGGC
53689 TGTTCCTGTAAACCATCCATTATGTTTCGG
1 TGTTCCTGTAAACCATCCATTATGTTTCGG
*
53719 TGTTCCTGTGAACCATCCATTATGTTTCGG
1 TGTTCCTGTAAACCATCCATTATGTTTCGG
53749 TGTTCCTG
1 TGTTCCTG
53757 CTTTCCCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (30 bp):
TGTTCCTGTAAACCATCCATTATGTTTCGG
Found at i:53850 original size:72 final size:72
Alignment explanation
Indices: 53764--53907 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
53754 CTGCTTTCCC
53764 TTTTTCCATTAGTAATTGTAGTTTTTCAGTAGAAAACATTTATTATAATTATTATATTTTATATA
1 TTTTTCCATTAGTAATTGTAGTTTTTCAGTAGAAAACATTTATTATAATTATTATATTTTATATA
53829 TTAATCA
66 TTAATCA
53836 TTTTTCCATTAGTAATTGTAGTTTTTCAGTAGAAAACATTTATTATAATTATTATATTTTATATA
1 TTTTTCCATTAGTAATTGTAGTTTTTCAGTAGAAAACATTTATTATAATTATTATATTTTATATA
53901 TTAATCA
66 TTAATCA
53908 ATTATGTTAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (72 bp):
TTTTTCCATTAGTAATTGTAGTTTTTCAGTAGAAAACATTTATTATAATTATTATATTTTATATA
TTAATCA
Found at i:54966 original size:41 final size:41
Alignment explanation
Indices: 54921--54999 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
54911 TATAAGGTAA
* *
54921 CGACATACATAATAATCCCCCAATAAAATAAGCACCAATAG
1 CGACATACATAATAATCACCCAATAAAATAAACACCAATAG
* *
54962 CGACATGCATAATGATCACCCAATAAAATAAACACCAA
1 CGACATACATAATAATCACCCAATAAAATAAACACCAA
55000 GATTTTACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.49, C:0.27, G:0.08, T:0.16
Consensus pattern (41 bp):
CGACATACATAATAATCACCCAATAAAATAAACACCAATAG
Found at i:55762 original size:20 final size:20
Alignment explanation
Indices: 55737--55775 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
55727 ATATTTTAAG
55737 TCAAAACCCCTTAATAAAGT
1 TCAAAACCCCTTAATAAAGT
55757 TCAAAACCCCTTAATAAAG
1 TCAAAACCCCTTAATAAAG
55776 GTAAAAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.26, G:0.05, T:0.23
Consensus pattern (20 bp):
TCAAAACCCCTTAATAAAGT
Found at i:55782 original size:20 final size:20
Alignment explanation
Indices: 55739--55782 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
55729 ATTTTAAGTC
* *
55739 AAAACCCCTTAATAAAGTTC
1 AAAACCCCTTAATAAAGGTA
55759 AAAACCCCTTAATAAAGGTA
1 AAAACCCCTTAATAAAGGTA
55779 AAAA
1 AAAA
55783 TCACGGGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.20, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAACCCCTTAATAAAGGTA
Found at i:57669 original size:22 final size:21
Alignment explanation
Indices: 57644--57711 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
57634 AAAGGCAATG
57644 AAATAAGATAAATAAATAAATA
1 AAATAAGA-AAATAAATAAATA
* * *
57666 AAATAGGAAAAATGAATCAAT-
1 AAATAAG-AAAATAAATAAATA
*
57687 AAATAAAGAAAATAAAAAAAATA
1 AAAT-AAGAAAAT-AAATAAATA
57710 AA
1 AA
57712 CAAAATGAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
21 9 0.26
22 23 0.66
23 3 0.09
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (21 bp):
AAATAAGAAAATAAATAAATA
Found at i:64847 original size:3 final size:3
Alignment explanation
Indices: 64839--64878 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
64829 GCTGTTAACC
64839 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
64879 TGTTGTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:66044 original size:19 final size:20
Alignment explanation
Indices: 66001--66045 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
65991 ATATTTTTAA
66001 TAAAAATACATAAATAAATT
1 TAAAAATACATAAATAAATT
* *
66021 T-AAAATATATAAA-AATTT
1 TAAAAATACATAAATAAATT
66039 TAAAAAT
1 TAAAAAT
66046 TCAGATGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 16 0.73
20 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAAATACATAAATAAATT
Found at i:67885 original size:166 final size:167
Alignment explanation
Indices: 67601--67944 Score: 440
Period size: 166 Copynumber: 2.1 Consensus size: 167
67591 CCCACCGGTT
* **
67601 GGGTTTTGAGCGGACGACGACGAGGAAGCTAAATATGGCGGCGGTGAGGCGAACGGAGGTCTGAG
1 GGGTTTTGAGAGGACGACGACGAGGAAGCTAAATAT-G-GGCGGTGAGGCGAACGGAGGTCCAAG
* * * *
67666 GCGGTCGAAATCGTCCAAAATTCGAGGCGTTGGGGTGGGTTTTCGGTGAAACTTTAAGGACTAGA
64 ACGGTCGAAATCGTCCAAAATTCGAGGAGTTGGGGTGGGTTTTCGGCGAAACTTCAAGGACTAGA
* * * *
67731 TTCCGGCTAACAACAACGGCTATCCACTAATTATTTTGG
129 TTCCGGCGAACAACAACGACTATCAACGAATTATTTTGG
* * * *
67770 GGGTTTTGAGATGACGGCGATGAGGAAGCTAACTAT-GGCGGTGAGGCGAACGGAGGTCCAAGAC
1 GGGTTTTGAGAGGACGACGACGAGGAAGCTAAATATGGGCGGTGAGGCGAACGGAGGTCCAAGAC
* * *
67834 GGTCGGAATCGTCCAAAA-TCTGAGGAGTTGGGGTGGGTTTTCGGCGAAACTTCAAGGGCTCGAT
66 GGTCGAAATCGTCCAAAATTC-GAGGAGTTGGGGTGGGTTTTCGGCGAAACTTCAAGGACTAGAT
*****
67898 TCCGGCGAACGGTGTCGACTATCAACGAATTATTTTGG
130 TCCGGCGAACAACAACGACTATCAACGAATTATTTTGG
67936 GGGTTTTGA
1 GGGTTTTGA
67945 TCATGGCGGC
Statistics
Matches: 151, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
165 2 0.01
166 118 0.78
169 31 0.21
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (167 bp):
GGGTTTTGAGAGGACGACGACGAGGAAGCTAAATATGGGCGGTGAGGCGAACGGAGGTCCAAGAC
GGTCGAAATCGTCCAAAATTCGAGGAGTTGGGGTGGGTTTTCGGCGAAACTTCAAGGACTAGATT
CCGGCGAACAACAACGACTATCAACGAATTATTTTGG
Found at i:70192 original size:3 final size:3
Alignment explanation
Indices: 70184--70230 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
70174 TTTTATTGTG
*
70184 ATA ATA ATA ATA ATA ATA ATA ATA ACA A-A TATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
70228 ATA
1 ATA
70231 TTATTATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
2 3 0.08
3 36 0.90
4 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:76226 original size:21 final size:21
Alignment explanation
Indices: 76201--76490 Score: 199
Period size: 21 Copynumber: 14.2 Consensus size: 21
76191 GATTTACATA
* *
76201 TTCGCATTGCGGTAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
76222 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
76243 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
76264 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
76283 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
76304 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
76323 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
76344 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
76363 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
76386 TT--CGTTGCGATAGTCGAAT
1 TTCGCGTTGCGATAGTCCAAG
** * *
76405 TTCGCGTTGCGATTTTTCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
76426 TT--CGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
** * *
76445 TTCATGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
76468 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
76487 TTCG
1 TTCG
76491 ATTTATTCCA
Statistics
Matches: 202, Mismatches: 51, Indels: 32
0.71 0.18 0.11
Matches are distributed among these distances:
19 75 0.37
21 111 0.55
23 16 0.08
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:76280 original size:40 final size:40
Alignment explanation
Indices: 76226--76559 Score: 480
Period size: 40 Copynumber: 8.3 Consensus size: 40
76216 TCCAAGTTCG
76226 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
76266 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
76306 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
76346 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
* *
76388 CGTTGCGATAGTCGAATTTCGCGTTGCGATTTTTCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
* **
76428 CGTTGCGATAGTCAAAGTTCATGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
* *
76470 CGTTGCGATAGTCGAAGTTCG-ATT----TATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
* * * *
76505 CGTTGCGATAGTCCAAGTTTGTGTTGCGCTTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCG-ATT-TTCCAAATT
76547 CGTTGCGATAGTC
1 CGTTGCGATAGTC
76560 CAAAATCGAA
Statistics
Matches: 268, Mismatches: 15, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
35 28 0.10
36 3 0.01
40 142 0.53
41 9 0.03
42 86 0.32
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:76434 original size:82 final size:82
Alignment explanation
Indices: 76226--76559 Score: 520
Period size: 82 Copynumber: 4.2 Consensus size: 82
76216 TCCAAGTTCG
76226 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
76291 GCGA-TT-TTCCAAATT
66 GCGATTTATTCCAAATT
76306 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
76371 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
* * * **
76388 CGTTGCGATAGTCGAATTTCGCGTTGCGATTTTTCAAATTCGTTGCGATAGTCAAAGTTCATGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
76453 GCGATTTATTCCAAATT
66 GCGATTTATTCCAAATT
* * * * *
76470 CGTTGCGATAGTCGAAGTTCG-ATT----TATTCCAAATTCGTTGCGATAGTCCAAGTTTGTGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
*
76530 GCGCTTTATTCCAAATT
66 GCGATTTATTCCAAATT
76547 CGTTGCGATAGTC
1 CGTTGCGATAGTC
76560 CAAAATCGAA
Statistics
Matches: 239, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
77 60 0.25
80 69 0.29
81 4 0.02
82 106 0.44
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (82 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATT
Found at i:76538 original size:77 final size:75
Alignment explanation
Indices: 76414--76559 Score: 238
Period size: 77 Copynumber: 1.9 Consensus size: 75
76404 TTTCGCGTTG
76414 CGATTTTTCAAATTCGTTGCGATAGTCAAAGTTCATGTTGCGATTTATTCCAAATTCGTTGCGAT
1 CGATTTTTCAAATTCGTTGCGATAGTCAAAGTTCATGTTGCGATTTATTCCAAATTCGTTGCGAT
76479 AGTCGAAGTT
66 AGTCGAAGTT
* ** *
76489 CGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTTGTGTTGCGCTTTATTCCAAATTCGTTGCG
1 CGATTT-TT-CAAATTCGTTGCGATAGTCAAAGTTCATGTTGCGATTTATTCCAAATTCGTTGCG
76554 ATAGTC
64 ATAGTC
76560 CAAAATCGAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
75 6 0.09
76 2 0.03
77 57 0.88
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (75 bp):
CGATTTTTCAAATTCGTTGCGATAGTCAAAGTTCATGTTGCGATTTATTCCAAATTCGTTGCGAT
AGTCGAAGTT
Found at i:76551 original size:21 final size:20
Alignment explanation
Indices: 76247--76553 Score: 74
Period size: 21 Copynumber: 15.3 Consensus size: 20
76237 TCGAAGTTCG
*
76247 CGTTGCGATT-TTCCAAATT
1 CGTTGCGTTTATTCCAAATT
* * * *
76266 CGTTGCG-ATAGTCGAAGTT
1 CGTTGCGTTTATTCCAAATT
*
76285 CGCGTTGCGATT-TTCCAAATT
1 --CGTTGCGTTTATTCCAAATT
* * * *
76306 CGTTGCG-ATAGTCGAAGTT
1 CGTTGCGTTTATTCCAAATT
*
76325 CGCGTTGCGATT-TTCCAAATT
1 --CGTTGCGTTTATTCCAAATT
* * * *
76346 CGTTGCG-ATAGTCGAAGTT
1 CGTTGCGTTTATTCCAAATT
76365 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCG-TTTATTCCAAATT
* * * *
76388 CGTTGCG-ATAGTCGAATTT
1 CGTTGCGTTTATTCCAAATT
76407 CGCGTTGCGATTT-TT-CAAATT
1 --CGTTGCG-TTTATTCCAAATT
* *
76428 CGTTGCG-ATAGT-CAAAGTT
1 CGTTGCGTTTATTCCAAA-TT
76447 CATGTTGCGATTTATTCCAAATT
1 C--GTTGCG-TTTATTCCAAATT
* * *
76470 CGTTGCG-ATAGT-CGAA--
1 CGTTGCGTTTATTCCAAATT
76486 -GTT-CGATTTATTCCAAATT
1 CGTTGCG-TTTATTCCAAATT
* * *
76505 CGTTGCG-ATAGTCCAAGTTT
1 CGTTGCGTTTATTCCAA-ATT
*
76525 GTGTTGCGCTTTATTCCAAATT
1 -CGTTGCG-TTTATTCCAAATT
76547 CGTTGCG
1 CGTTGCG
76554 ATAGTCCAAA
Statistics
Matches: 203, Mismatches: 50, Indels: 68
0.63 0.16 0.21
Matches are distributed among these distances:
14 2 0.01
15 3 0.01
16 3 0.01
17 4 0.02
18 11 0.05
19 67 0.33
20 5 0.02
21 77 0.38
22 5 0.02
23 22 0.11
24 4 0.02
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
CGTTGCGTTTATTCCAAATT
Found at i:78555 original size:15 final size:16
Alignment explanation
Indices: 78535--78572 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
78525 AATTAAATAT
*
78535 TATTTTA-AATAATTA
1 TATTTTACAATAATGA
78550 TATTTTTACAATAATGA
1 TA-TTTTACAATAATGA
78567 TATTTT
1 TATTTT
78573 CATCTCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 9 0.45
17 9 0.45
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
TATTTTACAATAATGA
Found at i:78562 original size:17 final size:16
Alignment explanation
Indices: 78537--78572 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
78527 TTAAATATTA
*
78537 TTTTAAATAATTATAT
1 TTTTAAATAATGATAT
78553 TTTTACAATAATGATAT
1 TTTTA-AATAATGATAT
78570 TTT
1 TTT
78573 CATCTCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTTAAATAATGATAT
Found at i:84816 original size:22 final size:22
Alignment explanation
Indices: 84790--84834 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
84780 GAAGATCAAC
84790 TATTAGGTTTAG-TTTAATATAT
1 TATTAGGTTTAGTTTTAA-ATAT
84812 TATTAGGTTTAGTTTTAAATAT
1 TATTAGGTTTAGTTTTAAATAT
84834 T
1 T
84835 GGTAATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (22 bp):
TATTAGGTTTAGTTTTAAATAT
Found at i:87003 original size:45 final size:48
Alignment explanation
Indices: 86936--87033 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 48
86926 TTTATTTTCG
86936 TTTTTCGAATAAATGCATGCGAACTAGATATCATACGGTTAGG-TTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATACGGTTAGGATTTA
* * * *
86983 TTTTTCGAA-CAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATACGGTTAGGATTTA
87029 TTTTT
1 TTTTT
87034 TAATAACAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
45 27 0.59
46 10 0.22
47 9 0.20
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATACGGTTAGGATTTA
Found at i:93974 original size:13 final size:13
Alignment explanation
Indices: 93956--93980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93946 CTTAGTAAAC
93956 CCATCAGTAAGTG
1 CCATCAGTAAGTG
93969 CCATCAGTAAGT
1 CCATCAGTAAGT
93981 CTTTTGAGCA
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:94028 original size:20 final size:20
Alignment explanation
Indices: 93968--94031 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
93958 ATCAGTAAGT
*
93968 GCCATCAGTAAGTCTTTTGA
1 GCCATCAGTAAGTCTTTCGA
* * *
93988 G-CATGATGATGAAGTCCTTCGG
1 GCCATCA-G-T-AAGTCTTTCGA
94010 GCCATCAGTAAGTCTTTCGA
1 GCCATCAGTAAGTCTTTCGA
94030 GC
1 GC
94032 ACGATGATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
19 4 0.12
20 13 0.39
21 2 0.06
22 10 0.30
23 4 0.12
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (20 bp):
GCCATCAGTAAGTCTTTCGA
Found at i:94032 original size:42 final size:42
Alignment explanation
Indices: 93968--94048 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
93958 ATCAGTAAGT
* * *
93968 GCCATCAGTAAGTCTTTTGAGCATGATGATGAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCACGATGATGAAATCCTTCGG
*
94010 GCCATCAGTAAGTCTTTCGAGCACGATGATTAAATCCTT
1 GCCATCAGTAAGTCTTTCGAGCACGATGATGAAATCCTT
94049 TGGGTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCACGATGATGAAATCCTTCGG
Found at i:94157 original size:42 final size:42
Alignment explanation
Indices: 94098--94185 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
94088 AATCCATCAA
* * *
94098 TAAGTCTTTCGAGCATGATGATGAAATCCTTCGGTTCATTTG
1 TAAGTCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTG
*
94140 TAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTG
1 TAAGTCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTG
94182 TAAG
1 TAAG
94186 ACTTCACCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (42 bp):
TAAGTCTTTCGAGCATGATGATGAAATCATTCGGGTAATTTG
Found at i:94191 original size:122 final size:122
Alignment explanation
Indices: 93969--94254 Score: 455
Period size: 122 Copynumber: 2.3 Consensus size: 122
93959 TCAGTAAGTG
* *
93969 CCATCAGTAAGTCTTTTGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAC
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAC
* * *
94034 GATGATTAAATCCTTTGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
66 GATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGTGAAGCAAAT
* ** ** *
94091 CCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGTTCATTTGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAC
94156 GATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGTGAAGCAAAT
66 GATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGTGAAGCAAAT
* *
94213 CCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
94255 TAATTTTTAA
Statistics
Matches: 149, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
122 149 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (122 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAC
GATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGTGAAGCAAAT
Found at i:94272 original size:80 final size:80
Alignment explanation
Indices: 94139--94464 Score: 526
Period size: 80 Copynumber: 4.1 Consensus size: 80
94129 CGGTTCATTT
*
94139 GTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
94204 GAAGCAAATCCATCA
66 GAAGCAAATCCATCA
* * * *
94219 GTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
*
94284 GAAGCAAACCCATCA
66 GAAGCAAATCCATCA
* *
94299 GTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGATTTCACCGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
94364 GAAGCAAATCCATCA
66 GAAGCAAATCCATCA
* * * * *
94379 GTAAGTCTTTCGACCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
*
94444 GAAGCAAATCCGTCA
66 GAAGCAAATCCATCA
94459 GTAAGT
1 GTAAGT
94465 GCCATCAATA
Statistics
Matches: 225, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 225 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (80 bp):
GTAAGTCTTTCGAGCATGATAATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
GAAGCAAATCCATCA
Found at i:94316 original size:160 final size:160
Alignment explanation
Indices: 94139--94464 Score: 616
Period size: 160 Copynumber: 2.0 Consensus size: 160
94129 CGGTTCATTT
94139 GTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
*
94204 GAAGCAAATCCATCAGTAAGTCTTTCGAGCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCT
66 GAAGCAAATCCATCAGTAAGTCTTTCGACCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCT
94269 TCACGGAAGAGTAGTGAAGCAAACCCATCA
131 TCACGGAAGAGTAGTGAAGCAAACCCATCA
*
94299 GTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGATTTCACCGAAGAGTAGT
1 GTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
94364 GAAGCAAATCCATCAGTAAGTCTTTCGACCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCT
66 GAAGCAAATCCATCAGTAAGTCTTTCGACCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCT
* *
94429 TCACGGAAGAGTAGTGAAGCAAATCCGTCA
131 TCACGGAAGAGTAGTGAAGCAAACCCATCA
94459 GTAAGT
1 GTAAGT
94465 GCCATCAATA
Statistics
Matches: 162, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (160 bp):
GTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTAATTTGTAAGACTTCACCGAAGAGTAGT
GAAGCAAATCCATCAGTAAGTCTTTCGACCATGATAATTAAATCCTTCGGGTAATTTTTAAGCCT
TCACGGAAGAGTAGTGAAGCAAACCCATCA
Found at i:94526 original size:42 final size:42
Alignment explanation
Indices: 94467--94553 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
94457 CAGTAAGTGC
94467 CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGT
1 CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGT
* * *
94509 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGT
1 CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGT
94551 CAT
1 CAT
94554 TTGTGAGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (42 bp):
CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGT
Found at i:94544 original size:22 final size:22
Alignment explanation
Indices: 94477--94547 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
94467 CATCAATAAG
*
94477 TCTTTCGAGCATGATGATGAAA
1 TCTTTCGAGCATGATGATTAAA
* * * *
94499 TCCTTCGGGTCATCA-G--TAAG
1 TCTTTCGAG-CATGATGATTAAA
94519 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGATTAAA
94541 TCTTTCG
1 TCTTTCG
94548 GGTCATTTGT
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
19 4 0.11
20 10 0.28
22 18 0.50
23 4 0.11
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (22 bp):
TCTTTCGAGCATGATGATTAAA
Found at i:94981 original size:53 final size:53
Alignment explanation
Indices: 94894--95101 Score: 274
Period size: 53 Copynumber: 3.9 Consensus size: 53
94884 AGAATCACAC
* * *
94894 CAGAAGATTGCTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCATAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAAG
* *
94947 CAGAAGATTGTTCGAGTTCTACTCCCTGATGCAAGAGGGAGTGAACCCATAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAAG
* * ***
95000 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCATTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAAG
* * *
95053 TAGAAGATTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGCGGACCC
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCC
95102 GTCATTTGAA
Statistics
Matches: 136, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
53 110 0.81
54 16 0.12
55 10 0.07
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAAG
Found at i:95114 original size:54 final size:51
Alignment explanation
Indices: 94896--95124 Score: 215
Period size: 53 Copynumber: 4.3 Consensus size: 51
94886 AATCACACCA
* * ***
94896 GAAGATTGCTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCATAGGCA
1 GAAGATTGTTCGAGTTCTACTCCCTGAA-CAAGAGGGAGCGAACCCATA-TTT
* * ***
94949 GAAGATTGTTCGAGTTCTACTCCCTGATGCAAGAGGGAGTGAACCCATAAGCA
1 GAAGATTGTTCGAGTTCTACTCCCTGA-ACAAGAGGGAGCGAACCCAT-ATTT
* * *
95002 GAAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCATTTTT
1 GAAGATTGTTCGAGTTCTACTCCCTGAA-CAAGAGGGAGCGAACCCATATTT
* * *
95054 AGAAGATTGTTCGAGTTCCTTAATCCCTGAACAAGAGGGAGCGGACCCGTCATTT
1 -GAAGATTGTTCGAGTT-C-TACTCCCTGAACAAGAGGGAGCGAACCCAT-ATTT
* *
95109 GAAGATTTTTCAAGTT
1 GAAGATTGTTCGAGTT
95125 TAATTTATCC
Statistics
Matches: 149, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
53 104 0.70
54 32 0.21
55 13 0.09
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (51 bp):
GAAGATTGTTCGAGTTCTACTCCCTGAACAAGAGGGAGCGAACCCATATTT
Found at i:96317 original size:22 final size:22
Alignment explanation
Indices: 96290--96334 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
96280 GAAGATCAAA
96290 TATTAGGTTTAG-TTTAATATAT
1 TATTAGGTTTAGTTTTAA-ATAT
96312 TATTAGGTTTAGTTTTAAATAT
1 TATTAGGTTTAGTTTTAAATAT
96334 T
1 T
96335 GGTAATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (22 bp):
TATTAGGTTTAGTTTTAAATAT
Found at i:96751 original size:12 final size:14
Alignment explanation
Indices: 96734--96766 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
96724 TATATGTGTG
96734 ATGTATA-ATATA-
1 ATGTATATATATAT
96746 ATGTATATATATAT
1 ATGTATATATATAT
96760 ATGTATA
1 ATGTATA
96767 CGTACTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 5 0.26
14 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (14 bp):
ATGTATATATATAT
Found at i:98476 original size:15 final size:15
Alignment explanation
Indices: 98456--98489 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
98446 TATATATTTA
98456 AAAAATAAT-TGACT
1 AAAAATAATATGACT
98470 CAAAAATAATATGACT
1 -AAAAATAATATGACT
98486 AAAA
1 AAAA
98490 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAATAATATGACT
Found at i:98907 original size:2 final size:2
Alignment explanation
Indices: 98900--98933 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
98890 TCTATAAATA
98900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
98934 GCATGCAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.