Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 131 of 175
Found at i:40834889 original size:25 final size:25
Alignment explanation
Indices: 40834825--40834893 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
40834815 ACATTTGTGC
40834825 GAGAAAGCCTTTT-GATT--CCATCT
1 GAGAAA-CCTTTTCGATTACCCATCT
*
40834848 GA-AAA-GTTCTTCGATTACCCATCT
1 GAGAAACCTT-TTCGATTACCCATCT
40834872 GAGAAACCTTTTCGATTACCCA
1 GAGAAACCTTTTCGATTACCCA
40834894 GCCATCTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 7 0.18
23 2 0.05
24 8 0.21
25 15 0.39
26 2 0.05
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (25 bp):
GAGAAACCTTTTCGATTACCCATCT
Found at i:40835448 original size:9 final size:9
Alignment explanation
Indices: 40835434--40835531 Score: 65
Period size: 9 Copynumber: 10.6 Consensus size: 9
40835424 ATCTGTTATG
40835434 TATGTATAT
1 TATGTATAT
*
40835443 TATGTATGT
1 TATGTATAT
40835452 TATGTATAT
1 TATGTATAT
*
40835461 TATTGTTTAT
1 TA-TGTATAT
*
40835471 GTCTGTATAT
1 -TATGTATAT
* *
40835481 TACGTATGT
1 TATGTATAT
40835490 TATGTAGTA-
1 TATGTA-TAT
40835499 TAT-TACTATT
1 TATGTA-TA-T
* *
40835509 TTTGTATTT
1 TATGTATAT
*
40835518 TATGTATGT
1 TATGTATAT
40835527 TATGT
1 TATGT
40835532 TATGTTTATT
Statistics
Matches: 68, Mismatches: 15, Indels: 12
0.72 0.16 0.13
Matches are distributed among these distances:
8 4 0.06
9 45 0.66
10 16 0.24
11 3 0.04
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.57
Consensus pattern (9 bp):
TATGTATAT
Found at i:40835472 original size:38 final size:38
Alignment explanation
Indices: 40835429--40835580 Score: 130
Period size: 38 Copynumber: 3.9 Consensus size: 38
40835419 AGTATATCTG
40835429 TTATGTATGTATATTATGTATGTTATGTATATTATTGT
1 TTATGTATGTATATTATGTATGTTATGTATATTATTGT
* * * *
40835467 TTATGTCTGTATATTACGTATGTTATGTAGTATATTACTAT
1 TTATGTATGTATATTATGTATGTTA--T-GTATATTATTGT
* * *
40835508 TTTTGTAT-TTTATGTATGTTATGTTATGTTTATTATTGT
1 TTATGTATGTATAT-TATG-TATGTTATGTATATTATTGT
* * *
40835547 TTATAATATGTATGTTTAT-CATG-TATGTATATTA
1 TTAT-GTATGTAT-ATTATGTATGTTATGTATATTA
40835581 CAATTTATAT
Statistics
Matches: 89, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
38 33 0.37
39 15 0.17
40 9 0.10
41 24 0.27
42 8 0.09
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (38 bp):
TTATGTATGTATATTATGTATGTTATGTATATTATTGT
Found at i:40838964 original size:14 final size:14
Alignment explanation
Indices: 40838945--40838976 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
40838935 CCATGGATAA
*
40838945 TTTGATGGTTTTAT
1 TTTGATGGTTCTAT
40838959 TTTGATGGTTCTAT
1 TTTGATGGTTCTAT
40838973 TTTG
1 TTTG
40838977 TTGGATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.22, T:0.62
Consensus pattern (14 bp):
TTTGATGGTTCTAT
Found at i:40854087 original size:15 final size:15
Alignment explanation
Indices: 40854066--40854108 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
40854056 AGAAGGGAAT
40854066 AAGAAAAGGAAAGAA
1 AAGAAAAGGAAAGAA
* * *
40854081 AATAAAAAGAAAGAG
1 AAGAAAAGGAAAGAA
40854096 AAGAAAAGTGAAA
1 AAGAAAAG-GAAA
40854109 AGGGAGTGAG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (15 bp):
AAGAAAAGGAAAGAA
Found at i:40865909 original size:12 final size:13
Alignment explanation
Indices: 40865884--40865912 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40865874 GATACAGTGT
40865884 AGAATAAGGGAGG
1 AGAATAAGGGAGG
40865897 AGAATAA-GGAGG
1 AGAATAAGGGAGG
40865909 AGAA
1 AGAA
40865913 ATGGAAGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.41, T:0.07
Consensus pattern (13 bp):
AGAATAAGGGAGG
Found at i:40868497 original size:9 final size:9
Alignment explanation
Indices: 40868478--40868562 Score: 68
Period size: 9 Copynumber: 9.1 Consensus size: 9
40868468 ATTAAATTTT
40868478 AATTA-AAA
1 AATTATAAA
*
40868486 AATTAGAAA
1 AATTATAAA
40868495 AATTATAAA
1 AATTATAAA
40868504 AATTAT-AA
1 AATTATAAA
40868512 AATCGTA-AAA
1 AAT--TATAAA
40868522 GAATTTATAAA
1 -AA-TTATAAA
*
40868533 TAATTTTAAA
1 -AATTATAAA
*
40868543 ATTTTATAAA
1 A-ATTATAAA
40868553 AATTATAAA
1 AATTATAAA
40868562 A
1 A
40868563 TATATAGAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
8 10 0.16
9 26 0.41
10 19 0.30
11 7 0.11
12 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (9 bp):
AATTATAAA
Found at i:40868503 original size:19 final size:19
Alignment explanation
Indices: 40868481--40868572 Score: 53
Period size: 20 Copynumber: 4.7 Consensus size: 19
40868471 AAATTTTAAT
40868481 TAAAAAATTAGAAAAATTA
1 TAAAAAATTAGAAAAATTA
* **
40868500 T-AAAAATTA-TAAAATCG
1 TAAAAAATTAGAAAAATTA
* *
40868517 TAAAAGAATTTATAAATAATTT
1 TAAAA-AA-TTAGAAA-AATTA
** *
40868539 TAAAATTTTATAAAAATTA
1 TAAAAAATTAGAAAAATTA
*
40868558 TAAAATATATAGAAA
1 TAAAAAAT-TAGAAA
40868573 TATAGAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
17 6 0.11
18 11 0.20
19 14 0.25
20 15 0.27
21 2 0.04
22 8 0.14
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (19 bp):
TAAAAAATTAGAAAAATTA
Found at i:40868592 original size:49 final size:49
Alignment explanation
Indices: 40868482--40868601 Score: 120
Period size: 49 Copynumber: 2.5 Consensus size: 49
40868472 AATTTTAATT
* * * * *
40868482 AAAAAATTAGAAAA-ATTATAAAAATTATAAAATCGTAAAAGAATTTAT
1 AAAAAATTATAAAATTTTATAAAAATTATAAAATCATAAAAGAATATAA
* * *
40868530 AAATAATTTTAAAATTTTATAAAAATTATAAAAT-AT-ATAGAAATATAGA
1 AAAAAATTATAAAATTTTATAAAAATTATAAAATCATAAAAG-AATATA-A
*
40868579 AAAAAATTATAAAATTGTATAAA
1 AAAAAATTATAAAATTTTATAAA
40868602 GTCGTAAGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
47 3 0.05
48 17 0.29
49 38 0.66
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.33
Consensus pattern (49 bp):
AAAAAATTATAAAATTTTATAAAAATTATAAAATCATAAAAGAATATAA
Found at i:40869781 original size:22 final size:22
Alignment explanation
Indices: 40869756--40869864 Score: 66
Period size: 22 Copynumber: 4.9 Consensus size: 22
40869746 ATTAAATATT
40869756 ATTTTAAATATAATTTAAAAAA
1 ATTTTAAATATAATTTAAAAAA
* *
40869778 A-TTTGAATAT-CTTTAAAAATA
1 ATTTTAAATATAATTTAAAAA-A
**
40869799 ATTTTAAA-A-AATTATATTTAAA
1 ATTTTAAATATAATT-TA-AAAAA
* **
40869821 ATTTTAAAAAATAATTT-TTAAA
1 ATTTT-AAATATAATTTAAAAAA
40869843 ATTTTAAAATATACATTTAAAA
1 ATTTT-AAATATA-ATTTAAAA
40869865 TATTATAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
20 8 0.12
21 13 0.19
22 31 0.46
23 9 0.13
24 3 0.04
25 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (22 bp):
ATTTTAAATATAATTTAAAAAA
Found at i:40869861 original size:21 final size:20
Alignment explanation
Indices: 40869798--40869865 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 20
40869788 CTTTAAAAAT
40869798 AATTTTAAAAAATTATATTTAA
1 AATTTTAAAAAA-TA-ATTTAA
40869820 AATTTTAAAAAATAATTTTTAA
1 AATTTTAAAAAATAA--TTTAA
*
40869842 AATTTTAAAATATACATTTAA
1 AATTTTAAAAAATA-ATTTAA
40869863 AAT
1 AAT
40869866 ATTATAAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
20 1 0.02
21 10 0.24
22 30 0.71
23 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTTAAAAAATAATTTAA
Found at i:40869955 original size:13 final size:13
Alignment explanation
Indices: 40869933--40869989 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
40869923 ATGTTTTATA
*
40869933 ATATTAAAAATAT
1 ATATTTAAAATAT
*
40869946 ATATTTAAAATTT
1 ATATTTAAAATAT
*
40869959 AAAATTTAAAATAT
1 -ATATTTAAAATAT
*
40869973 ACATTTAAAATAGT
1 ATATTTAAAATA-T
40869987 ATA
1 ATA
40869990 AAACAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
13 22 0.61
14 14 0.39
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAT
Found at i:40870005 original size:11 final size:11
Alignment explanation
Indices: 40869989--40870028 Score: 53
Period size: 11 Copynumber: 3.4 Consensus size: 11
40869979 AAAATAGTAT
40869989 AAAACAAATAA
1 AAAACAAATAA
40870000 AAAACAAATAAA
1 AAAACAAAT-AA
40870012 GAAGAACAAATAA
1 -AA-AACAAATAA
40870025 AAAA
1 AAAA
40870029 TTAAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.42
12 4 0.15
13 4 0.15
14 7 0.27
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.07
Consensus pattern (11 bp):
AAAACAAATAA
Found at i:40870021 original size:14 final size:12
Alignment explanation
Indices: 40869989--40870028 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 12
40869979 AAAATAGTAT
40869989 AAAACAAAT-AA
1 AAAACAAATAAA
40870000 AAAACAAATAAA
1 AAAACAAATAAA
40870012 GAAGAACAAATAAA
1 -AA-AACAAATAAA
40870026 AAA
1 AAA
40870029 TTAAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.35
12 3 0.12
13 4 0.15
14 10 0.38
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.07
Consensus pattern (12 bp):
AAAACAAATAAA
Found at i:40874811 original size:37 final size:37
Alignment explanation
Indices: 40874770--40874846 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
40874760 GGCTTGATCA
* *
40874770 ATTGATGTTTATATGAATATTAGAATAAGTTATGCGT
1 ATTGATGTCTATATGAATATTAGAATAAGTTATACGT
40874807 ATTGATGTCTATATGAATATTAGAATAAGTTATACGT
1 ATTGATGTCTATATGAATATTAGAATAAGTTATACGT
40874844 ATT
1 ATT
40874847 TTTTATCTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (37 bp):
ATTGATGTCTATATGAATATTAGAATAAGTTATACGT
Found at i:40875654 original size:16 final size:16
Alignment explanation
Indices: 40875635--40875676 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
40875625 GTGTATTAAC
40875635 TTTATTTTTCATTAT-T
1 TTTATTTTT-ATTATAT
*
40875651 TTTATTTTTATTTTAT
1 TTTATTTTTATTATAT
40875667 TTTATTTTTA
1 TTTATTTTTA
40875677 GCTACCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTTTATTATAT
Found at i:40876949 original size:13 final size:13
Alignment explanation
Indices: 40876931--40876964 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
40876921 ATTTTTTAAA
40876931 TTTTGTTTGTTCT-
1 TTTTGTTTGTT-TG
40876944 TTTTGTTTGTTTG
1 TTTTGTTTGTTTG
40876957 TTTTGTTT
1 TTTTGTTT
40876965 TCCACAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 19 0.95
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (13 bp):
TTTTGTTTGTTTG
Found at i:40879294 original size:21 final size:22
Alignment explanation
Indices: 40879252--40879294 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40879242 AACCAAACAA
*
40879252 TTTATTTAATGTTCTTTGTAGT
1 TTTATTTAATGTTCTATGTAGT
*
40879274 TTTATTTTATGTTC-ATGTAGT
1 TTTATTTAATGTTCTATGTAGT
40879295 CAGGATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.63
Consensus pattern (22 bp):
TTTATTTAATGTTCTATGTAGT
Found at i:40890686 original size:51 final size:49
Alignment explanation
Indices: 40890598--40890693 Score: 129
Period size: 51 Copynumber: 1.9 Consensus size: 49
40890588 GTTTTTCAAG
* *
40890598 TCATTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATTATT
1 TCATTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATTATT
***
40890647 TCATTTCTCTATTTTCATTTTAGAGAAAACTTTAATCATTTCCAAAT
1 TCATTT-TC-ATTTTCATTTTAGAGAAAACCACAATCATTTCCAAAT
40890694 GTTTCTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 6 0.15
50 2 0.05
51 32 0.80
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (49 bp):
TCATTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATTATT
Found at i:40890714 original size:51 final size:51
Alignment explanation
Indices: 40890598--40890712 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 51
40890588 GTTTTTCAAG
* *
40890598 TCATTT-T-CATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATTATT
1 TCATTTCTCCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATTATT
* ***
40890647 TCATTTCTCTATTTTCATTTTAGAGAAAACTTTAATCATTTCCAAATGT-TT
1 TCATTTCTCCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAAT-TATT
*
40890698 CTTATTTCTCCATTT
1 -TCATTTCTCCATTT
40890713 CACCATTTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
49 6 0.11
50 1 0.02
51 34 0.63
52 13 0.24
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (51 bp):
TCATTTCTCCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATTATT
Found at i:40894915 original size:16 final size:16
Alignment explanation
Indices: 40894894--40894940 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
40894884 CGCTGTATTA
40894894 GAATAGAGGCGTAATG
1 GAATAGAGGCGTAATG
*
40894910 GAATAGAAGCGTAATG
1 GAATAGAGGCGTAATG
40894926 GAATAGAGGCGTAAT
1 GAATAGAGGCGTAAT
40894941 AGCAAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.40, C:0.06, G:0.34, T:0.19
Consensus pattern (16 bp):
GAATAGAGGCGTAATG
Found at i:40894971 original size:45 final size:44
Alignment explanation
Indices: 40894920--40895016 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 44
40894910 GAATAGAAGC
40894920 GTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
40894965 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
*
40895009 GGAATGGA
1 GTAATGGA
40895017 GGTGTAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.50
45 23 0.48
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:40895244 original size:15 final size:14
Alignment explanation
Indices: 40895224--40895280 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
40895214 ATTTACTAAA
40895224 ATTATAATATATAAT
1 ATTATAA-ATATAAT
40895239 ATTATAAAATATAAT
1 ATTAT-AAATATAAT
*
40895254 -TTA-AAATA-ATT
1 ATTATAAATATAAT
40895265 ATTATTAAATATAAT
1 ATTA-TAAATATAAT
40895280 A
1 A
40895281 AACAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
11 2 0.06
12 8 0.23
14 8 0.23
15 15 0.43
16 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTATAAATATAAT
Found at i:40895293 original size:59 final size:58
Alignment explanation
Indices: 40895229--40895425 Score: 190
Period size: 59 Copynumber: 3.3 Consensus size: 58
40895219 CTAAAATTAT
40895229 AATATATAATATT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATAAAC-AA
1 AATATATAAT-TTAATAAAATATAATTTAAAATAATTATTATTAAATATAATAAACAAA
* * * * * * *
40895286 AATATATAATTTAATAAAATTTTTAGTATT-AAAT-ATTCTTATATGAATTTACTAAA-ATCAT
1 AATATATAATTTAATAAAA--TATAAT-TTAAAATAATTATTAT-TAAATATAATAAACA--AA
* *
40895347 AATATATAATACT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAACAAA
1 AATATATAAT-TTAATAAAATATAATTTAAAATAATTATTATTAAATATAA-TAAACAAA
40895406 AATATATAATTTAATAAAAT
1 AATATATAATTTAATAAAAT
40895426 TCTTATGATT
Statistics
Matches: 109, Mismatches: 17, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
56 2 0.02
57 16 0.15
58 10 0.09
59 50 0.46
60 12 0.11
61 18 0.17
62 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (58 bp):
AATATATAATTTAATAAAATATAATTTAAAATAATTATTATTAAATATAATAAACAAA
Found at i:40895340 original size:118 final size:120
Alignment explanation
Indices: 40895207--40895426 Score: 399
Period size: 118 Copynumber: 1.9 Consensus size: 120
40895197 TTTAATAAAA
* *
40895207 TATATGAATTTACTAAAATTATAATATATAATATTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
40895272 AATATAA-TAAAC-AAAATATATAATTTAATAAAATTTTTAGTATTAAATATTCT
66 AATATAATTAAACAAAAATATATAATTTAATAAAATTTTTAGTATTAAATATTCT
40895325 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
*
40895390 AATATAATTTAACAAAAATATATAATTTAATAAAATT
66 AATATAATTAAACAAAAATATATAATTTAATAAAATT
40895427 CTTATGATTG
Statistics
Matches: 97, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
118 70 0.72
119 4 0.04
120 23 0.24
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (120 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
AATATAATTAAACAAAAATATATAATTTAATAAAATTTTTAGTATTAAATATTCT
Found at i:40895364 original size:61 final size:61
Alignment explanation
Indices: 40895207--40895387 Score: 198
Period size: 59 Copynumber: 3.0 Consensus size: 61
40895197 TTTAATAAAA
*
40895207 TATATGAATTTACTAAAATTATAATATATAATATTATAAAA-TATAATTTAAAATAATTAT
1 TATATGAATTTACTAAAATCATAATATATAATATTATAAAATTATAATTTAAAATAATTAT
* * * * * * *
40895267 TAT-TAAATATAAT-AAA-CAAAATATATAAT-TTAATAAAATTTTTAGTATT-AAAT-ATTCT
1 TATATGAATTTACTAAAATCATAATATATAATATT-ATAAAA-TTATAAT-TTAAAATAATTAT
*
40895325 TATATGAATTTACTAAAATCATAATATATAATACTATAAAA-TATAATTTAAAATAATTAT
1 TATATGAATTTACTAAAATCATAATATATAATATTATAAAATTATAATTTAAAATAATTAT
40895385 TAT
1 TAT
40895388 TAAATATAAT
Statistics
Matches: 95, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
56 2 0.02
57 17 0.18
58 12 0.13
59 30 0.32
60 15 0.16
61 18 0.19
62 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (61 bp):
TATATGAATTTACTAAAATCATAATATATAATATTATAAAATTATAATTTAAAATAATTAT
Found at i:40898192 original size:17 final size:16
Alignment explanation
Indices: 40898154--40898185 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
40898144 ATCTAAATGA
40898154 ATAAAAGAAAAGAAAT
1 ATAAAAGAAAAGAAAT
40898170 ATAAAAGTAAAAGAAA
1 ATAAAAG-AAAAGAAA
40898186 ATGAAAACGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
ATAAAAGAAAAGAAAT
Found at i:40898892 original size:14 final size:14
Alignment explanation
Indices: 40898873--40898900 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40898863 AGGGAAAATC
40898873 GGCAGAAGGTAGAA
1 GGCAGAAGGTAGAA
40898887 GGCAGAAGGTAGAA
1 GGCAGAAGGTAGAA
40898901 AGAAGGAAGG
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:0.43, C:0.07, G:0.43, T:0.07
Consensus pattern (14 bp):
GGCAGAAGGTAGAA
Found at i:40905437 original size:22 final size:22
Alignment explanation
Indices: 40905402--40905443 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40905392 ATATATATCA
*
40905402 TTTATTAACATTATATACATTC
1 TTTATTAACATTATAAACATTC
40905424 TTTATTAA-ACTTATAAACAT
1 TTTATTAACA-TTATAAACAT
40905444 AAACAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTATTAACATTATAAACATTC
Found at i:40907714 original size:24 final size:23
Alignment explanation
Indices: 40907660--40907714 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
40907650 AAAAAATAAA
*
40907660 TAAATTTTATATTTTTATATTTT
1 TAAAATTTATATTTTTATATTTT
40907683 TAATAATTTATATTTTT-TAATTTTT
1 TAA-AATTTATATTTTTAT-A-TTTT
40907708 TAAAATT
1 TAAAATT
40907715 AAAAAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.14
24 17 0.61
25 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TAAAATTTATATTTTTATATTTT
Found at i:40909768 original size:41 final size:41
Alignment explanation
Indices: 40909709--40909828 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 41
40909699 TACCTTTTGC
* * *
40909709 GGCTTTAGCAGCACTTTTGAAAAAGAGCCGCTAATGCACGG
1 GGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCACGG
* * **
40909750 GGCTTTAGCGGCGTTTTTGAAAATGCGCCGCTAATGCTTGG
1 GGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCACGG
* * *
40909791 GGTTTTAGCGACATTTTTTGAAAAAGCGCTGCTAATGC
1 GGCTTTAGCGGCA-TTTTTGAAAAAGCGCCGCTAATGC
40909829 TCGGTGTTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 44 0.67
42 22 0.33
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (41 bp):
GGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCACGG
Found at i:40909825 original size:42 final size:41
Alignment explanation
Indices: 40909723--40909841 Score: 148
Period size: 41 Copynumber: 2.9 Consensus size: 41
40909713 TTAGCAGCAC
* * * *
40909723 TTTTGAAAAAGAGCCGCTAATGCACGGGGCTTTAGCGGCGT
1 TTTTGAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGACGT
* * *
40909764 TTTTGAAAATGCGCCGCTAATGCTTGGGGTTTTAGCGACATT
1 TTTTGAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGAC-GT
* *
40909806 TTTTGAAAAAGCGCTGCTAATGCTCGGTGTTTTAGC
1 TTTTGAAAAAGCGCCGCTAATGCTCGGGGTTTTAGC
40909842 AAAAACACCG
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 33 0.50
42 33 0.50
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (41 bp):
TTTTGAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGACGT
Found at i:40910285 original size:14 final size:15
Alignment explanation
Indices: 40910246--40910292 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
40910236 TATTTTAAGG
* *
40910246 TTTAGGGAGTATGAA
1 TTTAGGGATTATGGA
*
40910261 TTTAAGGATTATGGA
1 TTTAGGGATTATGGA
40910276 -TTAGGGATTATGG-
1 TTTAGGGATTATGGA
40910289 TTTA
1 TTTA
40910293 AGGGTTGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:40910304 original size:20 final size:21
Alignment explanation
Indices: 40910279--40910319 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40910269 TTATGGATTA
40910279 GGGATTAT-GGTTTAAGGGTT
1 GGGATTATAGGTTTAAGGGTT
* *
40910299 GGGATTTTAGGTTTAGGGGTT
1 GGGATTATAGGTTTAAGGGTT
40910320 AGGAGTTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.17, C:0.00, G:0.41, T:0.41
Consensus pattern (21 bp):
GGGATTATAGGTTTAAGGGTT
Found at i:40910330 original size:14 final size:16
Alignment explanation
Indices: 40910311--40910344 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
40910301 GATTTTAGGT
40910311 TTAGGGG-TTAGGA-G
1 TTAGGGGTTTAGGAGG
40910325 TTAGGGGTTTAGGAGG
1 TTAGGGGTTTAGGAGG
40910341 TTAG
1 TTAG
40910345 ACGTTAGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 6 0.33
16 5 0.28
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (16 bp):
TTAGGGGTTTAGGAGG
Found at i:40910338 original size:15 final size:15
Alignment explanation
Indices: 40910311--40910357 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
40910301 GATTTTAGGT
40910311 TTAGGGGTTAGGA-G
1 TTAGGGGTTAGGAGG
40910325 TTAGGGGTTTAGGAGG
1 TTAGGGG-TTAGGAGG
**
40910341 TTAGACGTTAGG-GG
1 TTAGGGGTTAGGAGG
40910355 TTA
1 TTA
40910358 AGAGTTAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 12 0.41
15 11 0.38
16 6 0.21
ACGTcount: A:0.21, C:0.02, G:0.45, T:0.32
Consensus pattern (15 bp):
TTAGGGGTTAGGAGG
Found at i:40910350 original size:23 final size:22
Alignment explanation
Indices: 40910308--40910356 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
40910298 TGGGATTTTA
40910308 GGTTTAGGGGTTAGGAGTTAGG
1 GGTTTAGGGGTTAGGAGTTAGG
40910330 GGTTTAGGAGGTTA-GACGTTAGG
1 GGTTTAGG-GGTTAGGA-GTTAGG
40910353 GGTT
1 GGTT
40910357 AAGAGTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33
Consensus pattern (22 bp):
GGTTTAGGGGTTAGGAGTTAGG
Found at i:40910610 original size:21 final size:22
Alignment explanation
Indices: 40910573--40910625 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
40910563 GAGTATGAAT
*
40910573 TTAGGGA-TTATGGTTTAAGGG
1 TTAGGGATTTAAGGTTTAAGGG
*
40910594 TT-GGGATTTAAGGTTTAGGGG
1 TTAGGGATTTAAGGTTTAAGGG
*
40910615 TTAGGGGTTTA
1 TTAGGGATTTA
40910626 GGGGTTAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 16 0.59
22 7 0.26
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (22 bp):
TTAGGGATTTAAGGTTTAAGGG
Found at i:40910625 original size:15 final size:15
Alignment explanation
Indices: 40910605--40910633 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40910595 TGGGATTTAA
40910605 GGTTTAGGGGTTAGG
1 GGTTTAGGGGTTAGG
40910620 GGTTTAGGGGTTAG
1 GGTTTAGGGGTTAG
40910634 ACATTATGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.52, T:0.34
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:40910811 original size:289 final size:292
Alignment explanation
Indices: 40910276--40910812 Score: 723
Period size: 289 Copynumber: 1.8 Consensus size: 292
40910266 GGATTATGGA
*
40910276 TTAGGGATTATGGTTTAAGGGTTGGGATTTTAGGTTTAGGGGTTAGGAGTTAGGGGTTTAGGAGG
1 TTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTA--GG-T-GGAGTTAGGGGTTTAGGAGG
* * *
40910341 TTAGACGTTAGGGGTTAAGAGTTAGAGATTTAGGGTTTAAGGATTCAGGAGTCGGGTTAGGGTTT
62 TTAGACATTAGGGGTTAAGAGTTAGAGATTTAAGGTTTAAGGATTCAGGAGTCGAGTTAGGGTTT
*
40910406 TAGGTTTAGATTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGA
127 TAGGTTTAGAGTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGA
* ** * * * *
40910471 TAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGTTGTT
192 TAATAATAAATTTATTTAGAATTATGAGTATA-GGTATATAATTAATTTAAGATTTAAGGTTGTT
40910536 TTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGAAT
256 TTAGGAGTTCATATTTTAAGGTTTAGGGAGTATGAAT
40910573 TTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTA-G-GG-GTTAGGGGTTTAGG-GGTTAG
1 TTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTAGGTGGAGTTAGGGGTTTAGGAGGTTAG
* * * * * *
40910634 ACATTATGGGTTAAGAGTTAGGGATTTAAGGTTT-AGAGATTTAGGGGTCGAGTTTGGGTTTTGG
66 ACATTAGGGGTTAAGAGTTAGAGATTTAAGGTTTAAG-GATTCAGGAGTCGAGTTAGGGTTTTAG
* *
40910698 GTTTAGAGTAATTATTTTTTAATTTTTATTTTGAATATGTTCTTATATAATTGTAAAAGAGATAA
130 GTTTAGAGTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAA
*
40910763 TAATAAATTAAATATATT-GAAATTATGAGTATA-GTTTA-AATT-ATTTAAGA
195 TAATAAATT---TAT-TTAG-AATTATGAGTATAGGTATATAATTAATTTAAGA
40910813 GATATATAAT
Statistics
Matches: 213, Mismatches: 21, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
288 2 0.01
289 137 0.64
290 17 0.08
291 6 0.03
292 3 0.01
293 10 0.05
294 1 0.00
297 37 0.17
ACGTcount: A:0.29, C:0.01, G:0.27, T:0.42
Consensus pattern (292 bp):
TTAGGGATTATGGTTTAAGGGTTGGGATTTAAGGTTTAGGTGGAGTTAGGGGTTTAGGAGGTTAG
ACATTAGGGGTTAAGAGTTAGAGATTTAAGGTTTAAGGATTCAGGAGTCGAGTTAGGGTTTTAGG
TTTAGAGTAATTATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAGATAAT
AATAAATTTATTTAGAATTATGAGTATAGGTATATAATTAATTTAAGATTTAAGGTTGTTTTAGG
AGTTCATATTTTAAGGTTTAGGGAGTATGAAT
Found at i:40911777 original size:13 final size:14
Alignment explanation
Indices: 40911745--40911778 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40911735 TCTCCTATTA
40911745 CCCTTTCCCCTCTC
1 CCCTTTCCCCTCTC
40911759 CCCTTTCCCCTCT-
1 CCCTTTCCCCTCTC
40911772 CCCTTTC
1 CCCTTTC
40911779 TCTCTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (14 bp):
CCCTTTCCCCTCTC
Found at i:40912984 original size:12 final size:12
Alignment explanation
Indices: 40912967--40912994 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40912957 ACTAGCCATG
40912967 ATGTTACTATTA
1 ATGTTACTATTA
40912979 ATGTTACTATTA
1 ATGTTACTATTA
40912991 ATGT
1 ATGT
40912995 ACTTAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (12 bp):
ATGTTACTATTA
Found at i:40914445 original size:43 final size:43
Alignment explanation
Indices: 40914383--40914479 Score: 131
Period size: 43 Copynumber: 2.3 Consensus size: 43
40914373 TTTGTGGAAC
* * * * *
40914383 CTTTAGCTGCATTTTTGGGAAAAGGGTTACTAAATGTCATGTT
1 CTTTAGCGGCGTTTGTGGGAAAAGGGCTACTAAAGGTCATGTT
*
40914426 CTTTAGCGGCGTTTGTGGGAAAAGTGCTACTAAAGGTCATGTT
1 CTTTAGCGGCGTTTGTGGGAAAAGGGCTACTAAAGGTCATGTT
*
40914469 GTTTAGCGGCG
1 CTTTAGCGGCG
40914480 ATTTTTTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.23, C:0.13, G:0.29, T:0.35
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGAAAAGGGCTACTAAAGGTCATGTT
Found at i:40915044 original size:2 final size:2
Alignment explanation
Indices: 40915037--40915064 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40915027 TTTATGGTTA
40915037 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40915065 AACAAGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:40918972 original size:16 final size:15
Alignment explanation
Indices: 40918939--40918982 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
40918929 CATGATGAAA
*
40918939 AATATTTTATCTTGAT
1 AATATTTT-TCTTAAT
40918955 AATTATTTTTCTTAAT
1 AA-TATTTTTCTTAAT
40918971 AATATTATTTCT
1 AATATT-TTTCT
40918983 AAAATTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 4 0.16
16 15 0.60
17 6 0.24
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (15 bp):
AATATTTTTCTTAAT
Found at i:40922239 original size:39 final size:41
Alignment explanation
Indices: 40922144--40922327 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
40922134 TTGAATGATG
*
40922144 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
40922183 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
40922223 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
40922262 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
40922302 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40922328 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:40922279 original size:79 final size:81
Alignment explanation
Indices: 40922144--40922327 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
40922134 TTGAATGATG
40922144 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
40922207 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
40922222 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
40922283 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
40922302 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40922328 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:40922349 original size:79 final size:79
Alignment explanation
Indices: 40922196--40922360 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
40922186 GGACTAAGAT
* ** *
40922196 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
40922261 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
40922275 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
40922337 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
40922354 CCGAAGG
1 CCGAAGG
40922361 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:40930228 original size:40 final size:40
Alignment explanation
Indices: 40930083--40930266 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
40930073 TTGAATGATG
* *
40930083 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * * *
40930122 TCCAGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
40930162 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40930201 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
40930242 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40930267 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
39 52 0.42
40 62 0.50
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40930288 original size:79 final size:79
Alignment explanation
Indices: 40930135--40930299 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
40930125 AGACTAAGAT
* ** *
40930135 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
40930200 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
40930214 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
40930276 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
40930293 CCGAAGG
1 CCGAAGG
40930300 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:40934512 original size:7 final size:8
Alignment explanation
Indices: 40934495--40934529 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
40934485 TCAAAGATGC
40934495 TTTCTTTT
1 TTTCTTTT
40934503 TTTCTTTT
1 TTTCTTTT
40934511 TTTC-TTT
1 TTTCTTTT
40934518 TTTCTTTT
1 TTTCTTTT
40934526 TTTC
1 TTTC
40934530 CCTCTTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTCTTTT
Found at i:40934520 original size:15 final size:16
Alignment explanation
Indices: 40934495--40934529 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
40934485 TCAAAGATGC
40934495 TTTCTTTTTTTCTTTT
1 TTTCTTTTTTTCTTTT
40934511 TTTC-TTTTTTCTTTT
1 TTTCTTTTTTTCTTTT
40934526 TTTC
1 TTTC
40934530 CCTCTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTCTTTTTTTCTTTT
Found at i:40939872 original size:57 final size:58
Alignment explanation
Indices: 40939784--40939901 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 58
40939774 ATAGAAATGG
* * * * *
40939784 TGAAAATGGATATATAAGAAACATTTAGAAATGATTATGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATAAGAAACATTTAGAAATAAATATGGTTTTCTCCAAAACGAAAA
* * *
40939842 TGAAAATGGAGAAAT-AGAATCATTTGGAAATAAATGTGGTTTTCTCCAAAACGAAAA
1 TGAAAATGGAGAAATAAGAAACATTTAGAAATAAATATGGTTTTCTCCAAAACGAAAA
40939899 TGA
1 TGA
40939902 CCTGAAAAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 39 0.75
58 13 0.25
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.29
Consensus pattern (58 bp):
TGAAAATGGAGAAATAAGAAACATTTAGAAATAAATATGGTTTTCTCCAAAACGAAAA
Found at i:40947029 original size:21 final size:21
Alignment explanation
Indices: 40947000--40947065 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
40946990 CGCGACATGC
40947000 ACCCTGTGTTGAGCCATAGCA
1 ACCCTGTGTTGAGCCATAGCA
* *
40947021 ACCCAGTGTTCAGCCATAG-A
1 ACCCTGTGTTGAGCCATAGCA
* *
40947041 AGCCTTGTGTTGAGCCATAACA
1 A-CCCTGTGTTGAGCCATAGCA
40947063 ACC
1 ACC
40947066 TTGCATTAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 2 0.05
21 33 0.89
22 2 0.05
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (21 bp):
ACCCTGTGTTGAGCCATAGCA
Found at i:40952082 original size:41 final size:41
Alignment explanation
Indices: 40952025--40952152 Score: 141
Period size: 41 Copynumber: 3.1 Consensus size: 41
40952015 CAATAGTTAT
40952025 CTGAT-TCACTACACTGGCACGAAGCCTGCTAGGCTCAAAGC
1 CTGATCTCA-TACACTGGCACGAAGCCTGCTAGGCTCAAAGC
* * * * *
40952066 CTGATTTCATGCACTGGCATGAGGCCTGCTAGGCTCAAGGC
1 CTGATCTCATACACTGGCACGAAGCCTGCTAGGCTCAAAGC
* * ** * *
40952107 CTAAACTGTTACACTGGCACGAAGCCTGCTAGGTTCAAAAC
1 CTGATCTCATACACTGGCACGAAGCCTGCTAGGCTCAAAGC
40952148 CTGAT
1 CTGAT
40952153 ACATGTCTCC
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
41 66 0.96
42 3 0.04
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (41 bp):
CTGATCTCATACACTGGCACGAAGCCTGCTAGGCTCAAAGC
Found at i:40954647 original size:37 final size:37
Alignment explanation
Indices: 40954597--40954671 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
40954587 GGCAAGGCTA
*
40954597 TAGGATTTCAGGTGATCTTTTGTACTCTATCTTTGGG
1 TAGGATTTCAGGTGATCTTTTGTACTCTACCTTTGGG
40954634 TAGGATTTCAGGTGATCTTTTGTACTCTACCTTTGGG
1 TAGGATTTCAGGTGATCTTTTGTACTCTACCTTTGGG
40954671 T
1 T
40954672 GATTGATGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.45
Consensus pattern (37 bp):
TAGGATTTCAGGTGATCTTTTGTACTCTACCTTTGGG
Found at i:40956102 original size:21 final size:21
Alignment explanation
Indices: 40956049--40956107 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
40956039 GGCTATCTAA
* *
40956049 CTCTATCACACAAGCGTATGC
1 CTCTATCACACGACCGTATGC
** *
40956070 CTCTGCCACACGACCGTGTGC
1 CTCTATCACACGACCGTATGC
* *
40956091 CTCTTTCACACGGCCGT
1 CTCTATCACACGACCGT
40956108 TGTAACAGCC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.24
Consensus pattern (21 bp):
CTCTATCACACGACCGTATGC
Found at i:40956161 original size:11 final size:11
Alignment explanation
Indices: 40956145--40956170 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40956135 GAATAGTGGC
40956145 TTTTAATATTA
1 TTTTAATATTA
40956156 TTTTAATATTA
1 TTTTAATATTA
40956167 TTTT
1 TTTT
40956171 TTGTGTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTAATATTA
Found at i:40959154 original size:16 final size:17
Alignment explanation
Indices: 40959133--40959165 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40959123 TTATTTTTTT
40959133 ATATGTTCTG-TATATG
1 ATATGTTCTGATATATG
*
40959149 ATATGTTTTGATATATG
1 ATATGTTCTGATATATG
40959166 CTAGAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (17 bp):
ATATGTTCTGATATATG
Found at i:40965366 original size:16 final size:16
Alignment explanation
Indices: 40965327--40965359 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40965317 AAAAAGATAA
*
40965327 AAAT-AAAATAAAATG
1 AAATGAAAATAAAACG
40965342 AAATGAAAATAAAACG
1 AAATGAAAATAAAACG
40965358 AA
1 AA
40965360 TAGAAAACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.73, C:0.03, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATGAAAATAAAACG
Found at i:40965414 original size:16 final size:16
Alignment explanation
Indices: 40965390--40965427 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
40965380 TTTGGTTCGC
* *
40965390 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
40965406 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
40965422 TGTAAT
1 TGTAAT
40965428 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:40965495 original size:44 final size:45
Alignment explanation
Indices: 40965406--40965500 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 45
40965396 GGATTAGAGG
* *
40965406 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGAAATAGAGGCGTAATAGCAAATCAACTGTTTGGTTGAA
* **
40965451 TGTAATGAAATAGAGGCGTAATAG-TAATCATGTGTTTGGTTGAA
1 TGTAATGAAATAGAGGCGTAATAGCAAATCAACTGTTTGGTTGAA
40965495 TGTAAT
1 TGTAAT
40965501 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 23 0.51
45 22 0.49
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (45 bp):
TGTAATGAAATAGAGGCGTAATAGCAAATCAACTGTTTGGTTGAA
Found at i:40965513 original size:39 final size:40
Alignment explanation
Indices: 40965409--40965515 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 40
40965399 TTAGAGGTGT
*
40965409 AATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTG
1 AATGTAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTG
* * **
40965449 AATGTAATGAAATAGAGGCGTAATAG-TAATCATGTGTTTGGTTG
1 AATG---T--AATAGAGGTGTAATAGCAAATCAACTGTTTGGTTG
40965493 AATGTAATAGAGGTGTAATAGCA
1 AATGTAATAGAGGTGTAATAGCA
40965516 TAATGGAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
39 15 0.28
40 4 0.07
41 1 0.02
44 19 0.35
45 15 0.28
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (40 bp):
AATGTAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTG
Found at i:40965682 original size:18 final size:17
Alignment explanation
Indices: 40965661--40965695 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40965651 TTATTATTAA
*
40965661 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40965679 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40965696 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40965764 original size:155 final size:157
Alignment explanation
Indices: 40965548--40965862 Score: 589
Period size: 155 Copynumber: 2.0 Consensus size: 157
40965538 TAGAATACCC
40965548 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
40965613 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
40965678 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
40965705 TTAGCATAAATTTGTTTTGGTAAATTA-T-TTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
40965768 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
40965833 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
40965860 TTA
1 TTA
40965863 ATATTCTTAC
Statistics
Matches: 155, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
155 128 0.83
156 1 0.01
157 26 0.17
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:40965833 original size:16 final size:16
Alignment explanation
Indices: 40965796--40965837 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40965786 TTAATCATAT
*
40965796 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
40965812 TT-AAATATATTATAA
1 TTAAAATATATTATAA
40965827 TTAAAATATAT
1 TTAAAATATAT
40965838 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:40965844 original size:14 final size:15
Alignment explanation
Indices: 40965805--40965846 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40965795 TTTAAACATA
*
40965805 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40965820 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40965834 A-TATAATTTAATA
1 ATTATAATTAAATA
40965847 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40965934 original size:120 final size:121
Alignment explanation
Indices: 40965794--40966091 Score: 469
Period size: 120 Copynumber: 2.5 Consensus size: 121
40965784 ATTTAATCAT
*
40965794 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
40965859 ATTAATATTCTTACATGAATTTACCCAAATCATAATATATGATACTGTAAAATATAA
66 ATTAATATTCTTACATGAATTTACCCAAATCATAATATATGATACTATAAAAGA-AA
40965916 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * **
40965979 ATTATTATTCTTATATGAATTTATTCAAATCATAATATATGATACTATAAAAGAAA
66 ATTAATATTCTTACATGAATTTACCCAAATCATAATATATGATACTATAAAAGAAA
* *
40966035 ATTTGAA-ATAATTAATATTAAATATATT-TAAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTAT-AATTAAAATATATAATTTAATAAAATT
40966092 TAAAATAATT
Statistics
Matches: 165, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
119 4 0.02
120 156 0.95
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTACATGAATTTACCCAAATCATAATATATGATACTATAAAAGAAA
Found at i:40965964 original size:14 final size:15
Alignment explanation
Indices: 40965915--40965966 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40965905 GTAAAATATA
40965915 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
40965930 TATTAAATATATTAT
1 AATTAAATATATTAT
40965945 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40965958 AATTTAATA
1 AATTAAATA
40965967 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40966190 original size:47 final size:46
Alignment explanation
Indices: 40966139--40966282 Score: 127
Period size: 47 Copynumber: 3.1 Consensus size: 46
40966129 TTGTATAATT
*
40966139 TAAAATAATAAATATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTAATATTA-ATATAATTTAATAATAATATATAATTTCA
** * ** * *
40966186 TAAAATTCTTAATAATAA-AT--TTTCTTATATGAATTTATACAATT--
1 TAAAATAATTAATATTAATATAATTTAATA-AT-AATATATA-ATTTCA
*
40966230 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTAATATT-AATATAATTTAATAATAATATATAATTTCA
40966277 TAAAAT
1 TAAAAT
40966283 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
43 5 0.07
44 15 0.21
45 14 0.19
46 12 0.17
47 21 0.29
48 5 0.07
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (46 bp):
TAAAATAATTAATATTAATATAATTTAATAATAATATATAATTTCA
Found at i:40966200 original size:101 final size:93
Alignment explanation
Indices: 40966034--40966314 Score: 304
Period size: 91 Copynumber: 3.0 Consensus size: 93
40966024 TATAAAAGAA
* * *
40966034 AATTTGAAATAATTAATATTAAATAT-ATTTAAATTAA-AATATATGATTTAATAAAATT-TAAA
1 AATTTAAAATAATTAATATTAAATATAATTT-AA-TAATAATATATAATTTCATAAAATTCT---
* * * *
40966096 ATAATTATAACTAATAAATTATATTTTATGAATTTGTAT
61 -T-A--ATAA-T-ATAAATTTTATTATATGAATTTATAC
* *
40966135 AATTTAAAATAATAAATATTACATATAATTTAATAATAATATATAATTTCATAAAATTCTTAAT-
1 AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
*
40966199 A-ATAAATTTTCTTATATGAATTTATAC
66 ATATAAATTTTATTATATGAATTTATAC
*
40966226 AATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATA
1 AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
* *
40966291 ATA-AAATGTTCTTATATGAATTTA
66 ATATAAATTTTATTATATGAATTTA
40966315 CTAAAATCAA
Statistics
Matches: 161, Mismatches: 14, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
91 82 0.51
92 21 0.13
93 1 0.01
94 1 0.01
95 2 0.01
97 1 0.01
98 1 0.01
100 3 0.02
101 44 0.27
102 5 0.03
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (93 bp):
AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
ATATAAATTTTATTATATGAATTTATAC
Found at i:40966202 original size:91 final size:91
Alignment explanation
Indices: 40966107--40966314 Score: 310
Period size: 91 Copynumber: 2.3 Consensus size: 91
40966097 TAATTATAAC
* * * *
40966107 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAATAAATATTACATATAATTTAATAAT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTTAATAAT
40966172 AATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
* * *
40966198 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTTAATAAT
*
40966263 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
40966289 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
40966315 CTAAAATCAA
Statistics
Matches: 107, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
91 87 0.81
92 19 0.18
93 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATAAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:40966274 original size:44 final size:43
Alignment explanation
Indices: 40966088--40966274 Score: 128
Period size: 44 Copynumber: 4.1 Consensus size: 43
40966078 GATTTAATAA
* * * *
40966088 AATTTAAAATAATTATAACTAATAAAT-TATATTTTATGAATTTGTAT
1 AATTTAAAATAA-T-TAA-TATTAAATATA-ATTTAAT-AATATATAT
* *
40966135 AATTTAAAATAATAAATATTACATATAATTTAATAATAATATAT
1 AATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATATAT
** * * * *
40966179 AATTTCATAAAATTCTTAATAATAAAT-T-TTCTTATATGAATTTATAC
1 AA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATATAT
40966226 AATTTAAAATAATTAATATTAAATATAATTTAATAATGATATAT
1 AATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATATAT
40966270 AATTT
1 AATTT
40966275 CATAAAATTC
Statistics
Matches: 109, Mismatches: 20, Indels: 25
0.71 0.13 0.16
Matches are distributed among these distances:
43 6 0.06
44 46 0.42
45 11 0.10
46 8 0.07
47 35 0.32
48 3 0.03
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (43 bp):
AATTTAAAATAATTAATATTAAATATAATTTAATAATATATAT
Found at i:40966289 original size:47 final size:47
Alignment explanation
Indices: 40966157--40966295 Score: 146
Period size: 47 Copynumber: 3.0 Consensus size: 47
40966147 TAAATATTAC
*
40966157 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
40966204 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
40966248 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
40966295 A
1 A
40966296 ATGTTCTTAT
Statistics
Matches: 70, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
44 21 0.30
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:40967727 original size:11 final size:11
Alignment explanation
Indices: 40967713--40967750 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
40967703 TTAGTACAAT
40967713 ACAAAAGTTTC
1 ACAAAAGTTTC
40967724 ACAAAAGTTTC
1 ACAAAAGTTTC
40967735 ACAAAAGTTTC
1 ACAAAAGTTTC
40967746 ACAAA
1 ACAAA
40967751 CTAATTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:40975478 original size:34 final size:35
Alignment explanation
Indices: 40975423--40975489 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
40975413 CAAACACCAG
*
40975423 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
40975458 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
40975490 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:40977246 original size:19 final size:19
Alignment explanation
Indices: 40977205--40977246 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
40977195 ATTAAATAAT
* *
40977205 AAATTTTAGAAAAATTATT
1 AAATTTTAGAAAAAATATA
40977224 AAATTTTA-ATAAAAATATA
1 AAATTTTAGA-AAAAATATA
40977243 AAAT
1 AAAT
40977247 ATATTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAATTTTAGAAAAAATATA
Found at i:40977604 original size:58 final size:58
Alignment explanation
Indices: 40977486--40977603 Score: 143
Period size: 56 Copynumber: 2.1 Consensus size: 58
40977476 TTTTACGAAA
* * *
40977486 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTGTAAAATGTTATATTTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATGTTAAATTTT
* * *
40977544 TTTATATTTCTATACA-TTT-TATAATTTT-TTATGATTTTTATAAAATTTTACAATTTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGA-CTTTATAAAATGTTA-AATTTT
40977601 TTT
1 TTT
40977604 TTACAATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
55 5 0.10
56 21 0.40
57 11 0.21
58 15 0.29
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (58 bp):
TTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATGTTAAATTTT
Found at i:40977625 original size:12 final size:13
Alignment explanation
Indices: 40977589--40977613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40977579 TTTTATAAAA
40977589 TTTTACAATTTTT
1 TTTTACAATTTTT
40977602 TTTTACAATTTT
1 TTTTACAATTTT
40977614 ACAATTTTTT
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTACAATTTTT
Found at i:40977631 original size:20 final size:20
Alignment explanation
Indices: 40977586--40977635 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
40977576 GATTTTTATA
40977586 AAATTTTACAATTTTTTTTT
1 AAATTTTACAATTTTTTTTT
40977606 ACAATTTTACAATTTTTTTTCT
1 A-AATTTTACAATTTTTTTT-T
*
40977628 AATTTTTA
1 AAATTTTA
40977636 ATATTTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (20 bp):
AAATTTTACAATTTTTTTTT
Found at i:40977641 original size:21 final size:21
Alignment explanation
Indices: 40977578--40977625 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
40977568 TTTTTTATGA
* *
40977578 TTTTTATAAAATTTTACAATT
1 TTTTTTTACAATTTTACAATT
40977599 TTTTTTTACAATTTTACAATT
1 TTTTTTTACAATTTTACAATT
40977620 TTTTTT
1 TTTTTT
40977626 CTAATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTTTACAATTTTACAATT
Found at i:40977709 original size:12 final size:12
Alignment explanation
Indices: 40977692--40977718 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40977682 TTGATTTTAA
40977692 TTTTTTCTAATT
1 TTTTTTCTAATT
40977704 TTTTTTCTAATT
1 TTTTTTCTAATT
40977716 TTT
1 TTT
40977719 AATAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTCTAATT
Found at i:40977834 original size:88 final size:89
Alignment explanation
Indices: 40977728--40977943 Score: 283
Period size: 88 Copynumber: 2.4 Consensus size: 89
40977718 TAATAAAAGA
* *
40977728 AGGGGCTTAATTACTTTTTTTGAAAAATTTTGAGGGTCTGTTTGATGCATTTTGAAAGTTCAAGT
1 AGGGGCTTAATTACTTTTTTTGAAAAAGTTTGAGGGCCTGTTTGATGCATTTTGAAAGTTCAAGT
* *
40977793 ACCCAATTAAGTGC-AAAAAAAGT
66 ACCCAAATAAGTGCGAAAAAAAAT
* * *
40977816 ATGGGCTTAATTGCTTTTTTT-AAAAAGGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCAAG
1 AGGGGCTTAATTACTTTTTTTGAAAAA-GTTTGAGGGCCTGTTTGATGCATTTTGAAAGTTCAAG
* * *
40977880 TATCTAAATGAGTGCGAAAAAAAAT
65 TACCCAAATAAGTGCGAAAAAAAAT
**
40977905 AGGGGCTTAAATTTTTTTTTTGTGAAAAAGTTTGAGGGC
1 AGGGGCTT-AATTACTTTTTT-TGAAAAAGTTTGAGGGC
40977944 TTTTTGCACC
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
87 5 0.05
88 64 0.58
89 15 0.14
90 10 0.09
91 11 0.10
92 5 0.05
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (89 bp):
AGGGGCTTAATTACTTTTTTTGAAAAAGTTTGAGGGCCTGTTTGATGCATTTTGAAAGTTCAAGT
ACCCAAATAAGTGCGAAAAAAAAT
Found at i:40978090 original size:31 final size:29
Alignment explanation
Indices: 40978033--40978090 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
40978023 AAAAAAATCA
* * *
40978033 TTTTAGTCTTTCATTTAATTTTTTGTCTC
1 TTTTAGTCTTTAACTTAATTATTTGTCTC
40978062 TTTTAGCTCTTTAACTTACATTATTTGTC
1 TTTTAG-TCTTTAACTTA-ATTATTTGTC
40978091 AAATTACCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 9 0.38
31 9 0.38
ACGTcount: A:0.17, C:0.16, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTTAGTCTTTAACTTAATTATTTGTCTC
Found at i:40983921 original size:43 final size:44
Alignment explanation
Indices: 40983839--40983921 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
40983829 TTTATTATAA
*
40983839 TATAATATATATAATATATATACTTAACATTTAAGTTTTAATAT
1 TATAATATATATAATATATATACTTAACATTTAAATTTTAATAT
**
40983883 TATAATAT-TATAATATATATTTTTAAC-TTTAAAATTTTA
1 TATAATATATATAATATATATACTTAACATTT-AAATTTTA
40983922 TAATAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 3 0.09
43 24 0.69
44 8 0.23
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.51
Consensus pattern (44 bp):
TATAATATATATAATATATATACTTAACATTTAAATTTTAATAT
Found at i:40989389 original size:22 final size:23
Alignment explanation
Indices: 40989355--40989398 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
40989345 AAATATATGA
40989355 AAAAAATAGAAATATGTATATAT
1 AAAAAATAGAAATATGTATATAT
*
40989378 AAAAATTA-AAATATGTATATA
1 AAAAAATAGAAATATGTATATA
40989399 GGTATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
AAAAAATAGAAATATGTATATAT
Found at i:40989820 original size:3 final size:3
Alignment explanation
Indices: 40989812--40989870 Score: 75
Period size: 3 Copynumber: 19.0 Consensus size: 3
40989802 ATATGTAAGT
*
40989812 ATA ATA ATA ATA GTA AGTA AT- ATA ATA ATA ATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
40989858 ATA ATA AGTA ATA
1 ATA ATA A-TA ATA
40989871 GTAGCAACGA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 2 0.04
3 39 0.78
4 9 0.18
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40991483 original size:45 final size:45
Alignment explanation
Indices: 40991430--40992633 Score: 1118
Period size: 45 Copynumber: 27.3 Consensus size: 45
40991420 ACCAATATGG
40991430 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * * * * *
40991475 GAATACAAGATTTGCTTTCTTCGATCTACTTCAC-GCCAATATAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* *
40991519 GAAGACAAGATCTGCTATCTTTGATCTACTTTACTGCCAGTACAG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * *
40991564 GAAGACAAGATCTGTTATCTTTGATCTACTTCACTGCTAGTACAG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* *
40991609 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* ** * * *
40991653 GAAGACAAGATTTAATATCTTCGATCTACTTCAC-GTCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* *
40991697 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * * *
40991741 GAAGATAAGATCTACTATCCTCTGATCTACTTCA-TGCTAGTACAT
1 GAAGACAAGATCTGCTAT-CTTTGATCTACTTCACTGCCAGTACAT
* **
40991786 GAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAGT--AT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * *
40991829 GGAAAGACAAGATTTGCTATCTTTGATTTACTTCAC-GCCAATACAT
1 -G-AAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * * *
40991875 GAAGACAAGATCTGCTTTATTTGATCTACTTCGCTGCCAGTACAG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
** * * * ** * ***
40991920 GAAGACAAGATCTATTTTCTTCGATCTACTTCGCCACTAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * * *
40991965 GAAGACAAGATCTGTTATCTTTGATCTACTTTAC-ACCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * * * *
40992009 GAAGATAAGATCTGCTTTATTTGATCTACATT-GCTGCCAGTACAG
1 GAAGACAAGATCTGCTATCTTTGATCTAC-TTCACTGCCAGTACAT
* * * * ** * ***
40992054 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAATATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * * *
40992099 GAAGACAAGATCTGCTTTATTTGATCTACTTCGCTGCCAGTACAG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * ***
40992144 GAAGACAAGA--T-CTAT-TTT-AT-T-C--GA-T--CTGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* *
40992177 GAAGACAAGATCTGCTATCTTTGATCTATTTCA-TGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* *
40992221 GAAGACAAGATCTGCTATTCTTCGATCTACTTCAC-GCCAATACAT
1 GAAGACAAGATCTGCTA-TCTTTGATCTACTTCACTGCCAGTACAT
* *
40992266 GAAGACAAGATCTGCTATCTTCGATCTACTTCA-TGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* *
40992310 GAAGACAAGATCTGTTATCCTCTGATCTACTTCA-TGCCAGTACAT
1 GAAGACAAGATCTGCTAT-CTTTGATCTACTTCACTGCCAGTACAT
* * * ** ** ***
40992355 AAAGACAAGATCTGCTTTCTTCGATCTACTTTGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * *
40992400 GAAGAC-A-ATCTGCTATATTTGATTTACTTCAC-GCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * * *
40992442 GAAGACAAGATCTGCTTTATTTGATCTACTTCGCTGCCAGTACAG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
** * * * ** ***
40992487 GAAGACAAGATCTATTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
*
40992532 GAAGACAAGATCTGCTATCTTTGATCTACTTCAC-GCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
* * * *
40992576 GAAGACAAGATCTGTTTTATTTGATCTACTTCACTGCCAGTACAG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
40992621 GAAGACAAGATCT
1 GAAGACAAGATCT
40992634 ATTTTCTTCG
Statistics
Matches: 957, Mismatches: 170, Indels: 64
0.80 0.14 0.05
Matches are distributed among these distances:
33 15 0.02
35 2 0.00
36 4 0.00
37 3 0.00
38 3 0.00
39 2 0.00
40 2 0.00
41 3 0.00
42 16 0.02
43 23 0.02
44 353 0.37
45 529 0.55
46 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (45 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACAT
Found at i:40991523 original size:89 final size:89
Alignment explanation
Indices: 40991402--40992676 Score: 1101
Period size: 89 Copynumber: 14.4 Consensus size: 89
40991392 AAGACTTGTA
* * ***
40991402 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGC
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGC
* *
40991467 CAGTACATGAATACAAGATTTGCTT
65 CAGTACATGAAGACAAGATCTGCTT
* *
40991492 TCTTCGATCTACTTCACGCCAATATATGAAGACAAGATCTGCTATCTTTGATCTACTTTACTGCC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCC
*
40991557 AGTACAGGAAGACAAGATCTG-TT
66 AGTACATGAAGACAAGATCTGCTT
* * * * *
40991580 ATCTTTGATCTACTTCACTGCTAGTACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-G
1 -TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTG
* * ** *
40991644 CCAATACATGAAGACAAGATTTAATA
64 CCAGTACATGAAGACAAGATCTGCTT
* *
40991670 TCTTCGATCTACTTCACGTCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCC
* * * *
40991734 AATACATGAAGATAAGATCTACTA
66 AGTACATGAAGACAAGATCTGCTT
* * * * * **
40991758 TCCTCTGATCTACTTCATGCTAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCAC
1 TCTTC-GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGC
* *
40991823 CAGT--ATGGAAAGACAAGATTTGCTA
65 CAGTACAT-G-AAGACAAGATCTGCTT
* * * * *
40991848 TCTTTGATTTACTTCACGCCAATACATGAAGACAAGATCTGCTTTATTTGATCTACTTCGCTGCC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCC
* **
40991913 AGTACAGGAAGACAAGATCTATTT
66 AGTACATGAAGACAAGATCTGCTT
* * * *
40991937 TCTTCGATCTACTT--CGCCACTAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTTAC-
1 TCTTCGATCTACTTCACGCCAATA-CAT--GAAGACAAGATCTGCTATCTTTGATCTACTTCACT
* * *
40991999 ACCAATACATGAAGATAAGATCTGCTT
63 GCCAGTACATGAAGACAAGATCTGCTT
* * * * * * * * * **
40992026 TATTTGATCTACATTGC-TGCCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
1 TCTTCGATCTAC-TT-CACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTG
* ***
40992090 CCAATATGGGAAGACAAGATCTGCTT
64 CCAGTACATGAAGACAAGATCTGCTT
* * * * * *
40992116 TATTTGATCTACTTCGCTGCCAGTACAGGAAGACAAGA--T-CTAT-TTT-AT-T-C--GA-T--
1 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGC
* *** *
40992169 CTGTATGGGAAGACAAGATCTGCTA
65 CAGTACATGAAGACAAGATCTGCTT
* * * *
40992194 TCTTTGATCTATTTCATGCCAATACATGAAGACAAGATCTGCTATTCTTCGATCTACTTCAC-GC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTA-TCTTTGATCTACTTCACTGC
* *
40992258 CAATACATGAAGACAAGATCTGCTA
65 CAGTACATGAAGACAAGATCTGCTT
* * *
40992283 TCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGTTATCCTCTGATCTACTTCA-TGC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTAT-CTTTGATCTACTTCACTGC
*
40992347 CAGTACATAAAGACAAGATCTGCTT
65 CAGTACATGAAGACAAGATCTGCTT
* * *** * *
40992372 TCTTCGATCTACTTTGC-CACCAGTATGGGAAGAC-A-ATCTGCTATATTTGATTTACTTCAC-G
1 TCTTCGATCTAC-TT-CACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTG
*
40992433 CCAATACATGAAGACAAGATCTGCTT
64 CCAGTACATGAAGACAAGATCTGCTT
* * * * * ** * * * **
40992459 TATTTGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTATTTTCTTCGATCTACTTCGCCAC
1 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGC
*** *
40992524 CAGTATGGGAAGACAAGATCTGCTA
65 CAGTACATGAAGACAAGATCTGCTT
* * * *
40992549 TCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTATTTGATCTACTTCACTGCC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCC
* **
40992614 AGTACAGGAAGACAAGATCTATTT
66 AGTACATGAAGACAAGATCTGCTT
* * * * *
40992638 TCTTCGATCTATTTCGCTACCAATATAGGAAGACAAGAT
1 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGAT
40992677 ATGTTACCTT
Statistics
Matches: 977, Mismatches: 166, Indels: 84
0.80 0.14 0.07
Matches are distributed among these distances:
77 18 0.02
78 35 0.04
79 1 0.00
80 3 0.00
81 1 0.00
82 2 0.00
83 3 0.00
84 2 0.00
85 4 0.00
86 5 0.01
87 70 0.07
88 86 0.09
89 510 0.52
90 228 0.23
91 3 0.00
92 6 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (89 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCC
AGTACATGAAGACAAGATCTGCTT
Found at i:40991640 original size:134 final size:133
Alignment explanation
Indices: 40991429--40992676 Score: 1138
Period size: 134 Copynumber: 9.4 Consensus size: 133
40991419 CACCAATATG
* * * * * * *
40991429 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACTGCCAGTACATGAATACAAGATTTGCTTTC
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGCTATC
* * *
40991494 TTCGATCTACTTCACGCCAATATATGAAGACAAGATCTGCTATCTTTGATCTACTTTACTGCCAG
65 TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACTGCCAG
40991559 TACA
130 TACA
* * *
40991563 GGAAGACAAGATCTGTTATCTTTGATCTACTTCACTGCTAGTACAGGAAGACAAGATCTGCTATC
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGCTATC
* ** * * * *
40991628 TTCGATCTACTTCACGCCAATACATGAAGACAAGATTTAATATCTTCGATCTACTTCAC-GTCAA
65 TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACTGCCAG
40991692 TACA
130 TACA
* * * * * *
40991696 TGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTACTATCC
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCT
* * * **
40991761 TCTGATCTACTTCATGCTAGTACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACCACCAG
66 TC-GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACTGCCAG
*
40991826 TA-T
130 TACA
* * * * * * *
40991829 GGAAAGACAAGATTTGCTATCTTTGATTTACTTCACGCCAATACATGAAGACAAGATCTGCTTTA
1 GG-AAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATC
* * * * ** * * ** *
40991894 TTTGATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTATTTTCTTCGATCTACTTCGCCACTA
65 TTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACTGCCA
**
40991959 GTATG
129 GTACA
* * * * * * *
40991964 GGAAGACAAGATCTGTTATCTTTGATCTACTTTACACCAATACATGAAGATAAGATCTGCTTTAT
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCT
* * * * * * * **
40992029 TTGATCTACATTGC-TGCCAGTACAGGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCA
66 TCGATCTAC-TT-CACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACTGCCA
* **
40992093 ATATG
129 GTACA
* * ** *
40992098 GGAAGACAAGATCTGCTTTAT-TT-GATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTATTT
1 GGAAGACAAGATCTG--TTATCTTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGCTA
* *** * *
40992161 TATTCGA--T-C-T---G----TATGGGAAGACAAGATCTGCTATCTTTGATCTATTTCA-TGCC
63 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACTGCC
*
40992214 AATACA
128 AGTACA
* * *
40992220 TGAAGACAAGATCTGCTATTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATC
1 GGAAGACAAGATCTGTTA-TCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATC
* *
40992285 TTCGATCTACTTCATGCCAATACATGAAGACAAGATCTG-TTATCCTCTGATCTACTTCA-TGCC
65 TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT-T-CTTTGATCTACTTCACTGCC
40992348 AGTACA
128 AGTACA
** * * **
40992354 TAAAGACAAGATCTGCTT-TCTTCGATCTACTTTGC-CACCAGTATGGGAAGAC-A-ATCTGCTA
1 GGAAGACAAGATCTG-TTATCTTCGATCTAC-TT-CACGCCAATACAGGAAGACAAGATCTGCTA
* * * * *
40992415 TATTTGATTTACTTCACGCCAATACATGAAGACAAGATCTGCTTTATTTGATCTACTTCGCTGCC
63 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACTGCC
40992480 AGTACA
128 AGTACA
* * * * * **
40992486 GGAAGACAAGATCTATTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATC
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTC-ACGCCAATACAGGAAGACAAGATCTGCTATC
* * *
40992551 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTATTTGATCTACTTCACTGCCAG
65 TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACTGCCAG
40992616 TACA
130 TACA
* * * * * *
40992620 GGAAGACAAGATCTATTTTCTTCGATCTATTTCGCTACCAATATAGGAAGACAAGAT
1 GGAAGACAAGATCTGTTATCTTCGATCTACTTCAC-GCCAATACAGGAAGACAAGAT
40992677 ATGTTACCTT
Statistics
Matches: 951, Mismatches: 126, Indels: 74
0.83 0.11 0.06
Matches are distributed among these distances:
120 2 0.00
121 1 0.00
122 50 0.05
123 42 0.04
124 1 0.00
125 1 0.00
126 1 0.00
127 1 0.00
129 1 0.00
130 2 0.00
131 16 0.02
132 125 0.13
133 133 0.14
134 535 0.56
135 35 0.04
136 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (133 bp):
GGAAGACAAGATCTGTTATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCT
TCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTTGATCTACTTCACTGCCAGT
ACA
Found at i:40992626 original size:221 final size:220
Alignment explanation
Indices: 40991400--40992628 Score: 923
Period size: 222 Copynumber: 5.6 Consensus size: 220
40991390 ATAAGACTTG
** *
40991400 TATCTTCGATCTACTTC-GCCACCAATATGGGAAGACAAGATCTGCTAT-CTTTGATCTACTTCA
1 TATCTTCGATCTACTTCAG---CCAATACAGGAAGACAAGATCTGCTATCCTCTGATCTACTTCA
* * * * * * * * *
40991463 CTGCCAGTACATGAATACAAGATTTGCTTTCTTCGATCTACTTCA-CGCCAATATATGAAGACAA
63 C-GCCAATACATAAAGACAAGATCTGCTTTATTCGATCTACTTCACCACCAGTACAGGAAGAC-A
* * * * *
40991527 GATCTGCTATCTTTGATCTACTTTACTGCCAGTACAGGAAGACAAGATCTGTTATCT-TT-GATC
126 -ATCTGCTATATTTGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTAT-TATTCGATC
* * *
40991590 TACTTCACTGCTAGTACAGGAAGACAAGATCTGC
188 TACTTCAC-GCCAATACAGGAAGACAAGATCTAC
* * ** *
40991624 TATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATTTAATATCTTC-GATCTACTTCACG
1 TATCTTCGATCTACTTCA-GCCAATACAGGAAGACAAGATCTGCTATCCTCTGATCTACTTCACG
* * * * * * * *
40991688 TCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CGCCAATACATGAAGATAAGAT
65 CCAATACATAAAGACAAGATCTGCTTTATTCGATCTACTTCACCACCAGTACAGGAAGA-CA-AT
* * * * * * * *
40991752 CTACTATCCTCTGATCTACTTCATGCTAGTACATGAAGACAAGATCTGCT-TTCTTTGATCTACT
128 CTGCTAT-ATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATTATTCGATCTACT
* * * * *
40991816 TCACCACCAGTA-TGGAAAGACAAGATTTGC
192 TCA-CGCCAATACAGG-AAGACAAGATCTAC
* * * ** * *
40991846 TATCTTTGATTTACTTCACGCCAATACATGAAGACAAGATCTGCT-TTATTTGATCTACTTCGCT
1 TATCTTCGATCTACTTCA-GCCAATACAGGAAGACAAGATCTGCTATCCTCTGATCTACTTCAC-
* ** ** * * * **
40991910 GCCAGTACAGGAAGACAAGATCTATTTTCTTCGATCTACTTCGCCACTAGTATGGGAAGACAAGA
64 GCCAATACATAAAGACAAGATCTGCTTTATTCGATCTACTTCACCACCAGTACAGGAAGAC-A-A
* * * * * *
40991975 TCTGTTATCTTTGATCTACTTTACACCAATACATGAAGATAAGATCTGCT-TTATTTGATCTACA
127 TCTGCTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATTATTCGATCTAC-
* * **
40992039 TTGC-TGCCAGTACAGGAAGACAAGATCTGT
191 TT-CACGCCAATACAGGAAGACAAGATCTAC
* ** ** * *
40992069 TTTCTTCGATCTACTTC-GCCACCAATATGGGAAGACAAGATCTGCT-TTATTTGATCTACTTCG
1 TATCTTCGATCTACTTCAG---CCAATACAGGAAGACAAGATCTGCTATCCTCTGATCTACTTCA
* ** ** **
40992132 CTGCCAGTACAGGAAGACAAGATCTATTTTATTCGA--T-C-T--------GTATGGGAAGACAA
63 C-GCCAATACATAAAGACAAGATCTGCTTTATTCGATCTACTTCACCACCAGTACAGGAAGAC-A
* * * *
40992185 GATCTGCTATCTTTGATCTATTTCATGCCAATACATGAAGACAAGATCTGCTATTCTTCGATCTA
126 -ATCTGCTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATTATTCGATCTA
* *
40992250 CTTCACGCCAATACATGAAGACAAGATCTGC
190 CTTCACGCCAATACAGGAAGACAAGATCTAC
* * *
40992281 TATCTTCGATCTACTTCATGCCAATACATGAAGACAAGATCTGTTATCCTCTGATCTACTTCATG
1 TATCTTCGATCTACTTCA-GCCAATACAGGAAGACAAGATCTGCTATCCTCTGATCTACTTCACG
* * ** **
40992346 CCAGTACATAAAGACAAGATCTGCTTTCTTCGATCTACTTTGCCACCAGTATGGGAAGACAATCT
65 CCAATACATAAAGACAAGATCTGCTTTATTCGATCTACTTCACCACCAGTACAGGAAGACAATCT
* * *
40992411 GCTATATTTGATTTACTTCACGCCAATACATGAAGACAAGATCTGCT-TTATTTGATCTACTTCG
130 GCTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATTATTCGATCTACTTCA
* *
40992475 CTGCCAGTACAGGAAGACAAGATCTAT
195 C-GCCAATACAGGAAGACAAGATCTAC
* ** *
40992502 TTTCTTCGATCTACTTC-GCCACCAGTATGGGAAGACAAGATCTGCTAT-CTTTGATCTACTTCA
1 TATCTTCGATCTACTTCAGCCA--A-TACAGGAAGACAAGATCTGCTATCCTCTGATCTACTTCA
* * * **
40992565 CGCCAATACATGAAGACAAGATCTGTTTTATTTGATCTACTTCACTGCCAGTACAGGAAGACAA
63 CGCCAATACATAAAGACAAGATCTGCTTTATTCGATCTACTTCACCACCAGTACAGGAAGACAA
40992629 GATCTATTTT
Statistics
Matches: 838, Mismatches: 127, Indels: 83
0.80 0.12 0.08
Matches are distributed among these distances:
211 51 0.06
212 113 0.13
213 12 0.01
214 2 0.00
215 1 0.00
219 4 0.00
220 17 0.02
221 160 0.19
222 187 0.22
223 174 0.21
224 115 0.14
225 1 0.00
226 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (220 bp):
TATCTTCGATCTACTTCAGCCAATACAGGAAGACAAGATCTGCTATCCTCTGATCTACTTCACGC
CAATACATAAAGACAAGATCTGCTTTATTCGATCTACTTCACCACCAGTACAGGAAGACAATCTG
CTATATTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATTATTCGATCTACTTCAC
GCCAATACAGGAAGACAAGATCTAC
Found at i:40994023 original size:13 final size:12
Alignment explanation
Indices: 40993966--40994023 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 12
40993956 CACCTTATCC
*
40993966 TTTTCATTTTACT
1 TTTTCATTTT-CA
40993979 TTTTCCATTTTTCA
1 TTTT-CA-TTTTCA
40993993 TTTCTCATTTCTCA
1 TTT-TCATTT-TCA
40994007 TTTTCACTTTTCA
1 TTTTCA-TTTTCA
40994020 TTTT
1 TTTT
40994024 TCCATTTCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 17 0.44
14 17 0.44
15 5 0.13
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTCATTTTCA
Found at i:40994025 original size:14 final size:13
Alignment explanation
Indices: 40993966--40994023 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
40993956 CACCTTATCC
* *
40993966 TTTTCATTTTACT
1 TTTTCATTTTTCA
40993979 TTTTCCATTTTTCA
1 TTTT-CATTTTTCA
*
40993993 TTTCTCATTTCTCA
1 TTT-TCATTTTTCA
*
40994007 TTTTCACTTTTCA
1 TTTTCATTTTTCA
40994020 TTTT
1 TTTT
40994024 TCCATTTCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 16 0.42
14 21 0.55
15 1 0.03
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:40994029 original size:21 final size:20
Alignment explanation
Indices: 40993966--40994034 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 20
40993956 CACCTTATCC
40993966 TTTTCATTTT-ACTTTTTCCA
1 TTTTCATTTTCA-TTTTTCCA
*
40993986 TTTTTCATTTCTCATTTCT-CA
1 -TTTTCATTT-TCATTTTTCCA
40994007 TTTTCACTTTTCATTTTTCCA
1 TTTTCA-TTTTCATTTTTCCA
40994028 -TTTCATT
1 TTTTCATT
40994035 ATTTTTACGA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
19 2 0.05
20 18 0.43
21 16 0.38
22 5 0.12
23 1 0.02
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTCATTTTCATTTTTCCA
Found at i:40999281 original size:3 final size:3
Alignment explanation
Indices: 40999273--40999315 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
40999263 ATATGTAAGT
40999273 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AGTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
40999316 GTAGCAACGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41006890 original size:17 final size:19
Alignment explanation
Indices: 41006858--41006893 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
41006848 TTATGTAATA
41006858 TATTATATTAATATAATTT
1 TATTATATTAATATAATTT
41006877 TATT-TATT-ATATAATTT
1 TATTATATTAATATAATTT
41006894 ATATAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTATATTAATATAATTT
Found at i:41010150 original size:11 final size:11
Alignment explanation
Indices: 41010120--41010154 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
41010110 TAGCTTTACG
41010120 GATTTTTCTTT
1 GATTTTTCTTT
*
41010131 GA-TTCTCTTT
1 GATTTTTCTTT
41010141 GATTTTTCTTT
1 GATTTTTCTTT
41010152 GAT
1 GAT
41010155 CGATGTCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.66
Consensus pattern (11 bp):
GATTTTTCTTT
Found at i:41012640 original size:11 final size:11
Alignment explanation
Indices: 41012624--41012649 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41012614 CATTATTTTC
41012624 TTTTCTTTCTT
1 TTTTCTTTCTT
41012635 TTTTCTTTCTT
1 TTTTCTTTCTT
41012646 TTTT
1 TTTT
41012650 GGGTGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:41016120 original size:20 final size:20
Alignment explanation
Indices: 41016032--41016125 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
41016022 TATATTAAGA
*
41016032 ATTTTATTAAATTATATATT
1 ATTTTATTAAATTATTTATT
41016052 ATTTTATTAAATTA--TATT
1 ATTTTATTAAATTATTTATT
** * **
41016070 -TAATAAT-AATTATGTTAAA
1 ATTTTATTAAATTAT-TTATT
* **
41016089 ATATGGTTAAATTATTTATT
1 ATTTTATTAAATTATTTATT
41016109 ATTTTATTAAATTATTT
1 ATTTTATTAAATTATTT
41016126 TTAATAATAA
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
16 5 0.09
17 4 0.07
18 4 0.07
19 2 0.04
20 34 0.62
21 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTATTAAATTATTTATT
Found at i:41016145 original size:57 final size:57
Alignment explanation
Indices: 41016014--41016147 Score: 189
Period size: 57 Copynumber: 2.3 Consensus size: 57
41016004 GTAAATTCAT
* **
41016014 ATAATAATTATATTAAGAATTTTATTAAATTATATATTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAA-AATATGGTTAAATTATATATTATTTTATTAAATTATATTTA
* * *
41016072 ATAATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTATTAAATTATTTTTA
1 ATAATAATTATATTAAAATATGGTTAAATTATATATTATTTTATTAAATTATATTTA
41016129 ATAATAATCT-TATTAAAAT
1 ATAATAAT-TATATTAAAAT
41016148 TTAATAACAA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
57 52 0.76
58 16 0.24
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (57 bp):
ATAATAATTATATTAAAATATGGTTAAATTATATATTATTTTATTAAATTATATTTA
Found at i:41021504 original size:5 final size:5
Alignment explanation
Indices: 41021494--41021522 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
41021484 GTTGAATGTC
41021494 TCTCT TCTCT TCTCT TCTCT TCTCT TCTC
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTC
41021523 CCATTCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
TCTCT
Found at i:41021655 original size:9 final size:10
Alignment explanation
Indices: 41021635--41021659 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41021625 TTTTTAGTCA
41021635 TTTAATTTTT
1 TTTAATTTTT
41021645 TTTAATTTTT
1 TTTAATTTTT
41021655 TTTAA
1 TTTAA
41021660 AATGCTTTAA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTAATTTTT
Found at i:41025307 original size:25 final size:24
Alignment explanation
Indices: 41025247--41025301 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 24
41025237 ATTTGTTATA
41025247 TATATATATATGCATGCATACATTTT
1 TATA-ATATATGCA-GCATACATTTT
41025273 TATAATATATGCA-CATA-ATTTT
1 TATAATATATGCAGCATACATTTT
41025295 GTATAAT
1 -TATAAT
41025302 TTATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.18
23 10 0.36
25 9 0.32
26 4 0.14
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (24 bp):
TATAATATATGCAGCATACATTTT
Found at i:41025866 original size:72 final size:72
Alignment explanation
Indices: 41025749--41025891 Score: 250
Period size: 72 Copynumber: 2.0 Consensus size: 72
41025739 TCTTTTCAAA
* *
41025749 CTCAAGTTTTAAACGATCCCGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCCCGGGAATTAAGAAAAGATCATGTCCTAACTTACTGGGCATGATCCC
41025814 TTTTTTT
66 TTTTTTT
* *
41025821 CTCAAGTTTTAAACTATCTCGGGAATTAAGAAAAGATCATGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCCCGGGAATTAAGAAAAGATCATGTCCTAACTTACTGGGCATGATCCC
41025886 TTTTTT
66 TTTTTT
41025892 AAATCTGAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (72 bp):
CTCAAGTTTTAAACGATCCCGGGAATTAAGAAAAGATCATGTCCTAACTTACTGGGCATGATCCC
TTTTTTT
Found at i:41033863 original size:56 final size:50
Alignment explanation
Indices: 41033792--41034088 Score: 272
Period size: 50 Copynumber: 5.8 Consensus size: 50
41033782 ATTTGGGTAA
* * *
41033792 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGACATCATTGAGATTGTG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAGA---TG
* * *
41033848 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
41033898 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
*** * * * *
41033948 AGAGGTCCCCCATAAGACCATGTCTGGGGCATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
** * * * ** * * * **
41033998 AGAAATCTCATGTAAGACCATATCTAGGATTTGGCATTGGTAGT-ACAAC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* ** *
41034047 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41034089 TGTTATTATC
Statistics
Matches: 198, Mismatches: 43, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
49 35 0.18
50 121 0.61
53 4 0.02
55 1 0.01
56 37 0.19
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
Found at i:41040669 original size:50 final size:50
Alignment explanation
Indices: 41040615--41040758 Score: 180
Period size: 50 Copynumber: 2.9 Consensus size: 50
41040605 ATTGAGATTG
* *
41040615 TGAGAGGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCACCGAGA
1 TGAGAGGTCCCATGTAAGACCATATCTAGGACATGGCATTGGCACCGAGA
** * * * *
41040665 TGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACTGATA
1 TGAGAGGTCCCATGTAAGACCATATCTAGGACATGGCATTGGCACCGAGA
** * *
41040715 TGAGAAATCTCATGTAAGACCATATCTAGGATATGGCATTGGCA
1 TGAGAGGTCCCATGTAAGACCATATCTAGGACATGGCATTGGCA
41040759 GTACAACAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
TGAGAGGTCCCATGTAAGACCATATCTAGGACATGGCATTGGCACCGAGA
Found at i:41047713 original size:44 final size:45
Alignment explanation
Indices: 41047622--41047716 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 45
41047612 AGCCATAAAC
* *
41047622 CTTATC-CCCCTAAAATTGCAATGGGGCAGGTTGAAATTACAAGT
1 CTTATCTCCCCTAAAATTGCAATAGAGCAGGTTGAAATTACAAGT
*
41047666 CTTATCTCCCC-AAAGTTGCAATAGAGCAGGTTGAAGA-TACCAA-T
1 CTTATCTCCCCTAAAATTGCAATAGAGCAGGTTGAA-ATTA-CAAGT
41047710 CTTATCT
1 CTTATCT
41047717 TCCTGAAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
44 37 0.82
45 8 0.18
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (45 bp):
CTTATCTCCCCTAAAATTGCAATAGAGCAGGTTGAAATTACAAGT
Found at i:41048892 original size:23 final size:23
Alignment explanation
Indices: 41048858--41048908 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
41048848 AGAGCTTGGT
*
41048858 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
41048881 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
41048904 AGTAA
1 TGTAA
41048909 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:41048969 original size:22 final size:22
Alignment explanation
Indices: 41048944--41048988 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41048934 TAAGGAAATA
41048944 AAGTGATAAAAAGAAAATTTTG
1 AAGTGATAAAAAGAAAATTTTG
* *
41048966 AAGTGATAAAAGGGAAATTTTG
1 AAGTGATAAAAAGAAAATTTTG
41048988 A
1 A
41048989 GTTATGGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (22 bp):
AAGTGATAAAAAGAAAATTTTG
Found at i:41051962 original size:45 final size:44
Alignment explanation
Indices: 41051886--41051986 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 44
41051876 CATATTTTTT
* * *
41051886 TTATAATTTATATATATACATACTTATATATATATTTATTATATC
1 TTATAATTTATATATATACATACATACATATATATTT-TTACATC
** * *
41051931 TTATAATTTATATATATATGTACATACATATATCTTTTTACATT
1 TTATAATTTATATATATACATACATACATATATATTTTTACATC
41051975 TTATAAGTTTAT
1 TTATAA-TTTAT
41051987 TCATTTTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 11 0.23
45 37 0.77
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (44 bp):
TTATAATTTATATATATACATACATACATATATATTTTTACATC
Found at i:41052458 original size:71 final size:72
Alignment explanation
Indices: 41052342--41052483 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 72
41052332 TCTTTTCAAA
*
41052342 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGA-TCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATTCC
41052406 TTTTTTT
66 TTTTTTT
*
41052413 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATTCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATTCC
41052478 TTTTTT
66 TTTTTT
41052484 AAATCCGAGA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 59 0.87
72 9 0.13
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (72 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATTCC
TTTTTTT
Found at i:41057556 original size:13 final size:13
Alignment explanation
Indices: 41057537--41057602 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
41057527 TAGATTTTTC
41057537 CTAAATATTATCA
1 CTAAATATTATCA
*
41057550 ATAAATA--ATC-
1 CTAAATATTATCA
41057560 CTAAATATTATCA
1 CTAAATATTATCA
*
41057573 CTAAATA--AT-T
1 CTAAATATTATCA
41057583 CTAAATATTATCA
1 CTAAATATTATCA
*
41057596 CTTAATA
1 CTAAATA
41057603 ATTCAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
10 13 0.31
11 5 0.12
12 5 0.12
13 19 0.45
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:41057605 original size:23 final size:23
Alignment explanation
Indices: 41057537--41057611 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
41057527 TAGATTTTTC
* *
41057537 CTAAATATTATCAATAAATAATC
1 CTAAATATTATCACTAAATAATT
41057560 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
41057583 CTAAATATTATCACTTAATAATT
1 CTAAATATTATCACTAAATAATT
*
41057606 CAAAAT
1 CTAAAT
41057612 TTAAAAATCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:41057758 original size:18 final size:18
Alignment explanation
Indices: 41057735--41057772 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
41057725 AATCTTTATC
*
41057735 CAGTCATCTTTTAGTCTT
1 CAGTCATCTTTGAGTCTT
41057753 CAGTCATCTTTGAGTCTT
1 CAGTCATCTTTGAGTCTT
41057771 CA
1 CA
41057773 TTCTTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.45
Consensus pattern (18 bp):
CAGTCATCTTTGAGTCTT
Found at i:41068357 original size:16 final size:16
Alignment explanation
Indices: 41068335--41068403 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
41068325 TTTGGTTCGC
41068335 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
41068351 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41068367 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
41068384 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41068400 TGTA
1 TGTA
41068404 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:41068381 original size:33 final size:32
Alignment explanation
Indices: 41068335--41068403 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
41068325 TTTGGTTCGC
41068335 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
41068367 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
41068400 TGTA
1 TGTA
41068404 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:41068468 original size:44 final size:45
Alignment explanation
Indices: 41068384--41068474 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
41068374 GGATTAGAGG
* * *
41068384 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
41068429 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
41068473 TG
1 TG
41068475 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:41068660 original size:18 final size:17
Alignment explanation
Indices: 41068639--41068673 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41068629 TTATTATTAA
*
41068639 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41068657 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41068674 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41068834 original size:119 final size:119
Alignment explanation
Indices: 41068622--41069206 Score: 1100
Period size: 120 Copynumber: 4.9 Consensus size: 119
41068612 ATCATATTTA
*
41068622 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAA-AAAATTCTTAATAATTAA
* *
41068687 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
65 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
41068742 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAAT
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAAT
41068807 GTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 GTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
41068861 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAA
41068926 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
65 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
41068981 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAA
*
41069046 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGT-AAATATAAATT
65 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
41069100 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAAT
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAAT
41069165 GTTCTTATATTAATTTACTCAAATCATAATATATGATACTGT
66 GTTCTTATATTAATTTACTCAAATCATAATATATGATACTGT
41069207 TGATGCTAGT
Statistics
Matches: 459, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
118 62 0.14
119 170 0.37
120 227 0.49
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (119 bp):
AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAAT
GTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:41069095 original size:239 final size:239
Alignment explanation
Indices: 41068622--41069206 Score: 1102
Period size: 239 Copynumber: 2.5 Consensus size: 239
41068612 ATCATATTTA
* *
41068622 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
* *
41068687 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
*
41068752 TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAATGTTCTTATAT
131 TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAATATTCTTATAT
41068817 TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
196 TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
41068861 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
41068926 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
41068991 TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAATATTCTTATA
131 TTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAATATTCTTATA
41069056 TTAATTTACTCAAATCATAATATATGATACTGT-AAATATAAATT
195 TTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
41069100 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT-AAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
41069164 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGT
66 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGT
41069207 TGATGCTAGT
Statistics
Matches: 340, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
238 63 0.19
239 215 0.63
240 62 0.18
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (239 bp):
AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
TTATTAAATATATTTTAATTAAACTATATAATTTAAAAAATTCTTAATAATTAATATTCTTATAT
TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Done.