Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 55 of 320
Found at i:15966188 original size:6 final size:6
Alignment explanation
Indices: 15966177--15966219 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
15966167 TAGGTTTAAA
* *
15966177 AAAATG AAAATG GAAGTG AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A
15966220 TCCATTTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:15972370 original size:17 final size:17
Alignment explanation
Indices: 15972348--15972381 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
15972338 TGTGTGCCAT
15972348 ACGGCCTAGAACATGGG
1 ACGGCCTAGAACATGGG
15972365 ACGGCCTAGAACATGGG
1 ACGGCCTAGAACATGGG
15972382 CCTGTGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.35, T:0.12
Consensus pattern (17 bp):
ACGGCCTAGAACATGGG
Found at i:15972794 original size:14 final size:14
Alignment explanation
Indices: 15972775--15972802 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15972765 TTTAATTTGG
15972775 TTAATAAATTATGA
1 TTAATAAATTATGA
15972789 TTAATAAATTATGA
1 TTAATAAATTATGA
15972803 AAAAGTAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TTAATAAATTATGA
Found at i:15980159 original size:22 final size:19
Alignment explanation
Indices: 15980129--15980175 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
15980119 AAAGATGATA
15980129 ATTATTAATATATAATTATATCT
1 ATTA-TAATATAT-ATTA-AT-T
15980152 ATTATAATATATATTAATT
1 ATTATAATATATATTAATT
15980171 ATTAT
1 ATTAT
15980176 CAACTGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 4 0.17
22 8 0.33
23 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTATAATATATATTAATT
Found at i:15980171 original size:16 final size:15
Alignment explanation
Indices: 15980131--15980172 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
15980121 AGATGATAAT
15980131 TATTAATATATAATTA
1 TATTAAT-TATAATTA
15980147 TATCT-ATTATAATATA
1 TAT-TAATTATAAT-TA
15980163 TATTAATTAT
1 TATTAATTAT
15980173 TATCAACTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:15982966 original size:15 final size:15
Alignment explanation
Indices: 15982946--15982975 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15982936 ATGCTCGATT
15982946 TAAAAGAAAAGAAAA
1 TAAAAGAAAAGAAAA
15982961 TAAAAGAAAAGAAAA
1 TAAAAGAAAAGAAAA
15982976 AAGAGCATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (15 bp):
TAAAAGAAAAGAAAA
Found at i:15983126 original size:36 final size:36
Alignment explanation
Indices: 15983079--15983153 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
15983069 CAAGCAAAGT
*
15983079 CTAGGGTTTTTAGCCTAAAAATTATTTATCTTCTAC
1 CTAGGGTTTTTAGCCTAAAAATTATCTATCTTCTAC
15983115 CTAGGGTTTTTAGCCTAAAAATTATCTATCTTCTAC
1 CTAGGGTTTTTAGCCTAAAAATTATCTATCTTCTAC
15983151 CTA
1 CTA
15983154 CCCCTAAACC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (36 bp):
CTAGGGTTTTTAGCCTAAAAATTATCTATCTTCTAC
Found at i:15984802 original size:39 final size:39
Alignment explanation
Indices: 15984748--15984829 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
15984738 GACACAGTAC
15984748 TTAATCAATGCATGTTTATTCTTCTAAGGTAGATGAAGT
1 TTAATCAATGCATGTTTATTCTTCTAAGGTAGATGAAGT
*
15984787 TTAATCAATGCATGTTTATTCTTCTAAGGTAGCTGAAGT
1 TTAATCAATGCATGTTTATTCTTCTAAGGTAGATGAAGT
15984826 TTAA
1 TTAA
15984830 ATTAGCATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (39 bp):
TTAATCAATGCATGTTTATTCTTCTAAGGTAGATGAAGT
Found at i:15986500 original size:55 final size:53
Alignment explanation
Indices: 15986314--15986568 Score: 245
Period size: 55 Copynumber: 4.8 Consensus size: 53
15986304 ACACGGGTAC
* * * *
15986314 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
* * *
15986363 CTTACCATTGCCATGTCTCGACATGATCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
* * * *
15986416 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-G-AA
* *
15986471 CTTATCAATGCCATGTATTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
* * * *
15986524 CCTTACCAATTTCTATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGTATCCTT
15986569 AAACCCTAAT
Statistics
Matches: 170, Mismatches: 25, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
49 36 0.21
50 1 0.01
52 2 0.01
53 47 0.28
54 10 0.06
55 72 0.42
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
Found at i:15986505 original size:108 final size:110
Alignment explanation
Indices: 15986361--15986561 Score: 300
Period size: 108 Copynumber: 1.8 Consensus size: 110
15986351 ATCCTTTTGA
* *
15986361 AACTTACCATTGCCATGTCTCGACATGATCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTATCGACATGATCTTACATGGTATCCTTGCCTTA-GAAACCTCACCAA
15986424 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * * *
15986469 AACTTATCAATGCCATGTATTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTATCGACATGATCTTACATGGTATCCTTGCCTTAGAAACCTCACCAAT
* *
15986534 TTCTATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
15986562 TATCCTTAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.59
109 7 0.09
110 26 0.32
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTATCGACATGATCTTACATGGTATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:15989201 original size:8 final size:9
Alignment explanation
Indices: 15989181--15989205 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
15989171 TGGTGTTGGC
15989181 TTTTGATGT
1 TTTTGATGT
15989190 TTTTGATGT
1 TTTTGATGT
15989199 TTTTGAT
1 TTTTGAT
15989206 ATCCTTGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.20, T:0.68
Consensus pattern (9 bp):
TTTTGATGT
Found at i:15989626 original size:38 final size:38
Alignment explanation
Indices: 15989583--15989658 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
15989573 AATTATGGAA
15989583 TATATTGGTTAATGTGATGATTTAAAGTAGTGAATTTT
1 TATATTGGTTAATGTGATGATTTAAAGTAGTGAATTTT
15989621 TATATTGGTTAATGTGATGATTTAAAGTAGTGAATTTT
1 TATATTGGTTAATGTGATGATTTAAAGTAGTGAATTTT
15989659 ATCATTTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (38 bp):
TATATTGGTTAATGTGATGATTTAAAGTAGTGAATTTT
Found at i:16004350 original size:39 final size:40
Alignment explanation
Indices: 16004233--16004417 Score: 189
Period size: 40 Copynumber: 4.7 Consensus size: 40
16004223 GCTACTCGTT
*
16004233 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
16004273 CAAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
16004313 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
16004352 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
* *
16004393 -AAAAGCCGTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
16004418 CATCATTCGA
Statistics
Matches: 119, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.27
40 76 0.64
41 9 0.08
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:16012340 original size:40 final size:40
Alignment explanation
Indices: 16012291--16012403 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 40
16012281 CAGAATTTAA
* * *
16012291 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGTACAAATGACTTCGGGACATAAC
* *
16012331 CCGGTTATAGTAACTCGTACAAATGACTTCGGGACTTAAC
1 CCGGATATAGTAACTCGTACAAATGACTTCGGGACATAAC
* * * *
16012371 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG
1 CCGGATATAGTAACTCGTACAAATGACTTCGGG
16012404 CTTAGCCTGG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
39 1 0.02
40 61 0.98
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGTACAAATGACTTCGGGACATAAC
Found at i:16012435 original size:39 final size:40
Alignment explanation
Indices: 16012310--16012439 Score: 129
Period size: 40 Copynumber: 3.3 Consensus size: 40
16012300 GCTACTCGTT
* * * **
16012310 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAACCCGGAAT-TAGTAACTCACA
* * *
16012350 CAAATGACTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCACA
* * * *
16012390 CCAATGCCTTCGGG-CTTAGCCTGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCACA
16012429 CAAATGCCTTC
1 CAAATGCCTTC
16012440 AGATCTTAGT
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 30 0.39
40 45 0.58
41 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCACA
Found at i:16036634 original size:18 final size:18
Alignment explanation
Indices: 16036611--16036646 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
16036601 CTAGTACTTG
16036611 ATAT-AACTATCACAAAAC
1 ATATAAACTATCA-AAAAC
16036629 ATATAAACTATCAAAAAC
1 ATATAAACTATCAAAAAC
16036647 TGAGCTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.22
Consensus pattern (18 bp):
ATATAAACTATCAAAAAC
Found at i:16038264 original size:48 final size:48
Alignment explanation
Indices: 16038196--16038482 Score: 279
Period size: 48 Copynumber: 6.0 Consensus size: 48
16038186 GAGGCTAAAT
* * *
16038196 TGCCGACGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAA
* * * * * * * *
16038244 TGCCGATGTCTTGTCTCAGACATGGTCTTATACTAGCTCTCGTCTCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAA
* * * *
16038292 TGCCGATGTCATGTCCTAGACATGGTCTTACACTAGCACACATATCAA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAA
** * * * * *
16038340 CACCAATGCCATGTCCCGGACATGGTCTTACACTGGCTCTCATAACAT
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAA
* * * * * *
16038388 TACTGATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATATC-G
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAA
* * *
16038435 TGGCCGACGCCATGTCCCAAACATGGTCTTACACTGGCACACATATCA
1 T-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCA
16038483 CCGAATGTCA
Statistics
Matches: 193, Mismatches: 44, Indels: 3
0.80 0.18 0.01
Matches are distributed among these distances:
47 1 0.01
48 192 0.99
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAA
Found at i:16039134 original size:24 final size:24
Alignment explanation
Indices: 16039104--16039154 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
16039094 GGAAAAACCC
16039104 TAGACTCTCAACCATTTTGCAAAA
1 TAGACTCTCAACCATTTTGCAAAA
16039128 TAGACTCTCAACCATTTTGCAAAA
1 TAGACTCTCAACCATTTTGCAAAA
16039152 TAG
1 TAG
16039155 TCCCCCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (24 bp):
TAGACTCTCAACCATTTTGCAAAA
Found at i:16040984 original size:22 final size:22
Alignment explanation
Indices: 16040956--16040997 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16040946 CTATATATAT
*
16040956 ACATATATATATACAAACCAAA
1 ACATATACATATACAAACCAAA
*
16040978 ACATATACATTTACAAACCA
1 ACATATACATATACAAACCA
16040998 TTTCTAATAT
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:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (22 bp):
ACATATACATATACAAACCAAA
Found at i:16043665 original size:43 final size:43
Alignment explanation
Indices: 16043617--16043702 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
16043607 GATTAACGAG
* ** *
16043617 ATGTGATTATGTGTTGGACCATGTCTGGGACATTGGTATCATT
1 ATGTGATTACGTGTAAGACCATGACTGGGACATTGGTATCATT
*
16043660 ATGTGATTACGTGTAAGATCATGACTGGGACATTGGTATCATT
1 ATGTGATTACGTGTAAGACCATGACTGGGACATTGGTATCATT
16043703 GTTTGATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACCATGACTGGGACATTGGTATCATT
Found at i:16043710 original size:43 final size:42
Alignment explanation
Indices: 16043636--16043723 Score: 122
Period size: 43 Copynumber: 2.1 Consensus size: 42
16043626 TGTGTTGGAC
*
16043636 CATGTCTGGGACATTGGTATCATTATGTGATTACGTGTAAGAT
1 CATGACTGGGACATTGGTATCATTATGTGATT-CGTGTAAGAT
* * **
16043679 CATGACTGGGACATTGGTATCATTGTTTGATTTTTGTAAGAT
1 CATGACTGGGACATTGGTATCATTATGTGATTCGTGTAAGAT
16043721 CAT
1 CAT
16043724 AGTTGGGCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 11 0.28
43 29 0.73
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (42 bp):
CATGACTGGGACATTGGTATCATTATGTGATTCGTGTAAGAT
Found at i:16045119 original size:18 final size:18
Alignment explanation
Indices: 16045079--16045120 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16045069 ACAATGTTAG
*
16045079 ATTGATGTTTATGTATGG
1 ATTGATGTTTATGTATGA
* *
16045097 GTTGATGTTTATGTATTA
1 ATTGATGTTTATGTATGA
16045115 ATTGAT
1 ATTGAT
16045121 TCTTGGATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (18 bp):
ATTGATGTTTATGTATGA
Found at i:16052614 original size:23 final size:21
Alignment explanation
Indices: 16052579--16052634 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
16052569 CACGGGTGAA
* *
16052579 CACACACTCGTGTGACTAAGT
1 CACACGCTCGTGTGTCTAAGT
16052600 CACACGCTCGTGTGTCTAAGT
1 CACACGCTCGTGTGTCTAAGT
*
16052621 TACACGCTCGTGTG
1 CACACGCTCGTGTG
16052635 CTAGGCCGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (21 bp):
CACACGCTCGTGTGTCTAAGT
Found at i:16054322 original size:29 final size:29
Alignment explanation
Indices: 16054280--16054340 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
16054270 AACTATCATC
16054280 AAGCTTTCATATTTCATCTTCAAACACCA
1 AAGCTTTCATATTTCATCTTCAAACACCA
16054309 AAGCTTTCATATTTCATCTTCAAACACCA
1 AAGCTTTCATATTTCATCTTCAAACACCA
16054338 AAG
1 AAG
16054341 TACACATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (29 bp):
AAGCTTTCATATTTCATCTTCAAACACCA
Found at i:16061324 original size:25 final size:25
Alignment explanation
Indices: 16061290--16061337 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
16061280 TTTTGAGTTA
16061290 GGTGCGACAACTAGGTGGCTAAAAG
1 GGTGCGACAACTAGGTGGCTAAAAG
* *
16061315 GGTGCGACAATTGGGTGGCTAAA
1 GGTGCGACAACTAGGTGGCTAAA
16061338 GGTGGAGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.38, T:0.19
Consensus pattern (25 bp):
GGTGCGACAACTAGGTGGCTAAAAG
Found at i:16066613 original size:25 final size:25
Alignment explanation
Indices: 16066585--16066634 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
16066575 AGGAGTAAGA
16066585 AAATTAATGCAGGAGAAAAATTTAC
1 AAATTAATGCAGGAGAAAAATTTAC
*
16066610 AAATTAATGCAGGAGAAAATTTTAC
1 AAATTAATGCAGGAGAAAAATTTAC
16066635 TTTAAATGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (25 bp):
AAATTAATGCAGGAGAAAAATTTAC
Found at i:16069927 original size:20 final size:19
Alignment explanation
Indices: 16069895--16069935 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
16069885 TAGATTTTGT
16069895 AAAAATAGAGTGAAATAGG
1 AAAAATAGAGTGAAATAGG
* *
16069914 AAAAATTAGTGTGATATAGG
1 AAAAA-TAGAGTGAAATAGG
16069934 AA
1 AA
16069936 CTATAAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (19 bp):
AAAAATAGAGTGAAATAGG
Found at i:16078837 original size:85 final size:84
Alignment explanation
Indices: 16078685--16078846 Score: 234
Period size: 85 Copynumber: 1.9 Consensus size: 84
16078675 GACATAGCTA
*
16078685 TAGAGGCATTAGTGGCATTTTAATAAAACGCCGCAATATATAAGAATTAGCAGCGCTTCTGTGAA
1 TAGAGGCATTAGTGGCATTTTAATAAAACGCCGCAATATATAAGAATTAGCAGCGCTTCTGTCAA
*
16078750 AACGCCGCAAAAGTGGCTG
66 AACGCCACAAAAGTGGCTG
* * * * * * *
16078769 TAGATGCATTAGTGGCGTTTTATATAAAACGCCGCAATATATCAGAATTAGCGGCGTTTGTTTCA
1 TAGAGGCATTAGTGGCATTTTA-ATAAAACGCCGCAATATATAAGAATTAGCAGCGCTTCTGTCA
16078834 AAACGCCACAAAA
65 AAACGCCACAAAA
16078847 TTATTGAGGG
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 20 0.29
85 48 0.71
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (84 bp):
TAGAGGCATTAGTGGCATTTTAATAAAACGCCGCAATATATAAGAATTAGCAGCGCTTCTGTCAA
AACGCCACAAAAGTGGCTG
Found at i:16079138 original size:21 final size:21
Alignment explanation
Indices: 16079105--16079148 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
16079095 ATGGTTTATC
*
16079105 TAGGGTTTAAAGTTTAGGGTT
1 TAGGATTTAAAGTTTAGGGTT
*
16079126 TAGGATTTTAAGTTTAGGGTT
1 TAGGATTTAAAGTTTAGGGTT
16079147 TA
1 TA
16079149 AGTTTTCGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (21 bp):
TAGGATTTAAAGTTTAGGGTT
Found at i:16079713 original size:18 final size:18
Alignment explanation
Indices: 16079690--16079729 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
16079680 TTGGGCTTTA
16079690 TGGTCTAGGATTTATGGT
1 TGGTCTAGGATTTATGGT
16079708 TGGTCTAGGATTTATGGT
1 TGGTCTAGGATTTATGGT
16079726 TGGT
1 TGGT
16079730 TTTAAGTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.05, G:0.35, T:0.45
Consensus pattern (18 bp):
TGGTCTAGGATTTATGGT
Found at i:16079744 original size:14 final size:14
Alignment explanation
Indices: 16079727--16079759 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16079717 ATTTATGGTT
16079727 GGTTTTAAGTTTGG
1 GGTTTTAAGTTTGG
16079741 GGTTTTAAGTTTGG
1 GGTTTTAAGTTTGG
*
16079755 TGTTT
1 GGTTT
16079760 GAGGTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (14 bp):
GGTTTTAAGTTTGG
Found at i:16083124 original size:62 final size:60
Alignment explanation
Indices: 16083056--16083249 Score: 213
Period size: 62 Copynumber: 3.2 Consensus size: 60
16083046 TTTTGTTCTC
*
16083056 TTTTATTTTATTTTCAAATTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATA
1 TTTTATTTT-TTTT-AAATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTTTAAATA
* * * * *
16083118 TTTTA-TTTTTTTGAATCA-CGAA--AAA-TAATTTTAATATTT-TA-TTTTATTTTAAATA
1 TTTTATTTTTTTTAAATTACCTAATTAAATTAA-ATT-ATATTTAAAGTTTTATTTTAAATA
*
16083173 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATA
1 TTTTATTTT-TTTTAA-ATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTTTAAATA
*
16083235 TTTCATTTTTTTTAA
1 TTTTATTTTTTTTAA
16083250 TCACGAAAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
55 21 0.19
56 9 0.08
57 11 0.10
58 6 0.06
59 7 0.06
60 9 0.08
61 15 0.14
62 30 0.28
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (60 bp):
TTTTATTTTTTTTAAATTACCTAATTAAATTAAATTATATTTAAAGTTTTATTTTAAATA
Found at i:16083166 original size:98 final size:98
Alignment explanation
Indices: 16083056--16084108 Score: 1519
Period size: 99 Copynumber: 10.7 Consensus size: 98
16083046 TTTTGTTCTC
* *
16083056 TTTTATTTTATTTTCAA-ATTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATT
1 TTTTATTTTATTTT-AACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
* *
16083120 TTATTTTTTTGAATCACGAAAAATAATTTTAATA
65 TCATTTTTTTGAATCACGAAAAATAATTTCAATA
* ** * * *
16083154 TTTTATTTTATTTTAAATATTTTATTTTATTTTAACATTACCTAATT-AAATTAAATTGTATTTA
1 TTTTATTTTATTTT-AACA--TTA-CCTA-ATTAA-ATTA---AATTGTATTTAAA--GT-TTT-
** *
16083218 AAGTTTTATTTTAAATATTTCATTTTTTTTAATCACGAAAAATAATTTCAATA
53 -A-TTTTAAAT-----ATTTCATTTTTTTGAATCACGAAAAATAATTTCAATA
16083271 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
* *
16083336 CATTTAATTTGAATCACGAAAAATAATTTTAATA
66 CATTT-TTTTGAATCACGAAAAATAATTTCAATA
16083370 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
*
16083435 CATTTTTTTGAATCATGAAAAATAATTTCAATA
66 CATTTTTTTGAATCACGAAAAATAATTTCAATA
*
16083468 TTTTATTTTAGTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
16083533 CATTTTTTT-AATCACGAAAAATAATTTCAATA
66 CATTTTTTTGAATCACGAAAAATAATTTCAATA
* *
16083565 ATTTATTATATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
*
16083630 CATTTAATTTGAATCACGAAAAATAATTTCAATA
66 CATTT-TTTTGAATCACGAAAAATAATTTCAATA
16083664 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
*
16083729 CATTTTTTTGAATCACGAAAAATAATTTTAATA
66 CATTTTTTTGAATCACGAAAAATAATTTCAATA
*
16083762 TTTTATTTTATTTTAACATTACCTAATTAAAATAAATTGTATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
*
16083827 CATTTTTTTTGAATCAAGAAAAATAATTTCAATA
66 CA-TTTTTTTGAATCACGAAAAATAATTTCAATA
16083861 TTTTA--TTA---T---A-T---T--TTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
* *
16083912 CATTTTTTTTGAATCACGAAAAATCATTTCAGTA
66 CA-TTTTTTTGAATCACGAAAAATAATTTCAATA
16083946 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
*
16084011 CATTTTTTTTGAATCAGGAAAAATAATTTCAATA
66 CA-TTTTTTTGAATCACGAAAAATAATTTCAATA
16084045 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
1 TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
16084109 CTATTTTATT
Statistics
Matches: 870, Mismatches: 46, Indels: 77
0.88 0.05 0.08
Matches are distributed among these distances:
85 74 0.09
87 4 0.00
90 2 0.00
91 1 0.00
93 1 0.00
94 2 0.00
97 93 0.11
98 218 0.25
99 355 0.41
101 3 0.00
102 2 0.00
103 10 0.01
104 5 0.01
106 9 0.01
107 6 0.01
108 6 0.01
109 8 0.01
111 5 0.01
112 10 0.01
113 2 0.00
114 3 0.00
116 3 0.00
117 48 0.06
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (98 bp):
TTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTT
CATTTTTTTGAATCACGAAAAATAATTTCAATA
Found at i:16083174 original size:19 final size:19
Alignment explanation
Indices: 16083145--16083188 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
16083135 ACGAAAAATA
16083145 ATTTT-AATATTTTATTTT
1 ATTTTAAATATTTTATTTT
16083163 ATTTTAAATATTTTATTTT
1 ATTTTAAATATTTTATTTT
16083182 ATTTTAA
1 ATTTTAA
16083189 CATTACCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTAAATATTTTATTTT
Found at i:16083260 original size:117 final size:117
Alignment explanation
Indices: 16083056--16083286 Score: 401
Period size: 117 Copynumber: 2.0 Consensus size: 117
16083046 TTTTGTTCTC
16083056 TTTTATTTTATTTTCAAATTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATTT
1 TTTTATTTTATTTTCAAATTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATTT
* *
16083121 TATTTTTTTGAATCACGAAAAATAATTTTAATATTTTATTTTATTTTAAATA
66 CATTTTTTTGAATCACGAAAAATAATTTCAATATTTTATTTTATTTTAAATA
* *
16083173 TTTTATTTTATTTT-AACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
1 TTTTATTTTATTTTCAA-ATTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATT
*
16083237 TCATTTTTTTTAATCACGAAAAATAATTTCAATATTTTATTTTATTTTAA
65 TCATTTTTTTGAATCACGAAAAATAATTTCAATATTTTATTTTATTTTAA
16083287 CATTACCTAA
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
116 2 0.02
117 106 0.98
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.55
Consensus pattern (117 bp):
TTTTATTTTATTTTCAAATTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTTAAATATTT
CATTTTTTTGAATCACGAAAAATAATTTCAATATTTTATTTTATTTTAAATA
Found at i:16083393 original size:197 final size:196
Alignment explanation
Indices: 16083163--16084108 Score: 1580
Period size: 197 Copynumber: 4.9 Consensus size: 196
16083153 ATTTTATTTT
16083163 ATTTTAAATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATT
1 ATTTT-AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATT
16083228 TTAAATATTTCATTTTTTTTAATCACGAAAAATAATTTCAATATTTTATTTTATTTTAACATTAC
65 TTAAATATTTCATTTTTTTTAATCACGAAAAATAATTTCAATATTTTATTTTATTTTAACATTAC
16083293 CTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTAATTTGAATCACGAAAA
130 CTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTT-ATTTGAATCACGAAAA
16083358 ATA
194 ATA
16083361 ATTTTAATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTT
1 ATTTTAATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTT
* * *
16083426 TAAATATTTCATTTTTTTGAATCATGAAAAATAATTTCAATATTTTATTTTAGTTTAACATTACC
66 TAAATATTTCATTTTTTTTAATCACGAAAAATAATTTCAATATTTTATTTTATTTTAACATTACC
*
16083491 TAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTT-TTTTAATCACGAAAAAT
131 TAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTATTTGAATCACGAAAAAT
16083555 A
196 A
* * *
16083556 ATTTCAATAATTTATTATATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTT
1 ATTTTAATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTT
* *
16083621 TAAATATTTCATTTAATTTGAATCACGAAAAATAATTTCAATATTTTATTTTATTTTAACATTAC
66 TAAATATTTCATTT-TTTTTAATCACGAAAAATAATTTCAATATTTTATTTTATTTTAACATTAC
*
16083686 CTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTTTTTGAATCACGAAAAA
130 CTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTATTTGAATCACGAAAAA
16083751 TA
195 TA
*
16083753 ATTTTAATATTTTATTTTATTTTAACATTACCTAATTAAAATAAATTGTATTTAAAGTTTTATTT
1 ATTTTAATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTT
*
16083818 TAAATATTTCATTTTTTTTGAATCAAGAAAAATAATTTCAATATTTTA--TTA---T---A-T--
66 TAAATATTTCATTTTTTTT-AATCACGAAAAATAATTTCAATATTTTATTTTATTTTAACATTAC
*
16083872 -T--TTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTTTTTTGAATCACGAAAA
130 CTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCA-TTTATTTGAATCACGAAAA
*
16083934 ATC
194 ATA
* *
16083937 ATTTCAGTATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTT
1 ATTTTAATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTT
*
16084002 TAAATATTTCATTTTTTTTGAATCAGGAAAAATAATTTCAATATTTTATTTTATTTTAACATTAC
66 TAAATATTTCATTTTTTTT-AATCACGAAAAATAATTTCAATATTTTATTTTATTTTAACATTAC
16084067 CTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
130 CTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATT
16084109 CTATTTTATT
Statistics
Matches: 707, Mismatches: 23, Indels: 36
0.92 0.03 0.05
Matches are distributed among these distances:
183 41 0.06
184 130 0.18
185 1 0.00
186 3 0.00
188 1 0.00
189 2 0.00
192 2 0.00
193 1 0.00
195 96 0.14
196 99 0.14
197 288 0.41
198 43 0.06
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.51
Consensus pattern (196 bp):
ATTTTAATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTT
TAAATATTTCATTTTTTTTAATCACGAAAAATAATTTCAATATTTTATTTTATTTTAACATTACC
TAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTATTTGAATCACGAAAAAT
A
Found at i:16083419 original size:99 final size:98
Alignment explanation
Indices: 16083169--16084108 Score: 1604
Period size: 99 Copynumber: 9.7 Consensus size: 98
16083159 TTTTATTTTA
16083169 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
1 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
*
16083234 ATTTCATTTTTTTTAATCACGAAAAATAATTTC
66 ATTTCATTTTTTTGAATCACGAAAAATAATTTC
16083267 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
1 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
* *
16083332 ATTTCATTTAATTTGAATCACGAAAAATAATTTT
66 ATTTCATTT-TTTTGAATCACGAAAAATAATTTC
16083366 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
1 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
*
16083431 ATTTCATTTTTTTGAATCATGAAAAATAATTTC
66 ATTTCATTTTTTTGAATCACGAAAAATAATTTC
*
16083464 AATATTTTATTTTAGTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
1 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
16083529 ATTTCATTTTTTT-AATCACGAAAAATAATTTC
66 ATTTCATTTTTTTGAATCACGAAAAATAATTTC
* *
16083561 AATAATTTATTATATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
1 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
*
16083626 ATTTCATTTAATTTGAATCACGAAAAATAATTTC
66 ATTTCATTT-TTTTGAATCACGAAAAATAATTTC
16083660 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
1 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
*
16083725 ATTTCATTTTTTTGAATCACGAAAAATAATTTT
66 ATTTCATTTTTTTGAATCACGAAAAATAATTTC
*
16083758 AATATTTTATTTTATTTTAACATTACCTAATTAAAATAAATTGTATTTAAAGTTTTATTTTAAAT
1 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
*
16083823 ATTTCATTTTTTTTGAATCAAGAAAAATAATTTC
66 ATTTCA-TTTTTTTGAATCACGAAAAATAATTTC
16083857 AATATTTTA--TTA---T---A-T---T--TTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
1 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
*
16083908 ATTTCATTTTTTTTGAATCACGAAAAATCATTTC
66 ATTTCA-TTTTTTTGAATCACGAAAAATAATTTC
*
16083942 AGTATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
1 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
*
16084007 ATTTCATTTTTTTTGAATCAGGAAAAATAATTTC
66 ATTTCA-TTTTTTTGAATCACGAAAAATAATTTC
16084041 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
1 AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
16084106 ATT
66 ATT
16084109 CTATTTTATT
Statistics
Matches: 798, Mismatches: 26, Indels: 35
0.93 0.03 0.04
Matches are distributed among these distances:
85 74 0.09
87 4 0.01
90 2 0.00
91 1 0.00
93 1 0.00
94 2 0.00
97 93 0.12
98 267 0.33
99 354 0.44
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.51
Consensus pattern (98 bp):
AATATTTTATTTTATTTTAACATTACCTAATTAAATTAAATTGTATTTAAAGTTTTATTTTAAAT
ATTTCATTTTTTTGAATCACGAAAAATAATTTC
Found at i:16083883 original size:85 final size:85
Alignment explanation
Indices: 16083788--16083966 Score: 304
Period size: 85 Copynumber: 2.1 Consensus size: 85
16083778 CATTACCTAA
*
16083788 TTAAAATAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTTTTTTGAATCAAGAAAAATAA
1 TTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTTTTTTGAATCAAGAAAAATAA
16083853 TTTCAATATTTTATTATATT
66 TTTCAATATTTTATTATATT
* *
16083873 TTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTTTTTTGAATCACGAAAAATCA
1 TTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTTTTTTGAATCAAGAAAAATAA
* *
16083938 TTTCAGTATTTTATTTTATT
66 TTTCAATATTTTATTATATT
16083958 TTAACATTA
1 TTAA-ATTA
16083967 CCTAATTAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
85 84 0.95
86 4 0.05
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (85 bp):
TTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTTTTTTGAATCAAGAAAAATAA
TTTCAATATTTTATTATATT
Found at i:16084002 original size:85 final size:85
Alignment explanation
Indices: 16083788--16083989 Score: 255
Period size: 85 Copynumber: 2.4 Consensus size: 85
16083778 CATTACCTAA
* * * *
16083788 TTAAAATAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTTTTTTGAATCAAGAAAAATAA
1 TTAAATTAAATTGAAATTAAAGTTGTATTTTAAATATTTCATTTTTTTTGAATCAAGAAAAATAA
16083853 TTTCAATATTTTATTATATT
66 TTTCAATATTTTATTATATT
* * * * *
16083873 TTAAATTAAATTGTATTTAAAGTTTTATTTTAAATATTTCATTTTTTTTGAATCACGAAAAATCA
1 TTAAATTAAATTGAAATTAAAGTTGTATTTTAAATATTTCATTTTTTTTGAATCAAGAAAAATAA
* *
16083938 TTTCAGTATTTTATTTTATT
66 TTTCAATATTTTATTATATT
16083958 TTAACATTACCTAATT-AAATTAAA-TTGTATTT
1 TTAA-ATTA---AATTGAAATTAAAGTTGTATTT
16083990 AAAGTTTTAT
Statistics
Matches: 105, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
85 84 0.80
86 4 0.04
87 7 0.07
88 6 0.06
89 4 0.04
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (85 bp):
TTAAATTAAATTGAAATTAAAGTTGTATTTTAAATATTTCATTTTTTTTGAATCAAGAAAAATAA
TTTCAATATTTTATTATATT
Found at i:16084232 original size:9 final size:9
Alignment explanation
Indices: 16084218--16084365 Score: 92
Period size: 9 Copynumber: 16.1 Consensus size: 9
16084208 CCAGCAACTA
16084218 ACATAATTT
1 ACATAATTT
16084227 ACATAATTT
1 ACATAATTT
16084236 ACATAA--T
1 ACATAATTT
*
16084243 ACATAACTT
1 ACATAATTT
*
16084252 ATATAATTT
1 ACATAATTT
*
16084261 AAAGTTCGAATTT
1 ACA--T--AATTT
*
16084274 -CATAACTT
1 ACATAATTT
16084282 ACATAATTT
1 ACATAATTT
*
16084291 TCATAATTT
1 ACATAATTT
16084300 ACATAA--T
1 ACATAATTT
* *
16084307 ACATGACTT
1 ACATAATTT
16084316 ACATAATTT
1 ACATAATTT
*
16084325 AAAGATCAAATTT
1 --ACAT--AATTT
*
16084338 -CATAACTT
1 ACATAATTT
16084346 ACATAATTT
1 ACATAATTT
16084355 ACATAAATTT
1 ACAT-AATTT
16084365 A
1 A
16084366 ACACACATGG
Statistics
Matches: 109, Mismatches: 15, Indels: 29
0.71 0.10 0.19
Matches are distributed among these distances:
7 13 0.12
8 8 0.07
9 64 0.59
10 9 0.08
11 4 0.04
12 1 0.01
13 10 0.09
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.40
Consensus pattern (9 bp):
ACATAATTT
Found at i:16084247 original size:16 final size:16
Alignment explanation
Indices: 16084226--16084322 Score: 56
Period size: 16 Copynumber: 6.1 Consensus size: 16
16084216 TAACATAATT
*
16084226 TACATAATTTACATAA
1 TACATAACTTACATAA
*
16084242 TACATAACTTATATAA
1 TACATAACTTACATAA
** * *
16084258 TTTA-AAGTT-CGA-AT
1 TACATAACTTAC-ATAA
*
16084272 TTCATAACTTACATAA
1 TACATAACTTACATAA
* *
16084288 TTTTCATAATTTACATAA
1 --TACATAACTTACATAA
*
16084306 TACATGACTTACATAA
1 TACATAACTTACATAA
16084322 T
1 T
16084323 TTAAAGATCA
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
14 4 0.07
15 10 0.16
16 32 0.52
18 15 0.25
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.40
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:16084280 original size:30 final size:29
Alignment explanation
Indices: 16084244--16084355 Score: 107
Period size: 30 Copynumber: 3.6 Consensus size: 29
16084234 TTACATAATA
*
16084244 CATAACTTATATAATTTAAAGTTCGAATTT
1 CATAACTTACATAATTTAAAGTTC-AATTT
* * *
16084274 CATAACTTACATAATTTTCATAATTTACATAATA
1 CATAACTTACATAA-TTT-A-AAGTT-CA-ATTT
* *
16084308 CATGACTTACATAATTTAAAGATCAAATTT
1 CATAACTTACATAATTTAAAGTTC-AATTT
16084338 CATAACTTACATAATTTA
1 CATAACTTACATAATTTA
16084356 CATAAATTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
30 33 0.50
31 7 0.11
32 2 0.03
33 8 0.12
34 16 0.24
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (29 bp):
CATAACTTACATAATTTAAAGTTCAATTT
Found at i:16084298 original size:64 final size:64
Alignment explanation
Indices: 16084213--16084365 Score: 243
Period size: 64 Copynumber: 2.4 Consensus size: 64
16084203 GTTCACCAGC
* * * *
16084213 AACTAACATAATTTACATAATTTACATAATACATAACTTATATAATTTAAAGTTCGAATTTCAT
1 AACTTACATAATTTACATAATTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCAT
* *
16084277 AACTTACATAATTTTCATAATTTACATAATACATGACTTACATAATTTAAAGATCAAATTTCAT
1 AACTTACATAATTTACATAATTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCAT
16084341 AACTTACATAATTTACATAAATTTA
1 AACTTACATAATTTACAT-AATTTA
16084366 ACACACATGG
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 75 0.93
65 6 0.07
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (64 bp):
AACTTACATAATTTACATAATTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCAT
Found at i:16084507 original size:9 final size:9
Alignment explanation
Indices: 16084493--16084564 Score: 60
Period size: 9 Copynumber: 8.2 Consensus size: 9
16084483 TCGTACATAA
16084493 TACATAACT
1 TACATAACT
*
16084502 TACATAATT
1 TACATAACT
16084511 TACATAACT
1 TACATAACT
16084520 TACATAA--
1 TACATAACT
*
16084527 TACATAA-A
1 TACATAACT
* * *
16084535 TATATATCA
1 TACATAACT
16084544 TATCATAACT
1 TA-CATAACT
*
16084554 GACATAACT
1 TACATAACT
16084563 TA
1 TA
16084565 ATTATACTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
7 7 0.14
8 5 0.10
9 34 0.67
10 5 0.10
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.35
Consensus pattern (9 bp):
TACATAACT
Found at i:16084516 original size:18 final size:18
Alignment explanation
Indices: 16084493--16084527 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
16084483 TCGTACATAA
16084493 TACATAACTTACATAATT
1 TACATAACTTACATAATT
16084511 TACATAACTTACATAAT
1 TACATAACTTACATAAT
16084528 ACATAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (18 bp):
TACATAACTTACATAATT
Found at i:16084551 original size:34 final size:34
Alignment explanation
Indices: 16084486--16084560 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
16084476 CTTTATATCG
* *
16084486 TACATAATACATAACTTACATAATTTACATAACT
1 TACATAATACATAAATTACATAATATACATAACT
* *
16084520 TACATAATACATAAATATATATCATAT-CATAACT
1 TACATAATACATAAAT-TACATAATATACATAACT
*
16084554 GACATAA
1 TACATAA
16084561 CTTAATTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 28 0.80
35 7 0.20
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.33
Consensus pattern (34 bp):
TACATAATACATAAATTACATAATATACATAACT
Found at i:16090084 original size:21 final size:21
Alignment explanation
Indices: 16090060--16090121 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
16090050 AACTTAGAGC
16090060 GGAGGCAGCGGCAGCAGCGAA
1 GGAGGCAGCGGCAGCAGCGAA
* *
16090081 GGAGGCAGCGGTAGCAGCGAG
1 GGAGGCAGCGGCAGCAGCGAA
* * *
16090102 GGAAGCAGAGGCAACAGCGA
1 GGAGGCAGCGGCAGCAGCGA
16090122 TGACAGTAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.47, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCGGCAGCAGCGAA
Found at i:16090399 original size:31 final size:31
Alignment explanation
Indices: 16090362--16090431 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
16090352 TTATTTTATT
* *
16090362 TTTCATGCTACATTTGTTGTTTTTGAATGGA
1 TTTCATGCTACATTTGCTATTTTTGAATGGA
* **
16090393 TTTCATGCTATATTTGCTATTTTTGGTTGGA
1 TTTCATGCTACATTTGCTATTTTTGAATGGA
*
16090424 TTTAATGC
1 TTTCATGC
16090432 AGGAAGGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.53
Consensus pattern (31 bp):
TTTCATGCTACATTTGCTATTTTTGAATGGA
Found at i:16103527 original size:68 final size:68
Alignment explanation
Indices: 16103360--16103535 Score: 184
Period size: 68 Copynumber: 2.6 Consensus size: 68
16103350 TAGTACCACC
* * * *
16103360 CATGTGACCTAGC--CA-ATTTATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGTGACCTAGCTACACATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAAT
16103422 CACA
65 CACA
** * *
16103426 CATGTGACCTAGCTACATTTATCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGT
1 CATGTGACCTAGCTACACATATATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGA
16103488 ATCACA
63 ATCACA
16103494 CATGTGACCTAGCTACTACATAGTATCTCGTAGCTCTCTTGT
1 CATGTGACCTAGCTAC-ACATA-TATCTCGTAGCTCTCTTGT
16103536 ACACATGATG
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
66 13 0.14
68 39 0.42
69 8 0.09
70 6 0.07
71 26 0.28
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (68 bp):
CATGTGACCTAGCTACACATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATC
ACA
Found at i:16107902 original size:29 final size:30
Alignment explanation
Indices: 16107869--16107926 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
16107859 GTAGTCGAAA
16107869 CTAG-TTAAATCGCACACTTAGTGCCAAAG
1 CTAGTTTAAATCGCACACTTAGTGCCAAAG
16107898 CTAGTTTAAATCGCACACTTAGTGCCAAA
1 CTAGTTTAAATCGCACACTTAGTGCCAAA
16107927 ACTTTCGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (30 bp):
CTAGTTTAAATCGCACACTTAGTGCCAAAG
Found at i:16114220 original size:29 final size:29
Alignment explanation
Indices: 16114138--16114232 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
16114128 CTAGTTTCCA
* * * *
16114138 TATAAGTG-AGCCTTTGTGGAAATATTTGT
1 TATAAG-GAAGCCTTTATGGCAATCTCTGT
* *
16114167 TATAATGAAGCCTTTATGATC-ATCTCTGT
1 TATAAGGAAGCCTTTATG-GCAATCTCTGT
*
16114196 TATAAGGAAGCCTTTATGGCAATCTCTGC
1 TATAAGGAAGCCTTTATGGCAATCTCTGT
*
16114225 TAAAAGGA
1 TATAAGGA
16114233 TTCCTTTGTG
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.04
29 51 0.96
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (29 bp):
TATAAGGAAGCCTTTATGGCAATCTCTGT
Found at i:16115568 original size:47 final size:48
Alignment explanation
Indices: 16115457--16115579 Score: 173
Period size: 47 Copynumber: 2.6 Consensus size: 48
16115447 TGTGTGCCAA
*
16115457 TGTAAGACCATGTCTGGGACATGGCATCGGCCATATTATGAAAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCATATGATGAAAGCTAG
16115505 TGTAAGACCATGTCTGGGACATGGCAT-GG-CAT-TGA-GACGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCATATGATGA--A-AGCTAG
*
16115552 TGTAGGACCATGTCTGGGACATGGCATC
1 TGTAAGACCATGTCTGGGACATGGCATC
16115580 TGCCTCGACA
Statistics
Matches: 69, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
44 2 0.03
45 2 0.03
46 4 0.06
47 34 0.49
48 27 0.39
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCCATATGATGAAAGCTAG
Found at i:16123036 original size:48 final size:48
Alignment explanation
Indices: 16122964--16123295 Score: 309
Period size: 48 Copynumber: 6.9 Consensus size: 48
16122954 GACATTTGGG
* * * *
16122964 TGATATGTGTGCCAGTGTAGGACCATGTCTGGAACATGGCATCGGCAT
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
* *
16123012 TGATATGTGCGATAGTGTAAGACCATGTCTGGGACATGGCATTGGCCACAT
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG---CAT
* *
16123063 T-ATGA-GTGC-C-AGTGTAAGACCATGTCTGGGACATTGCATCCGCCACAT
1 TGAT-ATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCAT-CG--GCAT
* * *
16123111 T-ATA--AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCAT
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
* * *
16123156 TGATGTGTACGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCAT
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
* * * * ** * * * *
16123204 TGAGACGAGGGCTAGTGTGGGACCATGTCTTGGACATAGCATCTGCCT
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
* * *
16123252 CGATATGTGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCG
1 TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
16123296 ATAATTCACC
Statistics
Matches: 227, Mismatches: 45, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
45 4 0.02
46 3 0.01
47 3 0.01
48 205 0.90
49 1 0.00
50 6 0.03
51 5 0.02
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (48 bp):
TGATATGTGCGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
Found at i:16123239 original size:144 final size:142
Alignment explanation
Indices: 16122977--16123294 Score: 406
Period size: 144 Copynumber: 2.2 Consensus size: 142
16122967 TATGTGTGCC
* * * *
16122977 AGTGTAGGACCATGTCTGGAACATGGCATCGGCATTGATATGTGCGATAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTACGATAGTGTAAGACCATGTCT
* * *
16123042 GGGACATGGCATTGGCCACATTATGAGTGCCAGTGTAAGACCATGTCTGGGACATTGCATCCGCC
66 GGGACATGGCATTGG-C-CATTACGAGGGCCAGTGTAAGACCATGTCTGGGACATAGCATCCGCC
16123107 AC-ATTATAAGAGCT
129 ACGA-TATAAGAGCT
* *
16123121 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATGTGTACGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTACGATAGTGTAAGACCATGTCT
* ** * *
16123186 GGGACATGGCATTGG-CATTGAGACGAGGGCTAGTGTGGGACCATGTCTTGGACATAGCATCTGC
66 GGGACATGGCATTGGCCATT---ACGAGGGCCAGTGTAAGACCATGTCTGGGACATAGCATCCGC
* **
16123250 CTCGATATGTGAGCT
128 CACGATATAAGAGCT
*
16123265 AGTGTAAGACCATGTTTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
16123295 GATAATTCAC
Statistics
Matches: 152, Mismatches: 18, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
141 4 0.03
144 147 0.97
145 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (142 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTACGATAGTGTAAGACCATGTCT
GGGACATGGCATTGGCCATTACGAGGGCCAGTGTAAGACCATGTCTGGGACATAGCATCCGCCAC
GATATAAGAGCT
Found at i:16128746 original size:40 final size:40
Alignment explanation
Indices: 16128688--16128867 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
16128678 GACAATCCGA
* *
16128688 CTATGTATGGCACTTAGTGTGTGATTCGAGATAGCTTCAG
1 CTATGTATGGCACTTAGTGTGTGATTCAAGATAGCTTCGG
* ** ** *
16128728 CTATGTATGGCACATAGTGTACGATTGGAGATAGCTTCGA
1 CTATGTATGGCACTTAGTGTGTGATTCAAGATAGCTTCGG
* * *
16128768 TTATGTATGGCACTTAGCGTGTGATTCAAGAAAGCTTCGG
1 CTATGTATGGCACTTAGTGTGTGATTCAAGATAGCTTCGG
*
16128808 CTATGTATGGCACTTAGTGTGTGAGATT-AAAATAGCTTCGG
1 CTATGTATGGCACTTAGTGTGT--GATTCAAGATAGCTTCGG
16128849 CTATGTATTGGCACTTAGT
1 CTATGTA-TGGCACTTAGT
16128868 TTGCGAGAAT
Statistics
Matches: 118, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 85 0.72
41 18 0.15
42 15 0.13
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (40 bp):
CTATGTATGGCACTTAGTGTGTGATTCAAGATAGCTTCGG
Found at i:16129067 original size:17 final size:17
Alignment explanation
Indices: 16129045--16129080 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
16129035 AAATTAACAA
*
16129045 GTTCAATTTGATGAATT
1 GTTCAATTTGATCAATT
16129062 GTTCAATTTGATCAATT
1 GTTCAATTTGATCAATT
16129079 GT
1 GT
16129081 GTGTTTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (17 bp):
GTTCAATTTGATCAATT
Found at i:16140641 original size:13 final size:13
Alignment explanation
Indices: 16140620--16140659 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
16140610 GCTCGACAGG
*
16140620 GACATGCCCGTGT
1 GACACGCCCGTGT
16140633 GACACGCCCGTGT
1 GACACGCCCGTGT
16140646 GACACGCCCGTGT
1 GACACGCCCGTGT
16140659 G
1 G
16140660 CGATTACTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.35, G:0.33, T:0.17
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:16151037 original size:22 final size:21
Alignment explanation
Indices: 16151009--16151058 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
16150999 TAAAAGATAT
16151009 ATATTTATATCATTT-TAATTTA
1 ATATTTA-AT-ATTTATAATTTA
*
16151031 ATATTTAATATTTAATAATTTC
1 ATATTTAATATTT-ATAATTTA
16151053 ATATTT
1 ATATTT
16151059 TTTTATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.16
21 2 0.08
22 19 0.76
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTTAATATTTATAATTTA
Found at i:16153082 original size:162 final size:163
Alignment explanation
Indices: 16152911--16153214 Score: 407
Period size: 162 Copynumber: 1.9 Consensus size: 163
16152901 CTAAACTACC
* * * **
16152911 TTTTTCTTTTAAGTGACTAAGGTTCATATTCTAAATAAAACTAAATAGCTTAAAAGTCCAAATGT
1 TTTTTCTTTTAAGTGACTAAGATACATATTCTAAATAAAACTAAATAGCCTAAAAGTCCAAACAT
* * *
16152976 TATAAAACTAGAAGTACGGATTAT-ACTAGATTGT-T-AATAACAGAAAGCTGTTCTTAATTCAA
66 TATAAAACTAGAAATACGGA-TATCACTAGATT-TCTCAATAACAGAAAGCTGTTCTCAACTCAA
16153038 ATACACCTGTCAATAAATTCCGAACCCCCCCCCCT
129 ATACACCTGTCAATAAATTCCGAACCCCCCCCCCT
* * * *
16153073 TTTTTCTTTTAAGTGACTATGATACATATTTTAAATAGAACTCAATAGCCTAAAAGTCCAAACAT
1 TTTTTCTTTTAAGTGACTAAGATACATATTCTAAATAAAACTAAATAGCCTAAAAGTCCAAACAT
* * * * *
16153138 TATAAAACTATAAATATGGATATCACTAGGTTTCTCAATAACAGGAAGCTGTTCTCAACTCAAGT
66 TATAAAACTAGAAATACGGATATCACTAGATTTCTCAATAACAGAAAGCTGTTCTCAACTCAAAT
*
16153203 GCACCTGTCAAT
131 ACACCTGTCAAT
16153215 TAATACTGAA
Statistics
Matches: 121, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
161 4 0.03
162 81 0.67
163 36 0.30
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (163 bp):
TTTTTCTTTTAAGTGACTAAGATACATATTCTAAATAAAACTAAATAGCCTAAAAGTCCAAACAT
TATAAAACTAGAAATACGGATATCACTAGATTTCTCAATAACAGAAAGCTGTTCTCAACTCAAAT
ACACCTGTCAATAAATTCCGAACCCCCCCCCCT
Found at i:16157621 original size:3 final size:3
Alignment explanation
Indices: 16157613--16157643 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16157603 GTGCAGTCTC
16157613 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
16157644 TTTTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:16160085 original size:17 final size:17
Alignment explanation
Indices: 16160029--16160086 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
16160019 TTTTTTGTAT
16160029 TATTTTTAA--AATTGAA
1 TATTTTTAATTAATT-AA
16160045 TATTTTGTAATTATATT-A
1 TATTTT-TAATTA-ATTAA
*
16160063 TGTTTTTAATTAATTAA
1 TATTTTTAATTAATTAA
16160080 TATTTTT
1 TATTTTT
16160087 TGAAGAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 9 0.26
17 16 0.46
18 6 0.17
19 1 0.03
20 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
TATTTTTAATTAATTAA
Found at i:16171585 original size:13 final size:13
Alignment explanation
Indices: 16171550--16171585 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
16171540 ATGACTTCAT
*
16171550 GAAAATTTCATTC
1 GAAAATTTCGTTC
16171563 GAAAATTTCGTTC
1 GAAAATTTCGTTC
16171576 GAAAATTTCG
1 GAAAATTTCG
16171586 ACGAATGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (13 bp):
GAAAATTTCGTTC
Found at i:16178011 original size:28 final size:28
Alignment explanation
Indices: 16177952--16178039 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
16177942 CATCTTGTAC
* * * * * *
16177952 TTCACCATTTTGTGGTGTAATCTCACAC
1 TTCACCACTTCGTGGTGTCATTTCGCAA
16177980 TTCACCACTTCGTGGTGTCATTTCGCAA
1 TTCACCACTTCGTGGTGTCATTTCGCAA
* * *
16178008 TTCACCACTTCGCGATGTCGTTTCGCAA
1 TTCACCACTTCGTGGTGTCATTTCGCAA
16178036 TTCA
1 TTCA
16178040 TCTCGTAACT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.36
Consensus pattern (28 bp):
TTCACCACTTCGTGGTGTCATTTCGCAA
Found at i:16180003 original size:14 final size:14
Alignment explanation
Indices: 16179984--16180011 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16179974 ACAATGAAGA
16179984 AGCAAGACAAATTC
1 AGCAAGACAAATTC
16179998 AGCAAGACAAATTC
1 AGCAAGACAAATTC
16180012 TTTCTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
AGCAAGACAAATTC
Found at i:16180458 original size:28 final size:28
Alignment explanation
Indices: 16180426--16180491 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
16180416 TGAAGACATC
*
16180426 TCACAGTTCACCACTTCGCAGTGTCATT
1 TCACAGTTCACCACTTCACAGTGTCATT
**
16180454 TCACAGTTCACCACTTCATGGTGTCATT
1 TCACAGTTCACCACTTCACAGTGTCATT
*
16180482 TCACAATTCA
1 TCACAGTTCA
16180492 TCTCGCAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.33
Consensus pattern (28 bp):
TCACAGTTCACCACTTCACAGTGTCATT
Found at i:16185793 original size:46 final size:46
Alignment explanation
Indices: 16185726--16185900 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
16185716 TGTAACCCGC
*
16185726 CCATAAGCGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
16185772 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACA-
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * *
16185821 AC-TCA-CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
** * **
16185865 CCATAAATGAACTCAGACTCAACTCAATAAGCTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG
16185901 ATGCCCAAAT
Statistics
Matches: 105, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 2 0.02
45 2 0.02
46 59 0.56
47 28 0.27
48 3 0.03
49 2 0.02
50 2 0.02
51 3 0.03
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.19
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:16185846 original size:93 final size:93
Alignment explanation
Indices: 16185733--16185905 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
16185723 CGCCCATAAG
* * * * *
16185733 CGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCA
*
16185798 ACGAGCTCGGATGCCTAGTTACAACTCA
66 ACAAGCTCGGATGCCTAGTTACAACTCA
16185826 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCA
*
16185891 ATAAGCTCGGATGCC
66 ACAAGCTCGGATGCC
16185906 CAAATATCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCAGACTCAACTCA
ACAAGCTCGGATGCCTAGTTACAACTCA
Found at i:16185853 original size:20 final size:19
Alignment explanation
Indices: 16185819--16185856 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
16185809 TGCCTAGTTA
16185819 CAACTCACGAACTCGGACT
1 CAACTCACGAACTCGGACT
*
16185838 CAACTCAACGAGCTCGGAC
1 CAACTC-ACGAACTCGGAC
16185857 ATTCGCATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.37, G:0.18, T:0.13
Consensus pattern (19 bp):
CAACTCACGAACTCGGACT
Found at i:16190502 original size:24 final size:24
Alignment explanation
Indices: 16190470--16190537 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
16190460 TCATTAGGGA
16190470 TTACCGATTGC-AGCTCGTGAGAGC
1 TTACCGATT-CTAGCTCGTGAGAGC
16190494 TTACCGATTCTTAGCTCGTGAGAGC
1 TTACCGATTC-TAGCTCGTGAGAGC
*
16190519 ATACC-AGTTCATAGCTCGT
1 TTACCGA-TTC-TAGCTCGT
16190538 ATGAGCATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 1 0.03
24 10 0.26
25 28 0.72
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (24 bp):
TTACCGATTCTAGCTCGTGAGAGC
Found at i:16190514 original size:25 final size:25
Alignment explanation
Indices: 16190481--16190547 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
16190471 TACCGATTGC
* *
16190481 AGCTCGTGAGAGCTTACC-GATTCTT
1 AGCTCGTGAGAGCATACCAG-TTCAT
16190506 AGCTCGTGAGAGCATACCAGTTCAT
1 AGCTCGTGAGAGCATACCAGTTCAT
16190531 AGCTCGT-ATGAGCATAC
1 AGCTCGTGA-GAGCATAC
16190548 ATGTACAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 1 0.03
25 36 0.95
26 1 0.03
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (25 bp):
AGCTCGTGAGAGCATACCAGTTCAT
Found at i:16206010 original size:44 final size:46
Alignment explanation
Indices: 16205904--16206029 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 46
16205894 GGTAGAATGC
* *
16205904 TGATGCTATGTCCCAGACATGGTCTTACACTAGCTTTCACATATTCGTGT
1 TGATGC-ATGTCCCAGACAT-GTCTTACACTAG--TACACATACTCGTGT
*
16205954 CGATGTCATGTCCCAGACATGTCTTACACT-G-ACACAT-CTCGTAGT
1 TGATG-CATGTCCCAGACATGTCTTACACTAGTACACATACTCGT-GT
*
16205999 TGATGCATGTCCCAGACATGTTTTACACTAG
1 TGATGCATGTCCCAGACATGTCTTACACTAG
16206030 CTCTTGTCTC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
44 27 0.40
45 12 0.18
48 1 0.01
49 10 0.15
50 17 0.25
51 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (46 bp):
TGATGCATGTCCCAGACATGTCTTACACTAGTACACATACTCGTGT
Found at i:16207780 original size:87 final size:86
Alignment explanation
Indices: 16207628--16207787 Score: 250
Period size: 87 Copynumber: 1.8 Consensus size: 86
16207618 TTTAAGTTCA
*
16207628 GTGAATTCATCAAGTCCGTCTTAATAGGACTACCCAAAATGTGGGATATGAACTCATTAAGAGTA
1 GTGAATTCATCAAGTCCGTCTCAATAGGACTACCCAAAATGTGGGATATGAACTCATTAAGAGTA
16207693 ATAAACTCAACCTCTCAAGTTG
66 A-AAACTCAACCTCTCAAGTTG
* * * *
16207715 GTGAATTCATCAAGTCTGTCTCAATAGGACTACCCAAAATTTGGGCTATGAATTCATT-AGAAGT
1 GTGAATTCATCAAGTCCGTCTCAATAGGACTACCCAAAATGTGGGATATGAACTCATTAAG-AGT
16207779 AAAAACTCA
65 AAAAACTCA
16207788 TCTTTATGCA
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
86 9 0.13
87 58 0.87
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (86 bp):
GTGAATTCATCAAGTCCGTCTCAATAGGACTACCCAAAATGTGGGATATGAACTCATTAAGAGTA
AAAACTCAACCTCTCAAGTTG
Found at i:16217422 original size:24 final size:24
Alignment explanation
Indices: 16217395--16217446 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16217385 TTAGTAAGTC
*
16217395 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
16217419 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
16217443 AAAT
1 AAAT
16217447 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:16219392 original size:24 final size:24
Alignment explanation
Indices: 16219365--16219416 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16219355 TTAGTAAGTC
*
16219365 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
16219389 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
16219413 AAAT
1 AAAT
16219417 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:16223695 original size:21 final size:22
Alignment explanation
Indices: 16223671--16223718 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
16223661 ATATTATTAC
16223671 AAAAAATGTA-AAAGA-AATTGT
1 AAAAAAT-TATAAAGACAATTGT
*
16223692 -AAAAATTATAAATACAATTGT
1 AAAAAATTATAAAGACAATTGT
16223713 AAAAAA
1 AAAAAA
16223719 ATATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.09
20 10 0.43
21 6 0.26
22 5 0.22
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (22 bp):
AAAAAATTATAAAGACAATTGT
Found at i:16223697 original size:20 final size:21
Alignment explanation
Indices: 16223672--16223717 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
16223662 TATTATTACA
16223672 AAAAATGTA-AAAGA-AATTGT
1 AAAAAT-TATAAAGACAATTGT
*
16223692 AAAAATTATAAATACAATTGT
1 AAAAATTATAAAGACAATTGT
16223713 AAAAA
1 AAAAA
16223718 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 2 0.09
20 10 0.43
21 11 0.48
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (21 bp):
AAAAATTATAAAGACAATTGT
Found at i:16224123 original size:20 final size:20
Alignment explanation
Indices: 16224073--16224140 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
16224063 CAAAAGTATT
*
16224073 ATTTAATATTTAA-ATATTTA
1 ATTTAAT-TTTAATATTTTTA
**
16224093 ATATTATATTTTTCTATTTTTA
1 AT-TTA-ATTTTAATATTTTTA
16224115 ATTTAATTTTAATATTTTTA
1 ATTTAATTTTAATATTTTTA
*
16224135 TTTTAA
1 ATTTAA
16224141 ATAAACTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 20 0.51
21 9 0.23
22 10 0.26
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTAATTTTAATATTTTTA
Found at i:16228609 original size:24 final size:24
Alignment explanation
Indices: 16228559--16228609 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
16228549 TTAGCAAGTC
**
16228559 AAATAAACTATACTAATAAATGTT
1 AAATAAACTATACTAATAAATACT
16228583 AAATATAA-TATACTAATAAATACT
1 AAATA-AACTATACTAATAAATACT
16228607 AAA
1 AAA
16228610 ACTTCTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:16233265 original size:16 final size:16
Alignment explanation
Indices: 16233244--16233275 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16233234 ATAAAGAGAC
16233244 TTTATTTTGGAAATCA
1 TTTATTTTGGAAATCA
16233260 TTTATTTTGGAAATCA
1 TTTATTTTGGAAATCA
16233276 ATGGCATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TTTATTTTGGAAATCA
Found at i:16238762 original size:27 final size:27
Alignment explanation
Indices: 16238732--16238844 Score: 75
Period size: 27 Copynumber: 4.2 Consensus size: 27
16238722 CTATCTAGCG
* *
16238732 AACAGGTGATTGGCGGACTGGCTCGCA
1 AACAGGTGACTGGCAGACTGGCTCGCA
* * *
16238759 AACAAGTGACTGGCAGACTGTCTCGCG
1 AACAGGTGACTGGCAGACTGGCTCGCA
* ** * * *
16238786 AACAGAG-GACTGGTAGGTTGCCTCACG
1 AACAG-GTGACTGGCAGACTGGCTCGCA
* * * *
16238813 AATAGGTGACTGGCAGATTGCCTCACA
1 AACAGGTGACTGGCAGACTGGCTCGCA
16238840 AACAG
1 AACAG
16238845 AGGACTGACG
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
26 1 0.01
27 66 0.97
28 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.19
Consensus pattern (27 bp):
AACAGGTGACTGGCAGACTGGCTCGCA
Found at i:16238850 original size:27 final size:28
Alignment explanation
Indices: 16238757--16238863 Score: 96
Period size: 27 Copynumber: 4.0 Consensus size: 28
16238747 GACTGGCTCG
* * *
16238757 CAAACA-AGTGACTGGCAGACTGTCTCG
1 CAAACAGAGTGACTGGCAGATTGCCTCA
* * *
16238784 CGAACAGAG-GACTGGTAGGTTGCCTCA
1 CAAACAGAGTGACTGGCAGATTGCCTCA
* *
16238811 CGAATAG-GTGACTGGCAGATTGCCTCA
1 CAAACAGAGTGACTGGCAGATTGCCTCA
* *
16238838 CAAACAGAG-GACTGACGGATTGCCTC
1 CAAACAGAGTGACTGGCAGATTGCCTC
16238864 GTGAACAGGA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
26 1 0.02
27 60 0.94
28 3 0.05
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.19
Consensus pattern (28 bp):
CAAACAGAGTGACTGGCAGATTGCCTCA
Found at i:16241761 original size:26 final size:26
Alignment explanation
Indices: 16241725--16241774 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
16241715 CCTGAACCAA
*
16241725 CTTAACTGCTGCAATAGTTCATTCTG
1 CTTAACTGCTGCAACAGTTCATTCTG
*
16241751 CTTAACTGCTGCTACAGTTCATTC
1 CTTAACTGCTGCAACAGTTCATTC
16241775 CTTAACATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (26 bp):
CTTAACTGCTGCAACAGTTCATTCTG
Found at i:16244939 original size:15 final size:15
Alignment explanation
Indices: 16244919--16244963 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
16244909 AAACCGAAAT
*
16244919 GGAGGAGTAAGCGGC
1 GGAGGAGGAAGCGGC
*
16244934 GGAGGAGGCAGCGGC
1 GGAGGAGGAAGCGGC
*
16244949 GGAGGAGGCAGCGGC
1 GGAGGAGGAAGCGGC
16244964 ATTGGAGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.22, C:0.18, G:0.58, T:0.02
Consensus pattern (15 bp):
GGAGGAGGAAGCGGC
Found at i:16244971 original size:18 final size:15
Alignment explanation
Indices: 16244928--16244963 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
16244918 TGGAGGAGTA
16244928 AGCGGCGGAGGAGGC
1 AGCGGCGGAGGAGGC
16244943 AGCGGCGGAGGAGGC
1 AGCGGCGGAGGAGGC
16244958 AGCGGC
1 AGCGGC
16244964 ATTGGAGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.22, G:0.58, T:0.00
Consensus pattern (15 bp):
AGCGGCGGAGGAGGC
Found at i:16252688 original size:25 final size:24
Alignment explanation
Indices: 16252655--16252704 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 24
16252645 AAACCTGATA
16252655 ATGACTATTTGTCACATTATATGTTT
1 ATGACTATTTGT-A-ATTATATGTTT
*
16252681 ATGA-TATTTGTATTTATATGTTT
1 ATGACTATTTGTAATTATATGTTT
16252704 A
1 A
16252705 ATAGTATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 7 0.30
26 4 0.17
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.54
Consensus pattern (24 bp):
ATGACTATTTGTAATTATATGTTT
Found at i:16259911 original size:52 final size:53
Alignment explanation
Indices: 16259845--16259947 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 53
16259835 ACTCCCAATC
16259845 AATTTCCTTCTTATTACATTTG-CTATCTTTGATTAACTTA-TCATTTCGAGTT
1 AATTTCCTTCTTATTACATTTGTC-ATCTTTGATTAACTTATTCATTTCGAGTT
* * *
16259897 AATTTCCTTTTTATTGCATTTGTCATCTTTGATTAATTTATTCATTTCGAG
1 AATTTCCTTCTTATTACATTTGTCATCTTTGATTAACTTATTCATTTCGAG
16259948 CTATGCTCCC
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 35 0.76
53 11 0.24
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (53 bp):
AATTTCCTTCTTATTACATTTGTCATCTTTGATTAACTTATTCATTTCGAGTT
Found at i:16260477 original size:46 final size:46
Alignment explanation
Indices: 16260331--16260470 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 46
16260321 CAGATCAATT
** * *
16260331 GATTGAAGAAGCCACAAATCCTATACCCTTGAGCTACAGTAGGATG
1 GATTGAAGAAGATACAAATCCTATACCCTTGAGTTACAGTGGGATG
* *
16260377 GATTGAAGAAGATACAAATCTTATACCCCTGAGTTACAGTGGGATG
1 GATTGAAGAAGATACAAATCCTATACCCTTGAGTTACAGTGGGATG
* *
16260423 GATTGAAGATGATACAAATCCTATACCCTTGAGTTGCAGTGGGATG
1 GATTGAAGAAGATACAAATCCTATACCCTTGAGTTACAGTGGGATG
16260469 GA
1 GA
16260471 CGGAAGAAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 84 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (46 bp):
GATTGAAGAAGATACAAATCCTATACCCTTGAGTTACAGTGGGATG
Found at i:16261081 original size:45 final size:46
Alignment explanation
Indices: 16260973--16261099 Score: 136
Period size: 44 Copynumber: 2.8 Consensus size: 46
16260963 ATTATGGCGG
* * *
16260973 ATCTTATCT-TCTTGAAGTTGCAACGGAGCAGATTGAAGCCACCAGC
1 ATCTTATCTCT-TTGAAGTTGCAGCGGAGCAGATTGAAGACACCAGA
* * * *
16261019 ATC--ATCTCTCTGAAGTTGTAGCGGAGCAGACTGAAGACAGC-GA
1 ATCTTATCTCTTTGAAGTTGCAGCGGAGCAGATTGAAGACACCAGA
* *
16261062 ATCTTATCTCTTTGAAGTTGCAGTGGAACAGATTGAAG
1 ATCTTATCTCTTTGAAGTTGCAGCGGAGCAGATTGAAG
16261100 CTACAAATTA
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
43 4 0.06
44 30 0.45
45 29 0.44
46 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (46 bp):
ATCTTATCTCTTTGAAGTTGCAGCGGAGCAGATTGAAGACACCAGA
Found at i:16261101 original size:143 final size:143
Alignment explanation
Indices: 16260829--16261248 Score: 592
Period size: 143 Copynumber: 2.9 Consensus size: 143
16260819 TGAATCCATA
*
16260829 AATCTCATCTTTC-TGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
1 AATCTTATC-TTCATGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTT
* * * * *
16260893 GCAGCGGAGCAAACTGAAGACAACGAATCTTA-CTTCCCTGACGTTGCAGTGGAATATATTAAAG
65 GCAGCGGAGCAGACTGAAGACAGCGAATCTTATC-TCCCTGAAGTTGCAGTGGAACAGATTAAAG
16260957 CTACAAATTATGGCG
129 CTACAAATTATGGCG
* * ** * * *
16260972 GATCTTATCTTCTTGAAGTTGCAACGGAGCAGATTGAAGCCACCAGCATCATCTCTCTGAAGTTG
1 AATCTTATCTTCATGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTG
* ** *
16261037 TAGCGGAGCAGACTGAAGACAGCGAATCTTATCTCTTTGAAGTTGCAGTGGAACAGATTGAAGCT
66 CAGCGGAGCAGACTGAAGACAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCT
16261102 ACAAATTATGGCG
131 ACAAATTATGGCG
* * *
16261115 AATCTTATCTTCATGAAGTTACAGTGGAGTAGATTTAAGCCACCAGCCTTATCTCCCTGAAGTTG
1 AATCTTATCTTCATGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTG
* * * *
16261180 CAGCGGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGAAGTTACAGAGGAACAGATTAAAGCT
66 CAGCGGAGCAGACTGAAGACAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCT
16261245 ACAA
131 ACAA
16261249 GTCACAAACC
Statistics
Matches: 241, Mismatches: 34, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
142 3 0.01
143 237 0.98
144 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (143 bp):
AATCTTATCTTCATGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTG
CAGCGGAGCAGACTGAAGACAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCT
ACAAATTATGGCG
Found at i:16262938 original size:3 final size:3
Alignment explanation
Indices: 16262930--16262966 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
16262920 TATTTACTTG
* *
16262930 TAT TAT TAT TAA TAT TAT TAT TGT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16262967 GAACCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:16263158 original size:18 final size:17
Alignment explanation
Indices: 16263122--16263163 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
16263112 GTCCTCATTG
*
16263122 TTAT-TTTATTATATGT
1 TTATATTTATTATATAT
*
16263138 TTAATATTTATTATTTAT
1 TT-ATATTTATTATATAT
16263156 TTATATTT
1 TTATATTT
16263164 TTAATATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 8 0.36
18 12 0.55
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTATATTTATTATATAT
Found at i:16265581 original size:47 final size:47
Alignment explanation
Indices: 16265527--16265623 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
16265517 AAGCCCTCAT
*
16265527 TCATACATTCATGTAAAATTGTGTTTAGATTAGAAATTGCATAGGGA
1 TCATACATTCATGTAAAATTGCGTTTAGATTAGAAATTGCATAGGGA
16265574 TCATACATTCATGTAAAATTGCGTTTAGATTAGAAATTGCATAGGGA
1 TCATACATTCATGTAAAATTGCGTTTAGATTAGAAATTGCATAGGGA
16265621 TCA
1 TCA
16265624 CTCCTTGCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (47 bp):
TCATACATTCATGTAAAATTGCGTTTAGATTAGAAATTGCATAGGGA
Found at i:16265928 original size:17 final size:17
Alignment explanation
Indices: 16265906--16265947 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
16265896 ATTGAATCAC
16265906 ATATTGATTGTATTGAT
1 ATATTGATTGTATTGAT
* * *
16265923 ATATTGTTTTTGTTGAT
1 ATATTGATTGTATTGAT
16265940 -TATTGATT
1 ATATTGATT
16265948 TAAATCATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.24, C:0.00, G:0.17, T:0.60
Consensus pattern (17 bp):
ATATTGATTGTATTGAT
Found at i:16267547 original size:6 final size:6
Alignment explanation
Indices: 16267536--16267571 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
16267526 ACACCGTAGG
16267536 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA
16267572 TTCATATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
GTAACA
Found at i:16271273 original size:18 final size:17
Alignment explanation
Indices: 16271246--16271282 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
16271236 GTTCTTTATT
*
16271246 TTATTAATATATTATAA
1 TTATTAATATAATATAA
16271263 TTATATAATATAATATAA
1 TTAT-TAATATAATATAA
16271281 TT
1 TT
16271283 TATTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATTAATATAATATAA
Found at i:16275859 original size:42 final size:41
Alignment explanation
Indices: 16275780--16275934 Score: 159
Period size: 42 Copynumber: 3.7 Consensus size: 41
16275770 TACCGAGGCT
* *
16275780 ATGTAAGACCATATTTGGGATATGGTATC-ATTATGAGACTTC
1 ATGTAAGACCATATCTGGGATATGGCATCGA-TATGAGA-TTC
* * * *
16275822 ATATAAGACCATATATGGGATGTGGCATCGATGTGAGATTTC
1 ATGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TTC
* * * * *
16275864 GTGTAAGACCATAGCTGGGTTATTGCCATCGATATGAGATCCC
1 ATGTAAGACCATATCTGGGATA-TGGCATCGATATGAGAT-TC
16275907 ATGTAAGACCATATCTGGGATATGGCAT
1 ATGTAAGACCATATCTGGGATATGGCAT
16275935 TGGTGTAGTA
Statistics
Matches: 91, Mismatches: 19, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
42 56 0.62
43 35 0.38
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (41 bp):
ATGTAAGACCATATCTGGGATATGGCATCGATATGAGATTC
Found at i:16278863 original size:42 final size:42
Alignment explanation
Indices: 16278800--16278911 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
16278790 TACTACACCA
* *
16278800 ATGCCATATCCCAGATATGGTCTTACATG-GGATCTCAT-ATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAG-TCTCATAAT-G
* *
16278842 ATGGCATATCCCAGATATGGTCTTACACGAAGTCTTATAATG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATAATG
16278884 ATGCCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
16278912 ATAGCCTTGG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
42 60 0.95
43 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATAATG
Found at i:16284920 original size:10 final size:10
Alignment explanation
Indices: 16284893--16284952 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
16284883 TTAAATTCTA
16284893 AAAGATAAAT
1 AAAGATAAAT
16284903 ACAA-ATAAAT
1 A-AAGATAAAT
*
16284913 AAAGATAATT
1 AAAGATAAAT
*
16284923 AAAGATAATT
1 AAAGATAAAT
16284933 AAAGATAAAT
1 AAAGATAAAT
16284943 GAAA-ATAAAT
1 -AAAGATAAAT
16284953 CCTAAATCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:16285753 original size:96 final size:96
Alignment explanation
Indices: 16285587--16285765 Score: 268
Period size: 96 Copynumber: 1.9 Consensus size: 96
16285577 TATATATATT
* * * * *
16285587 TTTTTCTTAAGAATATATTGAATCTTTTGACGTGAAGAGAGATGACAGCCAAGCACCCCACCCAG
1 TTTTTCTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAACAGCCAAGCACCCCACCCAG
*
16285652 ATTACTCAGCCTAACACACTCCTAATTTTTA
66 ATTACTCAGCCCAACACACTCCTAATTTTTA
* * *
16285683 TTTTTCTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAACAGTCAAGCACCTCACCCTG
1 TTTTTCTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAACAGCCAAGCACCCCACCCAG
*
16285748 GTTACTCAGCCCAACACA
66 ATTACTCAGCCCAACACA
16285766 TTCTTAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 73 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (96 bp):
TTTTTCTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAACAGCCAAGCACCCCACCCAG
ATTACTCAGCCCAACACACTCCTAATTTTTA
Found at i:16294521 original size:10 final size:10
Alignment explanation
Indices: 16294494--16294543 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
16294484 TTAAATTCTA
*
16294494 AAAGAGAAAT
1 AAAGATAAAT
16294504 ACAA-ATAAAT
1 A-AAGATAAAT
*
16294514 AAAGATAATT
1 AAAGATAAAT
16294524 AAAGATAAAT
1 AAAGATAAAT
16294534 GAAA-ATAAAT
1 -AAAGATAAAT
16294544 CCTAAATCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 27 0.79
11 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:16305658 original size:20 final size:20
Alignment explanation
Indices: 16305630--16305693 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
16305620 ATCTATGGAC
16305630 AAGCCACCAGTAATGCAGAT
1 AAGCCACCAGTAATGCAGAT
* * *
16305650 AAGCTACCAGTAATG-TGGT
1 AAGCCACCAGTAATGCAGAT
*
16305669 CAAGCCACTAGTAATGCAGAT
1 -AAGCCACCAGTAATGCAGAT
16305690 AAGC
1 AAGC
16305694 TGCCAGTACT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (20 bp):
AAGCCACCAGTAATGCAGAT
Found at i:16305701 original size:20 final size:20
Alignment explanation
Indices: 16305630--16305701 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
16305620 ATCTATGGAC
*
16305630 AAGCCACCAGTAATGCAGAT
1 AAGCTACCAGTAATGCAGAT
* *
16305650 AAGCTACCAGTAATG-TGGT
1 AAGCTACCAGTAATGCAGAT
* *
16305669 CAAGCCACTAGTAATGCAGAT
1 -AAGCTACCAGTAATGCAGAT
*
16305690 AAGCTGCCAGTA
1 AAGCTACCAGTA
16305702 CTTCTCCTTA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.05
20 36 0.90
21 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (20 bp):
AAGCTACCAGTAATGCAGAT
Found at i:16317354 original size:21 final size:21
Alignment explanation
Indices: 16317321--16317369 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
16317311 ATCATGTTAT
*
16317321 TTAT-TTTTATTTGATTTTG-
1 TTATGTTTTATTTGAATTTGA
16317340 TTATGTTTATATTTGAATTTGAA
1 TTATGTTT-TATTTGAATTTG-A
16317363 TTATGTT
1 TTATGTT
16317370 AGCACCACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 4 0.16
20 3 0.12
21 11 0.44
23 7 0.28
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.65
Consensus pattern (21 bp):
TTATGTTTTATTTGAATTTGA
Found at i:16335933 original size:67 final size:68
Alignment explanation
Indices: 16335787--16335941 Score: 260
Period size: 67 Copynumber: 2.3 Consensus size: 68
16335777 CACCATAGAA
*
16335787 ATTGCAGCGAAGG-AGCCAGATATTGTGACGAAGTCACCAGATACAGATATATGTAGCGAGGCCA
1 ATTGCAGCG-AGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATATGTAGCGAGGCCA
16335851 CCAG
65 CCAG
* *
16335855 ATTGCAACGAGGCTGCCAGATATTGTGACGAAGTCACCAGA-ATAGATATATGTAGCGAGGCCAC
1 ATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATATGTAGCGAGGCCAC
16335919 CAG
66 CAG
16335922 ATTGCAGCGAGGCTGCCAGA
1 ATTGCAGCGAGGCTGCCAGA
16335942 ACGCTTCCTC
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
67 47 0.57
68 35 0.43
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.18
Consensus pattern (68 bp):
ATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGATACAGATATATGTAGCGAGGCCAC
CAG
Found at i:16340808 original size:39 final size:39
Alignment explanation
Indices: 16340754--16340927 Score: 199
Period size: 40 Copynumber: 4.4 Consensus size: 39
16340744 AAACCAAGTA
* * * *
16340754 CCTTCGGAATTTAGCCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCGGATATAG-TAACTCGCACAAATG
*
16340793 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG
* *
16340833 CCTTTGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG
* * * *
16340873 CCTTCGGG-CTTAGCCCGAAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCGGATA-TAGTAACTCGCACAAATG
16340912 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
16340928 CGGTTATCAT
Statistics
Matches: 119, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
38 4 0.03
39 42 0.35
40 73 0.61
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG
Found at i:16340831 original size:40 final size:40
Alignment explanation
Indices: 16340787--16340934 Score: 228
Period size: 40 Copynumber: 3.7 Consensus size: 40
16340777 GCTACTTGCT
16340787 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
16340827 CAAATGCCTTTGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
** * *
16340867 CAAATGCCTTCGGG-CTTAGCCC-GAAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
16340906 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
16340935 CATCCGAATA
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
38 2 0.02
39 32 0.33
40 61 0.63
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:16340907 original size:79 final size:80
Alignment explanation
Indices: 16340787--16340934 Score: 228
Period size: 79 Copynumber: 1.9 Consensus size: 80
16340777 GCTACTTGCT
** * *
16340787 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTTGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
16340852 TTATAGTAACTCGCA
66 TTATAGTAACTCGCA
*
16340867 CAAATGCCTTCGGG-CTTAGCCCGAA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGAATA-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCG
16340930 GTTAT
65 GTTAT
16340935 CATCCGAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
78 1 0.02
79 47 0.76
80 14 0.23
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
TTATAGTAACTCGCA
Found at i:16343259 original size:28 final size:28
Alignment explanation
Indices: 16343196--16343346 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
16343186 ATATTAAGTC
*
16343196 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
16343223 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
16343251 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
16343279 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
16343307 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
16343336 CGCACACTTAG
1 CGCACACTTAG
16343347 CGCCAATCTC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 22 0.19
28 77 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:16351466 original size:28 final size:28
Alignment explanation
Indices: 16351403--16351553 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
16351393 ATATTAAGTC
*
16351403 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
16351430 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
16351458 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
16351486 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * * *
16351514 CGAACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
16351543 CGCACACTTAG
1 CGCACACTTAG
16351554 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 76 0.67
29 15 0.13
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:16356360 original size:21 final size:20
Alignment explanation
Indices: 16356304--16356375 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 20
16356294 CATAAATTCC
16356304 AAATCTCAAACTCAAA-CTT
1 AAATCTCAAACTCAAATCTT
* *
16356323 GAA-CTCAAACCCTAAATCTT
1 AAATCTCAAACTC-AAATCTT
*
16356343 AAATCTCAAACTTCAAATCTC
1 AAATCTCAAAC-TCAAATCTT
*
16356364 AAATATCAAACT
1 AAATCTCAAACT
16356376 TTGAACCTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 8 0.19
19 5 0.12
20 6 0.14
21 23 0.53
22 1 0.02
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.26
Consensus pattern (20 bp):
AAATCTCAAACTCAAATCTT
Found at i:16356560 original size:21 final size:20
Alignment explanation
Indices: 16356525--16356564 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16356515 AAATATCACT
16356525 AAATAATAATAAAAAGAAAAA
1 AAATAATAATAAAAA-AAAAA
*
16356546 AAATAATATTTAAAAAAAA
1 AAATAATA-ATAAAAAAAA
16356565 TCCAGCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (20 bp):
AAATAATAATAAAAAAAAAA
Found at i:16356944 original size:16 final size:16
Alignment explanation
Indices: 16356923--16356975 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
16356913 ATACATATTT
16356923 AAATATTAAAATTTAA
1 AAATATTAAAATTTAA
*
16356939 AAATATCAAAA-TTAA
1 AAATATTAAAATTTAA
*
16356954 AAAT-TTAAATTTTAGA
1 AAATATTAAAATTTA-A
16356970 AAATAT
1 AAATAT
16356976 AAGAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 4 0.13
15 11 0.35
16 15 0.48
17 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
AAATATTAAAATTTAA
Found at i:16356944 original size:30 final size:32
Alignment explanation
Indices: 16356910--16356976 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 32
16356900 CCTAATATTC
* * *
16356910 AATATACATATTTAAATA-TTAAAATTTA-AA
1 AATATACAAAATTAAAAATTTAAAATTTAGAA
*
16356940 AATAT-CAAAATTAAAAATTTAAATTTTAGAA
1 AATATACAAAATTAAAAATTTAAAATTTAGAA
16356971 AATATA
1 AATATA
16356977 AGAAAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 9 0.30
30 14 0.47
31 7 0.23
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (32 bp):
AATATACAAAATTAAAAATTTAAAATTTAGAA
Found at i:16358396 original size:24 final size:24
Alignment explanation
Indices: 16358369--16358422 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
16358359 TCATCCCATC
16358369 TCATAATCATTTGTTGAAATAATT
1 TCATAATCATTTGTTGAAATAATT
16358393 TCATAATCATTTGTTGAAATAATT
1 TCATAATCATTTGTTGAAATAATT
16358417 TCATAA
1 TCATAA
16358423 ATAATTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (24 bp):
TCATAATCATTTGTTGAAATAATT
Found at i:16358689 original size:20 final size:18
Alignment explanation
Indices: 16358664--16358709 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
16358654 TATATTTAAT
16358664 TAAAAAATTGTAAAAAAATA
1 TAAAAAATT-T-AAAAAATA
**
16358684 TAAAAAATTTCTAAAATA
1 TAAAAAATTTAAAAAATA
16358702 TAAAAAAT
1 TAAAAAAT
16358710 ATAATTTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 14 0.58
19 1 0.04
20 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
TAAAAAATTTAAAAAATA
Found at i:16358775 original size:22 final size:21
Alignment explanation
Indices: 16358729--16358786 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
16358719 CATTTTTTAG
*
16358729 ATTATAAA-AATAAAAAATAT
1 ATTAAAAATAATAAAAAATAT
16358749 ATTAAAAATAATAAAAAAT-T
1 ATTAAAAATAATAAAAAATAT
16358769 CATTTAAAAATAA-AAAAA
1 -A-TTAAAAATAATAAAAA
16358787 TTGAATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.24
21 16 0.47
22 10 0.29
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTAAAAATAATAAAAAATAT
Found at i:16358836 original size:26 final size:26
Alignment explanation
Indices: 16358778--16358837 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
16358768 TCATTTAAAA
**
16358778 ATAAAAAAATTGAATTTTTAAAAATT
1 ATAAAAAAATTGAATTTTTAAAAACC
16358804 ATAAAAAAATTAGAA-TTTTAAACAACC
1 ATAAAAAAATT-GAATTTTTAAA-AACC
16358831 ATAAAAA
1 ATAAAAA
16358838 TTATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (26 bp):
ATAAAAAAATTGAATTTTTAAAAACC
Found at i:16363300 original size:48 final size:47
Alignment explanation
Indices: 16363205--16363422 Score: 163
Period size: 48 Copynumber: 4.6 Consensus size: 47
16363195 ATTGCCAATA
* * * * ** * *
16363205 CCATGTTCCACACATGGTCTTACACTGGCTCACATGTCGAGGACGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-AAGTGGCCGATG
* * * *
16363253 CCGTGTCCTAGACATGGTTTTACACTAGCTCTCGTCTCAA-T-GCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTC--AT-AAGTGGCCGATG
* * * *
16363301 CCATGTCCCAAACATGGTCTTACATTGGCTCTCATAATGTGGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATAA-GTGGCCGATG
* **
16363349 CCATGTCCCAGACATGGTCTTACACTAGCTCTCATTACA-TTGTTGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTCA-TA-AGTGGCCGATG
* *
16363397 CCATGTTCCAAACATGGTCTTACACT
1 CCATGTCCCAGACATGGTCTTACACT
16363423 GGCACACATA
Statistics
Matches: 135, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
45 2 0.01
46 1 0.01
47 1 0.01
48 127 0.94
49 2 0.01
50 2 0.01
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.30
Consensus pattern (47 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAGTGGCCGATG
Found at i:16363372 original size:96 final size:96
Alignment explanation
Indices: 16363205--16363434 Score: 293
Period size: 96 Copynumber: 2.4 Consensus size: 96
16363195 ATTGCCAATA
* * * *
16363205 CCATGTTCCACACATGGTCTTACACTGGCTCACATGTCGAGGACGATGCCGTGTCCTAGACATGG
1 CCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGACGATGCCATGTCCCAGACATGG
* *
16363270 TTTTACACTAGCTCTCGTCT-CAATGCCGATG
66 TCTTACACTAGCTCTCAT-TACAATGCCGATG
* * * * *
16363301 CCATGTCCCAAACATGGTCTTACATTGGCTCTCATAAT-GTGGTCGATGCCATGTCCCAGACATG
1 CCATGTTCCAAACATGGTCTTACACTGGCTCACAT-ATCGAGGACGATGCCATGTCCCAGACATG
* **
16363365 GTCTTACACTAGCTCTCATTACATTGTTGATG
65 GTCTTACACTAGCTCTCATTACAATGCCGATG
*
16363397 CCATGTTCCAAACATGGTCTTACACTGGCACACATATC
1 CCATGTTCCAAACATGGTCTTACACTGGCTCACATATC
16363435 ACCCAAATGT
Statistics
Matches: 113, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
95 3 0.03
96 109 0.96
97 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (96 bp):
CCATGTTCCAAACATGGTCTTACACTGGCTCACATATCGAGGACGATGCCATGTCCCAGACATGG
TCTTACACTAGCTCTCATTACAATGCCGATG
Found at i:16366125 original size:60 final size:60
Alignment explanation
Indices: 16366006--16366132 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
16365996 TTGTATGAGA
* * * *
16366006 TTTGCACTTCGGTGCCTCTGTATACACTTCAGTGCCTCTGTATACACTTCGGTATCCCTG
1 TTTGCACTACGGTGCCCCTGTATACACTTCAGTGCCTCTGTATACACTTCAGTACCCCTG
* * * *
16366066 TTTGCACTACGGTGCCCCTGTCTACACATT-TGTGCC-CTTGTTTACACTTCAGTGCCCCTG
1 TTTGCACTACGGTGCCCCTGTATACAC-TTCAGTGCCTC-TGTATACACTTCAGTACCCCTG
16366126 TTATGCA
1 TT-TGCA
16366133 TCTATGATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.02
60 49 0.88
61 6 0.11
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.36
Consensus pattern (60 bp):
TTTGCACTACGGTGCCCCTGTATACACTTCAGTGCCTCTGTATACACTTCAGTACCCCTG
Done.