Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 60 of 214
Found at i:16930421 original size:14 final size:14
Alignment explanation
Indices: 16930404--16930463 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
16930394 TATTTTCATA
16930404 TTAGAGTTTTGAGT
1 TTAGAGTTTTGAGT
*
16930418 TTAGCGTTTATG-GT
1 TTAGAGTTT-TGAGT
* *
16930432 TTAGAGTTTGGGGT
1 TTAGAGTTTTGAGT
*
16930446 TTA-AGGTTTAGAGT
1 TTAGA-GTTTTGAGT
16930460 TTAG
1 TTAG
16930464 TATTTAAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 2 0.05
14 33 0.89
15 2 0.05
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.47
Consensus pattern (14 bp):
TTAGAGTTTTGAGT
Found at i:16930471 original size:21 final size:21
Alignment explanation
Indices: 16930409--16930463 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
16930399 TCATATTAGA
* *
16930409 GTTTTGAGTTTAGCGTTTATG
1 GTTTAGAGTTTAGCGTTTAAG
* *
16930430 GTTTAGAGTTTGGGGTTTAAG
1 GTTTAGAGTTTAGCGTTTAAG
16930451 GTTTAGAGTTTAG
1 GTTTAGAGTTTAG
16930464 TATTTAAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.47
Consensus pattern (21 bp):
GTTTAGAGTTTAGCGTTTAAG
Found at i:16930562 original size:7 final size:7
Alignment explanation
Indices: 16930536--16930754 Score: 64
Period size: 7 Copynumber: 31.0 Consensus size: 7
16930526 GTAGGTCTAT
16930536 GGTTTAG
1 GGTTTAG
*
16930543 GGTTTAA
1 GGTTTAG
**
16930550 TATTTAG
1 GGTTTAG
*
16930557 GGTTTAT
1 GGTTTAG
*
16930564 GATTTAG
1 GGTTTAG
* *
16930571 TGTTAAG
1 GGTTTAG
* *
16930578 AGATTAG
1 GGTTTAG
* *
16930585 TGTTTAC
1 GGTTTAG
*
16930592 GGATTAG
1 GGTTTAG
*
16930599 GGTGTA-
1 GGTTTAG
16930605 GGTTTAG
1 GGTTTAG
16930612 GGTTTAG
1 GGTTTAG
*
16930619 GGTTTAAA
1 GGTTT-AG
*
16930627 GG-TAAGG
1 GGTTTA-G
*
16930634 GGCTTAG
1 GGTTTAG
*
16930641 AGTTTAG
1 GGTTTAG
* *
16930648 GGTGTAA
1 GGTTTAG
** *
16930655 ATTTTAT
1 GGTTTAG
16930662 GGTTTAG
1 GGTTTAG
16930669 GGTTTAG
1 GGTTTAG
* *
16930676 ATGTTAAG
1 -GGTTTAG
*
16930684 GGCTTAG
1 GGTTTAG
*
16930691 AGTTTAG
1 GGTTTAG
* *
16930698 GGTGTAA
1 GGTTTAG
* *
16930705 AGTTTAT
1 GGTTTAG
*
16930712 AGTTTAG
1 GGTTTAG
*
16930719 GGTTTATA
1 GGTTTA-G
* *
16930727 CGCTTAG
1 GGTTTAG
*
16930734 GGTTTAT
1 GGTTTAG
16930741 GGTTTAG
1 GGTTTAG
*
16930748 TGTTTAG
1 GGTTTAG
16930755 TGTCCGATTT
Statistics
Matches: 142, Mismatches: 64, Indels: 12
0.65 0.29 0.06
Matches are distributed among these distances:
6 6 0.04
7 122 0.86
8 14 0.10
ACGTcount: A:0.23, C:0.02, G:0.32, T:0.42
Consensus pattern (7 bp):
GGTTTAG
Found at i:16930672 original size:50 final size:50
Alignment explanation
Indices: 16930595--16930724 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
16930585 TGTTTACGGA
* *
16930595 TTAGGGTGT-AGGTTTAGGGTTTAGGGTTTA-AAGGTAAGGGGCTTAGAGT
1 TTAGGGTGTAAAGTTTATGGTTTAGGGTTTAGAAGGTAA-GGGCTTAGAGT
* * *
16930644 TTAGGGTGTAAATTTTATGGTTTAGGGTTTAGATGTTAAGGGCTTAGAGT
1 TTAGGGTGTAAAGTTTATGGTTTAGGGTTTAGAAGGTAAGGGCTTAGAGT
*
16930694 TTAGGGTGTAAAGTTTATAGTTTAGGGTTTA
1 TTAGGGTGTAAAGTTTATGGTTTAGGGTTTA
16930725 TACGCTTAGG
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
49 9 0.12
50 58 0.81
51 5 0.07
ACGTcount: A:0.24, C:0.02, G:0.35, T:0.40
Consensus pattern (50 bp):
TTAGGGTGTAAAGTTTATGGTTTAGGGTTTAGAAGGTAAGGGCTTAGAGT
Found at i:16930735 original size:15 final size:14
Alignment explanation
Indices: 16930706--16930740 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
16930696 AGGGTGTAAA
*
16930706 GTTTATAGTTTAGG
1 GTTTATAGCTTAGG
16930720 GTTTATACGCTTAGG
1 GTTTATA-GCTTAGG
16930735 GTTTAT
1 GTTTAT
16930741 GGTTTAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.20, C:0.06, G:0.26, T:0.49
Consensus pattern (14 bp):
GTTTATAGCTTAGG
Found at i:16931721 original size:124 final size:125
Alignment explanation
Indices: 16931575--16931801 Score: 314
Period size: 125 Copynumber: 1.8 Consensus size: 125
16931565 AAACGGCGGC
* * * * * *
16931575 TTTCGGTACATGAATTTAA-TTTTTTAGTGGC-GTTTTTGCTGGAAACGTCGCAAAATGTAAGCA
1 TTTCAGTACAAGAATTTAATTTTTTTAGTGGCAGTTTTTG-TGAAAACGTCGCAAAAGGCAAGAA
* *
16931638 ATAGCAGCGTTTTGACCAAAAACGTCACAACTATGTATTAATATTTTTCAAAATGGTGTTG
65 ATAGCAGCGTTTGGACCAAAAACGCCACAACTATGTATTAATATTTTTCAAAATGGTGTTG
* *
16931699 TTTCAGTACAAGAATTTAATTTTTTTAGTGGCATTTTTTGTTAAAACGTCGCAAAAGGCAAGAAA
1 TTTCAGTACAAGAATTTAATTTTTTTAGTGGCAGTTTTTGTGAAAACGTCGCAAAAGGCAAGAAA
* * *
16931764 TAGCGGCGTTTGGACCTAAAACGCCGCAACTATGTATT
66 TAGCAGCGTTTGGACCAAAAACGCCACAACTATGTATT
16931802 TACTTTCTAA
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
124 17 0.19
125 65 0.74
126 6 0.07
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (125 bp):
TTTCAGTACAAGAATTTAATTTTTTTAGTGGCAGTTTTTGTGAAAACGTCGCAAAAGGCAAGAAA
TAGCAGCGTTTGGACCAAAAACGCCACAACTATGTATTAATATTTTTCAAAATGGTGTTG
Found at i:16931914 original size:42 final size:41
Alignment explanation
Indices: 16931848--16931935 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 41
16931838 CCGTCCCCTC
*
16931848 TCCCCTTAGCCCTTATACCCATCTCACA-ATCCAACTAAAAAA
1 TCCCTTTAGCCCTTATACCCATCTCACATAT--AACTAAAAAA
* * * *
16931890 TCCCTTTAGCCCTTATTCCGATCTCGCATATACCTAAAAAA
1 TCCCTTTAGCCCTTATACCCATCTCACATATAACTAAAAAA
16931931 TCCCT
1 TCCCT
16931936 AATTTCTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
41 14 0.35
42 24 0.60
43 2 0.05
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.28
Consensus pattern (41 bp):
TCCCTTTAGCCCTTATACCCATCTCACATATAACTAAAAAA
Found at i:16933769 original size:65 final size:66
Alignment explanation
Indices: 16933651--16933792 Score: 216
Period size: 65 Copynumber: 2.2 Consensus size: 66
16933641 TGGTTAAATA
* * *
16933651 GAATAAATTATCAAATTTTTAATTAATTGAATAAATTATGTTTGATTATTTTATTCGGTTTAATT
1 GAATAAATTATCAAATTTTCAATTAATTGAATAAATTATGTTTGATTAGTTTATTCGGTTTAATG
16933716 T
66 T
* *
16933717 GAATAAATTATC-GATTTTCGATTGAATTGAATAAA-TATGTTTGATTAGTTTATTCGGTTTAAT
1 GAATAAATTATCAAATTTTCAATT-AATTGAATAAATTATGTTTGATTAGTTTATTCGGTTTAAT
16933780 GT
65 GT
16933782 GAATAAATTAT
1 GAATAAATTAT
16933793 GTTTGATTAG
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
65 47 0.67
66 23 0.33
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.48
Consensus pattern (66 bp):
GAATAAATTATCAAATTTTCAATTAATTGAATAAATTATGTTTGATTAGTTTATTCGGTTTAATG
T
Found at i:16933799 original size:38 final size:38
Alignment explanation
Indices: 16933733--16933830 Score: 146
Period size: 38 Copynumber: 2.6 Consensus size: 38
16933723 ATTATCGATT
*
16933733 TTCGATTGAAT-TGAATAAA-TATGTTTGATTAGTTTA
1 TTCGATTTAATGTGAATAAATTATGTTTGATTAGTTTA
*
16933769 TTCGGTTTAATGTGAATAAATTATGTTTGATTAGTTTA
1 TTCGATTTAATGTGAATAAATTATGTTTGATTAGTTTA
* *
16933807 TTTGATTTTATGTGAATAAATTAT
1 TTCGATTTAATGTGAATAAATTAT
16933831 CAATTTTTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 9 0.16
37 8 0.15
38 38 0.69
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (38 bp):
TTCGATTTAATGTGAATAAATTATGTTTGATTAGTTTA
Found at i:16933839 original size:29 final size:28
Alignment explanation
Indices: 16933807--16933865 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
16933797 GATTAGTTTA
*
16933807 TTTGATTTTATGTGAATAAATTATCAATT
1 TTTGATTTAAT-TGAATAAATTATCAATT
*
16933836 TTTGATTTAATTGAATAAATTATCGATT
1 TTTGATTTAATTGAATAAATTATCAATT
16933864 TT
1 TT
16933866 ATATTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 18 0.64
29 10 0.36
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53
Consensus pattern (28 bp):
TTTGATTTAATTGAATAAATTATCAATT
Found at i:16934264 original size:8 final size:9
Alignment explanation
Indices: 16934224--16934404 Score: 94
Period size: 9 Copynumber: 20.9 Consensus size: 9
16934214 AAATTAATAT
*
16934224 ATAATTTAC
1 ATAACTTAC
*
16934233 ATAACTCAC
1 ATAACTTAC
16934242 ATAACTTAC
1 ATAACTTAC
16934251 ATAACTTA-
1 ATAACTTAC
16934259 ATAACTTAC
1 ATAACTTAC
16934268 ATAA-TT-C
1 ATAACTTAC
* *
16934275 ATAA-ATAT
1 ATAACTTAC
* *
16934283 ATATCATATC
1 ATAACTTA-C
*
16934293 ATAACTCAC
1 ATAACTTAC
*
16934302 ATCACTTAC
1 ATAACTTAC
*
16934311 ATAACTAAC
1 ATAACTTAC
16934320 ATAA--TAC
1 ATAACTTAC
* *
16934327 ATAA-ATAT
1 ATAACTTAC
* *
16934335 ATATCATATC
1 ATAACTTA-C
*
16934345 AAAACTTAC
1 ATAACTTAC
16934354 ATAACTTAC
1 ATAACTTAC
16934363 ATAA--TAC
1 ATAACTTAC
* *
16934370 ATAA-ATAT
1 ATAACTTAC
* * *
16934378 TTATCATATC
1 ATAACTTA-C
16934388 ATAACTTAC
1 ATAACTTAC
16934397 ATAACTTA
1 ATAACTTA
16934405 ATTATACTTG
Statistics
Matches: 133, Mismatches: 29, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
7 19 0.14
8 22 0.17
9 77 0.58
10 15 0.11
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:16934323 original size:52 final size:51
Alignment explanation
Indices: 16934241--16934404 Score: 211
Period size: 52 Copynumber: 3.4 Consensus size: 51
16934231 ACATAACTCA
*
16934241 CATAACTTACATAACTTA-ATAACTTACATAATTCATAAATATATATCATAT
1 CATAACTTACATAACTTACATAAC-TACATAATACATAAATATATATCATAT
* *
16934292 CATAACTCACATCACTTACATAACTAACATAATACATAAATATATATCATAT
1 CATAACTTACATAACTTACATAACT-ACATAATACATAAATATATATCATAT
*
16934344 CAAAACTTACATAACTTACATAA-TACAT-A-A-AT--AT-T-TATCATAT
1 CATAACTTACATAACTTACATAACTACATAATACATAAATATATATCATAT
16934387 CATAACTTACATAACTTA
1 CATAACTTACATAACTTA
16934405 ATTATACTTG
Statistics
Matches: 104, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
43 25 0.24
44 1 0.01
45 2 0.02
47 2 0.02
48 1 0.01
49 1 0.01
50 4 0.04
51 18 0.17
52 50 0.48
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (51 bp):
CATAACTTACATAACTTACATAACTACATAATACATAAATATATATCATAT
Found at i:16934403 original size:43 final size:43
Alignment explanation
Indices: 16934250--16934404 Score: 177
Period size: 43 Copynumber: 3.4 Consensus size: 43
16934240 ACATAACTTA
*
16934250 CATAACTTA-ATAACTTACATAATTCATAAATATATATCATATCATAACT
1 CATAACTTACATAACTTACATAATACAT-AA-ATAT-T--TATCAT-A-T
* * *
16934299 CACATCACTTACATAACTAACATAATACATAAATATATATCATAT
1 --CATAACTTACATAACTTACATAATACATAAATATTTATCATAT
*
16934344 CAAAACTTACATAACTTACATAATACATAAATATTTATCATAT
1 CATAACTTACATAACTTACATAATACATAAATATTTATCATAT
16934387 CATAACTTACATAACTTA
1 CATAACTTACATAACTTA
16934405 ATTATACTTG
Statistics
Matches: 94, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
43 56 0.60
45 1 0.01
46 1 0.01
47 6 0.06
50 4 0.04
51 10 0.11
52 16 0.17
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (43 bp):
CATAACTTACATAACTTACATAATACATAAATATTTATCATAT
Found at i:16940241 original size:43 final size:43
Alignment explanation
Indices: 16940194--16940285 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
16940184 GAATGGTACT
* *
16940194 TTTAGCAACGTTTGTGAAAAAAGCATCGCTAAAGGTCATGTTC
1 TTTAGCAACATTTGTGAAAAAAGCACCGCTAAAGGTCATGTTC
** * **
16940237 TTTAGCGGCATTTGTGAAAAAGGTGCCGCTAAAGGTCATGTTC
1 TTTAGCAACATTTGTGAAAAAAGCACCGCTAAAGGTCATGTTC
16940280 TTTAGC
1 TTTAGC
16940286 GGTGTTTATG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
TTTAGCAACATTTGTGAAAAAAGCACCGCTAAAGGTCATGTTC
Found at i:16940313 original size:45 final size:43
Alignment explanation
Indices: 16940204--16940314 Score: 141
Period size: 43 Copynumber: 2.5 Consensus size: 43
16940194 TTTAGCAACG
**
16940204 TTTGTGAAAAAAGCATCGCTAAAGGTCATGTTCTTTAGCGGCA
1 TTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCA
* * **
16940247 TTTGTGAAAAAGGTGCCGCTAAAGGTCATGTTCTTTAGCGGTGT
1 TTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGG-CA
*
16940291 TTATGTGAAAAAAACGCCGCTAAA
1 TT-TGTGAAAAAAGCGCCGCTAAA
16940315 ATTAGCGACA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 37 0.65
44 2 0.04
45 18 0.32
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (43 bp):
TTTGTGAAAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCA
Found at i:16947633 original size:13 final size:13
Alignment explanation
Indices: 16947615--16947640 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16947605 CTTTTGGAGA
16947615 TAAAATGAAAGAT
1 TAAAATGAAAGAT
16947628 TAAAATGAAAGAT
1 TAAAATGAAAGAT
16947641 GTTTGATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
TAAAATGAAAGAT
Found at i:16951020 original size:18 final size:17
Alignment explanation
Indices: 16950992--16951035 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
16950982 ACCAATGTCT
*
16950992 ATATTTCACATATATAC
1 ATATTTCACATATAAAC
16951009 ATATTATCACATATAAAC
1 ATATT-TCACATATAAAC
16951027 ATATATTCA
1 ATAT-TTCA
16951036 ATTCAATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.21
18 18 0.75
19 1 0.04
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATTTCACATATAAAC
Found at i:16954981 original size:20 final size:20
Alignment explanation
Indices: 16954956--16955037 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
16954946 GCTTGTACAG
*
16954956 GTTTGCATTTTGGTGCCTCT
1 GTTTGCACTTTGGTGCCTCT
16954976 GTTTGCACTTTGGTGCCTCT
1 GTTTGCACTTTGGTGCCTCT
* *
16954996 GTTTGCACTTCGGTGCCACT
1 GTTTGCACTTTGGTGCCTCT
* *
16955016 GTTACGCATCTTTGATGCCTCT
1 GTT-TGCA-CTTTGGTGCCTCT
16955038 AGTGTGGTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
20 40 0.75
21 3 0.06
22 10 0.19
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.43
Consensus pattern (20 bp):
GTTTGCACTTTGGTGCCTCT
Found at i:16960513 original size:21 final size:21
Alignment explanation
Indices: 16960489--16960529 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16960479 ATCATATAAA
16960489 TTATAACTCATAATTATTTTT
1 TTATAACTCATAATTATTTTT
* **
16960510 TTATAATTTTTAATTATTTT
1 TTATAACTCATAATTATTTT
16960530 CCAAATTTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATAACTCATAATTATTTTT
Found at i:16962923 original size:22 final size:22
Alignment explanation
Indices: 16962889--16962931 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16962879 CTAACTTTGT
* *
16962889 ATGTTTCGATACATTCAAGGGC
1 ATGTATCGATACATCCAAGGGC
*
16962911 ATGTATCGTTACATCCAAGGG
1 ATGTATCGATACATCCAAGGG
16962932 TTGTATTGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (22 bp):
ATGTATCGATACATCCAAGGGC
Found at i:16965764 original size:35 final size:35
Alignment explanation
Indices: 16965718--16965787 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
16965708 AATGAATTCG
16965718 ATGAGAGAATGATCAAATAGTTGCAAGGCGAGGTT
1 ATGAGAGAATGATCAAATAGTTGCAAGGCGAGGTT
16965753 ATGAGAGAATGATCAAATAGTTGCAAGGCGAGGTT
1 ATGAGAGAATGATCAAATAGTTGCAAGGCGAGGTT
16965788 GAGATGTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.09, G:0.31, T:0.23
Consensus pattern (35 bp):
ATGAGAGAATGATCAAATAGTTGCAAGGCGAGGTT
Found at i:16976202 original size:17 final size:17
Alignment explanation
Indices: 16976160--16976202 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
16976150 AAATTTTTTT
16976160 ATAAAGTTTTATATTTAA
1 ATAAA-TTTTATATTTAA
16976178 ATATAATTTTGAT-TTTAA
1 ATA-AATTTT-ATATTTAA
16976196 ATAAATT
1 ATAAATT
16976203 ATCTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.17
18 15 0.65
19 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
ATAAATTTTATATTTAA
Found at i:16981388 original size:20 final size:20
Alignment explanation
Indices: 16981363--16981402 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16981353 TTGTACTCTT
16981363 TTGAAATTC-AATATTTAATC
1 TTGAAATTCAAAT-TTTAATC
16981383 TTGAAATTCAAATTTTAATC
1 TTGAAATTCAAATTTTAATC
16981403 CAAGATGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (20 bp):
TTGAAATTCAAATTTTAATC
Found at i:16981728 original size:5 final size:5
Alignment explanation
Indices: 16981718--16981742 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
16981708 CTCTTTTTAA
16981718 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
16981743 CACAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:16984785 original size:26 final size:26
Alignment explanation
Indices: 16984756--16984805 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
16984746 AATAATATTA
16984756 TTAACAT-TTTTTTATAAATTATTTAT
1 TTAACATATTTTTTA-AAATTATTTAT
*
16984782 TTAATATATTTTTTAAAATTATTT
1 TTAACATATTTTTTAAAATTATTT
16984806 TGTTTTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TTAACATATTTTTTAAAATTATTTAT
Found at i:16984804 original size:13 final size:13
Alignment explanation
Indices: 16984763--16984806 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
16984753 TTATTAACAT
16984763 TTTTTTATAAATTA
1 TTTTTTA-AAATTA
*
16984777 TTTATTTAATA-TA
1 TTT-TTTAAAATTA
16984790 TTTTTTAAAATTA
1 TTTTTTAAAATTA
16984803 TTTT
1 TTTT
16984807 GTTTTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.23
13 11 0.42
14 5 0.19
15 4 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTTTAAAATTA
Found at i:16990047 original size:5 final size:6
Alignment explanation
Indices: 16990031--16990055 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16990021 GTAGAAATGC
16990031 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
16990056 GGGGGGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:16991009 original size:13 final size:12
Alignment explanation
Indices: 16990991--16991056 Score: 68
Period size: 13 Copynumber: 5.6 Consensus size: 12
16990981 TAGATTTTTC
16990991 CTAAATATTATCA
1 CTAAATA-TATCA
16991004 CTAAATA-ATC-
1 CTAAATATATCA
16991014 CTAAATATAATCA
1 CTAAATAT-ATCA
*
16991027 CTAAATA-AT-T
1 CTAAATATATCA
16991037 CTAAATATTATCA
1 CTAAATA-TATCA
16991050 CTAAATA
1 CTAAATA
16991057 ATTTAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
10 14 0.31
11 5 0.11
12 5 0.11
13 21 0.47
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
CTAAATATATCA
Found at i:16991016 original size:23 final size:23
Alignment explanation
Indices: 16990989--16991058 Score: 122
Period size: 23 Copynumber: 3.0 Consensus size: 23
16990979 GCTAGATTTT
16990989 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
16991012 TCCTAAATATAATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
16991035 TTCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
16991058 T
1 T
16991059 TTAAAATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:16995269 original size:23 final size:23
Alignment explanation
Indices: 16995242--16995317 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
16995232 AGTGTTATTG
16995242 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
16995265 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
16995288 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
16995311 ATCAGTG
1 ATCAGTG
16995318 TTGCACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:16999180 original size:13 final size:13
Alignment explanation
Indices: 16999162--16999227 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
16999152 TAGATTTTTC
16999162 CTAAATATTATCA
1 CTAAATATTATCA
16999175 CTAAATA-T-TC-
1 CTAAATATTATCA
* *
16999185 CTAACTATAATCA
1 CTAAATATTATCA
*
16999198 CTAAATA--AT-T
1 CTAAATATTATCA
*
16999208 CTAAATGTTATCA
1 CTAAATATTATCA
16999221 CTAAATA
1 CTAAATA
16999228 ATTCAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
10 12 0.30
11 4 0.10
12 5 0.12
13 19 0.47
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:16999228 original size:23 final size:23
Alignment explanation
Indices: 16999162--16999236 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
16999152 TAGATTTTTC
16999162 CTAAATATTATCACTAAAT-ATT
1 CTAAATATTATCACTAAATAATT
* *
16999184 CCTAACTATAATCACTAAATAATT
1 -CTAAATATTATCACTAAATAATT
*
16999208 CTAAATGTTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
16999231 CAAAAT
1 CTAAAT
16999237 TTAAAAATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:17001202 original size:15 final size:16
Alignment explanation
Indices: 17001178--17001210 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17001168 TTTGTATAAC
17001178 TTAATATA-TTTAATT
1 TTAATATATTTTAATT
*
17001193 TTAATTTATTTTAATT
1 TTAATATATTTTAATT
17001209 TT
1 TT
17001211 TATAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATATATTTTAATT
Found at i:17001323 original size:14 final size:14
Alignment explanation
Indices: 17001304--17001330 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17001294 TTATTTTTTA
17001304 TATTTAAATGTATT
1 TATTTAAATGTATT
17001318 TATTTAAATGTAT
1 TATTTAAATGTAT
17001331 ACAATTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
TATTTAAATGTATT
Found at i:17003837 original size:20 final size:20
Alignment explanation
Indices: 17003800--17003843 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
17003790 GTTTTGCTCG
**
17003800 TGTTATTTTACTTACATTAT
1 TGTTATTTTACACACATTAT
* *
17003820 TGTTATTTTACACCCATTTT
1 TGTTATTTTACACACATTAT
17003840 TGTT
1 TGTT
17003844 CAGATTTCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (20 bp):
TGTTATTTTACACACATTAT
Found at i:17005771 original size:19 final size:19
Alignment explanation
Indices: 17005747--17005793 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
17005737 TCTTTTTCTT
17005747 TTTGCATT-CATTCCATGCA
1 TTTGCATTACATTCCAT-CA
*
17005766 TTTGCATTACATTGCATCA
1 TTTGCATTACATTCCATCA
*
17005785 TATGCATTA
1 TTTGCATTA
17005794 GATTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTGCATTACATTCCATCA
Found at i:17008306 original size:7 final size:7
Alignment explanation
Indices: 17008294--17008342 Score: 80
Period size: 7 Copynumber: 6.7 Consensus size: 7
17008284 AAAAAAGGGC
17008294 AAAAAAG
1 AAAAAAG
17008301 AAAAAAAG
1 -AAAAAAG
17008309 AAAAAAG
1 AAAAAAG
17008316 AAAAAAG
1 AAAAAAG
17008323 AAAAAAG
1 AAAAAAG
17008330 AAAAGAAG
1 AAAA-AAG
17008338 AAAAA
1 AAAAA
17008343 GGAGAGGCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
7 26 0.65
8 14 0.35
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:17008312 original size:15 final size:15
Alignment explanation
Indices: 17008294--17008342 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
17008284 AAAAAAGGGC
17008294 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
17008309 AAAAAAG-AAAAAAG
1 AAAAAAGAAAAAAAG
*
17008323 AAAAAAGAAAAGAAG
1 AAAAAAGAAAAAAAG
17008338 AAAAA
1 AAAAA
17008343 GGAGAGGCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 14 0.44
15 18 0.56
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:17008319 original size:22 final size:22
Alignment explanation
Indices: 17008294--17008342 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
17008284 AAAAAAGGGC
17008294 AAAAAAGAAAAAAAGAAAA-AAG
1 AAAAAAG-AAAAAAGAAAAGAAG
17008316 AAAAAAGAAAAAAGAAAAGAAG
1 AAAAAAGAAAAAAGAAAAGAAG
17008338 AAAAA
1 AAAAA
17008343 GGAGAGGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAAAGAAAAGAAG
Found at i:17008973 original size:108 final size:106
Alignment explanation
Indices: 17008665--17008975 Score: 372
Period size: 108 Copynumber: 2.9 Consensus size: 106
17008655 TTTATTCTCA
* * ** *
17008665 TCGTAACTTAGCAAATTTGTTATCTTGATTATTTATTTATTGCGAGCTTTGTTCTCAATAAAATT
1 TCGTATCTTAGCAAATTTGCTATCTTGATTATTTATTTATTTAGAGCCTTGTTCTCAATAAAATT
* * *
17008730 CCATCTTGTCCATTGTGATAATCCTTTTCATCTTATTCATT
66 TCATCTTGTCCATTGTGATAATCTTTTTCATCTTATTCAGT
* * * * * * *
17008771 TTGAATCTTAGCATAATTCGCTATCCTGCTTAATTTATTTGTTTAGAG-CTCTGCTCTCAATAAA
1 TCGTATCTTAGCA-AATTTGCTATCTTGATT-ATTTATTTATTTAGAGCCT-TGTTCTCAATAAA
* *
17008835 ATTTCATCTTATCCACTGTGATAATCTTTTTCATCTTATTCAGT
63 ATTTCATCTTGTCCATTGTGATAATCTTTTTCATCTTATTCAGT
* * *
17008879 TCGTATCTTAGTAAGATTTGCTATCTTGATTGATTTATTCATTTTGAGCCTTGTTCTCAATAAAA
1 TCGTATCTTAGCAA-ATTTGCTATCTTGATT-ATTTATTTATTTAGAGCCTTGTTCTCAATAAAA
* *
17008944 TTTCATCTTGTCCATTTTGATAATATTTTTCA
64 TTTCATCTTGTCCATTGTGATAATCTTTTTCA
17008976 AGCAGTTTTC
Statistics
Matches: 168, Mismatches: 32, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
106 10 0.06
107 15 0.09
108 141 0.84
109 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.48
Consensus pattern (106 bp):
TCGTATCTTAGCAAATTTGCTATCTTGATTATTTATTTATTTAGAGCCTTGTTCTCAATAAAATT
TCATCTTGTCCATTGTGATAATCTTTTTCATCTTATTCAGT
Found at i:17010983 original size:46 final size:46
Alignment explanation
Indices: 17009855--17010977 Score: 1667
Period size: 46 Copynumber: 24.4 Consensus size: 46
17009845 AATGGACTAA
* * * * *
17009855 AAGATAACAGATCTTATCTTCCTGTATTTGGCAGCAGAGTAAATCT
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
17009901 AAGATATAGCAGATCTTATCTTCCTGTATTTGGCAGCAGAGTGGATCG
1 AAG--ATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
17009949 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
17009995 AAGATAGCAGATCTTGTCTTCCTGTATTTGGAAGCAGAGCAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
17010041 AAAATAGTAGATCTTGTCTTCTTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
17010087 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
17010133 AAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
17010179 AAGATAGCAGATCTTGTCTTTCTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
17010225 AAG-CAGCAGATCTTGTCTTCCTGTATTTGGTAGCGGAGGAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
17010270 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
17010316 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* *
17010362 AAGATAGCAGATCTTGTCTTCCTATATTTGGCAGCAGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
17010408 AAGATAGCGGATCTTGTCTTCCTG-ATTTGGCAGCAGAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
17010453 AAGATAGCAGATCTTGTCTTCCTGTATTTGGTAGTGGAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
17010499 AATATAGTAGATCTTGTTTTCCTGTATTTGGCAGCAGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
17010545 AAGATAGCAGATCTTGTTTTCCTGTATCTCGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
17010591 AAGATAGAAGATCTTGTCTTCCTGTATTTGACAGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
17010637 AAGATAGCATATCTTATCTTCCTGTATTTGGCAGCAGAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* *
17010683 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
17010729 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCA
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* ** *
17010775 AAGATAGCAGATCTTGTCTTCCTGTATTTGACAGCAAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * *
17010821 AAGATAGCAGATATTGTCTTTCTGTATTTGGCAGTGGAATAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
17010867 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGT-GATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * **
17010912 AAGTTAGCAGATCTTGTCTTCTTGTATTTGGCAGTAGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
17010958 AAGATTGCAGATCTTGTCTT
1 AAGATAGCAGATCTTGTCTT
17010978 TTTGTACTAG
Statistics
Matches: 982, Mismatches: 90, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
45 126 0.13
46 814 0.83
48 42 0.04
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (46 bp):
AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
Found at i:17011161 original size:44 final size:44
Alignment explanation
Indices: 17011102--17011207 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
17011092 GACGGCAAAT
* * *
17011102 CTTATCTTCCT-AAGTTGCAGTGGGGCAGGTTGAAATCACTAAC
1 CTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAATCACTAAC
* * * * **
17011145 CTTATCTCCCTGAAGTTACAATGGAGCATATTGAAATTACTAGT
1 CTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAATCACTAAC
*
17011189 CGTATCTTCCTGAAGTTGC
1 CTTATCTTCCTGAAGTTGC
17011208 GTTGAAGCGG
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
43 10 0.20
44 40 0.80
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (44 bp):
CTTATCTTCCTGAAGTTGCAATGGAGCAGATTGAAATCACTAAC
Found at i:17012406 original size:13 final size:13
Alignment explanation
Indices: 17012385--17012415 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
17012375 GGCACTACAG
*
17012385 CGGCGACCACGGC
1 CGGCAACCACGGC
17012398 CGGCAACCACGGC
1 CGGCAACCACGGC
17012411 CGGCA
1 CGGCA
17012416 GCCATGGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.45, G:0.35, T:0.00
Consensus pattern (13 bp):
CGGCAACCACGGC
Found at i:17013063 original size:30 final size:29
Alignment explanation
Indices: 17013027--17013103 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 29
17013017 AATATATATG
*
17013027 TATATATACACATGCATATTTTTATTTTTA
1 TATATATACACATACATATTTTTA-TTTTA
* *
17013057 TATATATACGTACTTATATATTTTTATTTTA
1 TATATATAC--ACATACATATTTTTATTTTA
*
17013088 TAATATTTACACATAC
1 T-ATATATACACATAC
17013104 CTACATACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
30 13 0.34
31 6 0.16
32 19 0.50
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52
Consensus pattern (29 bp):
TATATATACACATACATATTTTTATTTTA
Found at i:17013377 original size:2 final size:2
Alignment explanation
Indices: 17013370--17013400 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17013360 TTTCATAATT
*
17013370 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17013401 TTTTTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17013594 original size:20 final size:20
Alignment explanation
Indices: 17013557--17013600 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
17013547 GTTTTGCTCG
**
17013557 TGTTATTTTACTTACATTAT
1 TGTTATTTTACACACATTAT
* *
17013577 TGTTATTTTACACCCATTTT
1 TGTTATTTTACACACATTAT
17013597 TGTT
1 TGTT
17013601 TAGATTTCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (20 bp):
TGTTATTTTACACACATTAT
Found at i:17016418 original size:22 final size:23
Alignment explanation
Indices: 17016380--17016426 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
17016370 GATTTGCTAA
17016380 TTTAATTATAAATAATT-TTAAT
1 TTTAATTATAAATAATTATTAAT
*
17016402 TTTAATTAT-ATTAAATTATTAAT
1 TTTAATTATAAAT-AATTATTAAT
17016425 TT
1 TT
17016427 CATATGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 2 0.09
22 13 0.59
23 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTAATTATAAATAATTATTAAT
Found at i:17017060 original size:35 final size:35
Alignment explanation
Indices: 17017021--17017088 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
17017011 AAGTTTAGGG
*
17017021 TAGA-CCATTCTATGCCAACCTTAAAAAGGTTGGAA
1 TAGACCCA-TCTAAGCCAACCTTAAAAAGGTTGGAA
*
17017056 TAGACCCATCTAAGGCAACCTTAAAAAGGTTGG
1 TAGACCCATCTAAGCCAACCTTAAAAAGGTTGG
17017089 GATAAACGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (35 bp):
TAGACCCATCTAAGCCAACCTTAAAAAGGTTGGAA
Found at i:17026199 original size:22 final size:20
Alignment explanation
Indices: 17026160--17026217 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
17026150 TACATAATGT
*
17026160 AAAAAAAAAATTAGAATGCACACG
1 AAAAATAAAA-TA-AATGCA-A-G
17026184 AAAAATAAAATAAATGCAAG
1 AAAAATAAAATAAATGCAAG
*
17026204 ATAAATAAAA-AAAT
1 AAAAATAAAATAAAT
17026218 ATATAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.12
20 10 0.31
21 1 0.03
22 6 0.19
23 2 0.06
24 9 0.28
ACGTcount: A:0.69, C:0.07, G:0.09, T:0.16
Consensus pattern (20 bp):
AAAAATAAAATAAATGCAAG
Found at i:17026765 original size:23 final size:23
Alignment explanation
Indices: 17026739--17026808 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
17026729 AATTAATAGC
*
17026739 ATAATTATTTATATAATATTTAT
1 ATAATTATTTATATAATAATTAT
**
17026762 ATAATTACATATATAAATAATTAT
1 ATAATTATTTATAT-AATAATTAT
*
17026786 AT--TTATTTAATATAA-AAATAT
1 ATAATTATTT-ATATAATAATTAT
17026807 AT
1 AT
17026809 TGATGTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 7 0.18
22 6 0.15
23 16 0.41
24 10 0.26
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATTATTTATATAATAATTAT
Found at i:17028168 original size:29 final size:30
Alignment explanation
Indices: 17028120--17028178 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
17028110 GAACTGGATT
*
17028120 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
* * *
17028150 AAATC-AAAGTTCATTTATACAATTGCACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
17028179 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTACACA
Found at i:17038304 original size:45 final size:45
Alignment explanation
Indices: 17038211--17038315 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
17038201 AGGAGGAAGA
* * * *
17038211 ATTGGTGGCTTCGTCCACAACCTACATGGTAGTTTGTATGCAAAT
1 ATTGGTGGCTTTGTCCACAACCTACATGGCAGCTAGTATGCAAAT
* ** *
17038256 ATTGGTGGCTTTGTCCACAACCTACATGGCAGCTAGTCTGTGAGT
1 ATTGGTGGCTTTGTCCACAACCTACATGGCAGCTAGTATGCAAAT
17038301 ATTGGTGGCTTTGTC
1 ATTGGTGGCTTTGTC
17038316 TACATTAGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (45 bp):
ATTGGTGGCTTTGTCCACAACCTACATGGCAGCTAGTATGCAAAT
Found at i:17044198 original size:109 final size:109
Alignment explanation
Indices: 17043964--17044454 Score: 642
Period size: 109 Copynumber: 4.5 Consensus size: 109
17043954 GCTTTGACCA
** * * *
17043964 GCTCACGATGCTGCTCACACAAGCTACAGAGAATCCGCAAGAAATGCAGGATCTCAAGCCATCAT
1 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTC-AGCCATCAC
* * *
17044029 TACGGTCTGTATCACCCATACATAGTACTTGCTAAATAATCACCA
65 TACGGTCTGTATCACCCACACATAGTACCTGCTAAATAATCACCG
* *
17044074 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAAATGCAGGATCTCAGCCATCATT
1 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTCAGCCATCACT
* * **
17044139 ACGGTCTATATCACCCATACATAGTACCTGCTAAATAATCATTG
66 ACGGTCTGTATCACCCACACATAGTACCTGCTAAATAATCACCG
* * * * * * *
17044183 GCTCACGTTGTTGCTCACACAAGATGTAGAGAATCTGCAACAGATGCAAGATCTTAGCCATCGCT
1 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTCAGCCATCACT
*
17044248 ACGGTCTGTATCA-CCAGCACGTAGTACCTGCTAAATAATCACCG
66 ACGGTCTGTATCACCCA-CACATAGTACCTGCTAAATAATCACCG
* * * * * * *
17044292 GCTCAAGACGCTACTCACACAAGTTGTAGAGAATTCGCAACAGATGCAGGGTCTCAGCCATCGCT
1 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTCAGCCATCACT
*** *
17044357 ACGGTCTGTATCACTGGCACATAGTACCTGCTAAATAATCACTG
66 ACGGTCTGTATCACCCACACATAGTACCTGCTAAATAATCACCG
* *
17044401 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCTGCAATAGATGCAGGATCT
1 GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCT
17044455 ATTAAAGCCT
Statistics
Matches: 333, Mismatches: 46, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
108 3 0.01
109 278 0.83
110 52 0.16
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (109 bp):
GCTCACGATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTCAGCCATCACT
ACGGTCTGTATCACCCACACATAGTACCTGCTAAATAATCACCG
Found at i:17050877 original size:7 final size:7
Alignment explanation
Indices: 17050865--17050894 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
17050855 GTTGATAAAT
17050865 AAAATAA
1 AAAATAA
17050872 AAAATAA
1 AAAATAA
17050879 AAAATAA
1 AAAATAA
17050886 AAAATAA
1 AAAATAA
17050893 AA
1 AA
17050895 TAAAAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:17050885 original size:19 final size:19
Alignment explanation
Indices: 17050861--17050900 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
17050851 TTTAGTTGAT
17050861 AAATAAAATAA-AAAATAAA
1 AAATAAAA-AATAAAATAAA
17050880 AAATAAAAAATAAAATAAA
1 AAATAAAAAATAAAATAAA
17050899 AA
1 AA
17050901 TAGAATTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (19 bp):
AAATAAAAAATAAAATAAA
Found at i:17060186 original size:44 final size:44
Alignment explanation
Indices: 17060119--17060211 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 44
17060109 GAAGAAGTGA
17060119 TTGT-TCAGTTAGGCCATATTGTGGGCAACTTACACACTACTTC
1 TTGTATCAGTTAGGCCATATTGTGGGCAACTTACACACTACTTC
17060162 TTGTATCAGTTAGGCCATATTGTGGGCAACTTACACACTACTTC
1 TTGTATCAGTTAGGCCATATTGTGGGCAACTTACACACTACTTC
17060206 TTGTAT
1 TTGTAT
17060212 TGCACCCAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 4 0.08
44 45 0.92
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (44 bp):
TTGTATCAGTTAGGCCATATTGTGGGCAACTTACACACTACTTC
Found at i:17064182 original size:16 final size:16
Alignment explanation
Indices: 17064161--17064194 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
17064151 TCTACTTTCA
17064161 ATGGACTCTGACATAG
1 ATGGACTCTGACATAG
17064177 ATGGACTCTGACATAG
1 ATGGACTCTGACATAG
17064193 AT
1 AT
17064195 AGATGTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (16 bp):
ATGGACTCTGACATAG
Found at i:17064792 original size:23 final size:22
Alignment explanation
Indices: 17064738--17064792 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17064728 TACAGAATAC
*
17064738 GCCACACAAGCATCACAAAATAT
1 GCCACA-AAGCATCACAAAACAT
* * *
17064761 GCTATAAAGCATTTACAAAACAT
1 GCCACAAAGCA-TCACAAAACAT
17064784 GCCACAAAG
1 GCCACAAAG
17064793 AGCTTACAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.47, C:0.25, G:0.11, T:0.16
Consensus pattern (22 bp):
GCCACAAAGCATCACAAAACAT
Found at i:17066846 original size:45 final size:45
Alignment explanation
Indices: 17066783--17066927 Score: 184
Period size: 45 Copynumber: 3.2 Consensus size: 45
17066773 GGAGAATAAA
*
17066783 TAAGACCATGACTGAAAGACGTTATGGCATCATGATTCTATCGAG
1 TAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAG
* *
17066828 TAAGACCATGACTTAAAGATGTTATGGCATCACGATTCTATCGAG
1 TAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAG
* * * * * * *
17066873 TAAGGCCAT-AGCTGAAAGACGCTATGACATCACGAATCAAACGAA
1 TAAGACCATGA-CTGAAAGACGTTATGGCATCACGATTCTATCGAG
17066918 TAAGACCATG
1 TAAGACCATG
17066928 GTTGAAAAAC
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
44 1 0.01
45 84 0.99
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (45 bp):
TAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAG
Found at i:17066934 original size:45 final size:45
Alignment explanation
Indices: 17066781--17066992 Score: 149
Period size: 45 Copynumber: 4.7 Consensus size: 45
17066771 CCGGAGAATA
** * * * *
17066781 AATAAGACCATGACTGAAAGACGTTATGGCATCATGATTCTATCG
1 AATAAGACCATGGTTGAAAGACGCTATGGCATCACGATTCAAACG
* * * * * *
17066826 AGTAAGACCATGACTT-AAAGATGTTATGGCATCACGATTCTATCG
1 AATAAGACCATG-GTTGAAAGACGCTATGGCATCACGATTCAAACG
* * * * * *
17066871 AGTAAGGCCATAGCTGAAAGACGCTATGACATCACGAATCAAACG
1 AATAAGACCATGGTTGAAAGACGCTATGGCATCACGATTCAAACG
* * * *** *
17066916 AATAAGACCATGGTTGAAAAACACTATGGCAACACGACGGAAAATG
1 AATAAGACCATGGTTGAAAGACGCTATGGCATCACGA-TTCAAACG
* *
17066962 AAAAAGACCATGGTTGAAAGACAC-ATGGCAT
1 AATAAGACCATGGTTGAAAGACGCTATGGCAT
17066993 TAAGACAACA
Statistics
Matches: 134, Mismatches: 30, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
44 1 0.01
45 106 0.79
46 27 0.20
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (45 bp):
AATAAGACCATGGTTGAAAGACGCTATGGCATCACGATTCAAACG
Found at i:17075329 original size:20 final size:20
Alignment explanation
Indices: 17075306--17075359 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
17075296 ATACCAAATA
**
17075306 AAAAATATCGATACTTTTAT
1 AAAAATATCGATACTCGTAT
*
17075326 AAAAATATCGATACTCGTGT
1 AAAAATATCGATACTCGTAT
*
17075346 AAAAATATCAATAC
1 AAAAATATCGATAC
17075360 CATGGAGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAAATATCGATACTCGTAT
Found at i:17081468 original size:45 final size:45
Alignment explanation
Indices: 17081419--17081620 Score: 253
Period size: 45 Copynumber: 4.5 Consensus size: 45
17081409 ACCAGAAACG
*
17081419 AGTAAGACCATGATTGAAAGACGTTATGGCATCACGATTCTATCA
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCA
17081464 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCA
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCA
* *
17081509 AGTAAGACCATGACTGAAAGATGTTATGGCATCACGATTCTATCG
1 AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCA
* * *** * * * *
17081554 AGTAAAACCGT-AGCTGAAAGAAACTATCGCATCACGAATCAAACA
1 AGTAAGACCATGA-CTGAAAGACGTTATGGCATCACGATTCTATCA
* **
17081599 AATAAGACCATGGGTGAAAGAC
1 AGTAAGACCATGACTGAAAGAC
17081621 ACCATGGCAC
Statistics
Matches: 136, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
44 1 0.01
45 135 0.99
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCA
Found at i:17088007 original size:75 final size:75
Alignment explanation
Indices: 17087880--17088083 Score: 243
Period size: 75 Copynumber: 2.7 Consensus size: 75
17087870 AAGTGAGCAT
* * * * *
17087880 ATTATCTTATAATGATTAAAAATGATCAAATTCCAAAT-TTAATCATAATAGAGAGACCAAAACT
1 ATTATCTTATAATGACTAAAAAGGATTAAATCCCAAATGTTAA-CATAGTAGAGAGACCAAAACT
*
17087944 ACAATTTGATC
65 ACAATTTAATC
* * **
17087955 ATTATCTTATAATGACTAAAAAGGATTAAATCCCAAATGTGAACATAGTAGAGGGGTCAAAACTA
1 ATTATCTTATAATGACTAAAAAGGATTAAATCCCAAATGTTAACATAGTAGAGAGACCAAAACTA
*
17088020 TAATTTAATC
66 CAATTTAATC
* * * *
17088030 ATCATCTTAT-ACGACTAAAAGGGATTAAATCCCAAATGTTAGCATAGTA-AGAGA
1 ATTATCTTATAATGACTAAAAAGGATTAAATCCCAAATGTTAACATAGTAGAGAGA
17088084 TCGAAATTGA
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
73 3 0.03
74 35 0.32
75 69 0.63
76 3 0.03
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (75 bp):
ATTATCTTATAATGACTAAAAAGGATTAAATCCCAAATGTTAACATAGTAGAGAGACCAAAACTA
CAATTTAATC
Found at i:17088332 original size:16 final size:16
Alignment explanation
Indices: 17088313--17088343 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17088303 AATTAGATTC
*
17088313 AAATTTAAATTAAATA
1 AAATTTAAAATAAATA
17088329 AAATTTAAAATAAAT
1 AAATTTAAAATAAAT
17088344 TTATTACTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTTAAAATAAATA
Found at i:17089774 original size:14 final size:14
Alignment explanation
Indices: 17089739--17089780 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
17089729 TTTTAAAATT
17089739 TTTAAATTA-TAAA
1 TTTAAATTATTAAA
*
17089752 -TT-AACTATTAAA
1 TTTAAATTATTAAA
17089764 TTTAAATTATTAAA
1 TTTAAATTATTAAA
17089778 TTT
1 TTT
17089781 TAAGTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 4 0.17
12 6 0.25
13 2 0.08
14 12 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAATTATTAAA
Found at i:17094848 original size:6 final size:6
Alignment explanation
Indices: 17094837--17094867 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
17094827 GCATTGATGT
17094837 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA A
17094868 TGGTTTCGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:17096240 original size:22 final size:22
Alignment explanation
Indices: 17096209--17096259 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
17096199 TTTCCTCAAT
17096209 GTTTC-AATTTAGTCTCGAATC
1 GTTTCTAATTTAGTCTCGAATC
17096230 GTTTCTAATTTAGTCTCGAATC
1 GTTTCTAATTTAGTCTCGAATC
*
17096252 ATTTCTAA
1 GTTTCTAA
17096260 GGCCTTGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (22 bp):
GTTTCTAATTTAGTCTCGAATC
Found at i:17100762 original size:306 final size:308
Alignment explanation
Indices: 17100251--17100821 Score: 720
Period size: 306 Copynumber: 1.9 Consensus size: 308
17100241 TACAAAGATA
* *
17100251 TGTTTATAAATAACATACAATAAATAATGAAACGTATGATTTGAAACTAATTAATAATAACACAT
1 TGTTTAAAAATAACATACAATAAAT-ATGAAACATATGATTTGAAACTAATTAATAATAACACAT
* * * * **
17100316 GGAATTTATACGATATTAAAATGAAAATAAATTAGATTAACTTGTGAGTAAAACGAAATTTAATT
65 GAAATATATACGATATTAAAATGAAAAT--ATTAGATTAAATTGTGAGTAAAACAAAATTTAAAC
* * * *
17100381 GCATAAATACATCTGATTAATAATACTAAATCAATACATTTGTTTATCATGATGTTGTCATCAAT
128 GCATAAATACATCTGATTAAGAATACTAAATAAATACAATTGTTTATCATGATGTTGCCATCAAT
* * * ** * *
17100446 CTTGAGTTGGTGTCCATTTAATTTGTGACATCAACTCAATCAACAATATTA-TAATACTAGAAAT
193 CCTAAGTTGGTGTCAAGATAATTTGTGACACCAACTCAATCAACAACATTATTAATACTAGAAAT
17100510 TCTATCACACGTATATGCATCTACAAATCACATATTTAGAACAAAAATGTG
258 TCTATCACACGTATATGCATCTACAAATCACATATTTAGAACAAAAATGTG
* * * * *
17100561 TGTTTAAAAATAGCATATAATAAAT-TTAAACATATGGTTTGAAACTAATTAATAATAACACATT
1 TGTTTAAAAATAACATACAATAAATATGAAACATATGATTTGAAACTAATTAATAATAACACATG
* ** * *
17100625 AAATATGTGTGATATTAAAATGAAACGT-TTATATTAAATTGTGAGTAAAACAAAATTTAAACGC
66 AAATATATACGATATTAAAATGAAA-ATATTAGATTAAATTGTGAGTAAAACAAAATTTAAACGC
* * ** * *
17100689 ATAGATATATC-GTATTGGGAATACTAAATAAATATAATTGTTTATCATGGTGTTGCCAGT-AAT
130 ATAAATACATCTG-ATTAAGAATACTAAATAAATACAATTGTTTATCATGATGTTGCCA-TCAAT
* *
17100752 CCTAAGTTGGTGTCAAGATAATTTGTGACACCAATTCAATCAGCAACATTATTAATACTAGAAAT
193 CCTAAGTTGGTGTCAAGATAATTTGTGACACCAACTCAATCAACAACATTATTAATACTAGAAAT
17100817 TCTAT
258 TCTAT
17100822 TATATGTGTA
Statistics
Matches: 220, Mismatches: 37, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
305 1 0.00
306 122 0.55
307 19 0.09
308 55 0.25
309 1 0.00
310 22 0.10
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (308 bp):
TGTTTAAAAATAACATACAATAAATATGAAACATATGATTTGAAACTAATTAATAATAACACATG
AAATATATACGATATTAAAATGAAAATATTAGATTAAATTGTGAGTAAAACAAAATTTAAACGCA
TAAATACATCTGATTAAGAATACTAAATAAATACAATTGTTTATCATGATGTTGCCATCAATCCT
AAGTTGGTGTCAAGATAATTTGTGACACCAACTCAATCAACAACATTATTAATACTAGAAATTCT
ATCACACGTATATGCATCTACAAATCACATATTTAGAACAAAAATGTG
Found at i:17102668 original size:49 final size:50
Alignment explanation
Indices: 17102608--17102786 Score: 231
Period size: 50 Copynumber: 3.6 Consensus size: 50
17102598 TCATTCGATA
17102608 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTACAATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAATT
* * *
17102657 CACGTAGTAGCCTTCACATAGTACTACACACGTGAACAAGTTTTACGACT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAATT
* *
17102707 CACGTAGTAGCCTTCAC-TCAGTACTACACACGTGCTCAAGCTTCTT--AGTT
1 CACGTAGTAGCCTTCACAT-AGTACTACACACGTGATCAAG-TT-TTACAATT
* * *
17102757 CACATAGTAGCATTCACTTAGTACTACACA
1 CACGTAGTAGCCTTCACATAGTACTACACA
17102787 TATAACCGTA
Statistics
Matches: 115, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
49 37 0.32
50 73 0.63
51 3 0.03
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAATT
Found at i:17102720 original size:50 final size:50
Alignment explanation
Indices: 17102603--17102943 Score: 259
Period size: 51 Copynumber: 6.8 Consensus size: 50
17102593 TTTTATCATT
*
17102603 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
* *
17102652 CAATTCACGTAGTAGCCTTCACATAGTACTACACACGTGAACAAGTTTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
* *
17102702 CGACTCACGTAGTAGCCTTCAC-TCAGTACTACACACGTGCTCAAGCTTCTTA
1 CGATTCACGTAGTAGCCTTCACAT-AGTACTACACACGTGATCAAG-TT-TTA
* * * ** * * *
17102754 -G-TTCACATAGTAGCATTCACTTAGTACTACACATATAACCGTAG-TTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTA
** * * * * *
17102802 CCGAGACACGTGGTAGCATTCACACAGTACTACACATGTGCTCAAAGCTTCTT-
1 -CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TT-TTA
* * * * * * *
17102855 -GGTGCACATAGTAGCCTTCACTTAGTACCACACATGTGA-CCA-TTACTTA
1 CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTT--TTA
* *
17102904 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 -CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTG
17102944 TTCATCGATA
Statistics
Matches: 230, Mismatches: 46, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
47 2 0.01
48 6 0.03
49 42 0.18
50 77 0.33
51 97 0.42
52 3 0.01
53 1 0.00
54 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (50 bp):
CGATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
Found at i:17102913 original size:102 final size:99
Alignment explanation
Indices: 17102603--17102943 Score: 361
Period size: 102 Copynumber: 3.4 Consensus size: 99
17102593 TTTTATCATT
* * * * *
17102603 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AG-TT-TTACAATTCACGTAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTT--AGTGCACATAGT
* * *
17102665 AGCCTTCACATAGTACTACACACGTGAACAAGTT-TTA
64 AGCCTTCACTTAGTACTACACATGTG-ACCA-TTATTA
* *
17102702 CGACT-CACGTAGTAGCCTTCACTCAGTACTACACACGTGCTCAAGCTTCTTAGTTCACATAGTA
1 CGA-TACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTTAGTGCACATAGTA
* * * *
17102766 GCATTCACTTAGTACTACACATATAACC-GTAGTTTA
65 GCCTTCACTTAGTACTACACATGTGACCATTA--TTA
* * * * *
17102802 CCGAGACACGTGGTAGCATTCACACAGTACTACACATGTGCTCAAAGCTTCTTGGTGCACATAGT
1 -CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTC-AAGCTTCTTAGTGCACATAGT
*
17102867 AGCCTTCACTTAGTACCACACATGTGACCATTACTTA
64 AGCCTTCACTTAGTACTACACATGTGACCATTA-TTA
17102904 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 -CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
17102944 TTCATCGATA
Statistics
Matches: 201, Mismatches: 30, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
97 1 0.00
99 39 0.19
100 37 0.18
101 38 0.19
102 84 0.42
103 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (99 bp):
CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTTAGTGCACATAGTAG
CCTTCACTTAGTACTACACATGTGACCATTATTA
Found at i:17110262 original size:49 final size:50
Alignment explanation
Indices: 17110202--17110380 Score: 238
Period size: 50 Copynumber: 3.6 Consensus size: 50
17110192 TCATTCGATA
*
17110202 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTACAATT
1 CACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTACAATT
* * *
17110251 CACGTAGTAGCCTTCACTTAGTACTACACACGTGAACAAGTTTTACGACT
1 CACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTACAATT
* * * *
17110301 CACGTAGTAGCCTTCACTCAATACTACACACGTGCTCAAGCTTCTT--AGTT
1 CACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAG-TT-TTACAATT
*
17110351 CACATAGTAGCCTTCACTTAGTACTACACA
1 CACGTAGTAGCCTTCACTTAGTACTACACA
17110381 TATAACCGTA
Statistics
Matches: 113, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
49 35 0.31
50 74 0.65
51 2 0.02
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTACAATT
Found at i:17110314 original size:50 final size:50
Alignment explanation
Indices: 17110197--17110537 Score: 266
Period size: 51 Copynumber: 6.8 Consensus size: 50
17110187 TTTTATCATT
* *
17110197 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTA
1 CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTA
* *
17110246 CAATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGAACAAGTTTTA
1 CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTA
* * * *
17110296 CGACTCACGTAGTAGCCTTCACTCAATACTACACACGTGCTCAAGCTTCTTA
1 CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAG-TT-TTA
* ** * * *
17110348 -G-TTCACATAGTAGCCTTCACTTAGTACTACACATATAACCGTAG-TTTA
1 CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATC-AAGTTTTA
** * * ** *
17110396 CCGAGACACGTGGTAGCATTCACACAGTACTACACACGTGCTCAAAGCTTCTT-
1 -CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATC-AAG-TT-TTA
* * * * * *
17110449 -GGTGCACATAGTAGCCTTCACTTAGTACCACACATGTGA-CCA-TTACTTA
1 CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTT--TTA
* **
17110498 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 -CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTG
17110538 TTCATCGATA
Statistics
Matches: 225, Mismatches: 53, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
47 2 0.01
48 6 0.03
49 40 0.18
50 78 0.35
51 93 0.41
52 3 0.01
53 1 0.00
54 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (50 bp):
CGATTCACGTAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTA
Found at i:17110482 original size:102 final size:101
Alignment explanation
Indices: 17110201--17110537 Score: 362
Period size: 102 Copynumber: 3.3 Consensus size: 101
17110191 ATCATTCGAT
* * * * *
17110201 ACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AG-TT-TTACAATTCACGTAGTAGCC
1 ACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTT--AGTGCACATAGTAGCC
* ** * * *
17110263 TTCACTTAGTACTACACACGTGAACAAGT-TTTA-CGAC
64 TTCACTTAGTACCACACATAT-AACCAGTACTTACCGAG
* * * *
17110300 TCACGTAGTAGCCTTCACTCAATACTACACACGTGCTCAAGCTTCTTAGTTCACATAGTAGCCTT
1 ACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTTAGTGCACATAGTAGCCTT
* *
17110365 CACTTAGTACTACACATATAACC-GTAGTTTACCGAG
66 CACTTAGTACCACACATATAACCAGTA-CTTACCGAG
* * *
17110401 ACACGTGGTAGCATTCACACAGTACTACACACGTGCTCAAAGCTTCTTGGTGCACATAGTAGCCT
1 ACACGTAGTAGCCTTCACACAGTACTACACACGTGCTC-AAGCTTCTTAGTGCACATAGTAGCCT
* * * * *
17110466 TCACTTAGTACCACACATGTGACCATTACTTATCGAT
65 TCACTTAGTACCACACATATAACCAGTACTTACCGAG
17110503 ACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 ACACGTAGTAGCCTTCACACAGTACTACACACGTG
17110538 TTCATCGATA
Statistics
Matches: 203, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
98 2 0.01
99 36 0.18
100 39 0.19
101 38 0.19
102 86 0.42
103 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (101 bp):
ACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAGCTTCTTAGTGCACATAGTAGCCTT
CACTTAGTACCACACATATAACCAGTACTTACCGAG
Found at i:17121259 original size:25 final size:25
Alignment explanation
Indices: 17121221--17121268 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
17121211 TCATATTCAT
17121221 GTATGCTCATACGAGCTATGAATCA
1 GTATGCTCATACGAGCTATGAATCA
17121246 GTATGCTC-TCACGAGCTATGAAT
1 GTATGCTCAT-ACGAGCTATGAAT
17121269 TGGGAAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATGAATCA
Found at i:17126894 original size:36 final size:36
Alignment explanation
Indices: 17126854--17126927 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
17126844 GCTGAGAATA
*
17126854 AATTCTCTCTATTTTTCGGAAGAATAATAATATATC
1 AATTCTCTCAATTTTTCGGAAGAATAATAATATATC
* *
17126890 AATTCTCTCAATTTTTCGGTAGAATAATAATATCTC
1 AATTCTCTCAATTTTTCGGAAGAATAATAATATATC
17126926 AA
1 AA
17126928 AAGTCGTCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (36 bp):
AATTCTCTCAATTTTTCGGAAGAATAATAATATATC
Found at i:17133723 original size:28 final size:26
Alignment explanation
Indices: 17133690--17133755 Score: 96
Period size: 28 Copynumber: 2.5 Consensus size: 26
17133680 TTTTACTCTA
17133690 GTAAAATTTTGACGATTTTAAGCCCTCG
1 GTAAAATTTTGACGATTTTAA-CCCT-G
* *
17133718 GTAAAATTTTGACGATTTTAACTCTT
1 GTAAAATTTTGACGATTTTAACCCTG
17133744 GTAAAATTTTGA
1 GTAAAATTTTGA
17133756 AAAAATTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 12 0.33
27 3 0.08
28 21 0.58
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (26 bp):
GTAAAATTTTGACGATTTTAACCCTG
Found at i:17133928 original size:24 final size:24
Alignment explanation
Indices: 17133895--17133952 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
17133885 GGATTGCAAG
*
17133895 TTTCCATTTTCA-TTTTCATTTCCA
1 TTTCCATTTT-AGTTTTCATTTCAA
*
17133919 TTTCCGTTTTAGTTTTCATTTCAA
1 TTTCCATTTTAGTTTTCATTTCAA
*
17133943 TTTACATTTT
1 TTTCCATTTT
17133953 TGGAAACTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.17, C:0.19, G:0.03, T:0.60
Consensus pattern (24 bp):
TTTCCATTTTAGTTTTCATTTCAA
Found at i:17136138 original size:96 final size:96
Alignment explanation
Indices: 17135969--17136160 Score: 285
Period size: 96 Copynumber: 2.0 Consensus size: 96
17135959 TCGAGCAGAA
** *
17135969 CAGAAGAGCGCATCAGTCAGAATAGATCTGAAAGGCTACTAAATTGAATAGAGTTTACTCTTTCC
1 CAGAAGAGCGCATCAGTCAGAATAGATCCAAAAGGCTACTAAACTGAATAGAGTTTACTCTTTCC
*
17136034 TCTTGTTATTTATTTTAATTATGTTTTCTTT
66 TCTTGTTATTTATTTTAATTATGTTTGCTTT
* * ** * *
17136065 CAGAGGAGCGCATCAGTCAGACTAGATCCAAAAGGCTGTTCAACTGAATAGATTTTACTCTTTCC
1 CAGAAGAGCGCATCAGTCAGAATAGATCCAAAAGGCTACTAAACTGAATAGAGTTTACTCTTTCC
*
17136130 TCTTGTTATTTATTTTAGTTATGTTTGCTTT
66 TCTTGTTATTTATTTTAATTATGTTTGCTTT
17136161 GAGTTTATTA
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 85 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (96 bp):
CAGAAGAGCGCATCAGTCAGAATAGATCCAAAAGGCTACTAAACTGAATAGAGTTTACTCTTTCC
TCTTGTTATTTATTTTAATTATGTTTGCTTT
Found at i:17142232 original size:33 final size:33
Alignment explanation
Indices: 17142186--17142336 Score: 160
Period size: 33 Copynumber: 4.5 Consensus size: 33
17142176 TACTCTCTAG
*
17142186 TTGGTGTGCTGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
* * *
17142219 TTGTTGTGATGGTTGGTTTAGCTCTTATTAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
*
17142252 TTGGTGTGATGGTTGGATTAGCTATTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
*** * * *
17142285 CCAGTGTGATGGATGGATTGGCT-TGATTGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTA-TGAGCA
*
17142318 TCTGGTGTGTTTGGTTGGA
1 T-TGGTGTG-ATGGTTGGA
17142337 CTAATGATGT
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
32 2 0.02
33 82 0.85
34 5 0.05
35 7 0.07
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (33 bp):
TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
Found at i:17148750 original size:23 final size:22
Alignment explanation
Indices: 17148723--17148771 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
17148713 ACTTTAGTCC
17148723 TTAG-TTTTGAATTGATTGTAAAT
1 TTAGCTTTTGAA-TG-TTGTAAAT
*
17148746 TTAGTCTTTTGAATGTTGTAATT
1 TTAG-CTTTTGAATGTTGTAAAT
17148769 TTA
1 TTA
17148772 ATGCGATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 14 0.61
24 2 0.09
25 7 0.30
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.55
Consensus pattern (22 bp):
TTAGCTTTTGAATGTTGTAAAT
Found at i:17148861 original size:3 final size:3
Alignment explanation
Indices: 17148853--17148878 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17148843 ACAACTAAAC
17148853 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
17148879 GTACTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17149039 original size:13 final size:13
Alignment explanation
Indices: 17149023--17149051 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17149013 TTTAAGATAT
17149023 ATTATTATTTTTA
1 ATTATTATTTTTA
17149036 ATTATTATTTTTA
1 ATTATTATTTTTA
17149049 ATT
1 ATT
17149052 TATCATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTATTATTTTTA
Found at i:17149203 original size:16 final size:16
Alignment explanation
Indices: 17149178--17149212 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
17149168 TATCATATAC
*
17149178 ATTCTTTAATATTTTT
1 ATTCTATAATATTTTT
17149194 ATTCTATAATATTTTT
1 ATTCTATAATATTTTT
17149210 ATT
1 ATT
17149213 TAATTTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTCTATAATATTTTT
Found at i:17154222 original size:13 final size:13
Alignment explanation
Indices: 17154206--17154263 Score: 50
Period size: 12 Copynumber: 4.6 Consensus size: 13
17154196 AAAAAAAATC
17154206 AAAATCAAAATA-A
1 AAAATCAAAA-AGA
17154219 AAAA-CAAAAAGA
1 AAAATCAAAAAGA
***
17154231 AAAATCAAAGTCA
1 AAAATCAAAAAGA
*
17154244 AAAGT-AAAAAGA
1 AAAATCAAAAAGA
17154256 AAAATCAA
1 AAAATCAA
17154264 TCAAAGTCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
11 1 0.03
12 18 0.53
13 15 0.44
ACGTcount: A:0.74, C:0.09, G:0.07, T:0.10
Consensus pattern (13 bp):
AAAATCAAAAAGA
Found at i:17154235 original size:31 final size:31
Alignment explanation
Indices: 17154193--17154253 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
17154183 AGCTCGGATT
17154193 CAAAAAAAAAATCAAAATCAAAA-TAAAAAA
1 CAAAAAAAAAATCAAAATCAAAAGTAAAAAA
*
17154223 CAAAAAGAAAAATCAAAGTCAAAAGTAAAAA
1 CAAAAA-AAAAATCAAAATCAAAAGTAAAAA
17154254 GAAAAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 6 0.21
31 16 0.57
32 6 0.21
ACGTcount: A:0.75, C:0.10, G:0.05, T:0.10
Consensus pattern (31 bp):
CAAAAAAAAAATCAAAATCAAAAGTAAAAAA
Found at i:17154246 original size:25 final size:24
Alignment explanation
Indices: 17154192--17154263 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 24
17154182 GAGCTCGGAT
**
17154192 TCAAAAAAAAAATCAAAATCAAAA
1 TCAAAAAAAAAAGAAAAATCAAAA
* *
17154216 TAAAAAACAAAAAGAAAAATCAAAG
1 TCAAAAA-AAAAAGAAAAATCAAAA
*
17154241 TCAAAAGTAAAAAGAAAAATCAA
1 TCAAAA-AAAAAAGAAAAATCAA
17154264 TCAAAGTCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 6 0.15
25 34 0.85
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.11
Consensus pattern (24 bp):
TCAAAAAAAAAAGAAAAATCAAAA
Found at i:17155155 original size:6 final size:7
Alignment explanation
Indices: 17155136--17155191 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
17155126 AAAAAAAAGG
17155136 TGAAAAA
1 TGAAAAA
17155143 TGAAAAA
1 TGAAAAA
17155150 TGAAAAA
1 TGAAAAA
17155157 TG-AAAA
1 TGAAAAA
*
17155163 CGAAAAA
1 TGAAAAA
17155170 TG-AAAA
1 TGAAAAA
17155176 TGAAAAA
1 TGAAAAA
17155183 -GTAAAAA
1 TG-AAAAA
17155190 TG
1 TG
17155192 GAGAGGCTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
6 12 0.28
7 30 0.70
8 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.16, T:0.14
Consensus pattern (7 bp):
TGAAAAA
Found at i:17155162 original size:20 final size:19
Alignment explanation
Indices: 17155136--17155191 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
17155126 AAAAAAAAGG
17155136 TGAAAAATGAAAAATGAAAAA
1 TGAAAAA-GAAAAATG-AAAA
*
17155157 TGAAAACGAAAAATGAAAA
1 TGAAAAAGAAAAATGAAAA
17155176 TGAAAAAGTAAAAATG
1 TGAAAAAG-AAAAATG
17155192 GAGAGGCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 11 0.34
20 15 0.47
21 6 0.19
ACGTcount: A:0.68, C:0.02, G:0.16, T:0.14
Consensus pattern (19 bp):
TGAAAAAGAAAAATGAAAA
Found at i:17155188 original size:13 final size:13
Alignment explanation
Indices: 17155136--17155182 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
17155126 AAAAAAAAGG
17155136 TGAAAAATGAAAAA
1 TGAAAAATG-AAAA
17155150 TGAAAAATGAAAA
1 TGAAAAATGAAAA
*
17155163 CGAAAAATGAAAA
1 TGAAAAATGAAAA
17155176 TGAAAAA
1 TGAAAAA
17155183 GTAAAAATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 22 0.71
14 9 0.29
ACGTcount: A:0.70, C:0.02, G:0.15, T:0.13
Consensus pattern (13 bp):
TGAAAAATGAAAA
Found at i:17155189 original size:14 final size:13
Alignment explanation
Indices: 17155136--17155191 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
17155126 AAAAAAAAGG
17155136 TGAAAAATGAAAAA
1 TGAAAAAT-AAAAA
*
17155150 TGAAAAATGAAAA
1 TGAAAAATAAAAA
* *
17155163 CGAAAAATGAAAA
1 TGAAAAATAAAAA
17155176 TGAAAAAGTAAAAA
1 TGAAAAA-TAAAAA
17155190 TG
1 TG
17155192 GAGAGGCTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
13 22 0.59
14 15 0.41
ACGTcount: A:0.68, C:0.02, G:0.16, T:0.14
Consensus pattern (13 bp):
TGAAAAATAAAAA
Found at i:17156620 original size:44 final size:44
Alignment explanation
Indices: 17156554--17156666 Score: 156
Period size: 44 Copynumber: 2.6 Consensus size: 44
17156544 GGAAATGGTG
*
17156554 AATCTTATCTCCCTGATG-TTACAGTAGAGAAAATTAAAGCTAGA
1 AATCTTATCTCCCTGA-GATTACAGTAGAGAAAATTAAAGCAAGA
* * * * *
17156598 AATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCAAGT
1 AATCTTATCTCCCTGAGATTACAGTAGAGAAAATTAAAGCAAGA
17156642 AATCTTATCTCCCTGAGATTACAGT
1 AATCTTATCTCCCTGAGATTACAGT
17156667 GGAGCGGATT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 1 0.02
44 60 0.98
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTAGAGAAAATTAAAGCAAGA
Found at i:17156691 original size:44 final size:44
Alignment explanation
Indices: 17156554--17156701 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 44
17156544 GGAAATGGTG
* * * ** *
17156554 AATCTTATCTCCCTGATG-TTACAGTAGAGAAAATTAAAGCTAGA
1 AATCTTATCTCCCTGA-GATTACAGCAGAGCAGATTAAAGAAAGT
* *
17156598 AATCTTATCTCCCTGAGATTACAGCAGAGCAGATTGAAGCAAGT
1 AATCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAGAAAGT
** * *
17156642 AATCTTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG-
1 AATCTTATCTCCCTGAGATTACAGCAGAGCAGATT-AAAGAAAGT
* *
17156686 GATCTTATCTCTCTGA
1 AATCTTATCTCCCTGA
17156702 AGTTACAATA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
43 1 0.01
44 82 0.93
45 5 0.06
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGCAGAGCAGATTAAAGAAAGT
Found at i:17156857 original size:50 final size:50
Alignment explanation
Indices: 17156803--17157368 Score: 353
Period size: 50 Copynumber: 11.3 Consensus size: 50
17156793 GCAGTGGAGC
*
17156803 AGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * ** **
17156853 AGATTAAAGCCACAAC-GACGAATCTTACTTCTCTGGCGA-TGCAGTGGAGC
1 AGATTAAAGCCACAACAG-TGAATCTTGCTTCCCCGAC-ATTGCAGTTAAAA
* * * * * *
17156903 AGATTAAGGCCACATCGGCGAATCTCGCTTCCCCGAGATTGCAGTTAAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTT-AAAA
* * * * * * * * ** **
17156954 AAATTAAAGCTAAAACAGTGAATCTTACCTCCCTGGCGA-TGCAATGGAGC
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGAC-ATTGCAGTTAAAA
* * *
17157004 AGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAACATTGCAATTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * **
17157054 AGGTTAAAGCCACAGCGGCGAATCTTACTTCTCTGGCGA-TGCAG-TAGAGC
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGAC-ATTGCAGTTA-AAA
*** *
17157104 AGATTAAAGCCACATTGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * *** *
17157154 AGATTAATGCTACAACAGTGAATCTTAC-TCCCCAGGCGA-TGCAGCGGAAC
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCC-GAC-ATTGCAGTTAAAA
* *
17157204 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCAACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * *
17157254 AGATTAAAGCTACAACAGCGAATCTTAC-TCCCCAGGCGA-TGCAG-CAGAACA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCC-GAC-ATTGCAGTTA-AA-A
* * * *
17157305 A-ATTAAAGCCACGACGGTGTATCTTGCTTCCTCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* *
17157354 AGATTGAAGCTACAA
1 AGATTAAAGCCACAA
17157369 GCTACGAATC
Statistics
Matches: 376, Mismatches: 117, Indels: 46
0.70 0.22 0.09
Matches are distributed among these distances:
49 21 0.06
50 305 0.81
51 49 0.13
52 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:17156947 original size:100 final size:100
Alignment explanation
Indices: 17156774--17157368 Score: 753
Period size: 100 Copynumber: 5.9 Consensus size: 100
17156764 AGAATTACAG
* ** * *
17156774 ATCTTACCTCCCAAGCGGTGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGA
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
*
17156839 CATTGCAGTTAAAAAGATTAAAGCCACAAC-GACGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAG-CGA
* * * *
17156874 ATCTTACTTCTCTGGCGATGCAGTGGAGCAGATTAAGGCCACATCGGCGAATCTCGCTTCCCCGA
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
* * * *
17156939 GATTGCAGTTAAAAAAAATTAAAGCTAAAACAGTGA
66 CATTGCAGTT-AAAAAGATTAAAGCTACAACAGCGA
* * * *
17156975 ATCTTACCTCCCTGGCGATGCAATGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAA
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
* * * * *
17157040 CATTGCAATTAAAAAGGTTAAAGCCACAGCGGCGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
* * * *
17157075 ATCTTACTTCTCTGGCGATGCAGTAGAGCAGATTAAAGCCACATTGGTGAATCTCGCTTCCCCGA
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
* *
17157140 CATTGCAGTTAAAAAGATTAATGCTACAACAGTGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
* * * * * *
17157175 ATCTTACTCCCCAGGCGATGCAGCGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCAA
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
17157240 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
* * ** * * * *
17157275 ATCTTACTCCCCAGGCGATGCAGCAGAACAAATTAAAGCCACGA-CGGTGTATCTTGCTTCCTCG
1 ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCCG
*
17157339 ACATTGCAGTTAAAAAGATTGAAGCTACAA
65 ACATTGCAGTTAAAAAGATTAAAGCTACAA
17157369 GCTACGAATC
Statistics
Matches: 428, Mismatches: 64, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
100 342 0.80
101 85 0.20
102 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
ATCTTACTTCCCTGGCGATGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
Found at i:17157129 original size:201 final size:201
Alignment explanation
Indices: 17156774--17157354 Score: 835
Period size: 200 Copynumber: 2.9 Consensus size: 201
17156764 AGAATTACAG
* * *
17156774 ATCTTACCTCCCAAGCGGTGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCGA
1 ATCTTACCTCCCAGGCGATGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAA
* *
17156839 CATTGCAGTTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCTCTGGCGATGCAGTGGAGCA
66 CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCTCTGGCGATGCAGTAGAGCA
* * *
17156904 GATTAAGGCCACATCGGCGAATCTCGCTTCCCCGAGATTGCAGTTAAAAAAAATTAAAGCTAAAA
131 GATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAAAAAATTAAAGCTAAAA
17156969 CAGTGA
196 CAGTGA
* *
17156975 ATCTTACCTCCCTGGCGATGCAATGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAA
1 ATCTTACCTCCCAGGCGATGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAA
* * *
17157040 CATTGCAATTAAAAAGGTTAAAGCCACAGCGGCGAATCTTACTTCTCTGGCGATGCAGTAGAGCA
66 CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCTCTGGCGATGCAGTAGAGCA
* * * *
17157105 GATTAAAGCCACATTGGTGAATCTCGCTTCCCCGACATTGCAGTT-AAAAAGATTAATGCTACAA
131 GATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAAAAAATTAAAGCTAAAA
17157169 CAGTGA
196 CAGTGA
* * * *
17157175 ATCTTA-CTCCCCAGGCGATGCAGCGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCA
1 ATCTTACCT-CCCAGGCGATGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCA
* * * * * * *
17157239 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGATGCAGCAGAAC
65 ACATTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCTCTGGCGATGCAGTAGAGC
* * * *
17157304 AAATTAAAGCCACGA-CGGTGTATCTTGCTTCCTCGACATTGCAGTTAAAAA
130 AGATTAAAGCCAC-ATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAAA
17157355 GATTGAAGCT
Statistics
Matches: 339, Mismatches: 38, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
199 2 0.01
200 171 0.50
201 166 0.49
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (201 bp):
ATCTTACCTCCCAGGCGATGCAGTGGAGCAGATTAAAGCCACATCAGTGAATCTTGCTTCCCCAA
CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGAATCTTACTTCTCTGGCGATGCAGTAGAGCA
GATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAAAAAATTAAAGCTAAAA
CAGTGA
Found at i:17157953 original size:7 final size:7
Alignment explanation
Indices: 17157919--17157973 Score: 56
Period size: 8 Copynumber: 7.3 Consensus size: 7
17157909 ACAAAAGAAC
*
17157919 AAAAAGG
1 AAAAAAG
17157926 AAGAAAAG
1 AA-AAAAG
*
17157934 AAAACAG
1 AAAAAAG
17157941 AAAAAAGAG
1 -AAAAA-AG
17157950 AAAAAAG
1 AAAAAAG
17157957 AAAGAAAG
1 AAA-AAAG
17157965 AAAAAAG
1 AAAAAAG
17157972 AA
1 AA
17157974 CAGAAAAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
7 17 0.41
8 22 0.54
9 2 0.05
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:17157953 original size:16 final size:16
Alignment explanation
Indices: 17157919--17157979 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
17157909 ACAAAAGAAC
*
17157919 AAAAAGGAAGAAA-AG
1 AAAAAGAAAGAAAGAG
17157934 AAAACAGAAA-AAAGAG
1 AAAA-AGAAAGAAAGAG
17157950 AAAAAAGAAAGAAAGA-
1 -AAAAAGAAAGAAAGAG
17157966 AAAAAGAACAGAAA
1 AAAAAGAA-AGAAA
17157980 AGAGGACGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
15 15 0.38
16 16 0.40
17 9 0.22
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAGAG
Found at i:17157956 original size:9 final size:8
Alignment explanation
Indices: 17157911--17157970 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 8
17157901 CGCAGCACAC
17157911 AAAAGAACA
1 AAAAGAA-A
*
17157920 AAAAGGAAG
1 AAAA-GAAA
17157929 AAAAG-AA
1 AAAAGAAA
*
17157936 AACAG-AA
1 AAAAGAAA
17157943 AAAAGAGAA
1 AAAAGA-AA
17157952 AAAAGAAA
1 AAAAGAAA
*
17157960 GAAAGAAA
1 AAAAGAAA
17157968 AAA
1 AAA
17157971 GAACAGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
7 11 0.26
8 12 0.29
9 16 0.38
10 3 0.07
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:17157965 original size:31 final size:32
Alignment explanation
Indices: 17157911--17157973 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
17157901 CGCAGCACAC
* *
17157911 AAAAGAACAAAAAGGAAGAAAAGAAAACAGAA
1 AAAAGAACAAAAAGAAAGAAAAGAAAAAAGAA
17157943 AAAAGAGA-AAAAAGAAAG-AAAGAAAAAAGAA
1 AAAAGA-ACAAAAAGAAAGAAAAGAAAAAAGAA
17157974 CAGAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 12 0.43
32 15 0.54
33 1 0.04
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (32 bp):
AAAAGAACAAAAAGAAAGAAAAGAAAAAAGAA
Found at i:17157966 original size:24 final size:24
Alignment explanation
Indices: 17157919--17157982 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 24
17157909 ACAAAAGAAC
*
17157919 AAAAAG-GAAGAAAAGAAAACAGA
1 AAAAAGAGAAGAAAAGAAAAAAGA
17157942 AAAAAGAGAA-AAAAGAAAGAAAGA
1 AAAAAGAGAAGAAAAGAAA-AAAGA
17157966 AAAAAGA-ACAGAAAAGA
1 AAAAAGAGA-AGAAAAGA
17157983 GGACGATGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 15 0.42
24 15 0.42
25 6 0.17
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (24 bp):
AAAAAGAGAAGAAAAGAAAAAAGA
Found at i:17158743 original size:23 final size:22
Alignment explanation
Indices: 17158716--17158764 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
17158706 ACTTCAGTCC
17158716 TTAGT-TTTGAATTGATTGTAAAT
1 TTAGTCTTTGAA-TG-TTGTAAAT
*
17158739 TTAGTCCTTTGAATGTTGTAATT
1 TTAGT-CTTTGAATGTTGTAAAT
17158762 TTA
1 TTA
17158765 ATGCGATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 15 0.65
24 2 0.09
25 6 0.26
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.53
Consensus pattern (22 bp):
TTAGTCTTTGAATGTTGTAAAT
Found at i:17159173 original size:16 final size:16
Alignment explanation
Indices: 17159148--17159182 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
17159138 TATCATATAC
*
17159148 ATTCTTTAATATTTTT
1 ATTCTATAATATTTTT
17159164 ATTCTATAATATTTTT
1 ATTCTATAATATTTTT
17159180 ATT
1 ATT
17159183 TAATTTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTCTATAATATTTTT
Found at i:17161506 original size:10 final size:10
Alignment explanation
Indices: 17161467--17161557 Score: 84
Period size: 10 Copynumber: 9.3 Consensus size: 10
17161457 TCAAATAATT
17161467 AAAATT-TTA
1 AAAATTATTA
17161476 AAAATT-TTA
1 AAAATTATTA
*
17161485 AAAATTCTTTA
1 AAAATT-ATTA
17161496 AAAATTATTA
1 AAAATTATTA
*
17161506 AGAATTA-TA
1 AAAATTATTA
17161515 AATAATTA-TA
1 AA-AATTATTA
*
17161525 AATAATCATTA
1 AA-AATTATTA
17161536 AAAATT-TTA
1 AAAATTATTA
*
17161545 AAAAATATTA
1 AAAATTATTA
17161555 AAA
1 AAA
17161558 CCATACATAC
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
9 26 0.37
10 32 0.45
11 13 0.18
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (10 bp):
AAAATTATTA
Found at i:17164002 original size:48 final size:48
Alignment explanation
Indices: 17163962--17164083 Score: 190
Period size: 48 Copynumber: 2.5 Consensus size: 48
17163952 ACAGACTCTC
*
17163962 GGTGGCCTGCACATAGTCCGTGCCACCCTTATATCTTAACAGAATATT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTATATCTTAACAGAATATT
* * *
17164010 GGTGGCCTGCACACAATCCGTGCCACCCTTGTATCTTAAAAGAATATT
1 GGTGGCCTGCACACAGTCCGTGCCACCCTTATATCTTAACAGAATATT
* *
17164058 GGTGGCCTACACACAGCCCGTGCCAC
1 GGTGGCCTGCACACAGTCCGTGCCAC
17164084 ATATGCGACC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (48 bp):
GGTGGCCTGCACACAGTCCGTGCCACCCTTATATCTTAACAGAATATT
Found at i:17191564 original size:87 final size:86
Alignment explanation
Indices: 17191469--17191627 Score: 239
Period size: 87 Copynumber: 1.8 Consensus size: 86
17191459 TTAAGTTCAA
* *
17191469 TGAATTCATCAAGTCCATCTCAATAA-GACCACCCGAAATCTGAGATATGAACTCATTAACCGTA
1 TGAATTCATCAAGTCCATCTCAA-AAGGACCACCCAAAATCTGAGATATGAACTCATTAACAGTA
17191533 ATAAACTCAACCTCTCAAGTTGG
65 A-AAACTCAACCTCTCAAGTTGG
* * * *
17191556 TGAATTCATCAAGTCCATCTCAAAAGGACCACCCAAAATCTGGGCTATGAATTCATTAAGAGTAA
1 TGAATTCATCAAGTCCATCTCAAAAGGACCACCCAAAATCTGAGATATGAACTCATTAACAGTAA
17191621 AAACTCA
66 AAACTCA
17191628 TCCTTATGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
86 9 0.14
87 56 0.86
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (86 bp):
TGAATTCATCAAGTCCATCTCAAAAGGACCACCCAAAATCTGAGATATGAACTCATTAACAGTAA
AAACTCAACCTCTCAAGTTGG
Found at i:17194709 original size:21 final size:21
Alignment explanation
Indices: 17194685--17194724 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17194675 AACCACATGT
17194685 CCACAAAAT-CTTCAACAACCC
1 CCACAAAATCCTT-AACAACCC
*
17194706 CCACTAAATCCTTAACAAC
1 CCACAAAATCCTTAACAAC
17194725 TTTACATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.17
Consensus pattern (21 bp):
CCACAAAATCCTTAACAACCC
Found at i:17198030 original size:29 final size:28
Alignment explanation
Indices: 17197995--17198072 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
17197985 TCATGAGATT
17197995 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
17198025 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
17198052 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
17198073 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:17205607 original size:30 final size:30
Alignment explanation
Indices: 17205572--17205640 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
17205562 ATACAAAGAG
*
17205572 CACACGATCGTGTCACATGCCCGTGTGTGA
1 CACACGACCGTGTCACATGCCCGTGTGTGA
17205602 CACACGACCGTGTCACATGCCCGTGTGTGA
1 CACACGACCGTGTCACATGCCCGTGTGTGA
17205632 CACACGACC
1 CACACGACC
17205641 ATGTGTCAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.19
Consensus pattern (30 bp):
CACACGACCGTGTCACATGCCCGTGTGTGA
Found at i:17205612 original size:17 final size:17
Alignment explanation
Indices: 17205592--17205646 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
17205582 TGTCACATGC
17205592 CCGTGTGTGACACACGA
1 CCGTGTGTGACACACGA
* *
17205609 CC--GTGT--CACATGC
1 CCGTGTGTGACACACGA
17205622 CCGTGTGTGACACACGA
1 CCGTGTGTGACACACGA
*
17205639 CCATGTGT
1 CCGTGTGT
17205647 CAGCCTGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
13 7 0.24
15 8 0.28
17 14 0.48
ACGTcount: A:0.20, C:0.31, G:0.27, T:0.22
Consensus pattern (17 bp):
CCGTGTGTGACACACGA
Found at i:17207322 original size:17 final size:16
Alignment explanation
Indices: 17207291--17207329 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
17207281 TTTTGAGTTA
*
17207291 TTTTTAAATTTTTTAG
1 TTTTTAAATTATTTAG
17207307 TTTTTAATATTATTTAG
1 TTTTTAA-ATTATTTAG
17207324 TCTTTT
1 T-TTTT
17207330 TATAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTTTAAATTATTTAG
Found at i:17217961 original size:83 final size:83
Alignment explanation
Indices: 17217859--17218037 Score: 286
Period size: 83 Copynumber: 2.2 Consensus size: 83
17217849 TTCAGTTAAT
* ** * *
17217859 GGTTAATTCGGTTTGAAATCGATTAATTAACTGAACTTAATAAATAATATTATATATTATATGCA
1 GGTTAATTCAGTTCAAAATCGATTAATTAACCGAACTTAATAAATAATAGTATATATTATATGCA
*
17217924 TTAGGCTATTCCTAGTTC
66 TTAGGCTATTACTAGTTC
*
17217942 GGTTAATTCAGTTCAAAATCGATTAATTAACCGAATTTAATAAATAATAGTATATATTATATGCA
1 GGTTAATTCAGTTCAAAATCGATTAATTAACCGAACTTAATAAATAATAGTATATATTATATGCA
17218007 TTAGGCTATTACTAGTTC
66 TTAGGCTATTACTAGTTC
*
17218025 GGTTAATTTAGTT
1 GGTTAATTCAGTT
17218038 AATCCGATTA
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 88 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (83 bp):
GGTTAATTCAGTTCAAAATCGATTAATTAACCGAACTTAATAAATAATAGTATATATTATATGCA
TTAGGCTATTACTAGTTC
Found at i:17219273 original size:3 final size:3
Alignment explanation
Indices: 17219265--17219290 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17219255 GATGAAGTTT
17219265 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
17219291 AATTCTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:17238180 original size:19 final size:19
Alignment explanation
Indices: 17238158--17238197 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17238148 ATTAATTTTG
* *
17238158 ATCAAGTAAATTTAAATTA
1 ATCAAATAAATTAAAATTA
*
17238177 ATCAAATCAATTAAAATTA
1 ATCAAATAAATTAAAATTA
17238196 AT
1 AT
17238198 ATGATATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:17243169 original size:84 final size:84
Alignment explanation
Indices: 17243078--17243245 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
17243068 AGATCTTGTT
17243078 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
1 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
17243143 TTTTTCCAACATGCTTGCC
66 TTTTTCCAACATGCTTGCC
17243162 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
1 TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
17243227 TTTTTCCAACATGCTTGCC
66 TTTTTCCAACATGCTTGCC
17243246 ACAACAAGAC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (84 bp):
TTGAAAAAAAAATTAAACCTCTAATTTTTCCCTAAATTTATTTTCCGCTGCATTTTCCAAACCCA
TTTTTCCAACATGCTTGCC
Found at i:17245477 original size:27 final size:27
Alignment explanation
Indices: 17245390--17245488 Score: 96
Period size: 27 Copynumber: 3.6 Consensus size: 27
17245380 AAAGGTATAT
17245390 TTTCTTGTCCATAGTTTTGTGAATCGG
1 TTTCTTGTCCATAGTTTTGTGAATCGG
* * * *
17245417 TTTCTGGGT---TAGTTCCTTTATGTTATTGG
1 TTTCT-TGTCCATAG-T--TTTGTG-AATCGG
17245446 TTTCTTGTCCATAGTTTTGTGAATCGG
1 TTTCTTGTCCATAGTTTTGTGAATCGG
17245473 TTTCTTGTCCATAGTT
1 TTTCTTGTCCATAGTT
17245489 AGAAAGATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 25 0.45
28 14 0.25
29 9 0.16
30 1 0.02
31 3 0.05
ACGTcount: A:0.13, C:0.14, G:0.21, T:0.52
Consensus pattern (27 bp):
TTTCTTGTCCATAGTTTTGTGAATCGG
Found at i:17247312 original size:26 final size:26
Alignment explanation
Indices: 17247283--17247333 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
17247273 CCTCAAACTA
17247283 TAATCTAGATATTAAATTGGTCTCTC
1 TAATCTAGATATTAAATTGGTCTCTC
*
17247309 TAATCTAGATTTTAAATTGGTCTCT
1 TAATCTAGATATTAAATTGGTCTCT
17247334 ATAAATTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (26 bp):
TAATCTAGATATTAAATTGGTCTCTC
Found at i:17247693 original size:20 final size:20
Alignment explanation
Indices: 17247668--17247707 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17247658 AATATTTTTT
*
17247668 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
17247688 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
17247708 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:17249594 original size:27 final size:26
Alignment explanation
Indices: 17249540--17249594 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
17249530 TTATACACAT
*
17249540 TTATATATTTTTATATTTTTTAAAAA
1 TTATATATTTTTATATTTTCTAAAAA
*
17249566 TTAT-TATTTTTATAGATTTTCTAATAA
1 TTATATATTTTTAT--ATTTTCTAAAAA
17249593 TT
1 TT
17249595 TTTAGTGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.36
26 4 0.16
27 12 0.48
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTATATATTTTTATATTTTCTAAAAA
Found at i:17253640 original size:19 final size:20
Alignment explanation
Indices: 17253582--17253642 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
17253572 GAAGATAATA
* *
17253582 AAAAATATAAAA--ATTATG
1 AAAAATAGAAAATTATTATT
*
17253600 AAAAATAGAAAATTTTTATT
1 AAAAATAGAAAATTATTATT
17253620 AAAAATAGAAAGA-TATT-TT
1 AAAAATAGAAA-ATTATTATT
17253639 AAAA
1 AAAA
17253643 TCATAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.31
19 6 0.17
20 18 0.50
21 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (20 bp):
AAAAATAGAAAATTATTATT
Done.