Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 99 of 130
Found at i:19288731 original size:17 final size:18
Alignment explanation
Indices: 19288698--19288733 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19288688 AGAAAATAAG
19288698 AAAAGCCCAACAAAAAAT
1 AAAAGCCCAACAAAAAAT
*
19288716 AAAAGCCCGA-AAAAAAT
1 AAAAGCCCAACAAAAAAT
19288733 A
1 A
19288734 TAACCAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.19, G:0.08, T:0.06
Consensus pattern (18 bp):
AAAAGCCCAACAAAAAAT
Found at i:19290821 original size:24 final size:25
Alignment explanation
Indices: 19290779--19290835 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
19290769 TTGATTCCAT
* *
19290779 ATTTTTTTCATTAATACAAGTCAAA
1 ATTTGTTTCATTAACACAAGTCAAA
* *
19290804 A-TTGTTTCATTTACACAAGTGAAA
1 ATTTGTTTCATTAACACAAGTCAAA
19290828 ATTTGTTT
1 ATTTGTTT
19290836 ATATATACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.46
Consensus pattern (25 bp):
ATTTGTTTCATTAACACAAGTCAAA
Found at i:19290845 original size:24 final size:24
Alignment explanation
Indices: 19290784--19290855 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
19290774 TCCATATTTT
19290784 TTTCAT-TAATACAAGTCAAAATTG
1 TTTCATAT-ATACAAGTCAAAATTG
* * *
19290808 TTTCATTTACACAAGTGAAAATTTG
1 TTTCATATATACAAGTCAAAA-TTG
*
19290833 TTT-ATATATACAAATCCAAAATT
1 TTTCATATATACAAGT-CAAAATT
19290856 TTTTATTTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 28 0.72
25 11 0.28
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (24 bp):
TTTCATATATACAAGTCAAAATTG
Found at i:19290986 original size:21 final size:21
Alignment explanation
Indices: 19290959--19291028 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
19290949 AAAGAAACAC
19290959 AGTTTTTGACAACAAAGACAAT
1 AGTTTTTGACAA-AAAGACAAT
* *
19290981 -GTTTTTTACTAAAA-AC-AT
1 AGTTTTTGACAAAAAGACAAT
* *
19290999 AGTTTTTGATAATAAAGACAAC
1 AGTTTTTGACAA-AAAGACAAT
*
19291021 ATTTTTTG
1 AGTTTTTG
19291029 CCTAAAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 2 0.05
19 10 0.27
20 6 0.16
21 11 0.30
22 8 0.22
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (21 bp):
AGTTTTTGACAAAAAGACAAT
Found at i:19291026 original size:40 final size:40
Alignment explanation
Indices: 19290935--19291036 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 40
19290925 ATGAATAGAT
*
19290935 AACATTTTGTTATTAAAGAAACACAGTTTTTGACAACAAAGAC
1 AACATTTT-TTACT-AA-AAACACAGTTTTTGACAACAAAGAC
** * * *
19290978 AATGTTTTTTACTAAAAACATAGTTTTTGATAATAAAGAC
1 AACATTTTTTACTAAAAACACAGTTTTTGACAACAAAGAC
*
19291018 AACATTTTTTGCCTAAAAA
1 AACATTTTTT-ACTAAAAA
19291037 TTTAGTATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
40 30 0.61
41 9 0.18
42 4 0.08
43 6 0.12
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (40 bp):
AACATTTTTTACTAAAAACACAGTTTTTGACAACAAAGAC
Found at i:19291048 original size:41 final size:40
Alignment explanation
Indices: 19290935--19291051 Score: 99
Period size: 40 Copynumber: 2.8 Consensus size: 40
19290925 ATGAATAGAT
* * *
19290935 AACATTTTGTTATTAAAGAAACACAGTTTTTGACAACAAAGAC
1 AACATTTT-TTACT-AA-AAACATAGTATTTGACAACAAAGAC
** * * *
19290978 AATGTTTTTTACTAAAAACATAGTTTTTGATAATAAAGAC
1 AACATTTTTTACTAAAAACATAGTATTTGACAACAAAGAC
* **
19291018 AACATTTTTTGCCTAAAAATTTAGTATTTGACAA
1 AACATTTTTT-ACTAAAAACATAGTATTTGACAA
19291052 TTTATTAAAG
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
40 30 0.50
41 20 0.33
42 4 0.07
43 6 0.10
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (40 bp):
AACATTTTTTACTAAAAACATAGTATTTGACAACAAAGAC
Found at i:19291405 original size:38 final size:38
Alignment explanation
Indices: 19291362--19291447 Score: 136
Period size: 38 Copynumber: 2.3 Consensus size: 38
19291352 ATAGAATGCC
*
19291362 AATGTAATTATAATATTGAAACAATAGAAAATATTATG
1 AATGTAATTATAATATTGAAACAATAGAAAACATTATG
* * *
19291400 AATGTAGTTATAATATTGAAACAATATAAAGCATTATG
1 AATGTAATTATAATATTGAAACAATAGAAAACATTATG
19291438 AATGTAATTA
1 AATGTAATTA
19291448 CAAAATGCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (38 bp):
AATGTAATTATAATATTGAAACAATAGAAAACATTATG
Found at i:19293770 original size:22 final size:23
Alignment explanation
Indices: 19293742--19293785 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
19293732 AGGAAGATGG
19293742 AAAGAAAAAA-GAATAAAAAAAA
1 AAAGAAAAAAGGAATAAAAAAAA
*
19293764 AAAGAAAAAAGGCATAAAAAAA
1 AAAGAAAAAAGGAATAAAAAAA
19293786 GTTACAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.82, C:0.02, G:0.11, T:0.05
Consensus pattern (23 bp):
AAAGAAAAAAGGAATAAAAAAAA
Found at i:19294340 original size:12 final size:13
Alignment explanation
Indices: 19294301--19294341 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
19294291 TATTTATTTA
*
19294301 AAAAATAATCATAC
1 AAAAAT-ATTATAC
19294315 AAAAATATTATAC
1 AAAAATATTATAC
19294328 AAAAATATT-TAC
1 AAAAATATTATAC
19294340 AA
1 AA
19294342 TTAAGATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 5 0.19
13 15 0.58
14 6 0.23
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAATATTATAC
Found at i:19294475 original size:6 final size:6
Alignment explanation
Indices: 19294419--19294486 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
19294409 CTAATCAAAT
* * * *
19294419 AAATAA AATTAA AAA-CA TAATAA AGATAA AAAT-A AAATAA AAATAGTA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATA--A
*
19294467 AAATAA AAACAA AAA-AA AAA
1 AAATAA AAATAA AAATAA AAA
19294487 ACTTACCAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
5 13 0.27
6 30 0.61
8 6 0.12
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:19294481 original size:26 final size:26
Alignment explanation
Indices: 19294429--19294487 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
19294419 AAATAAAATT
* *
19294429 AAAAACATAATAAAGATAAAAATAAA
1 AAAAAAATAATAAAGATAAAAAAAAA
* *
19294455 ATAAAAATAGTAAA-ATAAAAACAAAA
1 AAAAAAATAATAAAGATAAAAA-AAAA
19294481 AAAAAAA
1 AAAAAAA
19294488 CTTACCAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (26 bp):
AAAAAAATAATAAAGATAAAAAAAAA
Found at i:19294927 original size:27 final size:26
Alignment explanation
Indices: 19294878--19294928 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
19294868 ATAAAATTAG
* *
19294878 TTAAAAAAATCTTTTATTGAAGAATA
1 TTAAAAAAATCTTTAATTAAAGAATA
*
19294904 TTAAGAAAATCTTTAAATTAAAGAA
1 TTAAAAAAATCTTT-AATTAAAGAA
19294929 ATATCTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (26 bp):
TTAAAAAAATCTTTAATTAAAGAATA
Found at i:19297808 original size:145 final size:145
Alignment explanation
Indices: 19297595--19297994 Score: 409
Period size: 145 Copynumber: 2.7 Consensus size: 145
19297585 TTAAAACACA
* *** * * *
19297595 AAAAATCATGAAATATTATGAAATTAAGATCTGAAAAGTTTCCTAAAAATTTGAGTTCGAGAAGG
1 AAAAATCATGAAATATTATAAAATTAAGATAAAAAAAGTTTCATAAAATTTTGAGCTCGAGAAGG
19297660 TTAAATTACAAAAATA-CTCTTATAAAGATATTTTTA-TAATTTCATAC-TTTTTAAGG-TACTG
66 TTAAATTACAAAAATATCTCTTA-AAAGATA-TTTTAGTAATTT--TACATTTTTAAGGATACTG
* * * *
19297721 CTATAATTTTAGATGTATC
127 CTATAATTTCAAATGCACC
19297740 AAAAATCATGAAATATTATAAAATTAAGATAAAAAAAGTTTCATAAAATTTTGAGCTCGAGAAGG
1 AAAAATCATGAAATATTATAAAATTAAGATAAAAAAAGTTTCATAAAATTTTGAGCTCGAGAAGG
** ** * *
19297805 TTAAATTATGAAAATATCTCTTAAAAGATATTTTAGTAATTTTACATTTTTTGGGATATTGCTGT
66 TTAAATTACAAAAATATCTCTTAAAAGATATTTTAGTAATTTTACATTTTTAAGGATACTGCTAT
**
19297870 TGTTTCAAATGCACC
131 AATTTCAAATGCACC
* * ** * *
19297885 AAAAATTATGAAATATTATAAAATTAAGATTCTAAAAAA-TTTCATGAAAA-TTCAAGCTTGAAA
1 AAAAATCATGAAATATTATAAAATTAAGA-T-AAAAAAAGTTTCAT-AAAATTTTGAGCTCGAGA
* * * *
19297948 AGATCAAATTACAAGAATATCCTCTATAAAAG-TATTTTAATAATTTT
63 AGGTTAAATTACAAAAATAT-CTCT-TAAAAGATATTTTAGTAATTTT
19297995 GCCTTTCTTG
Statistics
Matches: 215, Mismatches: 31, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
143 3 0.01
144 12 0.06
145 129 0.60
146 37 0.17
147 28 0.13
148 6 0.03
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (145 bp):
AAAAATCATGAAATATTATAAAATTAAGATAAAAAAAGTTTCATAAAATTTTGAGCTCGAGAAGG
TTAAATTACAAAAATATCTCTTAAAAGATATTTTAGTAATTTTACATTTTTAAGGATACTGCTAT
AATTTCAAATGCACC
Found at i:19301367 original size:12 final size:12
Alignment explanation
Indices: 19301350--19301376 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19301340 TTTAAAATTA
19301350 TAATAAAATATT
1 TAATAAAATATT
19301362 TAATAAAATATT
1 TAATAAAATATT
19301374 TAA
1 TAA
19301377 ATTTTAAAAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAAAATATT
Found at i:19301402 original size:29 final size:31
Alignment explanation
Indices: 19301344--19301415 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 31
19301334 AATAATTTTA
19301344 AAATTATAATAAAATATTTAATAAAATATTT
1 AAATTATAATAAAATATTTAATAAAATATTT
* * *
19301375 AAATTTTAA-AAAAT-TTTAATATATTATTT
1 AAATTATAATAAAATATTTAATAAAATATTT
*
19301404 GAATTATGAATA
1 AAATTAT-AATA
19301416 TATTAATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 18 0.53
30 7 0.21
31 9 0.26
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (31 bp):
AAATTATAATAAAATATTTAATAAAATATTT
Found at i:19301428 original size:20 final size:20
Alignment explanation
Indices: 19301392--19301429 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19301382 AAAAAATTTT
*
19301392 AATATATTATTTGAATTATG
1 AATATATTATATGAATTATG
19301412 AATATATTAATAT-AATTA
1 AATATATT-ATATGAATTA
19301430 ATTTTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AATATATTATATGAATTATG
Found at i:19303063 original size:14 final size:14
Alignment explanation
Indices: 19303044--19303071 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19303034 ATCTTTCTTC
19303044 TTTTTTGATTTTTT
1 TTTTTTGATTTTTT
19303058 TTTTTTGATTTTTT
1 TTTTTTGATTTTTT
19303072 CTTTAATGGA
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:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (14 bp):
TTTTTTGATTTTTT
Found at i:19303298 original size:20 final size:22
Alignment explanation
Indices: 19303256--19303301 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
19303246 CCAAAGCTCC
*
19303256 ATATTGAAATTAAAAATATTGA
1 ATATTGAAATTAAAAATACTGA
*
19303278 ATATTTAAA-TAAAAAT-CTGA
1 ATATTGAAATTAAAAATACTGA
19303298 ATAT
1 ATAT
19303302 GTCAAAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (22 bp):
ATATTGAAATTAAAAATACTGA
Found at i:19303527 original size:30 final size:29
Alignment explanation
Indices: 19303448--19303528 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
19303438 ACATAATGAA
19303448 AATGAAGATTTTTCATTTTATAGAATATTG
1 AATGAAGATTTTT-ATTTTATAGAATATTG
* * * * *
19303478 TATGATATATCTGTGTTTTATAGAATATATG
1 AATGA-AGATTTTTATTTTATAGAATAT-TG
*
19303509 AATGAAGATTTTTTTTTTAT
1 AATGAAGATTTTTATTTTAT
19303529 TTTTTGAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
30 28 0.72
31 11 0.28
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (29 bp):
AATGAAGATTTTTATTTTATAGAATATTG
Found at i:19304106 original size:36 final size:36
Alignment explanation
Indices: 19304061--19304130 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
19304051 GAACTAGGCA
* *
19304061 TTAGTCAATATGATTTAGATGGAAGGAGGGAAGGTG
1 TTAGCCAATATGATTTAGATGGAAGGAGAGAAGGTG
19304097 TTAGCCAATATGATTTAGATGGAAGGAGAGAAGG
1 TTAGCCAATATGATTTAGATGGAAGGAGAGAAGG
19304131 AGGGAGAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.36, C:0.04, G:0.34, T:0.26
Consensus pattern (36 bp):
TTAGCCAATATGATTTAGATGGAAGGAGAGAAGGTG
Found at i:19304218 original size:25 final size:25
Alignment explanation
Indices: 19304190--19304240 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
19304180 TTTAAAAAAA
*
19304190 TGAAATTCACTTAGAACATCACTCT
1 TGAAATTCACTTAGAACATAACTCT
*
19304215 TGAAATTTACTTAGAACATAACTCT
1 TGAAATTCACTTAGAACATAACTCT
19304240 T
1 T
19304241 TTATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (25 bp):
TGAAATTCACTTAGAACATAACTCT
Found at i:19321229 original size:38 final size:35
Alignment explanation
Indices: 19321187--19321259 Score: 83
Period size: 38 Copynumber: 2.0 Consensus size: 35
19321177 CTATTTGTAC
* * *
19321187 ATTTATTTTTATTTTATATATTTTACTATTAAATACAT
1 ATTTAATTTAATTTT-TATATTTT--TACTAAATACAT
*
19321225 ATTTAATTTAATTTTTTTATTTTTACTAAATACAT
1 ATTTAATTTAATTTTTATATTTTTACTAAATACAT
19321260 CCTGTGCCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 11 0.35
37 7 0.23
38 13 0.42
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (35 bp):
ATTTAATTTAATTTTTATATTTTTACTAAATACAT
Found at i:19321757 original size:34 final size:34
Alignment explanation
Indices: 19321716--19321921 Score: 98
Period size: 34 Copynumber: 6.2 Consensus size: 34
19321706 ACGAAAAACC
*
19321716 AAAAATTTAAAGATTTTTTAAAAATTTATTTTCA
1 AAAAATTTAAAGATTTTTTGAAAATTTATTTTCA
* * * *
19321750 AGAAATTTTAAA-A-TCTTTCAAAA---A---TCT
1 A-AAAATTTAAAGATTTTTTGAAAATTTATTTTCA
* *
19321777 AAAAGTTTAAAGATTTTTTTGAAAATTTATTTTTA
1 AAAAATTTAAAGA-TTTTTTGAAAATTTATTTTCA
* * * *
19321812 ATAAACCTTT-GAG-TTTCTTGAAAATCTCT-TTTTGA
1 A-AAA-ATTTAAAGATTTTTTGAAAAT-T-TATTTTCA
* ***
19321847 GAAACCCTAAAG-TTTTTTGAAAATTTATTTTCA
1 AAAAATTTAAAGATTTTTTGAAAATTTATTTTCA
*
19321880 AAAAATCTTAAA-ATTTCTT-AAAATTTTATTTTCA
1 AAAAAT-TTAAAGATTTTTTGAAAA-TTTATTTTCA
19321914 AAAAATTT
1 AAAAATTT
19321922 GATTTTAAAA
Statistics
Matches: 129, Mismatches: 24, Indels: 39
0.67 0.12 0.20
Matches are distributed among these distances:
26 9 0.07
27 4 0.03
29 8 0.06
30 1 0.01
32 2 0.02
33 25 0.19
34 54 0.42
35 17 0.13
36 6 0.05
37 3 0.02
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (34 bp):
AAAAATTTAAAGATTTTTTGAAAATTTATTTTCA
Found at i:19321918 original size:16 final size:16
Alignment explanation
Indices: 19321866--19321931 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
19321856 AAGTTTTTTG
19321866 AAAA-TTTATTTTCAA
1 AAAATTTTATTTTCAA
* * **
19321881 AAAATCTTAAAATTTCTT
1 AAAAT-TT-TATTTTCAA
19321899 AAAATTTTATTTTCAA
1 AAAATTTTATTTTCAA
*
19321915 AAAATTTGATTTT-AA
1 AAAATTTTATTTTCAA
19321930 AA
1 AA
19321932 TTTTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
15 8 0.21
16 17 0.44
17 4 0.10
18 10 0.26
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (16 bp):
AAAATTTTATTTTCAA
Found at i:19326723 original size:31 final size:31
Alignment explanation
Indices: 19326688--19326775 Score: 167
Period size: 31 Copynumber: 2.8 Consensus size: 31
19326678 CATGCTCATA
*
19326688 TTTGTTACTTGATTCAAGTGTCTCAATGAGC
1 TTTGTTTCTTGATTCAAGTGTCTCAATGAGC
19326719 TTTGTTTCTTGATTCAAGTGTCTCAATGAGC
1 TTTGTTTCTTGATTCAAGTGTCTCAATGAGC
19326750 TTTGTTTCTTGATTCAAGTGTCTCAA
1 TTTGTTTCTTGATTCAAGTGTCTCAA
19326776 CAAACAATCA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (31 bp):
TTTGTTTCTTGATTCAAGTGTCTCAATGAGC
Found at i:19327352 original size:2 final size:2
Alignment explanation
Indices: 19327347--19327372 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19327337 ATTTTGCTCA
19327347 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19327373 TTATGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19327955 original size:21 final size:21
Alignment explanation
Indices: 19327911--19327957 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
19327901 AATAAAATGA
*
19327911 TTTTTTAGTCAAAATTAAGAT
1 TTTTTTAGTCAAAATTAACAT
* * *
19327932 TTTTTTATTCAAAATTACCCT
1 TTTTTTAGTCAAAATTAACAT
19327953 TTTTT
1 TTTTT
19327958 AAAGTAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTTTAGTCAAAATTAACAT
Found at i:19328238 original size:25 final size:25
Alignment explanation
Indices: 19328193--19328240 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
19328183 ATTTTGTTTC
* *
19328193 TTTATATAATTTTAATTTAAAATAA
1 TTTATATAATTTGAATCTAAAATAA
19328218 TTTATATAA-TTGAGATCTAAAAT
1 TTTATATAATTTGA-ATCTAAAAT
19328241 TTAGTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (25 bp):
TTTATATAATTTGAATCTAAAATAA
Found at i:19328446 original size:38 final size:35
Alignment explanation
Indices: 19328375--19328454 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 35
19328365 GAAAAAATAG
*
19328375 GAAAAAAAA-AGAAAAAGAAAAAAGAAGAGAAGAA
1 GAAAAAAAACGGAAAAAGAAAAAAGAAGAGAAGAA
* * *
19328409 TGAAACAAAAACGGAAAAATGAAGAAAGGAGATAAGAA
1 -GAAA-AAAAACGGAAAAA-GAAAAAAGAAGAGAAGAA
19328447 GAAAAAAA
1 GAAAAAAA
19328455 TACTATTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
35 4 0.11
36 9 0.24
37 10 0.26
38 15 0.39
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.04
Consensus pattern (35 bp):
GAAAAAAAACGGAAAAAGAAAAAAGAAGAGAAGAA
Found at i:19329069 original size:22 final size:21
Alignment explanation
Indices: 19329044--19329095 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
19329034 TGGAACTATG
19329044 TGTACATTCCTCTTTTATTATA
1 TGTACATT-CTCTTTTATTATA
*
19329066 TGTACATATTTCTTTTATTATA
1 TGTACAT-TCTCTTTTATTATA
*
19329088 TATACATT
1 TGTACATT
19329096 TGCTAAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (21 bp):
TGTACATTCTCTTTTATTATA
Found at i:19331273 original size:21 final size:21
Alignment explanation
Indices: 19331225--19331273 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
19331215 GAAATAATAG
*
19331225 GAAAGAAAAAAGAATAACTAA
1 GAAAGAAAAAAGAAGAACTAA
19331246 -AAA-AAAAAA-AAGAACATAA
1 GAAAGAAAAAAGAAGAAC-TAA
19331265 GAAAGAAAA
1 GAAAGAAAA
19331274 GAACCCAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 5 0.21
19 9 0.38
20 6 0.25
21 4 0.17
ACGTcount: A:0.78, C:0.04, G:0.12, T:0.06
Consensus pattern (21 bp):
GAAAGAAAAAAGAAGAACTAA
Found at i:19333299 original size:104 final size:105
Alignment explanation
Indices: 19333112--19333328 Score: 355
Period size: 104 Copynumber: 2.1 Consensus size: 105
19333102 CAAAATGAAA
* *
19333112 GCATTCTAGGTGAGTTCTTCATCGAATTAAAAATCAATTGATTGCATATTATATATGAATTATAA
1 GCATTCTAGGTGAG-T-TTCATCGAATTAAAAATCAATTGATTGCATATTAAATATGAATTACAA
* *
19333177 TATGTATTATCTGAAGTATCCCTTTCATAATCAGTATCTTCT
64 TATGTATTATCCGAAGTATCCCCTTCATAATCAGTATCTTCT
*
19333219 GCATTCTAGGTGAG-TTCATCGAATTAAAAATCAATTGATTGCATGTTAAATATGAATTACAATA
1 GCATTCTAGGTGAGTTTCATCGAATTAAAAATCAATTGATTGCATATTAAATATGAATTACAATA
*
19333283 TGTATTATCCGTAGTATCCCCTTCATAATCAGTATCTTCT
66 TGTATTATCCGAAGTATCCCCTTCATAATCAGTATCTTCT
19333323 GCATTC
1 GCATTC
19333329 ATTAATTATT
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
104 90 0.87
107 14 0.13
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (105 bp):
GCATTCTAGGTGAGTTTCATCGAATTAAAAATCAATTGATTGCATATTAAATATGAATTACAATA
TGTATTATCCGAAGTATCCCCTTCATAATCAGTATCTTCT
Found at i:19333996 original size:1 final size:1
Alignment explanation
Indices: 19333990--19334032 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
19333980 ATAAATAACC
* * * *
19333990 AAAAAAAAAAAAAAAAAACAAAAAAGAAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19334033 GCACCAAGCA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.91, C:0.02, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:19334013 original size:19 final size:19
Alignment explanation
Indices: 19333989--19334032 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
19333979 GATAAATAAC
19333989 CAAAAAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAAA
* *
19334008 CAAAAAAGAAAAAGAAAAA
1 CAAAAAAAAAAAAAAAAAA
*
19334027 GAAAAA
1 CAAAAA
19334033 GCACCAAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.89, C:0.05, G:0.07, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAAAAAAAAAA
Found at i:19335513 original size:30 final size:30
Alignment explanation
Indices: 19335479--19335538 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
19335469 TGTTAAATTC
* *
19335479 ATAAGTCACTGAGTTGTGGACCTTTAAAAT
1 ATAAGTCACAGAGTAGTGGACCTTTAAAAT
19335509 ATAAGTCACAGAGTAGTGGACCTTTAAAAT
1 ATAAGTCACAGAGTAGTGGACCTTTAAAAT
19335539 TTCTATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (30 bp):
ATAAGTCACAGAGTAGTGGACCTTTAAAAT
Found at i:19337700 original size:39 final size:38
Alignment explanation
Indices: 19337575--19337707 Score: 135
Period size: 39 Copynumber: 3.4 Consensus size: 38
19337565 CAACCGTGGG
* * * *
19337575 AGAACATTTAATTAAAAATTTCAATGTCTTAA-TTATGAG
1 AGAACATTTTATTTAAAATTTC-ATGTC-TAAGTTGTGAA
* * *
19337614 AGAACATTTTATTTAAAGTTTCAAG-CTACAGTTGTAAA
1 AGAACATTTTATTTAAAATTTCATGTCTA-AGTTGTGAA
* *
19337652 AGTATATTTTATTTAAAATTTCGATGTCTAAGTTGTGAA
1 AGAACATTTTATTTAAAATTTC-ATGTCTAAGTTGTGAA
19337691 AGAACATTTTATTTAAA
1 AGAACATTTTATTTAAA
19337708 GTTTTAAACT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
36 2 0.03
37 2 0.03
38 25 0.33
39 44 0.58
40 3 0.04
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.41
Consensus pattern (38 bp):
AGAACATTTTATTTAAAATTTCATGTCTAAGTTGTGAA
Found at i:19338001 original size:6 final size:6
Alignment explanation
Indices: 19337988--19338053 Score: 71
Period size: 6 Copynumber: 11.2 Consensus size: 6
19337978 AAAGCTCAAA
* * * *
19337988 AATTTT AGTTTT -AGTTT AATTTT AATTTT GATTTT AATTTT AATGTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
* *
19338035 ATTTTT AATTTT ATTTTT A
1 AATTTT AATTTT AATTTT A
19338054 GAGTCAAAGT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
5 3 0.06
6 45 0.94
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:19339388 original size:18 final size:18
Alignment explanation
Indices: 19339365--19339425 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
19339355 ATAGGTTTTA
* *
19339365 TTTTATTTTATTTTCTAT
1 TTTTATTTTATTTTATGT
* *
19339383 TTTTATTTTGTTTTGTGT
1 TTTTATTTTATTTTATGT
*
19339401 TGTTATTTTATTTTATGT
1 TTTTATTTTATTTTATGT
19339419 TTTTATT
1 TTTTATT
19339426 AATTGTGTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.13, C:0.02, G:0.08, T:0.77
Consensus pattern (18 bp):
TTTTATTTTATTTTATGT
Found at i:19340406 original size:20 final size:20
Alignment explanation
Indices: 19340381--19340454 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
19340371 GGCATTAATA
* *
19340381 ATTATTAATATGTTTGCATG
1 ATTATTAATATATTTGAATG
19340401 ATTATTAATATATTTGAATG
1 ATTATTAATATATTTGAATG
*
19340421 ATTATTAAT-TAATT-ATATG
1 ATTATTAATATATTTGA-ATG
19340440 ATTATTAATATATTT
1 ATTATTAATATATTT
19340455 ATTTGTGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 16 0.33
20 31 0.65
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.53
Consensus pattern (20 bp):
ATTATTAATATATTTGAATG
Found at i:19340470 original size:44 final size:44
Alignment explanation
Indices: 19340422--19340563 Score: 236
Period size: 44 Copynumber: 3.3 Consensus size: 44
19340412 ATTTGAATGA
*
19340422 TTATTAATTAATTATATGATTATTAATATATTTATTTGTGTAAT
1 TTATTAATTAATTACATGATTATTAATATATTTATTTGTGTAAT
* *
19340466 TTATTAATTAATT-GA-G-TTATTATTATATTTATTTGTGTAAT
1 TTATTAATTAATTACATGATTATTAATATATTTATTTGTGTAAT
19340507 TTATTAATTAATTACATGATTATTAATATATTTATTTGTGTAAT
1 TTATTAATTAATTACATGATTATTAATATATTTATTTGTGTAAT
19340551 TTATTAATTAATT
1 TTATTAATTAATT
19340564 GATTGTTAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
41 37 0.41
42 2 0.02
43 2 0.02
44 50 0.55
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (44 bp):
TTATTAATTAATTACATGATTATTAATATATTTATTTGTGTAAT
Found at i:19340498 original size:41 final size:40
Alignment explanation
Indices: 19340399--19340582 Score: 223
Period size: 41 Copynumber: 4.5 Consensus size: 40
19340389 TATGTTTGCA
* *
19340399 TGATTATTAATATATTTGA-ATGAT-T-ATTAATTAATT-AT
1 TGATTATTAATATATTT-ATTTG-TGTAATTTATTAATTAAT
19340437 ATGATTATTAATATATTTATTTGTGTAATTTATTAATTAAT
1 -TGATTATTAATATATTTATTTGTGTAATTTATTAATTAAT
*
19340478 TGAGTTATTATTATATTTATTTGTGTAATTTATTAATTAATT
1 TGA-TTATTAATATATTTATTTGTGTAATTTATTAATTAA-T
19340520 ACATGATTATTAATATATTTATTTGTGTAATTTATTAATTAAT
1 ---TGATTATTAATATATTTATTTGTGTAATTTATTAATTAAT
* *
19340563 TGATTGTTAATATTTTTATT
1 TGATTATTAATATATTTATT
19340583 AGTATCTATT
Statistics
Matches: 130, Mismatches: 6, Indels: 17
0.85 0.04 0.11
Matches are distributed among these distances:
38 2 0.02
39 20 0.15
40 31 0.24
41 37 0.28
42 1 0.01
43 1 0.01
44 35 0.27
45 3 0.02
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.57
Consensus pattern (40 bp):
TGATTATTAATATATTTATTTGTGTAATTTATTAATTAAT
Found at i:19340520 original size:85 final size:84
Alignment explanation
Indices: 19340422--19340582 Score: 277
Period size: 85 Copynumber: 1.9 Consensus size: 84
19340412 ATTTGAATGA
*
19340422 TTATTAATTAATTATATGATTATTAATATATTTATTTGTGTAATTTATTAATTAATTGAGTTATT
1 TTATTAATTAATTACATGATTATTAATATATTTATTTGTGTAATTTATTAATTAATTGA-TTATT
*
19340487 ATTATATTTATTTGTGTAAT
65 AATATATTTATTTGTGTAAT
*
19340507 TTATTAATTAATTACATGATTATTAATATATTTATTTGTGTAATTTATTAATTAATTGATTGTTA
1 TTATTAATTAATTACATGATTATTAATATATTTATTTGTGTAATTTATTAATTAATTGATTATTA
*
19340572 ATATTTTTATT
66 ATATATTTATT
19340583 AGTATCTATT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 14 0.19
85 58 0.81
ACGTcount: A:0.34, C:0.01, G:0.07, T:0.58
Consensus pattern (84 bp):
TTATTAATTAATTACATGATTATTAATATATTTATTTGTGTAATTTATTAATTAATTGATTATTA
ATATATTTATTTGTGTAAT
Found at i:19348901 original size:76 final size:77
Alignment explanation
Indices: 19348811--19348964 Score: 292
Period size: 76 Copynumber: 2.0 Consensus size: 77
19348801 GATCATGAAT
*
19348811 ACAGGCTCAACCCGTTGAAAGCCTAATAGTCTTTATTTAATTGATGAAAAAGAGTGCATGATC-A
1 ACAGGCTCAACCCGTTGAAAGCCTAATAGTCTTTATTTAATTGATGAAAAAGAGTCCATGATCAA
19348875 AAAAGGAGTCTA
66 AAAAGGAGTCTA
19348887 ACAGGCTCAACCCGTTGAAAGCCTAATAGTCTTTATTTAATTGATGAAAAAGAGTCCATGATCAA
1 ACAGGCTCAACCCGTTGAAAGCCTAATAGTCTTTATTTAATTGATGAAAAAGAGTCCATGATCAA
19348952 AAAAGGAGTCTA
66 AAAAGGAGTCTA
19348964 A
1 A
19348965 GGAGTCCAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
76 62 0.82
77 14 0.18
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (77 bp):
ACAGGCTCAACCCGTTGAAAGCCTAATAGTCTTTATTTAATTGATGAAAAAGAGTCCATGATCAA
AAAAGGAGTCTA
Found at i:19353640 original size:59 final size:58
Alignment explanation
Indices: 19353549--19353684 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 58
19353539 TTTAGGGTTT
* * *
19353549 AATTTTTT-GTTATAAATTTGTTGAAATTTGTTTAGGTTTTAATTATATATTTGTTGA
1 AATTTTTTCGTTATATATTTATTGAAATTTGTTTAGATTTTAATTATATATTTGTTGA
** * * **
19353606 GTTTTTGTTCGTTATATATTTATTTAACTTTGTTTAGATTTTGGTTATATATTTGTTGA
1 AATTTT-TTCGTTATATATTTATTGAAATTTGTTTAGATTTTAATTATATATTTGTTGA
*
19353665 AATTTTTTGGTTATATATTT
1 AATTTTTTCGTTATATATTT
19353685 TTGTTGGATT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
57 4 0.06
58 15 0.23
59 46 0.71
ACGTcount: A:0.24, C:0.01, G:0.14, T:0.60
Consensus pattern (58 bp):
AATTTTTTCGTTATATATTTATTGAAATTTGTTTAGATTTTAATTATATATTTGTTGA
Found at i:19353702 original size:25 final size:27
Alignment explanation
Indices: 19353644--19353699 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
19353634 TTTGTTTAGA
19353644 TTTTGG-T-TATATATTTGTTGAAATT
1 TTTTGGTTATATATATTTGTTGAAATT
* *
19353669 TTTTGGTTATATATTTTTGTTG-GATT
1 TTTTGGTTATATATATTTGTTGAAATT
19353695 TTTTG
1 TTTTG
19353700 TTAAGTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 6 0.22
26 9 0.33
27 12 0.44
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (27 bp):
TTTTGGTTATATATATTTGTTGAAATT
Found at i:19353708 original size:25 final size:27
Alignment explanation
Indices: 19353644--19353699 Score: 82
Period size: 25 Copynumber: 2.2 Consensus size: 27
19353634 TTTGTTTAGA
19353644 TTTTGGTTATATA--TTTGTTGAAATT
1 TTTTGGTTATATATTTTTGTTGAAATT
*
19353669 TTTTGGTTATATATTTTTGTTG-GATT
1 TTTTGGTTATATATTTTTGTTGAAATT
19353695 TTTTG
1 TTTTG
19353700 TTAAGTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 13 0.46
26 8 0.29
27 7 0.25
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (27 bp):
TTTTGGTTATATATTTTTGTTGAAATT
Found at i:19353804 original size:23 final size:22
Alignment explanation
Indices: 19353754--19353797 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19353744 TTTTAGTATT
*
19353754 TTGAGGAA-TTTTTTTTATTTG
1 TTGAGTAATTTTTTTTTATTTG
19353775 TTGAGTAATTTTTTTTTATTTG
1 TTGAGTAATTTTTTTTTATTTG
19353797 T
1 T
19353798 GAAAGTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (22 bp):
TTGAGTAATTTTTTTTTATTTG
Found at i:19353975 original size:19 final size:21
Alignment explanation
Indices: 19353938--19353976 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
19353928 AATATTTTCT
19353938 AAATTATAATAATAATTATAG
1 AAATTATAATAATAATTATAG
*
19353959 AAATTA-AA-AATATTTATA
1 AAATTATAATAATAATTATA
19353977 TTGATTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
AAATTATAATAATAATTATAG
Found at i:19354025 original size:23 final size:23
Alignment explanation
Indices: 19353999--19354050 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
19353989 TATAATTGGG
19353999 TTTGATGTAGAA-TAAGATTTATA
1 TTTGAT-TAGAAGTAAGATTTATA
* **
19354022 TTTGATTTGAAGTAATTTTTATA
1 TTTGATTAGAAGTAAGATTTATA
19354045 TTTGAT
1 TTTGAT
19354051 AGTTTAGTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (23 bp):
TTTGATTAGAAGTAAGATTTATA
Found at i:19354143 original size:14 final size:16
Alignment explanation
Indices: 19354110--19354142 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19354100 TGTATTGATC
*
19354110 AAATATAATATAAATA
1 AAATAAAATATAAATA
19354126 AAATAAAATA-AAATA
1 AAATAAAATATAAATA
19354141 AA
1 AA
19354143 TTATTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAAATATAAATA
Found at i:19361046 original size:19 final size:19
Alignment explanation
Indices: 19361022--19361064 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
19361012 AAATTGAAAT
19361022 TTATAGGTTTCTTAAATAA
1 TTATAGGTTTCTTAAATAA
* * *
19361041 TTATAGGTTTTTTGAGTAA
1 TTATAGGTTTCTTAAATAA
19361060 TTATA
1 TTATA
19361065 AATATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (19 bp):
TTATAGGTTTCTTAAATAA
Found at i:19369051 original size:30 final size:30
Alignment explanation
Indices: 19368989--19369053 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
19368979 TAGATTAACA
* *
19368989 TGAAATTAAATGCAAGAAATTGAAAATGCT
1 TGAAAGTAAATGCAAGAAATTGAAAATACT
* *
19369019 TGAAAGTAAATGTAAGAAA-TGTAAAGTACT
1 TGAAAGTAAATGCAAGAAATTG-AAAATACT
19369049 TGAAA
1 TGAAA
19369054 ATTGAAACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (30 bp):
TGAAAGTAAATGCAAGAAATTGAAAATACT
Found at i:19379113 original size:21 final size:21
Alignment explanation
Indices: 19379081--19379140 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 21
19379071 AATACAAGTT
*
19379081 TCAG-TTTCATTTCTTTACTG
1 TCAGCTTTTATTTCTTTACTG
** *
19379101 TCAGCTTTTATTT-TTTGTTT
1 TCAGCTTTTATTTCTTTACTG
19379121 TCAGCTTTTAATTTTCTTTA
1 TCAGCTTTT-A-TTTCTTTA
19379141 TTTTTCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 17 0.55
21 8 0.26
22 3 0.10
23 3 0.10
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (21 bp):
TCAGCTTTTATTTCTTTACTG
Found at i:19387381 original size:23 final size:23
Alignment explanation
Indices: 19387331--19387382 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
19387321 ATGGAAATGA
*
19387331 TAAATTTTAGAAATAATAAAAAC
1 TAAATTTTAGAAATAAGAAAAAC
* *
19387354 AAAATTTT-GAAATAAGAATAAAG
1 TAAATTTTAGAAATAAGAA-AAAC
19387377 TAAATT
1 TAAATT
19387383 CAATGATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (23 bp):
TAAATTTTAGAAATAAGAAAAAC
Found at i:19390828 original size:2 final size:2
Alignment explanation
Indices: 19390821--19390849 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19390811 ACACATGCAC
19390821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19390850 CACGTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19394620 original size:2 final size:2
Alignment explanation
Indices: 19394613--19394641 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19394603 TCGAGGCTTT
19394613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19394642 GTGAAAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19395059 original size:12 final size:12
Alignment explanation
Indices: 19395027--19395059 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
19395017 CAAAATGGAT
19395027 TTTCGAGAAGTC
1 TTTCGAGAAGTC
19395039 TTT-GAGAAGTC
1 TTTCGAGAAGTC
19395050 TTTCGAGAAG
1 TTTCGAGAAG
19395060 GCTTAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.33
Consensus pattern (12 bp):
TTTCGAGAAGTC
Found at i:19397792 original size:11 final size:11
Alignment explanation
Indices: 19397759--19397799 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
19397749 GGTTATTAAT
*
19397759 TTTATATTTAC
1 TTTATATTTAG
*
19397770 TTCAT-TTT-G
1 TTTATATTTAG
19397779 TTTATATTTAG
1 TTTATATTTAG
19397790 TTTATATTTA
1 TTTATATTTA
19397800 TCAAATATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
9 4 0.16
10 6 0.24
11 15 0.60
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TTTATATTTAG
Found at i:19400236 original size:12 final size:12
Alignment explanation
Indices: 19400219--19400243 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19400209 GAACAAAATG
19400219 GAAAAAGAAGAA
1 GAAAAAGAAGAA
19400231 GAAAAAGAAGAA
1 GAAAAAGAAGAA
19400243 G
1 G
19400244 GTATATGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAAAAGAAGAA
Found at i:19401397 original size:2 final size:2
Alignment explanation
Indices: 19401390--19401418 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19401380 ATTGTCTATT
19401390 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19401419 TTTATAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19401544 original size:14 final size:14
Alignment explanation
Indices: 19401525--19401575 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
19401515 TTTTTAAAAA
19401525 ATATATTAATTTTT
1 ATATATTAATTTTT
*
19401539 ATATATTTATTTTT
1 ATATATTAATTTTT
* *
19401553 A-AAATTAATATTT
1 ATATATTAATTTTT
*
19401566 ATTTATTAAT
1 ATATATTAAT
19401576 GAGATAGCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATATATTAATTTTT
Found at i:19401654 original size:2 final size:2
Alignment explanation
Indices: 19401647--19401680 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19401637 TATAAACTCT
19401647 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19401681 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19402946 original size:21 final size:22
Alignment explanation
Indices: 19402920--19402961 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
19402910 TGAATATTTT
19402920 AAAATT-AAAATATGATTTTAA
1 AAAATTAAAAATATGATTTTAA
19402941 AAAATTCAAAAATATGATTTT
1 AAAATT-AAAAATATGATTTT
19402962 CTTTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (22 bp):
AAAATTAAAAATATGATTTTAA
Found at i:19402998 original size:18 final size:19
Alignment explanation
Indices: 19402948--19402999 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
19402938 TAAAAAATTC
* *
19402948 AAAAATATGATTTTCTTTT
1 AAAAATATAATATTCTTTT
*
19402967 AAAAATTAAAATATT-TTTT
1 AAAAA-TATAATATTCTTTT
*
19402986 AAAAATATTATATT
1 AAAAATATAATATT
19403000 GATAATTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 7 0.26
19 14 0.52
20 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
AAAAATATAATATTCTTTT
Found at i:19405681 original size:16 final size:16
Alignment explanation
Indices: 19405660--19405718 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
19405650 TACTAATAAA
19405660 TAAATAGATTTTATTT
1 TAAATAGATTTTATTT
*
19405676 TAAAT--ATTTTA-AT
1 TAAATAGATTTTATTT
* *
19405689 TAAATAAATTTTATTC
1 TAAATAGATTTTATTT
*
19405705 TAATTATGATTTTA
1 TAAATA-GATTTTA
19405719 CAACTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 6 0.18
14 6 0.18
15 6 0.18
16 10 0.29
17 6 0.18
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (16 bp):
TAAATAGATTTTATTT
Found at i:19413973 original size:15 final size:15
Alignment explanation
Indices: 19413953--19413984 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19413943 AGTTCTAAGT
19413953 ACACTACCAAACAGG
1 ACACTACCAAACAGG
19413968 ACACTACCAAACAGG
1 ACACTACCAAACAGG
19413983 AC
1 AC
19413985 CAATAATTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.34, G:0.12, T:0.06
Consensus pattern (15 bp):
ACACTACCAAACAGG
Found at i:19414740 original size:27 final size:26
Alignment explanation
Indices: 19414690--19414740 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
19414680 TATTATTCTT
*
19414690 AAAATATTATTTATTAATATAATAAA
1 AAAATATTATTTATTAATAAAATAAA
*
19414716 AAAATATATATTTATTATTAAAATA
1 AAAATAT-TATTTATTAATAAAATA
19414741 TTAAAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAAATATTATTTATTAATAAAATAAA
Found at i:19414746 original size:27 final size:26
Alignment explanation
Indices: 19414688--19414746 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
19414678 ATTATTATTC
*
19414688 TTAAAATATTATTTATTAATATAATA
1 TTAAAATATTATTTATTAATAAAATA
** *
19414714 AAAAAATATATATTTATTATTAAAATA
1 TTAAAATAT-TATTTATTAATAAAATA
19414741 TTAAAA
1 TTAAAA
19414747 ACATTTACAC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TTAAAATATTATTTATTAATAAAATA
Found at i:19415231 original size:42 final size:48
Alignment explanation
Indices: 19415138--19415231 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 48
19415128 CATATTCATT
*
19415138 TAATGAAAATAATAATATTATTATATTATTTAATATTAATTATTAAAA
1 TAATGAAAATAATAATATTAATATATTATTTAATATTAATTATTAAAA
*
19415186 TAATGAAAATAGT-AT-TTAATATATTA-TT-AT-TT-ATTATTAAAA
1 TAATGAAAATAATAATATTAATATATTATTTAATATTAATTATTAAAA
19415228 TAAT
1 TAAT
19415232 ATTATAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
42 14 0.32
43 2 0.05
44 2 0.05
45 2 0.05
46 10 0.23
47 2 0.05
48 12 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (48 bp):
TAATGAAAATAATAATATTAATATATTATTTAATATTAATTATTAAAA
Found at i:19415618 original size:171 final size:170
Alignment explanation
Indices: 19415296--19415624 Score: 396
Period size: 171 Copynumber: 1.9 Consensus size: 170
19415286 AATTGAAATA
* *
19415296 TTTAAAATTAAAATATCCAAAGATTGTTAATGTTAATATTTTAATTTTTTAATTAAAATTAAATA
1 TTTAAAATTAAAATATCAAAAGATTGTTAATATTAATATTTTAATTTTTTAATTAAAATTAAATA
* * * * * * *
19415361 AAAATATTTTTTATTAATATAACAATATTTCATTTAGGATTAAATCAAGTTTAAACTTAAAATAT
66 AAAATATTTTTTATTAATATAACAATATTTCAGTCAAGATCAAATCAAATCTAAACTTAAAAAAT
**
19415426 CATATTCAAAATCTTACTTGAATAGAACTATAAAAATATTT
131 CATATTCAAAATCCGACTTGAATA-AACTATAAAAATATTT
* *
19415467 TTTAAAATTAAAATATTAAAAGATTTTTAATATTAATATTTTAATTTTTTTACA-T-AAATTAAA
1 TTTAAAATTAAAATATCAAAAGATTGTTAATATTAATATTTTAA-TTTTTTA-ATTAAAATTAAA
* * * **
19415530 TAAAAATA-TTTTTATTAATATAATAATATTTCAAGTCAAG-TCAAATTAAATCTGAGTTTGAAA
64 TAAAAATATTTTTTATTAATATAACAATATTTC-AGTCAAGATCAAATCAAATCTAAACTT-AAA
* **
19415593 AAATCATGTTCAAGGTCCGACTTGAATAAACT
127 AAATCATATTCAAAATCCGACTTGAATAAACT
19415625 TGTACTCACG
Statistics
Matches: 133, Mismatches: 21, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
170 39 0.29
171 85 0.64
172 8 0.06
173 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (170 bp):
TTTAAAATTAAAATATCAAAAGATTGTTAATATTAATATTTTAATTTTTTAATTAAAATTAAATA
AAAATATTTTTTATTAATATAACAATATTTCAGTCAAGATCAAATCAAATCTAAACTTAAAAAAT
CATATTCAAAATCCGACTTGAATAAACTATAAAAATATTT
Found at i:19418874 original size:2 final size:2
Alignment explanation
Indices: 19418869--19418893 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19418859 TACTAAATAA
19418869 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19418894 GCGTAGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19420755 original size:17 final size:17
Alignment explanation
Indices: 19420722--19420757 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
19420712 TGAGTGATTA
*
19420722 TTTATGTATTTTATTTT
1 TTTATGTATTTAATTTT
19420739 TTTAT-TATTTAATTTT
1 TTTATGTATTTAATTTT
19420755 TTT
1 TTT
19420758 GTCATGCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTATGTATTTAATTTT
Found at i:19421284 original size:21 final size:22
Alignment explanation
Indices: 19421241--19421284 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
19421231 TTATAATTGT
*
19421241 TAACATATGTATATTTTTTAAA
1 TAACATATGTATATTTTTGAAA
19421263 TAACAT-TGTA-ATTATTTGAAA
1 TAACATATGTATATT-TTTGAAA
19421284 T
1 T
19421285 TAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 11 0.55
22 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (22 bp):
TAACATATGTATATTTTTGAAA
Found at i:19421346 original size:16 final size:16
Alignment explanation
Indices: 19421299--19421348 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
19421289 ATATATTTAA
*
19421299 CAAAATTTTTTAATTGAT
1 CAAAATTTTATAATT--T
*
19421317 TAAAATTTTA-AATTT
1 CAAAATTTTATAATTT
19421332 CAAAATTTTATAATTT
1 CAAAATTTTATAATTT
19421348 C
1 C
19421349 TACAAAGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 10 0.36
16 6 0.21
17 4 0.14
18 8 0.29
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (16 bp):
CAAAATTTTATAATTT
Found at i:19421419 original size:80 final size:85
Alignment explanation
Indices: 19421329--19421511 Score: 225
Period size: 87 Copynumber: 2.2 Consensus size: 85
19421319 AAATTTTAAA
* *
19421329 TTTCAAAATTTTATAATTTCT-ACAAAGAC-TA-TAAA-A-TGAAAATGTAATTTTTGTTGAAAA
1 TTTCAAAATTTTATAATTT-TAACAAAGACATATTAAAGATTAAAAATGTAATATTTGTTGAAAA
*
19421389 TATACTAGGAAAAAAT-TATT
65 TAAACTAGGAAAAAATGTATT
* *
19421409 TTTCAAAATTTTATAATTTTAATAAAGACTATATTCTAAAGATTAAAAATGTAGTATTTGTTGAA
1 TTTCAAAATTTTATAATTTTAACAAAGAC-ATA-T-TAAAGATTAAAAATGTAATATTTGTTGAA
* *
19421474 AATAAATTATGAAAAAATGTATT
63 AATAAACTAGGAAAAAATGTATT
19421497 TTTCAAAATTTTATA
1 TTTCAAAATTTTATA
19421512 GTTTAAAAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
79 1 0.01
80 26 0.30
82 2 0.02
85 4 0.05
86 1 0.01
87 34 0.39
88 19 0.22
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (85 bp):
TTTCAAAATTTTATAATTTTAACAAAGACATATTAAAGATTAAAAATGTAATATTTGTTGAAAAT
AAACTAGGAAAAAATGTATT
Found at i:19421638 original size:93 final size:88
Alignment explanation
Indices: 19421373--19421705 Score: 232
Period size: 88 Copynumber: 3.7 Consensus size: 88
19421363 AATGAAAATG
* * * * * * * * *
19421373 TAATTTTTGTTGAAAATATACTAGGAAAAAA-TTATTTTTCAAAATTTTATAATTTTAATAAAGA
1 TAATCTTTATTGAAAATATATTATGAAAAAATTTATTTTTCTAAATTTTATAGTTTCAACAAAAA
* * **
19421437 CTATA--TTCTAAAGATTAAAAATG
66 CTA-AGCTTGT-AAGATAAAAAACA
* * * * * *
19421460 TAGTATTTGTTGAAAATAAATTATGAAAAAATGTATTTTTCAAAATTTTATAGTTT-AA-AAAAA
1 TAATCTTTATTGAAAATATATTATGAAAAAATTTATTTTTCTAAATTTTATAGTTTCAACAAAAA
* *
19421523 TTACGCTTGTAAGATAAAAAAAAAAACA
66 CTAAGCTTGTAAGAT-----AAAAAACA
* *
19421551 TAATTTTTATTGAAAATATATTATAAAAAAAATTTTATTTTTCTAAATTTTATAGTTTCAACAAA
1 TAATCTTTATTGAAAATATATTAT-GAAAAAA-TTTATTTTTCTAAATTTTATAGTTTCAACAAA
* * *
19421616 GACTAAGTTTTTAAGACT-AAAAACA
64 AACTAAGCTTGTAAGA-TAAAAAACA
* * * *
19421641 TTATCTTTGTTGAAAATATATTATGAGAAAATTTATTTTT-TAAAATTCTATA-TCTTCAACAAA
1 TAATCTTTATTGAAAATATATTATGAAAAAATTTATTTTTCT-AAATTTTATAGT-TTCAACAAA
19421704 AA
64 AA
19421706 TGATATTTTT
Statistics
Matches: 198, Mismatches: 33, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
86 11 0.06
87 33 0.17
88 50 0.25
89 5 0.03
90 28 0.14
91 25 0.13
92 6 0.03
93 23 0.12
94 2 0.01
95 14 0.07
96 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (88 bp):
TAATCTTTATTGAAAATATATTATGAAAAAATTTATTTTTCTAAATTTTATAGTTTCAACAAAAA
CTAAGCTTGTAAGATAAAAAACA
Found at i:19421758 original size:152 final size:154
Alignment explanation
Indices: 19421564--19421839 Score: 366
Period size: 152 Copynumber: 1.8 Consensus size: 154
19421554 TTTTTATTGA
* *
19421564 AAATATATTATAAAAAAAATTTTATTTTTCTAAATTTTATAGTTTCAACAAAGACTA-AGTTTTT
1 AAATATATTATAAAAAAAATTTTATTTTTCAAAATTTTATAGTTTCAACAAAAACTACA-TTTTT
* * * *
19421628 AAGACTAAAAACATTATCTT-TGTTGAAAATATATTATGAGAAA-ATTTATTTTTT-AAAATTCT
65 AA-AATAAAAACATAAT-TTATGTTAAAAATATATTATGA-AAATAATTATTTTTTGAAAATTCT
19421690 ATATCTTCAACAAAAATGATATTTTTTT
127 ATATCTTCAACAAAAATGATATTTTTTT
* * * * *
19421718 AAATATATTAT-GAAGAAA-TTTATTTTTCAAAATTTTATAGTTTTAATAAAAATTACATTTTTA
1 AAATATATTATAAAAAAAATTTTATTTTTCAAAATTTTATAGTTTCAACAAAAACTACATTTTTA
*
19421781 AAATGAAAACATAATTTATGTTAAAAATATATTATGAAAATAATTATTTTTTGAAAATT
66 AAATAAAAACATAATTTATGTTAAAAATATATTATGAAAATAATTATTTTTTGAAAATT
19421840 TCACAATTTC
Statistics
Matches: 106, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
150 5 0.05
151 39 0.37
152 45 0.42
153 6 0.06
154 11 0.10
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (154 bp):
AAATATATTATAAAAAAAATTTTATTTTTCAAAATTTTATAGTTTCAACAAAAACTACATTTTTA
AAATAAAAACATAATTTATGTTAAAAATATATTATGAAAATAATTATTTTTTGAAAATTCTATAT
CTTCAACAAAAATGATATTTTTTT
Found at i:19421769 original size:64 final size:64
Alignment explanation
Indices: 19421654--19421779 Score: 166
Period size: 64 Copynumber: 2.0 Consensus size: 64
19421644 TCTTTGTTGA
* *
19421654 AAATATATTATGAGAAAATTTATTTTTTAAAATTCTATATCTTCAACAAAAATGATATTTTTTT
1 AAATATATTATGAGAAAATTTATTTTTCAAAATTCTATATCTTCAACAAAAATGACATTTTTTT
* * * *
19421718 AAATATATTATGA-AGAAATTTATTTTTCAAAATTTTATAGT-TTTAATAAAAATTACATTTTT
1 AAATATATTATGAGA-AAATTTATTTTTCAAAATTCTATA-TCTTCAACAAAAATGACATTTTT
19421780 AAAATGAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
63 1 0.02
64 52 0.96
65 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (64 bp):
AAATATATTATGAGAAAATTTATTTTTCAAAATTCTATATCTTCAACAAAAATGACATTTTTTT
Found at i:19422162 original size:29 final size:30
Alignment explanation
Indices: 19422129--19422200 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
19422119 TCACAAATAT
* *
19422129 TAAATAAAATCA-TTTACATGTTAAATAAG
1 TAAATAAAATAATTTTACATGTTAAATAAA
19422158 TAAAT-AAATAATTTTACATGTTAAATAAA
1 TAAATAAAATAATTTTACATGTTAAATAAA
*
19422187 TAACT-AAATAATTT
1 TAAATAAAATAATTT
19422201 AAATATAAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (30 bp):
TAAATAAAATAATTTTACATGTTAAATAAA
Found at i:19422647 original size:82 final size:82
Alignment explanation
Indices: 19422557--19422707 Score: 239
Period size: 82 Copynumber: 1.8 Consensus size: 82
19422547 TGTTATTCAC
* * ** *
19422557 GTGACATCAACTAATAATATAACTAAGGCAATATAGTTAAAGATGTTATTATTCCCCTAATCAAA
1 GTGACATCAACTAATAATACAACAAAAACAATATAGTAAAAGATGTTATTATTCCCCTAATCAAA
19422622 TATAACAACCCTAAAAT
66 TATAACAACCCTAAAAT
* *
19422639 GTGACATCAACTAATAATACAACAAAAATAATATAGTAAAAGATGTTATTGTTCCCCTAATCAAA
1 GTGACATCAACTAATAATACAACAAAAACAATATAGTAAAAGATGTTATTATTCCCCTAATCAAA
19422704 TATA
66 TATA
19422708 GCACCCCCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 62 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (82 bp):
GTGACATCAACTAATAATACAACAAAAACAATATAGTAAAAGATGTTATTATTCCCCTAATCAAA
TATAACAACCCTAAAAT
Found at i:19423242 original size:18 final size:17
Alignment explanation
Indices: 19423211--19423245 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19423201 TAGTATTTAA
*
19423211 TGTTTTTCCTTTTTTTT
1 TGTTTTTCCCTTTTTTT
19423228 TGTTTATTCCCTTTTTTT
1 TGTTT-TTCCCTTTTTTT
19423246 AGGTTTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.03, C:0.14, G:0.06, T:0.77
Consensus pattern (17 bp):
TGTTTTTCCCTTTTTTT
Found at i:19423538 original size:22 final size:24
Alignment explanation
Indices: 19423508--19423555 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
19423498 AGACCCAAAC
19423508 AAAGCCCA-TTTAA-AGCTAATAA
1 AAAGCCCATTTTAAGAGCTAATAA
* *
19423530 AAAGGCCATTTTAAGAGCTTATAA
1 AAAGCCCATTTTAAGAGCTAATAA
19423554 AA
1 AA
19423556 TGCATCGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 5 0.23
24 10 0.45
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (24 bp):
AAAGCCCATTTTAAGAGCTAATAA
Found at i:19424084 original size:144 final size:145
Alignment explanation
Indices: 19423927--19424247 Score: 409
Period size: 145 Copynumber: 2.2 Consensus size: 145
19423917 AATTTTTATA
* * **
19423927 AAACTTTTTAGATCTTAATTTCATAATATTTCATGTTTTTTGGTGCATTTGAAATCACAGTAGTA
1 AAACTTTTTAGATCCTAATTTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAACAGTA
*
19423992 T-CCCAAAAATGAAAAATTA-CTAAAATACCCCTAT-AAGGTTATTTTCATAATTTGA-CCTTC-
66 TACCCAAAAATGAAAAATTATC-AAAATACCCATATAAAGG-TATTTTCATAATTT-ATCCTTCT
*
19424052 CTGAGTTTGGACTTTCATG
128 C-GAGTTTGAACTTTCATG
* *
19424071 AAACTTTTCAGATCCTAATGTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAACAGTA
1 AAACTTTTTAGATCCTAATTTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAACAGTA
* * ** * *
19424136 TACCGAAAAGTGTGAAATTATCAAAATACTCATATAAAGGTATTTTTATAATTTATCCTTCTCGA
66 TACCCAAAAATGAAAAATTATCAAAATACCCATATAAAGGTATTTTCATAATTTATCCTTCTCGA
*
19424201 GTTTGAATTTTCATG
131 GTTTGAACTTTCATG
* *
19424216 AAACTTTTTAGATCGTAATTTTATAAGTATTT
1 AAACTTTTTAGATCCTAATTTCATAA-TATTT
19424248 GAAATCACAA
Statistics
Matches: 152, Mismatches: 19, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
144 61 0.40
145 80 0.53
146 11 0.07
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (145 bp):
AAACTTTTTAGATCCTAATTTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAACAGTA
TACCCAAAAATGAAAAATTATCAAAATACCCATATAAAGGTATTTTCATAATTTATCCTTCTCGA
GTTTGAACTTTCATG
Found at i:19424216 original size:145 final size:143
Alignment explanation
Indices: 19423860--19424234 Score: 423
Period size: 144 Copynumber: 2.6 Consensus size: 143
19423850 GAAGAAGTAC
*** * * * * * * *
19423860 AAAATTACTAAAATACATTTTTGAAGGTATTTTTGTAATTTGACTTTTTCAAGCTTGAATTTTTA
1 AAAATTACTAAAATACCCATAT-AAGGTATTTTTATAATTTGACCTTCTCGAGTTTGAATTTTCA
* * * * **
19423925 TAAAACTTTTTAGATCTTAATTTCATAATATTTCATGTTTTTTGGTGCATTTGAAATCACAGTAG
65 TGAAACTTTTTAGATCCTAATGTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAACAG
19423990 TATCCCAAAAATGA
130 TATCCCAAAAATGA
* * * *
19424004 AAAATTACTAAAATACCCCTATAAGGTTATTTTCATAATTTGACCTTC-CTGAGTTTGGACTTTC
1 AAAATTACTAAAATACCCATATAAGG-TATTTTTATAATTTGACCTTCTC-GAGTTTGAATTTTC
*
19424068 ATGAAACTTTTCAGATCCTAATGTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAACA
64 ATGAAACTTTTTAGATCCTAATGTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAACA
* * *
19424133 GTATACCGAAAAGTGT
129 GTAT-CCCAAAAATGA
* *
19424149 GAAATTA-TCAAAATACTCATATAAAGGTATTTTTATAATTT-ATCCTTCTCGAGTTTGAATTTT
1 AAAATTACT-AAAATACCCATAT-AAGGTATTTTTATAATTTGA-CCTTCTCGAGTTTGAATTTT
*
19424212 CATGAAACTTTTTAGATCGTAAT
63 CATGAAACTTTTTAGATCCTAAT
19424235 TTTATAAGTA
Statistics
Matches: 193, Mismatches: 31, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
143 5 0.03
144 108 0.56
145 75 0.39
146 5 0.03
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (143 bp):
AAAATTACTAAAATACCCATATAAGGTATTTTTATAATTTGACCTTCTCGAGTTTGAATTTTCAT
GAAACTTTTTAGATCCTAATGTCATAATATTTCATGATTTTTGGTGCATTTGAAATCACAACAGT
ATCCCAAAAATGA
Found at i:19424460 original size:271 final size:270
Alignment explanation
Indices: 19423973--19424517 Score: 662
Period size: 271 Copynumber: 2.0 Consensus size: 270
19423963 TTTTTGGTGC
** *
19423973 ATTTGAAATCACAGTAGTATCCCAAAAATGAAAAATTACTAAAATACCCCTATAAGGTTATTTTC
1 ATTTGAAATCACAACAGTATCCCAAAAATGAAAAATTACTAAAATACCCCTAAAAGGTTATTTTC
* * *
19424038 ATAATTTGACCTTCCTGAGTTTGGACTTTCATGAAACTTTTCAGATCCTAATGTCATAATATTTC
66 ATAATTTGACCTTCCTAAGTCTCGACTTTCATGAAACTTTTCAGATCCTAATGTCATAATATTTC
* *
19424103 ATGATTTTTGGTGCATTTGAAATCACAACAGTATACCGAAAAGTGTGAAATTATCAAAATACTCA
131 ATGATTTTTGATGCATTTGAAATCACAACAATATACCGAAAAGTGTGAAATTATCAAAATACTCA
* * * *
19424168 TATAAAGGTATTTTTATAATTT-ATCCTTCTCGAG-TTTGAATTTTCATGAAACTTTTTAGATCG
196 TATAAAGGTATTTTCATAATTTGA-CCTTCCCGAGCTTAG-ATTTTCATGAAACTTTTCAGAT-G
19424231 T-AATTTTATAAGT
258 TCAATTTTATAA-T
* * *
19424244 ATTTGAAATCACAACAGTA-CCTCGAAAAGTGTAAAATTA-TCAAAATATCCCTAAAAGGTTATT
1 ATTTGAAATCACAACAGTATCC-C-AAAAATGAAAAATTACT-AAAATACCCCTAAAAGGTTATT
* * * * * * *
19424307 TTCGTAATTTGACCTTCTTAAG-CTCGATTTTCATGAAACTTTTCATATCTTAATTTTATAATAT
63 TTCATAATTTGACCTTCCTAAGTCTCGACTTTCATGAAACTTTTCAGATCCTAATGTCATAATAT
* * *
19424371 TTTATGATTTTTGATGCATTTGAAGTCACAGCAATAT--CGCAAGAAGTGTGAAATTA-CTAAAA
128 TTCATGATTTTTGATGCATTTGAAATCACAACAATATACCG-AA-AAGTGTGAAATTATC-AAAA
* *
19424433 TA-TCCCTAT-AGGGATATTTTCATAATTTGACCTTCCCGAGCTTAGATTTTCATGAAACTTTTC
190 TACT-CATATAAAGG-TATTTTCATAATTTGACCTTCCCGAGCTTAGATTTTCATGAAACTTTTC
19424496 AGATGTCAATTTTATAAT
253 AGATGTCAATTTTATAAT
19424514 ATTT
1 ATTT
19424518 CACGATTTTT
Statistics
Matches: 236, Mismatches: 27, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
269 2 0.01
270 16 0.07
271 162 0.69
272 56 0.24
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (270 bp):
ATTTGAAATCACAACAGTATCCCAAAAATGAAAAATTACTAAAATACCCCTAAAAGGTTATTTTC
ATAATTTGACCTTCCTAAGTCTCGACTTTCATGAAACTTTTCAGATCCTAATGTCATAATATTTC
ATGATTTTTGATGCATTTGAAATCACAACAATATACCGAAAAGTGTGAAATTATCAAAATACTCA
TATAAAGGTATTTTCATAATTTGACCTTCCCGAGCTTAGATTTTCATGAAACTTTTCAGATGTCA
ATTTTATAAT
Found at i:19432733 original size:28 final size:29
Alignment explanation
Indices: 19432692--19432761 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
19432682 CACTCAAGTA
*
19432692 TTAAGCCCAATTTAGCTAGTA-ATAAATT
1 TTAAGCCCAGTTTAGCTAGTACATAAATT
* * *
19432720 TTAAGCCTAGTTTAGCTAGTACTTAAGTT
1 TTAAGCCCAGTTTAGCTAGTACATAAATT
19432749 TTAAGCCCAGTTT
1 TTAAGCCCAGTTT
19432762 TTCTGACACC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 19 0.53
29 17 0.47
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (29 bp):
TTAAGCCCAGTTTAGCTAGTACATAAATT
Found at i:19432761 original size:29 final size:29
Alignment explanation
Indices: 19432662--19432757 Score: 104
Period size: 29 Copynumber: 3.3 Consensus size: 29
19432652 TCCATGAAAA
** * *
19432662 TTTAAGCCCAATTTAATTAGCACTCAAGT
1 TTTAAGCCCAATTTAGCTAGTACTTAAGT
* * *
19432691 ATTAAGCCCAATTTAGCTAGTA-ATAAAT
1 TTTAAGCCCAATTTAGCTAGTACTTAAGT
* *
19432719 TTTAAGCCTAGTTTAGCTAGTACTTAAGT
1 TTTAAGCCCAATTTAGCTAGTACTTAAGT
19432748 TTTAAGCCCA
1 TTTAAGCCCA
19432758 GTTTTTCTGA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 22 0.42
29 31 0.58
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (29 bp):
TTTAAGCCCAATTTAGCTAGTACTTAAGT
Found at i:19433622 original size:66 final size:67
Alignment explanation
Indices: 19433552--19433700 Score: 157
Period size: 66 Copynumber: 2.3 Consensus size: 67
19433542 TCCCAGCCAT
*
19433552 TTATTTCGACTTACAATG-T-AGTCTCGG-TCATCTTTATTTCAACTT-GTGATTCAGTTTCAGT
1 TTATTTCGACTTACAATGCTCAGTCCCGGCT-ATCTTTATTTCAACTTAG-GA-TCAGTTTCAGT
19433613 CATCC
63 CATCC
* * *
19433618 TTATTTGGACTTAC-A-GCTCAGTCCCTGCTATCTTTATTTCAATTTACGGATCAGTTTCAGTCA
1 TTATTTCGACTTACAATGCTCAGTCCCGGCTATCTTTATTTCAACTTA-GGATCAGTTTCAGTCA
*
19433681 TTC
65 TCC
* *
19433684 TTATTTTGACTTTCAAT
1 TTATTTCGACTTACAAT
19433701 TCAATCCTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
64 1 0.01
65 2 0.03
66 61 0.88
67 4 0.06
68 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (67 bp):
TTATTTCGACTTACAATGCTCAGTCCCGGCTATCTTTATTTCAACTTAGGATCAGTTTCAGTCAT
CC
Found at i:19433786 original size:33 final size:33
Alignment explanation
Indices: 19433678--19433840 Score: 101
Period size: 33 Copynumber: 4.9 Consensus size: 33
19433668 TCAGTTTCAG
* * * * * **
19433678 TCATTCTTATTTTGACTTTCAATTCAATCCTAA
1 TCATCCTTATTTTAACTTACGATTCAGTCCCGA
* * * * **
19433711 TCATCCTTACTTTGACTTATGGTTCAGTTTCGA
1 TCATCCTTATTTTAACTTACGATTCAGTCCCGA
*
19433744 TCATCCTTATTTTAACTTACGATTCAGTCCCGG
1 TCATCCTTATTTTAACTTACGATTCAGTCCCGA
* * * ***
19433777 TCATCCTTATTTTTTGACTTAAGATTTAGTCTTAA
1 TCATCCTTA--TTTTAACTTACGATTCAGTCCCGA
* * *
19433812 TCATCCTTATTTCAACTTATGATTTAGTC
1 TCATCCTTATTTTAACTTACGATTCAGTC
19433841 TTAATCATCT
Statistics
Matches: 100, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
33 74 0.74
35 26 0.26
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (33 bp):
TCATCCTTATTTTAACTTACGATTCAGTCCCGA
Found at i:19433876 original size:35 final size:33
Alignment explanation
Indices: 19433699--19433877 Score: 128
Period size: 33 Copynumber: 5.3 Consensus size: 33
19433689 TTGACTTTCA
* * *
19433699 ATTCAATCCTAATCATCCTTACTTT-GACTTATG
1 ATTCAGTCTTAATCATCCTTA-TTTCAACTTATG
* * * *
19433732 GTTCAGT-TTCGATCATCCTTATTTTAACTTACG
1 ATTCAGTCTT-AATCATCCTTATTTCAACTTATG
**** ** *
19433765 ATTCAGTCCCGGTCATCCTTATTTTTTGACTTAAG
1 ATTCAGTCTTAATCATCCTTA--TTTCAACTTATG
*
19433800 ATTTAGTCTTAATCATCCTTATTTCAACTTATG
1 ATTCAGTCTTAATCATCCTTATTTCAACTTATG
* *
19433833 ATTTAGTCTTAATCATCTTTATTTCATAACTTATG
1 ATTCAGTCTTAATCATCCTTATTTC--AACTTATG
*
19433868 GTTCAGTCTT
1 ATTCAGTCTT
19433878 TGTTATTCTT
Statistics
Matches: 116, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
32 4 0.03
33 70 0.60
35 42 0.36
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.46
Consensus pattern (33 bp):
ATTCAGTCTTAATCATCCTTATTTCAACTTATG
Found at i:19433876 original size:68 final size:69
Alignment explanation
Indices: 19433668--19433877 Score: 160
Period size: 68 Copynumber: 3.1 Consensus size: 69
19433658 AATTTACGGA
* * ** * * * * * *
19433668 TCAGT-TTCAGTCATTCTTATTTTGACTTTCAATTCAATCCTAATCATCCTTACTT--TGACTTA
1 TCAGTCTTCAATCATCCTTATTTCAACTTACGATTCAGTCCCAATCATCCTTATTTCATAACTTA
19433730 TGGT
66 TGGT
* * ** ** *
19433734 TCAGT-TTCGATCATCCTTATTTTAACTTACGATTCAGTCCCGGTCATCCTTATTTTTTGACTTA
1 TCAGTCTTCAATCATCCTTATTTCAACTTACGATTCAGTCCCAATCATCCTTATTTCATAACTTA
* *
19433798 AGAT
66 TGGT
* * * ** *
19433802 TTAGTCTT-AATCATCCTTATTTCAACTTATGATTTAGTCTTAATCATCTTTATTTCATAACTTA
1 TCAGTCTTCAATCATCCTTATTTCAACTTACGATTCAGTCCCAATCATCCTTATTTCATAACTTA
19433866 TGGT
66 TGGT
19433870 TCAGTCTT
1 TCAGTCTT
19433878 TGTTATTCTT
Statistics
Matches: 112, Mismatches: 29, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
66 44 0.39
68 66 0.59
69 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (69 bp):
TCAGTCTTCAATCATCCTTATTTCAACTTACGATTCAGTCCCAATCATCCTTATTTCATAACTTA
TGGT
Found at i:19437182 original size:23 final size:24
Alignment explanation
Indices: 19437129--19437175 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
19437119 AATAAGTATA
*
19437129 ATAATAATAATAATAAAAGAAAAT
1 ATAAAAATAATAATAAAAGAAAAT
*
19437153 ATAAAAATAA-AATAAATGAAAAT
1 ATAAAAATAATAATAAAAGAAAAT
19437176 GAAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (24 bp):
ATAAAAATAATAATAAAAGAAAAT
Found at i:19439943 original size:40 final size:40
Alignment explanation
Indices: 19439867--19439943 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
19439857 ATTCAGTTTC
* * *
19439867 TTTCAAGTTAATTTAAATTTCTGTAACTTTAGTTTAAAAT
1 TTTCAAGTAAATTTAAATTTCTGTAAATTTAATTTAAAAT
19439907 TTTCAAG-AAATTTAAATTT-TGTTACAATTTAATTTAA
1 TTTCAAGTAAATTTAAATTTCTG-TA-AATTTAATTTAA
19439944 GTTCAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.06
39 13 0.41
40 17 0.53
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (40 bp):
TTTCAAGTAAATTTAAATTTCTGTAAATTTAATTTAAAAT
Found at i:19449852 original size:65 final size:62
Alignment explanation
Indices: 19449747--19449882 Score: 139
Period size: 64 Copynumber: 2.1 Consensus size: 62
19449737 TAATTGATCA
* * * ** *
19449747 ATCATTTAAGGCGTTTCTGTAGACAAATGTTTTAACTGATCTACATTATAATTTTA-AATTGATG
1 ATCAATTAAAGCGTTTCTGTAAACAAATGTCGTAACTGATCT-CATTATAAATTTATAA-TGA-G
* * * *
19449811 ATTAATTAAAGCGTTTGTGTAAACTAAATGTCGTAATTGATCTTATTATAAATTTATAATGAG
1 ATCAATTAAAGCGTTTCTGTAAAC-AAATGTCGTAACTGATCTCATTATAAATTTATAATGAG
19449874 ATCAATTAA
1 ATCAATTAA
19449883 GGCATTGGCG
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
63 9 0.15
64 33 0.56
65 17 0.29
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (62 bp):
ATCAATTAAAGCGTTTCTGTAAACAAATGTCGTAACTGATCTCATTATAAATTTATAATGAG
Found at i:19457355 original size:15 final size:15
Alignment explanation
Indices: 19457335--19457365 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19457325 TTGTGCATGT
19457335 TTCTTTTTCATTTTC
1 TTCTTTTTCATTTTC
*
19457350 TTCTTTTTCTTTTTC
1 TTCTTTTTCATTTTC
19457365 T
1 T
19457366 CTTGAATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTTTCATTTTC
Found at i:19459461 original size:375 final size:375
Alignment explanation
Indices: 19458771--19459518 Score: 1406
Period size: 375 Copynumber: 2.0 Consensus size: 375
19458761 ATTACAAACT
19458771 TACCTTCTTCAAACTCTTGTACACATTGATTGTCAGCAGCAGCAGCATATGCTTAATTGCTCTTG
1 TACCTTCTTCAAACTCTTGTACACATTGATTGTCAGCAGCAGCAGCATATGCTTAATTGCTCTTG
*
19458836 ACCTCCTTACTGATCTGCTGAATATTTGCAATAAAAGCCTTTTTATCATCACTAGCTTGGGCTTC
66 ACCTCCTTACTGATCTGCCGAATATTTGCAATAAAAGCCTTTTTATCATCACTAGCTTGGGCTTC
19458901 TTGTGATAGTGGCACTAAAAGCCTCGATTTAACATTTTTTGAGAGTATAAGGATCCAATTTATCC
131 TTGTGATAGTGGCACTAAAAGCCTCGATTTAACATTTTTTGAGAGTATAAGGATCCAATTTATCC
*
19458966 AGACAATAGGGTAGGGGTTAAACCCAATATTTTTGTATGATACAGGGACTAAAGTCAAAATTTGA
196 AGACAATAGGGTAGGGGTTAAACCCAATATTTTTGTATAATACAGGGACTAAAGTCAAAATTTGA
19459031 ACTTCTACATGCATCTTTTTATGGAAGTCCTCGGCCTCTATTCTCACTCTGCCCCCATTTCCAGG
261 ACTTCTACATGCATCTTTTTATGGAAGTCCTCGGCCTCTATTCTCACTCTGCCCCCATTTCCAGG
19459096 CCATCTAACAATCGCTGTTCCAATCCAACACAAATAGCAAGCTATACTAG
326 CCATCTAACAATCGCTGTTCCAATCCAACACAAATAGCAAGCTATACTAG
* * *
19459146 TACCTTCTTCAAACTTTTGTCCATATTGATTGTCAGCAGCAGCAGCATATGCTTAATTGCTCTTG
1 TACCTTCTTCAAACTCTTGTACACATTGATTGTCAGCAGCAGCAGCATATGCTTAATTGCTCTTG
*
19459211 ACCTCCTTACTGATCTGCCGAATATTTGCAATAAAAGCCTTTTTATTATCACTAGCTTGGGCTTC
66 ACCTCCTTACTGATCTGCCGAATATTTGCAATAAAAGCCTTTTTATCATCACTAGCTTGGGCTTC
*
19459276 TTGTGATAGTGGCACTAAAAGCCTTGATTTAACATTTTTTGAGAGTATAAGGATCCAATTTATCC
131 TTGTGATAGTGGCACTAAAAGCCTCGATTTAACATTTTTTGAGAGTATAAGGATCCAATTTATCC
*
19459341 AGACAATAGTGTAGGGGTTAAACCCAATATTTTTGTATAATACAGGGACTAAAGTCAAAATTTGA
196 AGACAATAGGGTAGGGGTTAAACCCAATATTTTTGTATAATACAGGGACTAAAGTCAAAATTTGA
*
19459406 ACTTCTACATGCATCTTTTTATGGAAGTTCTCGGCCTCTATTCTCACTCTGCCCCCATTTCCAGG
261 ACTTCTACATGCATCTTTTTATGGAAGTCCTCGGCCTCTATTCTCACTCTGCCCCCATTTCCAGG
*
19459471 CCATCTAACAATCGCTGTTCCAATCCAACACAAATAGCAAGTTATACT
326 CCATCTAACAATCGCTGTTCCAATCCAACACAAATAGCAAGCTATACT
19459519 GGTCTAGTAT
Statistics
Matches: 363, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
375 363 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (375 bp):
TACCTTCTTCAAACTCTTGTACACATTGATTGTCAGCAGCAGCAGCATATGCTTAATTGCTCTTG
ACCTCCTTACTGATCTGCCGAATATTTGCAATAAAAGCCTTTTTATCATCACTAGCTTGGGCTTC
TTGTGATAGTGGCACTAAAAGCCTCGATTTAACATTTTTTGAGAGTATAAGGATCCAATTTATCC
AGACAATAGGGTAGGGGTTAAACCCAATATTTTTGTATAATACAGGGACTAAAGTCAAAATTTGA
ACTTCTACATGCATCTTTTTATGGAAGTCCTCGGCCTCTATTCTCACTCTGCCCCCATTTCCAGG
CCATCTAACAATCGCTGTTCCAATCCAACACAAATAGCAAGCTATACTAG
Found at i:19465446 original size:24 final size:25
Alignment explanation
Indices: 19465401--19465450 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
19465391 ATGGACCAAA
19465401 GTGTGAAAAATTAAGAAATAAAACT
1 GTGTGAAAAATTAAGAAATAAAACT
*
19465426 GTGTGAAAAATTAAG-AGTAAAACT
1 GTGTGAAAAATTAAGAAATAAAACT
19465450 G
1 G
19465451 AATGTATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.24
Consensus pattern (25 bp):
GTGTGAAAAATTAAGAAATAAAACT
Found at i:19465628 original size:22 final size:22
Alignment explanation
Indices: 19465593--19465634 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19465583 TTTTTTGTCT
*
19465593 TTAATTCTAGAGATATAAATGC
1 TTAATTCTAAAGATATAAATGC
*
19465615 TTAATTTTAAAGATATAAAT
1 TTAATTCTAAAGATATAAAT
19465635 ATAAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (22 bp):
TTAATTCTAAAGATATAAATGC
Found at i:19474479 original size:19 final size:20
Alignment explanation
Indices: 19474436--19474472 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
19474426 GATATTTTAT
19474436 TGATTAAAATAATAAAAATA
1 TGATTAAAATAATAAAAATA
19474456 T-ATTAAAAT-ATAAAAAT
1 TGATTAAAATAATAAAAAT
19474473 TCGATTACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 8 0.47
20 1 0.06
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
TGATTAAAATAATAAAAATA
Found at i:19483366 original size:11 final size:12
Alignment explanation
Indices: 19483341--19483366 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19483331 CTTCTAGATC
19483341 TTTTTCATAATT
1 TTTTTCATAATT
19483353 TTTTTCATAATT
1 TTTTTCATAATT
19483365 TT
1 TT
19483367 CATTTTCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTCATAATT
Found at i:19487642 original size:202 final size:201
Alignment explanation
Indices: 19487281--19487662 Score: 500
Period size: 202 Copynumber: 1.9 Consensus size: 201
19487271 AAGGGTTATA
* * *
19487281 TAATTACTCCACTTTTAACACCATTATCCACCTACTTAATGGTCTTTCTATTATCATATCTTTAA
1 TAATTACTCCACTCTTAACACCATTATCCAACAACTTAATGGTCTTTCTATTATCATATCTTTAA
* **
19487346 TAATAAACTCTAAGTGATGGCGCTCAATAAGTGTGGTGAAATTGGCTATATAACCTACCCCAAGC
66 TAATAAACTCTAAATGATGGCGCTCAATAAGTGTAATGAAATTGGCTATATAACCTACCCCAAGC
* * *
19487411 GATGTCTTCAACATAGCTCTAACTGAACTAAGGTAGGTGTGCATTGGCTTCAATACCAATGAAAA
131 AATGTCTTCAACATAGCACTAACTGAACTAAGGTAGGTATGCATTGGCTTCAATACCAATGAAAA
19487476 AGCATG
196 AGCATG
* *
19487482 TAATTGCTCCACTCTTAACACC-TTCATCCAACAACTTGATGG-CTTTTCTATTTATCATATCTT
1 TAATTACTCCACTCTTAACACCATT-ATCCAACAACTTAATGGTC-TTTCTA-TTATCATATCTT
* * * * * * *
19487545 TAATAATAAATTCTAAAT-AGTGGTGCTCAGTGAGTGTAATGAAATTGGCTATGTGACCTACCTC
63 TAATAATAAACTCTAAATGA-TGGCGCTCAATAAGTGTAATGAAATTGGCTATATAACCTACCCC
* * ***
19487609 AAGTAATGTCTTCAATATAGCACTGGTTGAACTAAGGTAGGTATGCATTGGCTT
127 AAGCAATGTCTTCAACATAGCACTAACTGAACTAAGGTAGGTATGCATTGGCTT
19487663 TAGTACTAGT
Statistics
Matches: 154, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
200 3 0.02
201 41 0.27
202 110 0.71
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (201 bp):
TAATTACTCCACTCTTAACACCATTATCCAACAACTTAATGGTCTTTCTATTATCATATCTTTAA
TAATAAACTCTAAATGATGGCGCTCAATAAGTGTAATGAAATTGGCTATATAACCTACCCCAAGC
AATGTCTTCAACATAGCACTAACTGAACTAAGGTAGGTATGCATTGGCTTCAATACCAATGAAAA
AGCATG
Found at i:19504852 original size:203 final size:202
Alignment explanation
Indices: 19504490--19504868 Score: 571
Period size: 203 Copynumber: 1.9 Consensus size: 202
19504480 AAGGGTTATA
* * * *
19504490 TAATTACTCCACTTTTAACACCATTATCCACCCATTTAATGGTCTTTCTGTTACCATATCTTCAA
1 TAATTACTCCACTCTTAACACCATTATCCACCCACTTAACGGCCTTTCTGTTACCATATCTTCAA
* *
19504555 TAATAAACTCTAAGTGATGGTGCTTAATAAGTGTGGTGAAATTGGCTATATAACCTACCCCAAGC
66 TAATAAACTCTAAGTGATGGTGCTTAATAAGTGTAGTAAAATTGGCTATATAACCTACCCCAAGC
*
19504620 AATTTCTTCAATATAGCACTAACTGAACTAAGGTAGGTGTGCATTGGCTTCAATACCATTGAAAA
131 AATGTCTTCAATATAGCACTAACTGAACTAAGGTAGGTGTGCATTGGCTTCAATACCATTGAAAA
19504685 AAGCACG
196 AAGCACG
* * * *
19504692 TAATTGCTCCACTCTTAACACC-TTCATCCACCCACTTAACGGCCTTTTTATTTACCATATCTTT
1 TAATTACTCCACTCTTAACACCATT-ATCCACCCACTTAACGGCCTTTCT-GTTACCATATCTTC
* * * * *
19504756 AATAATAAATTCTAAGTGATGGTGCTTAGTGAGTGTAGTAAAATTGGCTATGTGACCTACCCCAA
64 AATAATAAACTCTAAGTGATGGTGCTTAATAAGTGTAGTAAAATTGGCTATATAACCTACCCCAA
**
19504821 GCAATGTCTTCAATATAGCACTAGGTGAACTAAGGTAGGTGTGCATTG
129 GCAATGTCTTCAATATAGCACTAACTGAACTAAGGTAGGTGTGCATTG
19504869 ACTTTAGTAC
Statistics
Matches: 157, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
201 2 0.01
202 40 0.25
203 115 0.73
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (202 bp):
TAATTACTCCACTCTTAACACCATTATCCACCCACTTAACGGCCTTTCTGTTACCATATCTTCAA
TAATAAACTCTAAGTGATGGTGCTTAATAAGTGTAGTAAAATTGGCTATATAACCTACCCCAAGC
AATGTCTTCAATATAGCACTAACTGAACTAAGGTAGGTGTGCATTGGCTTCAATACCATTGAAAA
AAGCACG
Found at i:19511639 original size:12 final size:12
Alignment explanation
Indices: 19511622--19511646 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19511612 GTGCTAGAAA
19511622 ACAAATATCAAT
1 ACAAATATCAAT
19511634 ACAAATATCAAT
1 ACAAATATCAAT
19511646 A
1 A
19511647 GATAGCCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ACAAATATCAAT
Found at i:19512681 original size:17 final size:18
Alignment explanation
Indices: 19512659--19512692 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
19512649 TAAGGACATT
19512659 TATGCATCATTT-TGAGC
1 TATGCATCATTTATGAGC
19512676 TATGCATCATTTATGAG
1 TATGCATCATTTATGAG
19512693 GAAGGGTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (18 bp):
TATGCATCATTTATGAGC
Found at i:19514033 original size:21 final size:20
Alignment explanation
Indices: 19514009--19514061 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
19513999 GCTTTAAACT
19514009 TTTGGATGTGAATCTCTAAAA
1 TTTGGATGTGAATCT-TAAAA
* *
19514030 TTT-GAGTGAGAATCTTTAAA
1 TTTGGA-TGTGAATCTTAAAA
19514050 TGTTGGATGTGA
1 T-TTGGATGTGA
19514062 GCCTTGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 7 0.27
21 17 0.65
22 2 0.08
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTGGATGTGAATCTTAAAA
Found at i:19514141 original size:23 final size:25
Alignment explanation
Indices: 19514108--19514158 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
19514098 TTTGGATGAG
19514108 AATCTTACAAATGTGAA-TCTTG-A
1 AATCTTACAAATGTGAATTCTTGCA
* *
19514131 AATCTTGCAAATTTGAATTCTTGCA
1 AATCTTACAAATGTGAATTCTTGCA
19514156 AAT
1 AAT
19514159 TTGAATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.62
24 5 0.21
25 4 0.17
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (25 bp):
AATCTTACAAATGTGAATTCTTGCA
Found at i:19514152 original size:16 final size:16
Alignment explanation
Indices: 19514127--19514171 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
19514117 AATGTGAATC
*
19514127 TTGAAATCTTGCAAAT
1 TTGAATTCTTGCAAAT
19514143 TTGAATTCTTGCAAAT
1 TTGAATTCTTGCAAAT
19514159 TTGAATTCTTGCA
1 TTGAATTCTTGCA
19514172 TATCTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (16 bp):
TTGAATTCTTGCAAAT
Found at i:19514424 original size:43 final size:43
Alignment explanation
Indices: 19514373--19514848 Score: 538
Period size: 43 Copynumber: 11.1 Consensus size: 43
19514363 AGGAGCTTTT
* * *
19514373 TTTTTCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTCTTTA
1 TTTTTCAAAGTTGTTGAGCCTCTATTTAGAGGAGCATTATTTA
* *
19514416 TTTTTCAAAGTTGTTGAGCCTCTATTTAGATGAGCCTTATTT-
1 TTTTTCAAAGTTGTTGAGCCTCTATTTAGAGGAGCATTATTTA
* * * *
19514458 TTTTTCGAAAGTTGTTGAGCCTCTATTTCGAGAAGCCTTGTTTA
1 TTTTTC-AAAGTTGTTGAGCCTCTATTTAGAGGAGCATTATTTA
* * *
19514502 TTTTCCAAAAGTTG-TGAGCCTCTATTTATAGGAGCTTTATTTA
1 TTTTTC-AAAGTTGTTGAGCCTCTATTTAGAGGAGCATTATTTA
* * * *
19514545 TTTTTCAAAGTTGTTAAGCTTTTACTTAGAGGAGCATTATTTA
1 TTTTTCAAAGTTGTTGAGCCTCTATTTAGAGGAGCATTATTTA
**
19514588 TTTTTCAAAGTTGTTGAGCCTCTGCTTAGAGGAGCATTATTTA
1 TTTTTCAAAGTTGTTGAGCCTCTATTTAGAGGAGCATTATTTA
* * *
19514631 TTTTCCAAAAATTGTTGAGCCTCTGA-TTAGAGGGGCATTATTTA
1 TTTTTC-AAAGTTGTTGAGCCTCT-ATTTAGAGGAGCATTATTTA
*
19514675 TTTTTCAAAGTTGTTGAGCCTCTGA-TTAGAGGAGC---CTTTA
1 TTTTTCAAAGTTGTTGAGCCTCT-ATTTAGAGGAGCATTATTTA
* * *
19514715 TTTTTCCAAAGTTGTTGAGCCTTTACTTAGAAGAGCATTATTTA
1 TTTTT-CAAAGTTGTTGAGCCTCTATTTAGAGGAGCATTATTTA
* * *
19514759 TTTTTCAAAGTCGTTGAGCCTCTACTTAGAGGAGTATTATTTA
1 TTTTTCAAAGTTGTTGAGCCTCTATTTAGAGGAGCATTATTTA
** * *
19514802 TTTTTCAAAGTCATTGAGCCTATGTTTAGA-GAGTCA-TATTTA
1 TTTTTCAAAGTTGTTGAGCCTCTATTTAGAGGAG-CATTATTTA
19514844 TTTTT
1 TTTTT
19514849 TTCCAAAAGT
Statistics
Matches: 376, Mismatches: 46, Indels: 23
0.84 0.10 0.05
Matches are distributed among these distances:
40 10 0.03
41 26 0.07
42 27 0.07
43 254 0.68
44 59 0.16
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.44
Consensus pattern (43 bp):
TTTTTCAAAGTTGTTGAGCCTCTATTTAGAGGAGCATTATTTA
Found at i:19514934 original size:9 final size:9
Alignment explanation
Indices: 19514922--19514965 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 9
19514912 ACTTAAAAAC
19514922 AAAAAAAGA
1 AAAAAAAGA
19514931 AAAAAAAGGA
1 AAAAAAA-GA
*
19514941 AACAAAAG-
1 AAAAAAAGA
19514949 AAAAAAAGCA
1 AAAAAAAG-A
19514959 AAAAAAA
1 AAAAAAA
19514966 AAGCAAGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 7 0.23
9 8 0.27
10 15 0.50
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:19515701 original size:18 final size:19
Alignment explanation
Indices: 19515660--19515699 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
19515650 AAAATTTGGA
*
19515660 AAATTTCTAGATTTTGGTG
1 AAATTTCTAGATTTTGATG
19515679 AAATTTCTAG-TTTTCGATG
1 AAATTTCTAGATTTT-GATG
19515698 AA
1 AA
19515700 TTATCAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (19 bp):
AAATTTCTAGATTTTGATG
Found at i:19515797 original size:19 final size:19
Alignment explanation
Indices: 19515773--19515810 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19515763 TTTCTAGAAT
19515773 TCGGTGGAAAATTTCGATG
1 TCGGTGGAAAATTTCGATG
**
19515792 TCGGTGGAATTTTTCGATG
1 TCGGTGGAAAATTTCGATG
19515811 AACTTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.11, G:0.32, T:0.37
Consensus pattern (19 bp):
TCGGTGGAAAATTTCGATG
Found at i:19516213 original size:12 final size:12
Alignment explanation
Indices: 19516198--19516240 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
19516188 TTAGTTTTTT
19516198 TATTTTATATAG
1 TATTTTATATAG
*
19516210 TATTTTATTTATG
1 TATTTTATATA-G
* *
19516223 TGTTTTTTATAG
1 TATTTTATATAG
19516235 TATTTT
1 TATTTT
19516241 TGCATGATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (12 bp):
TATTTTATATAG
Found at i:19520121 original size:7 final size:6
Alignment explanation
Indices: 19520090--19520120 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
19520080 AAAAGAGAAG
19520090 AAAAGA AAAAGA AAAAGA AAAAGA TAAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA -AAAAGA
19520121 TGACTTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:19521756 original size:19 final size:19
Alignment explanation
Indices: 19521722--19521772 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
19521712 TTTGATTTTT
**
19521722 AATTTTAATTGCTAA-TTG
1 AATTTTAATTTTTAATTTG
*
19521740 AGATTTTAATTTTTAATTTT
1 A-ATTTTAATTTTTAATTTG
19521760 AATTTTAATTTTT
1 AATTTTAATTTTT
19521773 TTGAGTGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 24 0.86
20 3 0.11
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (19 bp):
AATTTTAATTTTTAATTTG
Found at i:19521757 original size:32 final size:31
Alignment explanation
Indices: 19521682--19521763 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 31
19521672 AACCTTGATG
* *
19521682 TTAATTTCTAATTTTAATTTCAATTAAGACT
1 TTAATTTTTAATTTTAATTGCAATTAAGACT
* * *
19521713 TTGATTTTTAATTTTAATTGCTAATTGAGATT
1 TTAATTTTTAATTTTAATTGC-AATTAAGACT
19521745 TTAATTTTTAATTTTAATT
1 TTAATTTTTAATTTTAATT
19521764 TTAATTTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 18 0.41
32 26 0.59
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.57
Consensus pattern (31 bp):
TTAATTTTTAATTTTAATTGCAATTAAGACT
Found at i:19521772 original size:7 final size:6
Alignment explanation
Indices: 19521682--19521771 Score: 58
Period size: 6 Copynumber: 14.3 Consensus size: 6
19521672 AACCTTGATG
* * * *
19521682 TTAATT TCTAATT TTAATT TCAA-T TAAGACTT TGATTT TTAATT TTAATT
1 TTAATT T-TAATT TTAATT TTAATT TTA-A-TT TTAATT TTAATT TTAATT
* *
19521732 GCTAA-T TGAGATT TTAATTT TTAATT TTAATT TTAATT TT
1 -TTAATT TTA-ATT TTAA-TT TTAATT TTAATT TTAATT TT
19521772 TTTGAGTGGA
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.06
6 41 0.62
7 18 0.27
8 3 0.05
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (6 bp):
TTAATT
Found at i:19522766 original size:27 final size:27
Alignment explanation
Indices: 19522736--19522792 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
19522726 TATTATCATG
19522736 TTTTCAATTTTTTT-TTTCATATCT-TTA
1 TTTTCAATTTTTTTATTT-AT-TCTATTA
*
19522763 TTTTCCATTTTTTTATTTATTCTATTA
1 TTTTCAATTTTTTTATTTATTCTATTA
19522790 TTT
1 TTT
19522793 ATTAATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 3 0.11
27 21 0.78
28 3 0.11
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTCAATTTTTTTATTTATTCTATTA
Found at i:19522912 original size:20 final size:20
Alignment explanation
Indices: 19522889--19522965 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
19522879 ATTTATATGA
*
19522889 TTGCATGTTTATATTATTAT
1 TTGCATGATTATATTATTAT
*
19522909 TTGCATGATTATA-TATTTAA
1 TTGCATGATTATATTA-TTAT
* *
19522929 TTACAAGATTTATATATTATTAT
1 TTGCATGA--T-TATATTATTAT
19522952 TTGCATGATTATAT
1 TTGCATGATTATAT
19522966 ATTTAATTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
19 2 0.04
20 26 0.58
21 1 0.02
22 1 0.02
23 13 0.29
24 2 0.04
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.53
Consensus pattern (20 bp):
TTGCATGATTATATTATTAT
Found at i:19522927 original size:28 final size:28
Alignment explanation
Indices: 19522870--19522931 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
19522860 GCATGGTTTA
* * *
19522870 TATATTATTATTTATATGATTGCATGTT
1 TATATTATTATTTACATGATTACATATT
* *
19522898 TATATTATTATTTGCATGATTATATATT
1 TATATTATTATTTACATGATTACATATT
19522926 TA-ATTA
1 TATATTA
19522932 CAAGATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.56
Consensus pattern (28 bp):
TATATTATTATTTACATGATTACATATT
Found at i:19522975 original size:55 final size:55
Alignment explanation
Indices: 19522916--19523138 Score: 184
Period size: 55 Copynumber: 4.1 Consensus size: 55
19522906 TATTTGCATG
* *
19522916 ATTATATATTTAATTACAAGATTTATATATTATTATTTGCATGATTATATATTTA
1 ATTACATATTTATTTACAAGATTTATATATTATTATTTGCATGATTATATATTTA
* * * * *
19522971 ATTATATGTTTATTTA-AATGGTTTATGTATTACTATTTGCATGATTATATATATTTA
1 ATTACATATTTATTTACAA-GATTTATATATTATTATTTGCATGA-T-TATATATTTA
* * ** * * * *
19523028 ACTGCATATTTATTTGTATGGTATATATA-TATTTATTTGCATGATTATATAGTTA
1 ATTACATATTTATTTACAAGATTTATATATTA-TTATTTGCATGATTATATATTTA
* * * * * * *
19523083 ATTACATGTTTATTTGCATGA-TT-TACATTATTAATTGCATGATTATGTGTTTA
1 ATTACATATTTATTTACAAGATTTATATATTATTATTTGCATGATTATATATTTA
19523136 ATT
1 ATT
19523139 GGATGTCTAT
Statistics
Matches: 136, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
53 25 0.18
54 5 0.04
55 61 0.45
56 4 0.03
57 40 0.29
58 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.52
Consensus pattern (55 bp):
ATTACATATTTATTTACAAGATTTATATATTATTATTTGCATGATTATATATTTA
Done.