Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 192 of 218
Found at i:56953160 original size:29 final size:28
Alignment explanation
Indices: 56953118--56953172 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
56953108 TTAATATAAT
* **
56953118 TATTGATATAATATTTTTTATATTTAAA
1 TATTGATACAATATTAATTATATTTAAA
56953146 TATTGCATACAATATTAATTATATTTA
1 TATTG-ATACAATATTAATTATATTTA
56953173 TCTAATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (28 bp):
TATTGATACAATATTAATTATATTTAAA
Found at i:56954400 original size:20 final size:21
Alignment explanation
Indices: 56954375--56954416 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
56954365 CAAAAGTAAA
56954375 TAAATAATTTTATAA-ATTTT
1 TAAATAATTTTATAATATTTT
*
56954395 TAAATAATTTTTTAATATTTT
1 TAAATAATTTTATAATATTTT
56954416 T
1 T
56954417 TTTAGAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAAATAATTTTATAATATTTT
Found at i:56957457 original size:8 final size:8
Alignment explanation
Indices: 56957444--56957468 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
56957434 AAATTTATGT
56957444 TCAATTTC
1 TCAATTTC
56957452 TCAATTTC
1 TCAATTTC
56957460 TCAATTTC
1 TCAATTTC
56957468 T
1 T
56957469 TCCGCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCAATTTC
Found at i:56959049 original size:98 final size:98
Alignment explanation
Indices: 56958878--56959074 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
56958868 GTGCAATAAA
*
56958878 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
56958943 CCTCTAAAATCCCAAACTCAAAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCAAAATATTTCCTTT
56958976 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* **
56959041 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCAAAATATTTCCTTT
56959074 A
1 A
56959075 TTATTTTTAA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCAAAATATTTCCTTT
Found at i:56959743 original size:20 final size:20
Alignment explanation
Indices: 56959715--56959761 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
56959705 ATATGTGTAT
* *
56959715 ATATATATATAAATTATAAA
1 ATATATATAGAAAGTATAAA
* *
56959735 ATATGTATAGAAAGTATAAT
1 ATATATATAGAAAGTATAAA
56959755 ATATATA
1 ATATATA
56959762 CACGTACATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (20 bp):
ATATATATAGAAAGTATAAA
Found at i:56964687 original size:23 final size:23
Alignment explanation
Indices: 56964657--56964853 Score: 265
Period size: 23 Copynumber: 8.7 Consensus size: 23
56964647 CTACCCTGTT
*
56964657 TTGGACAGCTTTTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
* *
56964680 TTGGACAGCATTTATATACCAAA
1 TTGGACAGCATTTATACATCAAA
*
56964703 TTGGACAGCATTTATACTTCAAA
1 TTGGACAGCATTTATACATCAAA
*
56964726 TTGGGCAGCATTTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
*
56964749 TTAGG-CAGCA--TATACACCAAA
1 TT-GGACAGCATTTATACATCAAA
**
56964770 TTGGACAAAATTTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
*
56964793 TTAGACAGCATTTATACATCAAA
1 TTGGACAGCATTTATACATCAAA
* *
56964816 TTGGACAACATTTATACATTAAA
1 TTGGACAGCATTTATACATCAAA
56964839 TTGGACAGCATTTAT
1 TTGGACAGCATTTAT
56964854 TATACATGTA
Statistics
Matches: 151, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
20 2 0.01
21 15 0.10
23 132 0.87
24 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (23 bp):
TTGGACAGCATTTATACATCAAA
Found at i:56964786 original size:67 final size:68
Alignment explanation
Indices: 56964657--56964845 Score: 247
Period size: 67 Copynumber: 2.8 Consensus size: 68
56964647 CTACCCTGTT
* * ** *
56964657 TTGGACAGCTTTTATACATCAAATTGGACAGCATTTATATACCAAATTGGACAGCATTTATACTT
1 TTGGACAGCATTTATACATCAAATTGGACAGCA-TTATACACCAAATTGGACAAAATTTATACAT
56964722 CAAA
65 CAAA
*
56964726 TTGGGCAGCATTTATACATCAAATTAGG-CAGCA-TATACACCAAATTGGACAAAATTTATACAT
1 TTGGACAGCATTTATACATCAAATT-GGACAGCATTATACACCAAATTGGACAAAATTTATACAT
56964789 CAAA
65 CAAA
* * **
56964793 TTAGACAGCATTTATACATCAAATTGGACAACATTTATACATTAAATTGGACA
1 TTGGACAGCATTTATACATCAAATTGGACAGCA-TTATACACCAAATTGGACA
56964846 GCATTTATTA
Statistics
Matches: 105, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
66 2 0.02
67 57 0.54
69 44 0.42
70 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.31
Consensus pattern (68 bp):
TTGGACAGCATTTATACATCAAATTGGACAGCATTATACACCAAATTGGACAAAATTTATACATC
AAA
Found at i:56964828 original size:90 final size:90
Alignment explanation
Indices: 56964669--56964849 Score: 256
Period size: 90 Copynumber: 2.0 Consensus size: 90
56964659 GGACAGCTTT
* ** * * * * *
56964669 TATACATCAAATTGGACAGCATTTATATACCAAATTGGACAGCATTTATACTTCAAATTGGGCAG
1 TATACACCAAATTGGACAAAATTTATACACCAAATTAGACAGCATTTATACATCAAATTGGACAA
56964734 CATTTATACATCAAATTAGG-CAGCA
66 CATTTATACATCAAATT-GGACAGCA
*
56964759 TATACACCAAATTGGACAAAATTTATACATCAAATTAGACAGCATTTATACATCAAATTGGACAA
1 TATACACCAAATTGGACAAAATTTATACACCAAATTAGACAGCATTTATACATCAAATTGGACAA
*
56964824 CATTTATACATTAAATTGGACAGCA
66 CATTTATACATCAAATTGGACAGCA
56964849 T
1 T
56964850 TTATTATACA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
89 2 0.03
90 78 0.98
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (90 bp):
TATACACCAAATTGGACAAAATTTATACACCAAATTAGACAGCATTTATACATCAAATTGGACAA
CATTTATACATCAAATTGGACAGCA
Found at i:56965732 original size:40 final size:40
Alignment explanation
Indices: 56965601--56965736 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 40
56965591 TATTATAATC
* * * * **
56965601 TCGCACAGTAAGTGCCTTACATAGCTGAAGCTATCTCAGTT
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTC-GAA
* *
56965642 TCGCACACTAAGTGCCATATATAGCCGAAGCTAT-TCCCAA
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCT-CGAA
56965682 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAA
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAA
* *
56965722 TCACATACTAAGTGC
1 TCGCACACTAAGTGC
56965737 TAAACATAGT
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
40 50 0.61
41 32 0.39
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCGAA
Found at i:56969017 original size:19 final size:19
Alignment explanation
Indices: 56968993--56969105 Score: 163
Period size: 19 Copynumber: 5.8 Consensus size: 19
56968983 AATTTTTGAG
56968993 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
56969012 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
56969031 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
56969052 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
56969071 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
56969090 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
56969106 ATATATGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 65 0.79
21 17 0.21
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:56969038 original size:40 final size:40
Alignment explanation
Indices: 56968994--56969100 Score: 173
Period size: 40 Copynumber: 2.7 Consensus size: 40
56968984 ATTTTTGAGG
*
56968994 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
**
56969034 ATATGCAATCTTAGATATGATATGCAATCTTAGAGATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
56969074 ATAT--AATCTTAGATATGATATGCAATC
1 ATATGCAATCTTAGATATGATATGCAATC
56969101 TTAGAATATA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
38 23 0.36
40 41 0.64
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
Found at i:56969489 original size:22 final size:22
Alignment explanation
Indices: 56969443--56969490 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
56969433 AATTAAGTTT
* *
56969443 TTTTATTTTTTTTAATTTACCA
1 TTTTATTTATTTTAAATTACCA
56969465 TTTTATTTATTTTAAATT-CCA
1 TTTTATTTATTTTAAATTACCA
*
56969486 ATTTA
1 TTTTA
56969491 ATCCTTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTATTTATTTTAAATTACCA
Found at i:56970514 original size:98 final size:98
Alignment explanation
Indices: 56970390--56970586 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
56970380 TTAAAAATAA
* *
56970390 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCTTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
56970455 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
56970488 TAAAGGAAGTATTTCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
56970553 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
56970586 T
1 T
56970587 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:56975290 original size:13 final size:14
Alignment explanation
Indices: 56975274--56975324 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 14
56975264 AAAATATTTC
56975274 AAAA-AAAAAGAGA
1 AAAAGAAAAAGAGA
56975287 AAAA-AGAAAAG-GA
1 AAAAGA-AAAAGAGA
56975300 AAAAGGAAAAA-AGA
1 AAAA-GAAAAAGAGA
56975314 AAAAGAAAAAG
1 AAAAGAAAAAG
56975325 TAAAAGGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 17 0.52
14 15 0.45
15 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAGA
Found at i:56975294 original size:7 final size:7
Alignment explanation
Indices: 56975274--56975323 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
56975264 AAAATATTTC
56975274 AAAAA-A
1 AAAAAGA
*
56975280 AAAGAGA
1 AAAAAGA
56975287 AAAAAG-
1 AAAAAGA
*
56975293 AAAAGGA
1 AAAAAGA
*
56975300 AAAAGGA
1 AAAAAGA
56975307 AAAAAG-
1 AAAAAGA
56975313 AAAAAGA
1 AAAAAGA
56975320 AAAA
1 AAAA
56975324 GTAAAAGGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 15 0.41
7 22 0.59
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:56975308 original size:20 final size:20
Alignment explanation
Indices: 56975274--56975329 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
56975264 AAAATATTTC
56975274 AAAA-AAAAAGAGAAAAAAGA
1 AAAAGAAAAAG-GAAAAAAGA
*
56975294 AAAGGAAAAAGGAAAAAAGA
1 AAAAGAAAAAGGAAAAAAGA
*
56975314 AAAAGAAAAAGTAAAA
1 AAAAGAAAAAGGAAAA
56975330 GGAGAGGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAAGGAAAAAAGA
Found at i:56975329 original size:7 final size:6
Alignment explanation
Indices: 56975274--56975330 Score: 53
Period size: 6 Copynumber: 9.0 Consensus size: 6
56975264 AAAATATTTC
*
56975274 AAAAA- AAAAGAG AAAAAAG AAAAGG AAAAAGG AAAAAAG AAAAAG AAAAAG
1 AAAAAG AAAA-AG -AAAAAG AAAAAG AAAAA-G -AAAAAG AAAAAG AAAAAG
*
56975325 TAAAAG
1 AAAAAG
56975331 GAGAGGACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
5 4 0.09
6 27 0.61
7 4 0.09
8 9 0.20
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:56976717 original size:44 final size:43
Alignment explanation
Indices: 56976544--56977106 Score: 183
Period size: 44 Copynumber: 12.8 Consensus size: 43
56976534 AGTGAAAATT
* * *
56976544 GTAGATCTTATCTCCCTAAACAGTAGTTGAGCAGATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
* * *
56976587 GGT-GAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTTAAGCCAC
1 -GTAG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--AC
** * * * * * *
56976633 CAAG-CCTTGTCTCCCTAAGCAGCAGTGGAGAAGGTTGAAGATT
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-C
*
56976676 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
* * *
56976719 AG-CGAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCAC
1 -GTAG-ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--AC
** * * * * * * * *
56976765 CAAG-CCTTGTCTCCCTAAGCAGCAGCGGAGAAGGTTGAAAATT
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-C
*
56976808 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
* * *
56976851 G-ACGAATCTTATATTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCAC
1 GTA-G-ATCTTAT-CTCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--AC
** * * * * * * * *
56976897 CAAG-TCTTGTCTCCCTGAGCAGCAGCGGAGAAGGTTGAAAATT
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-C
*
56976940 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
* * * * *
56976983 GACAAATCTTATCTTTCC-AA--AATAGTGGGAAGCAGATTTAAGCCAC
1 G-TAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--AC
** * * * * * * * * *
56977029 CAAG-TCTTGTTTCACTGAGCAGGAGCGGAGTAGGTTGAAGATT
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-C
56977072 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
56977107 CAAGACGACA
Statistics
Matches: 359, Mismatches: 111, Indels: 98
0.63 0.20 0.17
Matches are distributed among these distances:
42 22 0.06
43 34 0.09
44 257 0.72
45 24 0.07
46 21 0.06
47 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (43 bp):
GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAC
Found at i:56976778 original size:132 final size:132
Alignment explanation
Indices: 56976536--56977146 Score: 1003
Period size: 132 Copynumber: 4.6 Consensus size: 132
56976526 AACAGATCAG
* * **
56976536 TGAAAATTGTAGATCTTATCTCCCTAAACAGTAGTTGAGCAGATCGAAGACGGTGAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCT
* *
56976601 TTCCAAGATAGTGGGAAGCAAATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGTGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAG
56976666 GT
131 GT
*
56976668 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC-AGCGAATCTTATC
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGA-CGAATCTTATC
56976732 TTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAA
65 TTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAA
56976797 GGT
130 GGT
*
56976800 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATAT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCT
* *
56976865 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGTCTTGTCTCCCTGAGCAGCAGCGGAGAAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAG
56976930 GT
131 GT
*
56976932 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCT
* * * * * * *
56976997 TTCCAAAATAGTGGGAAGCAGATTTAAGCCACCAAGTCTTGTTTCACTGAGCAGGAGCGGAGTAG
66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAG
56977062 GT
131 GT
* * *
56977064 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-C-AAGACGACAAATCATATCT
1 TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCT
56977127 TTCCAAGATAGTGGGAAGCA
66 TTCCAAGATAGTGGGAAGCA
56977147 AATTAAAGTC
Statistics
Matches: 456, Mismatches: 21, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
130 37 0.08
131 1 0.00
132 417 0.91
133 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (132 bp):
TGAAAATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCT
TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAGCAGCAGCGGAGAAG
GT
Found at i:56977196 original size:44 final size:44
Alignment explanation
Indices: 56977143--56978018 Score: 344
Period size: 44 Copynumber: 20.2 Consensus size: 44
56977133 GATAGTGGGA
* *
56977143 AGCAAATTAAAGTCGACAATCCTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* * * *
56977187 AGCGGATTAAAATC-ACAGATCTTATC-CCTCTGAAGTTACAG-AG
1 AGCAGATTAAAGTCGACA-ATCTTATCTCC-CTGAAGTTGCAGTGG
*** * *
56977230 AGCAGATCGCA-TC--TAGTCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* ** * * *
56977271 AGCAGACT-AAGTAAACAAGTCTTATC-CTTCTAAAGTTACAGT-G
1 AGCAGATTAAAGTCGACAA-TCTTATCTC-CCTGAAGTTGCAGTGG
* * * *
56977314 AGGCAGACTGAAGAT-GGCAAATCTTATCTTCCTGAAGTTGCAGTGG
1 A-GCAGATTAAAG-TCGAC-AATCTTATCTCCCTGAAGTTGCAGTGG
* * * *
56977360 AGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* * * ** *
56977404 AGCAGATTAAAAT-TACAGATCTTATCTCTCTGAAGTTATA-TAG
1 AGCAGATTAAAGTCGACA-ATCTTATCTCCCTGAAGTTGCAGTGG
*** * * *
56977447 AGCAGATCGCA-TC--TAGTCTTATCTCCCTGAAGTTGCGGTGG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* * *
56977488 A-CAAGACT-AAGT-AAGCAAGTCTTATC-CTCCTGAAGTTACAGT-G
1 AGC-AGATTAAAGTCGA-CAA-TCTTATCTC-CCTGAAGTTGCAGTGG
* * *
56977531 AGGCAGACTGAAGAT-GACAAATCTTATCTTCCTGAAGTTGCAGTGG
1 A-GCAGATTAAAG-TCGAC-AATCTTATCTCCCTGAAGTTGCAGTGG
* *
56977577 AGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * * *
56977621 AGCGGATTAAAAT-TACAGATCTTATCTCTCTGAAGTTACAG-AG
1 AGCAGATTAAAGTCGACA-ATCTTATCTCCCTGAAGTTGCAGTGG
*** * * *
56977664 AGCAGATCGCA-TC--TAGTCTTATCTCCCTGAAGTTGC-GATAG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAG-TGG
* * * *
56977705 A-CAAGACT-AAGT-AAGCAAGTCTTATC-CTTCTGAAGTTACAGT-G
1 AGC-AGATTAAAGTCGA-CAA-TCTTATCTC-CCTGAAGTTGCAGTGG
* * * * *
56977748 AGGCAGACTGAAGAT-GGCAAATCTTATCTGCCTGAAGTTGCAGAGG
1 A-GCAGATTAAAG-TCGAC-AATCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
56977794 AGCAGATTAAAGCCGATAATCCTATCTCCTTGAAGTTGCAGTAG
1 AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
56977838 AGCGGATTAAAATC-ACAGATCTTATCTCTCTAAAGTTGCAG-AG
1 AGCAGATTAAAGTCGACA-ATCTTATCTCCCTGAAGTTGCAGTGG
** ** *
56977881 AGCA-A--ATCG-CTTCTAGTCTTATCTCCCTGAAGTTGCAGTGG
1 AGCAGATTAAAGTCGAC-AATCTTATCTCCCTGAAGTTGCAGTGG
* * ** * *
56977922 AGCAGACTAAGGAAG-CAAGTTTTATC-CTCCTGAAGTTGTAGT-G
1 AGCAGATTAAAGTCGACAA-TCTTATCTC-CCTGAAGTTGCAGTGG
* * * *
56977965 AGGCAAACTGAAGAT-GGCAAGTCTTATCTCCCTGAAGTTGCAGTGG
1 A-GCAGATTAAAG-TCGACAA-TCTTATCTCCCTGAAGTTGCAGTGG
*
56978011 AGTAGATT
1 AGCAGATT
56978019 GAAGCACTAA
Statistics
Matches: 619, Mismatches: 144, Indels: 137
0.69 0.16 0.15
Matches are distributed among these distances:
39 2 0.00
40 80 0.13
41 33 0.05
42 6 0.01
43 59 0.10
44 290 0.47
45 130 0.21
46 19 0.03
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AGCAGATTAAAGTCGACAATCTTATCTCCCTGAAGTTGCAGTGG
Found at i:56977357 original size:89 final size:87
Alignment explanation
Indices: 56977246--56977799 Score: 297
Period size: 89 Copynumber: 6.4 Consensus size: 87
56977236 TCGCATCTAG
*
56977246 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAGTCTTATC-CTTCTAAAGTTAC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAACAAGTCTTATCTC-TCTGAAGTTAC
56977310 AGTGAGGCAGACTGAAGATGGCAAA
64 AGTG-GGCAGACTGAAGATGGCAAA
* * ** * * * * *
56977335 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAA-AGCCGATAATCCTATCTCCCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAAC-A-AGTCTTATCTCTCTGAAGTTAC
* * ** *
56977399 AGTGGAGCAGA-TTAAAATTACAGA
64 AGTGG-GCAGACTGAAGATGGCAAA
* ** * * * * * * * *
56977423 TCTTATCTCTCTGAAGTTATA-TAGAGCAGA-T-CGCATCTAGTCTTATCTCCCTGAAGTTGCGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAACAAGTCTTATCTCTCTGAAGTTACAG
* * *
56977485 TGGACAAGACT-AAG-TAAGCAAG
66 TGGGC-AGACTGAAGAT-GGCAAA
* * *
56977507 TCTTATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGACAAATCTTATCT-TCCTGAAGT
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AACAAGTCTTATCTCT-CTGAAGT
* * * ** *
56977569 TGCAGTGGAGCAGATTAAAGCCGAC-AA
61 TACAGTGG-GCAGACTGAAGATGGCAAA
* * *
56977596 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AATTAC-AGATCTTATCTCTCTGAAGTTA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAA--ACAAG-TCTTATCTCTCTGAAGTTA
* * * * *
56977659 CAGAGAGCAGA-TCG--CAT--CTAG
63 CAGTGGGCAGACT-GAAGATGGCAAA
* *
56977680 TCTTATCTCCCTGAAGTTGC-GATAGA-CAAGACTAAGTAAGCAAGTCTTATC-CTTCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAG-TGGAGC-AGACTAAG-AAACAAGTCTTATCTC-TCTGAAGTT
56977742 ACAGTGAGGCAGACTGAAGATGGCAAA
62 ACAGTG-GGCAGACTGAAGATGGCAAA
* *
56977769 TCTTATCTGCCTGAAGTTGCAGAGGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
56977800 TTAAAGCCGA
Statistics
Matches: 348, Mismatches: 76, Indels: 82
0.69 0.15 0.16
Matches are distributed among these distances:
83 7 0.02
84 99 0.28
85 15 0.04
86 7 0.02
87 19 0.05
88 52 0.15
89 138 0.40
90 11 0.03
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (87 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAACAAGTCTTATCTCTCTGAAGTTACAG
TGGGCAGACTGAAGATGGCAAA
Found at i:56977404 original size:217 final size:217
Alignment explanation
Indices: 56977143--56978023 Score: 1399
Period size: 217 Copynumber: 4.1 Consensus size: 217
56977133 GATAGTGGGA
* *
56977143 AGCAAATTAAAGTCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
1 AGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
*
56977208 TTATCCCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
66 TTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGA-
* * *
56977273 C-AGACTAAGTAAACAAGTCTTATCCTTCTAAAGTTACAGTGAGGCAGACTGAAGATGGCAAATC
130 CAAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATC
56977337 TTATCTTCCTGAAGTTGCAGTGG
195 TTATCTTCCTGAAGTTGCAGTGG
* * * *
56977360 AGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATTACAGATC
1 AGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
* * *
56977425 TTATCTCTCTGAAGTTATATAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCGGTGGAC
66 TTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAC
*
56977490 AAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGACAAATCT
131 AAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
56977555 TATCTTCCTGAAGTTGCAGTGG
196 TATCTTCCTGAAGTTGCAGTGG
*
56977577 AGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATC
1 AGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
*
56977642 TTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGC-GATAGA
66 TTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG-TGGA
*
56977706 CAAGACTAAGTAAGCAAGTCTTATCCTTCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATC
130 CAAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATC
* *
56977771 TTATCTGCCTGAAGTTGCAGAGG
195 TTATCTTCCTGAAGTTGCAGTGG
* * *
56977794 AGCAGATTAAAGCCGATAATCCTATCTCCTTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATC
1 AGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
* * * *
56977859 TTATCTCTCTAAAGTTGCAGAGAGCAAATCGCTTCTAGTCTTATCTCCCTGAAGTTGCAGTGGAG
66 TTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGA-
* * ** * *
56977924 C-AGACTAAGGAAGCAAGTTTTATCCTCCTGAAGTTGTAGTGAGGCAAACTGAAGATGGCAAGTC
130 CAAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATC
*
56977988 TTATCTCCCTGAAGTTGCAGTGG
195 TTATCTTCCTGAAGTTGCAGTGG
* *
56978011 AGTAGATTGAAGC
1 AGCAGATTAAAGC
56978024 ACTAATTCCT
Statistics
Matches: 616, Mismatches: 44, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
216 2 0.00
217 612 0.99
218 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (217 bp):
AGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATC
TTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAC
AAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTACAGTGAGGCAGACTGAAGATGGCAAATCT
TATCTTCCTGAAGTTGCAGTGG
Found at i:56977699 original size:84 final size:86
Alignment explanation
Indices: 56977165--56977699 Score: 245
Period size: 84 Copynumber: 6.2 Consensus size: 86
56977155 TCGACAATCC
* * *
56977165 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCCCTCTGAAGTTACAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGACAGATCTTATCTCTCTGAAGTTACAGAG
*
56977230 AGCAGA-TCG-CATCTAGTCT
66 AGCAGATTAGACATCTAGTCT
* *
56977249 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAA--ACA-AGTCTTATC-CTTCTAAAGTTAC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATGACAGA-TCTTATCTC-TCTGAAGTTAC
* * * * *
56977310 AGTGAGGCAGACT-GAAGATGGCAAATCT
62 AGAGA-GCAGATTAG-ACAT--CTAGTCT
* ** * * * * *
56977338 TATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA-ATCCTATCTCCCTAAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATGACAGATCTTATCTCTCTGAAGTTACAG-
* *
56977402 GGAGCAGATTA-AAAT-TACAGATCT
64 AGAGCAGATTAGACATCT--AG-TCT
* ** * *** * * * *
56977426 TATCTCTCTGAAGTTATA-TAGAGCAGA-TCGCAT--CTAG-TCTTATCTCCCTGAAGTTGCGGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGAC-AGATCTTATCTCTCTGAAGTTACAGA
* * *
56977486 G-GACAAGACTAAGTA-AGCAAGTCT
65 GAG-C-AGA-TTAG-ACATCTAGTCT
* * * * *
56977510 TATC-CTCCTGAAGTTACAGT-GAGGCAGACTGAAGATGACAAATCTTATCT-TCCTGAAGTTGC
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATGACAGATCTTATCTCT-CTGAAGTTAC
* * * *
56977572 AGTGGAGCAGATTAAAGCCGA-C-AATCC
62 AG-AGAGCAGATT--AGAC-ATCTAGTCT
* *
56977599 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTACAGATCTTATCTCTCTGAAGTTACAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGACAGATCTTATCTCTCTGAAGTTACAGAG
*
56977664 AGCAGA-TCG-CATCTAGTCT
66 AGCAGATTAGACATCTAGTCT
56977683 TATCTCCCTGAAGTTGC
1 TATCTCCCTGAAGTTGC
56977700 GATAGACAAG
Statistics
Matches: 342, Mismatches: 62, Indels: 94
0.69 0.12 0.19
Matches are distributed among these distances:
82 2 0.01
83 7 0.02
84 117 0.34
85 16 0.05
86 6 0.02
87 22 0.06
88 50 0.15
89 106 0.31
90 14 0.04
91 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (86 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGACAGATCTTATCTCTCTGAAGTTACAGAG
AGCAGATTAGACATCTAGTCT
Found at i:56977947 original size:84 final size:88
Alignment explanation
Indices: 56977461--56978012 Score: 205
Period size: 89 Copynumber: 6.3 Consensus size: 88
56977451 GATCGCATCT
* *
56977461 AGTCTTATCTCCCTGAAGTTGCGGTGGA-CAAGACTAAGTAAGCA-AG-TCTTATCCTCCTGAAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGC-AGACTAA--AAGCACAGATCTTATCCTCCTAAAG
* * * *
56977523 TTACAGTGAGGCAGACTGAAGATGACA
63 TTGCAGAGAGGCAAACT-AAGATGGCA
* * * * *
56977550 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGA-TTAAAGCCGACA-ATCCTAT-CTCCCTGAAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAG-C-ACAGATCTTATCCT-CCTAAAG
* ** * * **
56977612 TTGCAGTG-GAGCGGATTAAAATTAC-
63 TTGCAGAGAG-GCAAACTAAGATGGCA
* * * * *
56977637 AGATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T---CGCATCTAG-TCTTAT-CTCCCTGAA
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAGCA-C-AGATCTTATCCT-CCTAAA
* * *
56977695 GTTGC-GATAGACAAGACTAAG-TAAGCA
62 GTTGCAGAGAGGCAA-ACTAAGAT-GGCA
* * * *
56977722 AGTCTTATC-CTTCTGAAGTTACAGT-GAGGCAGACTGAAGATGGCA-A-ATCTTAT-CTGCCTG
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AA-A-AGCACAGATCTTATCCT-CCTA
* * *
56977782 AAGTTGCAGAG-GAGCAGATTAA-A-GCCGA
60 AAGTTGCAGAGAG-GCAAACTAAGATGGC-A
* * * * * * *
56977810 TAATCCTATCTCCTTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCTTAT-CTCTCTAAAGT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAGCACAGATCTTATCCTC-CTAAAGT
* * * *
56977874 TGCAGAGA-GCAAA-T-CGCT-TCT
64 TGCAGAGAGGCAAACTAAGATGGCA
* *
56977895 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGGAAGCA-AG-TTTTATCCTCCTGAAGT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AAGCACAGATCTTATCCTCCTAAAGT
* *
56977958 TGTAGTGAGGCAAACTGAAGATGGCA
64 TGCAGAGAGGCAAACT-AAGATGGCA
56977984 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
56978013 TAGATTGAAG
Statistics
Matches: 352, Mismatches: 64, Indels: 94
0.69 0.13 0.18
Matches are distributed among these distances:
82 1 0.00
83 6 0.02
84 97 0.28
85 17 0.05
86 13 0.04
87 18 0.05
88 58 0.16
89 131 0.37
90 8 0.02
92 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAGCACAGATCTTATCCTCCTAAAGTTG
CAGAGAGGCAAACTAAGATGGCA
Found at i:56978250 original size:19 final size:19
Alignment explanation
Indices: 56978226--56978338 Score: 163
Period size: 19 Copynumber: 5.8 Consensus size: 19
56978216 AATTTTTGAG
56978226 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
56978245 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
56978264 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
56978285 GATATGCAATCTTAGAGAT
1 GATATGCAATCTTAGATAT
**
56978304 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
56978323 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
56978339 ATATATGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 65 0.79
21 17 0.21
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:56978271 original size:40 final size:40
Alignment explanation
Indices: 56978227--56978333 Score: 173
Period size: 40 Copynumber: 2.7 Consensus size: 40
56978217 ATTTTTGAGG
*
56978227 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
**
56978267 ATATGCAATCTTAGATATGATATGCAATCTTAGAGATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
56978307 ATAT--AATCTTAGATATGATATGCAATC
1 ATATGCAATCTTAGATATGATATGCAATC
56978334 TTAGAATATA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
38 23 0.36
40 41 0.64
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGAGATGAT
Found at i:56979716 original size:98 final size:98
Alignment explanation
Indices: 56979596--56979792 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
56979586 TTAAAAATAA
* *
56979596 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
56979661 TTAAATCTTGGTTAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
56979694 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
56979759 TTAAATCTTGGATGAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
56979792 T
1 T
56979793 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:56988327 original size:18 final size:19
Alignment explanation
Indices: 56988285--56988328 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
56988275 CTATAATAAT
56988285 AATATATTTTAATTTTAGGA
1 AATATATTTTAATTTTA-GA
* *
56988305 CATATATTTTATTTTTA-A
1 AATATATTTTAATTTTAGA
56988323 AATATA
1 AATATA
56988329 ATTATATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (19 bp):
AATATATTTTAATTTTAGA
Found at i:56993383 original size:38 final size:38
Alignment explanation
Indices: 56993341--56993417 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 38
56993331 AAAAAAATAT
56993341 TTTTAAACAGTTACGATTTGACAA-AATTAGAATCTAGC
1 TTTTAAACAGTTACGATTTGA-AAGAATTAGAATCTAGC
*
56993379 TTTTAAACGGTTACGATTTGAAAGAATTAGAATCTAGC
1 TTTTAAACAGTTACGATTTGAAAGAATTAGAATCTAGC
56993417 T
1 T
56993418 ATTGAGATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
37 2 0.05
38 35 0.95
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (38 bp):
TTTTAAACAGTTACGATTTGAAAGAATTAGAATCTAGC
Found at i:56999735 original size:24 final size:24
Alignment explanation
Indices: 56999673--56999724 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
56999663 TTTCTAGAAG
* *
56999673 ATTTAGTATTTATGAGA-ATAATAT
1 ATTTAGCATTTATTA-ACATAATAT
56999697 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATTAACATAATAT
56999721 ATTT
1 ATTT
56999725 GACTTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATTAACATAATAT
Found at i:57002991 original size:21 final size:21
Alignment explanation
Indices: 57002967--57003010 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
57002957 AAGTTATATA
57002967 TAAGTT-TATATATAAGTCATG
1 TAAGTTAT-TATATAAGTCATG
* *
57002988 TAAGTTATTATGTAAGTTATG
1 TAAGTTATTATATAAGTCATG
57003009 TA
1 TA
57003011 TTGTGCAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.45
Consensus pattern (21 bp):
TAAGTTATTATATAAGTCATG
Found at i:57003048 original size:59 final size:60
Alignment explanation
Indices: 57002954--57003067 Score: 153
Period size: 59 Copynumber: 1.9 Consensus size: 60
57002944 ATGAAAGTTA
* *
57002954 TGCAAGTTATATATAAGTTTATATATAAGTCATGTAAG-TTATTATGTAAGTTATGTATTG
1 TGCAAGTTATATATAAATTTATATATAAGTCATGTAAGTTTA-TATATAAGTTATGTATTG
* *
57003014 TGCAAGTTTATATATAAATTT-TATTTATGT-ATGTAAGTTTATATATAAGTTATG
1 TGCAAG-TTATATATAAATTTATATATAAGTCATGTAAGTTTATATATAAGTTATG
57003068 ATATGATTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 19 0.40
60 16 0.33
61 13 0.27
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (60 bp):
TGCAAGTTATATATAAATTTATATATAAGTCATGTAAGTTTATATATAAGTTATGTATTG
Found at i:57003139 original size:15 final size:15
Alignment explanation
Indices: 57003119--57003148 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57003109 TGATAAATTT
57003119 TTAAAAAAATATATA
1 TTAAAAAAATATATA
*
57003134 TTAAAAAAGTATATA
1 TTAAAAAAATATATA
57003149 AATATTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
TTAAAAAAATATATA
Found at i:57003188 original size:24 final size:22
Alignment explanation
Indices: 57003150--57003195 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
57003140 AAGTATATAA
*
57003150 ATATTAATAAGTTATGTAAGTTAT
1 ATATTAAAAAGTTA--TAAGTTAT
*
57003174 ATATTAAAAATTTATAAGTTAT
1 ATATTAAAAAGTTATAAGTTAT
57003196 GTAAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
24 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (22 bp):
ATATTAAAAAGTTATAAGTTAT
Found at i:57004968 original size:240 final size:240
Alignment explanation
Indices: 57004544--57004981 Score: 729
Period size: 240 Copynumber: 1.8 Consensus size: 240
57004534 TGATAGAACC
57004544 CATGCATATCCACATACAAATTTAGGCATTTTAAAACAGTTAAGCAAAAAGGAAAAAAAAAAAAG
1 CATGCATATCCACATACAAATTTAGGCATTTTAAAACAGTTAAGCAAAAAGG-AAAAAAAAAAAG
* * *
57004609 AATAACCATCGAAAAAATCCCAAATTTGATAGAAACAAAACCGTAAATGTAGATCGACAATCGAT
65 AATAACCATCGAAAAAATCCCAAATTTGACAGAAACAAAACCCTAAATGTAGATCAACAATCGAT
* *
57004674 AAAAAAAGGCTTATCTGGGATACAAATTTTCCAGCTTTGAATGCTCGATTCAACCCTTGCTTCGG
130 AAAAAAAGGCTTACCTGGGATACAAATTTTCCAGCTTTGAATGATCGATTCAACCCTTGCTTCGG
57004739 TTCAGTTGATTTCTGAGTTCTCCTATGTTTCTTTTTCTTTGTATTT
195 TTCAGTTGATTTCTGAGTTCTCCTATGTTTCTTTTTCTTTGTATTT
* *
57004785 CATGCATATCCACATACAAATTTAGGCATTTTAAAACAGTTAAGTAAAAAGG-AAAAAAAGAAGA
1 CATGCATATCCACATACAAATTTAGGCATTTTAAAACAGTTAAGCAAAAAGGAAAAAAAAAAAGA
*
57004849 ATAACGATCGAAAAAAATCCCAAATTTGACAGAAACAAAACCCTAAATGTAGATCAACAATCGAT
66 ATAACCATCG-AAAAAATCCCAAATTTGACAGAAACAAAACCCTAAATGTAGATCAACAATCGAT
* *
57004914 AGAAAAAGGCTTACCTGGGATACAAA-TTTCGCAGCTTTG-GTAGATCGATTCAACCCTTGCTTC
130 AAAAAAAGGCTTACCTGGGATACAAATTTTC-CAGCTTTGAAT-GATCGATTCAACCCTTGCTTC
57004977 GGTTC
193 GGTTC
57004982 TGAGTTCTCC
Statistics
Matches: 184, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
239 25 0.14
240 108 0.59
241 51 0.28
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (240 bp):
CATGCATATCCACATACAAATTTAGGCATTTTAAAACAGTTAAGCAAAAAGGAAAAAAAAAAAGA
ATAACCATCGAAAAAATCCCAAATTTGACAGAAACAAAACCCTAAATGTAGATCAACAATCGATA
AAAAAAGGCTTACCTGGGATACAAATTTTCCAGCTTTGAATGATCGATTCAACCCTTGCTTCGGT
TCAGTTGATTTCTGAGTTCTCCTATGTTTCTTTTTCTTTGTATTT
Found at i:57005730 original size:21 final size:21
Alignment explanation
Indices: 57005706--57005757 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
57005696 CTCTTAAACT
*
57005706 CTAAACCTTAACCCCAAACCC
1 CTAAACCTTAACCACAAACCC
* *
57005727 CTAACCCTTAACCACTAACCC
1 CTAAACCTTAACCACAAACCC
57005748 CTAAACCTTA
1 CTAAACCTTA
57005758 TTTAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.44, G:0.00, T:0.19
Consensus pattern (21 bp):
CTAAACCTTAACCACAAACCC
Found at i:57005900 original size:146 final size:146
Alignment explanation
Indices: 57005608--57005883 Score: 394
Period size: 146 Copynumber: 1.9 Consensus size: 146
57005598 TATATAAGAA
* * *
57005608 CTTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACATTAAACCCTAACCTGACCCTGA
1 CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACACTAAACCCTAACCTAACCCTGA
* * *
57005673 ATTTCTAAACCCTAAATCAATAACTCTTAAACTCTAAACCTTAACCCCAAACCCCTAACCCTTAA
66 ATCTCTAAACCCTAAATCAATAACTCTTAAACCCTAAACCTTAACCCCAAACCCCTAAACCTTAA
57005738 CCACTAACCCCTAAAC
131 CCACTAACCCCTAAAC
*
57005754 CTTATTTAATATATAAATTAAAAAACACTAATTAATTTAAAC-CTAAACCCTAACCTAACCCCTG
1 CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACACTAAACCCTAACCTAA-CCCTG
* ** * ** *
57005818 AATCTCTAAACCTTAAATCCCTAACTCTTAACCCCT-AATGTCTAACCCCTAACCCCTAAACCTT
65 AATCTCTAAACCCTAAATCAATAACTCTTAAACCCTAAACCT-TAACCCCAAACCCCTAAACCTT
57005882 AA
129 AA
57005884 ATCCCAACCC
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
145 17 0.15
146 97 0.85
ACGTcount: A:0.41, C:0.29, G:0.01, T:0.28
Consensus pattern (146 bp):
CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACACTAAACCCTAACCTAACCCTGA
ATCTCTAAACCCTAAATCAATAACTCTTAAACCCTAAACCTTAACCCCAAACCCCTAAACCTTAA
CCACTAACCCCTAAAC
Found at i:57005916 original size:21 final size:22
Alignment explanation
Indices: 57005864--57005919 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
57005854 AATGTCTAAC
* *
57005864 CCCTAACCCCTAAACCTTAAAT
1 CCCTAACCCTTAAACCATAAAT
57005886 CCC-AACCCTTAAACCAT-AAT
1 CCCTAACCCTTAAACCATAAAT
*
57005906 CCCTAAACCTTAAA
1 CCCTAACCCTTAAA
57005920 ATAGTAACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.20
21 21 0.70
22 3 0.10
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.21
Consensus pattern (22 bp):
CCCTAACCCTTAAACCATAAAT
Found at i:57006474 original size:41 final size:41
Alignment explanation
Indices: 57006315--57006513 Score: 215
Period size: 41 Copynumber: 4.9 Consensus size: 41
57006305 TCACGGCACT
* * * *
57006315 GAGCATTAGCGGCACTTTTTCAAAAATGCCGCTAAAGCCCCA
1 GAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAA-ACCCA
* * *
57006357 -AACATTAGCGGCGCTTTTTAAAAATCGCCGCTAAAACCAA
1 GAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCA
*
57006397 GAGCATTAGTGGCGCTTTTTAAAAAACGCCGCTAAAACCCA
1 GAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCA
* * * **
57006438 GAGCATTAGCGACGCTTTTTCAAAACCGCCTTTAAAACACC-
1 GAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAAC-CCA
* * *
57006479 GAGCATTAGCGGCACTTTTT-TAAAACGCAGCTAAA
1 GAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAA
57006514 GCCCCGATAG
Statistics
Matches: 131, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
40 13 0.10
41 116 0.89
42 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCA
Found at i:57006607 original size:40 final size:40
Alignment explanation
Indices: 57006552--57006638 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 40
57006542 TGGGCTTTGG
* * *
57006552 TTTTTTGCAGCGTTTTTCCAAAAAATGCCGCGAATGCTC-A
1 TTTTTAGCAGCG-TTTTACAAAAAACGCCGCGAATGCTCGA
* * *
57006592 TTTTTAGCAGTGTTTTACAAGAAACGCCGCTAATGCTCGA
1 TTTTTAGCAGCGTTTTACAAAAAACGCCGCGAATGCTCGA
*
57006632 TCTTTAG
1 TTTTTAG
57006639 TGGTGGTTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 22 0.56
40 17 0.44
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (40 bp):
TTTTTAGCAGCGTTTTACAAAAAACGCCGCGAATGCTCGA
Found at i:57010469 original size:31 final size:31
Alignment explanation
Indices: 57010434--57010495 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
57010424 TGGAAAATTA
*
57010434 CAAGAGTAATTGAATTCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
57010465 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
57010496 AAAATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:57020923 original size:19 final size:19
Alignment explanation
Indices: 57020901--57020953 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
57020891 TTATTTTACC
57020901 TCCAATAATTCATTTTTGG
1 TCCAATAATTCATTTTTGG
57020920 TCCAATAATTCATTTTTGG
1 TCCAATAATTCATTTTTGG
57020939 TCCAATAATTCATTT
1 TCCAATAATTCATTT
57020954 ACATTATCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (19 bp):
TCCAATAATTCATTTTTGG
Found at i:57021404 original size:16 final size:17
Alignment explanation
Indices: 57021372--57021404 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57021362 ATAATTTATC
*
57021372 AATTTATATTTTTTAGA
1 AATTTATATTATTTAGA
57021389 AATTTATA-TATTTAGA
1 AATTTATATTATTTAGA
57021405 TGGGTTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
AATTTATATTATTTAGA
Found at i:57021844 original size:22 final size:22
Alignment explanation
Indices: 57021793--57021847 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
57021783 AAAAATTAGG
* *
57021793 AGAGAATATC--AAAAAGTATG
1 AGAGAATATCAAAAAAAATATA
57021813 AGA-AAGTATCAAAAAAAATATA
1 AGAGAA-TATCAAAAAAAATATA
57021835 AGAGAATATCAAA
1 AGAGAATATCAAA
57021848 TATTAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 7 0.24
22 18 0.62
23 2 0.07
ACGTcount: A:0.62, C:0.05, G:0.15, T:0.18
Consensus pattern (22 bp):
AGAGAATATCAAAAAAAATATA
Found at i:57021938 original size:21 final size:22
Alignment explanation
Indices: 57021909--57021949 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
57021899 ATTATTTGTA
*
57021909 TATATAAAAAAATTT-TATTAG
1 TATACAAAAAAATTTATATTAG
*
57021930 TATACAAAAATATTTATATT
1 TATACAAAAAAATTTATATT
57021950 TATATTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
TATACAAAAAAATTTATATTAG
Found at i:57021953 original size:20 final size:18
Alignment explanation
Indices: 57021886--57021953 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 18
57021876 ATTTTTTATT
* *
57021886 TTTTATTT-TAAATATTA
1 TTTTATTTATAAAAAATA
*
57021903 TTTGTATATATAAAAAA-A
1 TTT-TATTTATAAAAAATA
57021921 TTTTATTAGTATACAAAAATA
1 TTTTATT--TATA-AAAAATA
57021942 TTTATATTTATA
1 TTT-TATTTATA
57021954 TTAAAAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
17 6 0.15
18 8 0.20
19 9 0.22
20 9 0.22
21 4 0.10
22 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTATTTATAAAAAATA
Found at i:57021960 original size:22 final size:22
Alignment explanation
Indices: 57021895--57021963 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
57021885 TTTTTATTTT
57021895 AAATA-TTAT-TTGTATATATAAA
1 AAATATTTATATT-TATAT-TAAA
57021917 AAA-ATTT-TA-TTAGTA-TACAA
1 AAATATTTATATTTA-TATTA-AA
57021937 AAATATTTATATTTATATTAAA
1 AAATATTTATATTTATATTAAA
57021959 AAATA
1 AAATA
57021964 AATTTTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
19 2 0.05
20 7 0.18
21 9 0.23
22 16 0.41
23 5 0.13
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (22 bp):
AAATATTTATATTTATATTAAA
Found at i:57022052 original size:19 final size:19
Alignment explanation
Indices: 57022026--57022071 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
57022016 GAGAATACTA
57022026 AAAATTAT-AAGCATAACC
1 AAAATTATAAAGCATAACC
*
57022044 AATAATTATGAAAGCATACCC
1 AA-AATTAT-AAAGCATAACC
57022065 AAAATTA
1 AAAATTA
57022072 GGAAGGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.08
19 6 0.25
20 5 0.21
21 11 0.46
ACGTcount: A:0.54, C:0.15, G:0.07, T:0.24
Consensus pattern (19 bp):
AAAATTATAAAGCATAACC
Found at i:57022381 original size:20 final size:21
Alignment explanation
Indices: 57022343--57022382 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
57022333 AAAACATTAA
57022343 AAATCATAAAAATTTATAATG
1 AAATCATAAAAATTTATAATG
57022364 AAATC-TAACAAA-TTATAAT
1 AAATCATAA-AAATTTATAAT
57022383 TTTTTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (21 bp):
AAATCATAAAAATTTATAATG
Found at i:57022452 original size:20 final size:18
Alignment explanation
Indices: 57022429--57022473 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
57022419 TTAAAATGTT
57022429 ATAAAAACTAATAAAAATTC
1 ATAAAAA-TAATAAAAA-TC
* *
57022449 ATAAAAATTATTAAAATC
1 ATAAAAATAATAAAAATC
57022467 ATAAAAA
1 ATAAAAA
57022474 AATTATAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 7 0.30
20 7 0.30
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (18 bp):
ATAAAAATAATAAAAATC
Found at i:57022456 original size:40 final size:40
Alignment explanation
Indices: 57022387--57022465 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
57022377 TATAATTTTT
* *
57022387 TTATAAAATTAATAAAAATATATTTAAAATGT-TTAAAATG
1 TTATAAAACTAATAAAAATATATTAAAAAT-TATTAAAATG
57022427 TTATAAAAACTAATAAAAAT-TCA-TAAAAATTATTAAAAT
1 TTAT-AAAACTAATAAAAATAT-ATTAAAAATTATTAAAAT
57022466 CATAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 1 0.03
40 18 0.53
41 15 0.44
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (40 bp):
TTATAAAACTAATAAAAATATATTAAAAATTATTAAAATG
Found at i:57022459 original size:29 final size:28
Alignment explanation
Indices: 57022427--57022502 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 28
57022417 GTTTAAAATG
57022427 TTATAAAAAC-TAATAAAAATTCATAAAAA
1 TTATAAAAACATAA-AAAAATT-ATAAAAA
* *
57022456 TTATTAAAATCATAAAAAAATTATAACAA
1 TTA-TAAAAACATAAAAAAATTATAAAAA
* **
57022485 TTATTAAAATTTAAAAAA
1 TTATAAAAACATAAAAAA
57022503 GAAAAAAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 11 0.28
29 12 0.31
30 13 0.33
31 3 0.08
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (28 bp):
TTATAAAAACATAAAAAAATTATAAAAA
Found at i:57022573 original size:39 final size:38
Alignment explanation
Indices: 57022441--57022581 Score: 106
Period size: 39 Copynumber: 3.6 Consensus size: 38
57022431 AAAAACTAAT
* * * * *
57022441 AAAAATTCATAAAAATTATTAAAATCATAAAAAAATTAT
1 AAAAATTTATAAAACTTATAAAAATAATAAAAAAA-TAC
* * * *
57022480 AACAA-TTATTAAAATTTA-AAAAAGAAAAAAGAAAATAC
1 AAAAATTTA-TAAAACTTATAAAAATAATAAA-AAAATAC
* * * *
57022518 TAGAATTGATATAAACTTATAAAAATTATAAAAAAATCAC
1 AAAAATTTATA-AAACTTATAAAAATAATAAAAAAAT-AC
57022558 AAAAATTTATAAAACTTATAAAAA
1 AAAAATTTATAAAACTTATAAAAA
57022582 CTACCTAACA
Statistics
Matches: 78, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
38 17 0.22
39 42 0.54
40 19 0.24
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (38 bp):
AAAAATTTATAAAACTTATAAAAATAATAAAAAAATAC
Found at i:57026196 original size:3 final size:3
Alignment explanation
Indices: 57026188--57026245 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
57026178 GTAGGCTTCT
57026188 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57026236 TAA TAA TAA T
1 TAA TAA TAA T
57026246 TGTAACACCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:57030542 original size:27 final size:26
Alignment explanation
Indices: 57030506--57030781 Score: 291
Period size: 27 Copynumber: 10.2 Consensus size: 26
57030496 GGAGGTCGAT
*
57030506 AAATGATCGAAATACCTCCATAGGGTA
1 AAATGACCGAAATACC-CCATAGGGTA
* *
57030533 AAATGATCGAAATACCCCTATAAGGTA
1 AAATGACCGAAATACCCC-ATAGGGTA
57030560 AAATGACCGAAATACGCCCATAGGGTA
1 AAATGACCGAAATAC-CCCATAGGGTA
* *
57030587 GAATGACCGAAATACCCTTATAGGGTA
1 AAATGACCGAAATACCC-CATAGGGTA
* *
57030614 AAATGACCAAAATAGCCCTATAGGGTA
1 AAATGACCGAAATA-CCCCATAGGGTA
* * *
57030641 AAATAACCAAAATACCCCATTAGGATA
1 AAATGACCGAAATACCCCA-TAGGGTA
* *
57030668 AAATGACTGAAATACCCTCATAGGTTA
1 AAATGACCGAAATACCC-CATAGGGTA
* * *
57030695 GAATGACCAAAATACCTCCATTGGGTA
1 AAATGACCGAAATACC-CCATAGGGTA
* * *
57030722 AAATAACTGAAATACCCCCTTAGGGTA
1 AAATGACCGAAATA-CCCCATAGGGTA
*
57030749 AAATGACCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATA-CCCCATAGGGTA
57030776 AAATGA
1 AAATGA
57030782 TTTTTATACC
Statistics
Matches: 212, Mismatches: 29, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
26 8 0.04
27 193 0.91
28 11 0.05
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (26 bp):
AAATGACCGAAATACCCCATAGGGTA
Found at i:57031195 original size:28 final size:28
Alignment explanation
Indices: 57031155--57031288 Score: 173
Period size: 28 Copynumber: 4.8 Consensus size: 28
57031145 CATTGTTACA
*
57031155 GTATTGGGCTAAGGCCTACACTAATTCT
1 GTATTGGGCTAAGGCCCACACTAATTCT
*
57031183 GTATTGGGCTAAGGCCCACACTGATTCT
1 GTATTGGGCTAAGGCCCACACTAATTCT
57031211 GTATTGGGCTAAGGCCCACACT-ATTACT
1 GTATTGGGCTAAGGCCCACACTAATT-CT
* ** *
57031239 GTATTGGGCTAA-GCCTACACTGCTACT
1 GTATTGGGCTAAGGCCCACACTAATTCT
* *
57031266 GTAATGGGCCAAGGCCCACACTA
1 GTATTGGGCTAAGGCCCACACTA
57031289 TATTGATACT
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
27 23 0.24
28 71 0.76
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (28 bp):
GTATTGGGCTAAGGCCCACACTAATTCT
Found at i:57031232 original size:56 final size:56
Alignment explanation
Indices: 57031155--57031288 Score: 191
Period size: 55 Copynumber: 2.4 Consensus size: 56
57031145 CATTGTTACA
* *
57031155 GTATTGGGCTAAGGCCTACACTAATT-CTGTATTGGGCTAAGGCCCACACTGATTCT
1 GTATTGGGCTAAGGCCCACACTAATTACTGTATTGGGCTAA-GCCCACACTGATACT
* *
57031211 GTATTGGGCTAAGGCCCACACT-ATTACTGTATTGGGCTAAGCCTACACTGCTACT
1 GTATTGGGCTAAGGCCCACACTAATTACTGTATTGGGCTAAGCCCACACTGATACT
* *
57031266 GTAATGGGCCAAGGCCCACACTA
1 GTATTGGGCTAAGGCCCACACTA
57031289 TATTGATACT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
55 35 0.50
56 35 0.50
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (56 bp):
GTATTGGGCTAAGGCCCACACTAATTACTGTATTGGGCTAAGCCCACACTGATACT
Found at i:57033805 original size:113 final size:114
Alignment explanation
Indices: 57033558--57033814 Score: 290
Period size: 113 Copynumber: 2.3 Consensus size: 114
57033548 CCTGAACATC
* * * **
57033558 TAGTGGCGTTTTTTAAAAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATATGTAAGCGCCGC
1 TAGTGGCGTTTATTAAAAAACGCCGTAAAAGAACATCATTAGCGGCGTTTACATAAAAGCGCCGC
** * * *
57033623 AAAATACCTTAACCAAAACGCGGCGTTTGGTTTTTAGGTATATTAGTAT
66 AAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAGTAT
** * *
57033672 TAGTGGCGTTTACGAGAAAACGTCGCT-AAAGAACAGT-ATTAGCGGCGTATTACA-AAAAGCGC
1 TAGTGGCGTTTATTAAAAAACGCCG-TAAAAGAACA-TCATTAGCGGCGT-TTACATAAAAGCGC
*
57033734 CGC-AAATATCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAG-AGT
63 CGCAAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAGTA-T
* *
57033785 TAGTGGCGCTTATTAAAAAACGCCGCAAAA
1 TAGTGGCGTTTATTAAAAAACGCCGTAAAA
57033815 TATTGGGACA
Statistics
Matches: 117, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
112 1 0.01
113 63 0.54
114 47 0.40
115 6 0.05
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (114 bp):
TAGTGGCGTTTATTAAAAAACGCCGTAAAAGAACATCATTAGCGGCGTTTACATAAAAGCGCCGC
AAAATACCTTAACCAAAACGCACCGTTTGGTCTTGAGGTAGATTAGTAT
Found at i:57036795 original size:20 final size:20
Alignment explanation
Indices: 57036770--57036808 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
57036760 TCTTTCTGCA
57036770 ATTTCCCCTCATCCTTTCTG
1 ATTTCCCCTCATCCTTTCTG
*
57036790 ATTTCCCCTCGTCCTTTCT
1 ATTTCCCCTCATCCTTTCT
57036809 TCATCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.41, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTTCCCCTCATCCTTTCTG
Found at i:57038522 original size:17 final size:17
Alignment explanation
Indices: 57038500--57038532 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
57038490 TTATTTTCTA
57038500 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
*
57038517 TATAAGTTTTGTAAAT
1 TATAAGTTTTCTAAAT
57038533 AATTATTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:57038563 original size:16 final size:15
Alignment explanation
Indices: 57038542--57038580 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
57038532 TAATTATTCC
57038542 AAATTTATTAGTATAA
1 AAATTTATTAGTAT-A
* *
57038558 AAATTTAGTAGTATT
1 AAATTTATTAGTATA
57038573 AAATTTAT
1 AAATTTAT
57038581 AAGTTTTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (15 bp):
AAATTTATTAGTATA
Found at i:57038580 original size:61 final size:61
Alignment explanation
Indices: 57038511--57038660 Score: 169
Period size: 61 Copynumber: 2.5 Consensus size: 61
57038501 ATAAGTTTTC
57038511 TAAATTTATAAGTTTTGTAAATAATTATTCCAAATTTATTAGT-ATAAAAATTTAGT-AGTAT
1 TAAATTTATAAGTTTTGTAAATAATTATTCCAAATTTATTAGTAAT-AAAATTTA-TAAGTAT
* * * * * * *
57038572 TAAATTTATAAGTTTTCTAAAAAAGTGTTCTAGATTTATTATTAATAAAATTTATAAGTAT
1 TAAATTTATAAGTTTTGTAAATAATTATTCCAAATTTATTAGTAATAAAATTTATAAGTAT
* * * *
57038633 CAATTTTACACGTTTTGTAAATAATTAT
1 TAAATTTATAAGTTTTGTAAATAATTAT
57038661 ATTTTTTAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
60 1 0.01
61 69 0.96
62 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (61 bp):
TAAATTTATAAGTTTTGTAAATAATTATTCCAAATTTATTAGTAATAAAATTTATAAGTAT
Found at i:57038896 original size:8 final size:7
Alignment explanation
Indices: 57038883--57038928 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
57038873 CAACGTATAT
57038883 ATAATAAC
1 ATAAT-AC
57038891 ATAATA-
1 ATAATAC
*
57038897 A-ATTAC
1 ATAATAC
57038903 ATAATAC
1 ATAATAC
57038910 ATAATAAC
1 ATAAT-AC
57038918 ATAATAC
1 ATAATAC
57038925 ATAA
1 ATAA
57038929 CTTATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:57038916 original size:95 final size:95
Alignment explanation
Indices: 57038804--57039008 Score: 295
Period size: 95 Copynumber: 2.2 Consensus size: 95
57038794 AATCATTTGC
* *
57038804 TTACTTAATACATAATAACACAATACATAA-TTGGTATATAAGCTTGCATAACTTACATAATAAC
1 TTACATAATACATAATAACACAATACATAACTT-ATATATAAGCTTGCATAACTTACATAATAAC
57038868 TTCCACAACGTATATATAATAACATAATAAA
65 TTCCACAACGTATATATAATAACATAATAAA
* *
57038899 TTACATAATACATAATAACATAATACATAACTTATATATAAGCTTGTATAACTTACATAATAACT
1 TTACATAATACATAATAACACAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACT
* * * *** *
57038964 TTCATAACTTATATATAATCTGATAATACA
66 TCCACAACGTATATATAATAACATAATAAA
57038994 TTACATAATACATAA
1 TTACATAATACATAA
57039009 CTTATATTAT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 96 0.98
96 2 0.02
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (95 bp):
TTACATAATACATAATAACACAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACT
TCCACAACGTATATATAATAACATAATAAA
Found at i:57038921 original size:15 final size:15
Alignment explanation
Indices: 57038883--57038928 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
57038873 CAACGTATAT
57038883 ATAATAACATAAT--
1 ATAATAACATAATAC
*
57038896 A-AATTACATAATAC
1 ATAATAACATAATAC
57038910 ATAATAACATAATAC
1 ATAATAACATAATAC
57038925 ATAA
1 ATAA
57038929 CTTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
14 1 0.04
15 16 0.57
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAACATAATAC
Found at i:57038950 original size:21 final size:20
Alignment explanation
Indices: 57038924--57039055 Score: 76
Period size: 21 Copynumber: 6.5 Consensus size: 20
57038914 TAACATAATA
57038924 CATAACTTATATATAAGCTTGT
1 CATAACTTATATATAA-CTT-T
*
57038946 -ATAACTTACATAATAACTTT
1 CATAACTTATAT-ATAACTTT
*
57038966 CATAACTTATATATAA-TCT
1 CATAACTTATATATAACTTT
* * * *
57038985 GATAA-TACATTACATAA--TA
1 CATAACT-TA-TATATAACTTT
*
57039004 CATAACTTATATTATAATCTTG
1 CATAACTTATA-TATAA-CTTT
* *
57039026 CATAACTTACATAATAACTTC
1 CATAACTTATAT-ATAACTTT
57039047 CATAACTTA
1 CATAACTTA
57039056 ATACACCACT
Statistics
Matches: 86, Mismatches: 14, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
18 3 0.03
19 16 0.19
20 12 0.14
21 36 0.42
22 19 0.22
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (20 bp):
CATAACTTATATATAACTTT
Found at i:57039036 original size:38 final size:36
Alignment explanation
Indices: 57038916--57039041 Score: 137
Period size: 38 Copynumber: 3.2 Consensus size: 36
57038906 ATACATAATA
*
57038916 ACATAATACATAACTTATATATAAGCTTGTATAACTT
1 ACATAATACATAACTTATATATAATCTTG-ATAACTT
57038953 ACATAATAACTTTCATAACTTATATATAATC-TGATAATACATT
1 ACATAAT-A----CATAACTTATATATAATCTTGAT-A-AC-TT
57038996 ACATAATACATAACTTATATTATAATCTTGCATAACTT
1 ACATAATACATAACTTATA-TATAATCTTG-ATAACTT
57039034 ACATAATA
1 ACATAATA
57039042 ACTTCCATAA
Statistics
Matches: 77, Mismatches: 1, Indels: 21
0.78 0.01 0.21
Matches are distributed among these distances:
37 7 0.09
38 22 0.29
39 9 0.12
40 5 0.06
41 5 0.06
42 20 0.26
43 9 0.12
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.38
Consensus pattern (36 bp):
ACATAATACATAACTTATATATAATCTTGATAACTT
Found at i:57039156 original size:9 final size:9
Alignment explanation
Indices: 57039142--57039668 Score: 345
Period size: 9 Copynumber: 59.4 Consensus size: 9
57039132 CATACATTAA
57039142 ATAACTTAC
1 ATAACTTAC
57039151 ATAACTTAC
1 ATAACTTAC
* *
57039160 ATAAATTAA
1 ATAACTTAC
57039169 ATAACTTAC
1 ATAACTTAC
*
57039178 ATAACCTAC
1 ATAACTTAC
* *
57039187 ATAAATTAA
1 ATAACTTAC
57039196 ATAACTTAC
1 ATAACTTAC
* *
57039205 ATAAATTAA
1 ATAACTTAC
57039214 ATAACTTAC
1 ATAACTTAC
57039223 ATAACTTAC
1 ATAACTTAC
* *
57039232 ATAAATTCC
1 ATAACTTAC
* *
57039241 GTGGACTTAC
1 AT-AACTTAC
*
57039251 ATAACCTAC
1 ATAACTTAC
* * *
57039260 ACAAATTAA
1 ATAACTTAC
57039269 ATAACTTAC
1 ATAACTTAC
57039278 ATAACTTAC
1 ATAACTTAC
57039287 ATAACTTAC
1 ATAACTTAC
57039296 ATAACTTAC
1 ATAACTTAC
* *
57039305 ATAA-ATAGTT
1 ATAACTTA--C
* *
57039315 ATAAATTAG
1 ATAACTTAC
57039324 ATAACTTAC
1 ATAACTTAC
57039333 ATAACTTAC
1 ATAACTTAC
*
57039342 AT-ACATTAA
1 ATAAC-TTAC
* *
57039351 ATTACTTAT
1 ATAACTTAC
57039360 ATAACTTAC
1 ATAACTTAC
*
57039369 ATTA--TAC
1 ATAACTTAC
57039376 ATAACTTAC
1 ATAACTTAC
* *
57039385 ATAAATTAA
1 ATAACTTAC
57039394 ATAACTTAC
1 ATAACTTAC
57039403 ATAACTTAC
1 ATAACTTAC
* *
57039412 ATAAATTCC
1 ATAACTTAC
* **
57039421 GTGGGCTTAC
1 AT-AACTTAC
*
57039431 ATAACCTAC
1 ATAACTTAC
* * *
57039440 ACAAATTAA
1 ATAACTTAC
57039449 ATAACTTAC
1 ATAACTTAC
57039458 ATAACTTAC
1 ATAACTTAC
57039467 ATAACTTAC
1 ATAACTTAC
* *
57039476 ATAA-ATAGTT
1 ATAACTTA--C
* *
57039486 ATAAATTAA
1 ATAACTTAC
57039495 ATAACTTAC
1 ATAACTTAC
57039504 ATAACTTAC
1 ATAACTTAC
*
57039513 AT-ACATTAA
1 ATAAC-TTAC
*
57039522 ATTACTTAC
1 ATAACTTAC
57039531 ATAACTTAC
1 ATAACTTAC
*
57039540 ATAA-ATA-
1 ATAACTTAC
*
57039547 GTAACCTT-C
1 ATAA-CTTAC
*
57039556 TTAACTTAC
1 ATAACTTAC
*
57039565 ATTA--TAC
1 ATAACTTAC
** *
57039572 ACGACTCAC
1 ATAACTTAC
57039581 ATAA-TTA-
1 ATAACTTAC
*
57039588 AT-ATTATAC
1 ATAACT-TAC
*
57039597 ACAACTTAC
1 ATAACTTAC
*
57039606 ATAA-TAAC
1 ATAACTTAC
**
57039614 -TTTCTTAC
1 ATAACTTAC
57039622 ATAACTTAC
1 ATAACTTAC
*
57039631 ATTACTTAC
1 ATAACTTAC
57039640 AGT-ACTTAC
1 A-TAACTTAC
57039649 ATAA--TAC
1 ATAACTTAC
57039656 ATAACTTAC
1 ATAACTTAC
57039665 ATAA
1 ATAA
57039669 TACATAAAAA
Statistics
Matches: 393, Mismatches: 95, Indels: 60
0.72 0.17 0.11
Matches are distributed among these distances:
6 1 0.00
7 25 0.06
8 24 0.06
9 315 0.80
10 24 0.06
11 4 0.01
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:57039269 original size:55 final size:54
Alignment explanation
Indices: 57039142--57039515 Score: 254
Period size: 55 Copynumber: 6.9 Consensus size: 54
57039132 CATACATTAA
* * * * * ** * *
57039142 ATAACTTACATAACTTACATAAATTAAATAACTTACATAACCTACATAAATTAA
1 ATAACATACATAAATTAAATAACTTACATAACTTACATAAATTACATAACTTAC
* * * *
57039196 ATAACTTACATAAATTAAATAACTTACATAACTTACATAAATTCCGTGGACTTAC
1 ATAACATACATAAATTAAATAACTTACATAACTTACATAAATTACAT-AACTTAC
* * *
57039251 ATAACCTACACAAATTAAATAACTTACATAACTTACATAACTTACATAACTTAC
1 ATAACATACATAAATTAAATAACTTACATAACTTACATAAATTACATAACTTAC
* * * * * *
57039305 ATAA-ATAGTTATAAATTAGATAACTTACATAACTTACATACATTAAATTACTTAT
1 ATAACATA--CATAAATTAAATAACTTACATAACTTACATAAATTACATAACTTAC
* * * * * *
57039360 ATAACTTACAT-TA-TACATAACTTACATAAATTAAATAACTTACATAACTTAC
1 ATAACATACATAAATTAAATAACTTACATAACTTACATAAATTACATAACTTAC
* * *** * * * * * *
57039412 ATAA-ATTCCGTGGGCTTACATAACCTACACAAATTAAATAACTTACATAACTTAC
1 ATAACA-TACAT-AAATTAAATAACTTACATAACTTACATAAATTACATAACTTAC
* * * * *
57039467 ATAACTTACATAAA-TAGTTATAAATTAAATAACTTACATAACTTACATA
1 ATAACATACATAAATTA--AATAACTTACATAACTTACATAAATTACATA
57039516 CATTAAATTA
Statistics
Matches: 252, Mismatches: 57, Indels: 21
0.76 0.17 0.06
Matches are distributed among these distances:
52 38 0.15
53 5 0.02
54 51 0.20
55 156 0.62
56 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (54 bp):
ATAACATACATAAATTAAATAACTTACATAACTTACATAAATTACATAACTTAC
Found at i:57039378 original size:43 final size:43
Alignment explanation
Indices: 57039248--57039413 Score: 159
Period size: 43 Copynumber: 4.0 Consensus size: 43
57039238 TCCGTGGACT
* * *
57039248 TACATAACCTACACAAATTAAATAACTTACATAACTTACATAA
1 TACATAACTTACATAAATTAAATAACTTACATAACTTACATTA
* * *
57039291 CTTACATAACTTACATAAA-TAGTTATAAATTAGAT-A---AC--T-
1 --TACATAACTTACATAAATTA--AATAACTTACATAACTTACATTA
* * *
57039330 TACATAACTTACATACATTAAATTACTTATATAACTTACATTA
1 TACATAACTTACATAAATTAAATAACTTACATAACTTACATTA
57039373 TACATAACTTACATAAATTAAATAACTTACATAACTTACAT
1 TACATAACTTACATAAATTAAATAACTTACATAACTTACAT
57039414 AAATTCCGTG
Statistics
Matches: 97, Mismatches: 14, Indels: 22
0.73 0.11 0.17
Matches are distributed among these distances:
36 8 0.08
37 17 0.18
38 2 0.02
40 2 0.02
42 3 0.03
43 38 0.39
44 2 0.02
45 16 0.16
46 9 0.09
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.34
Consensus pattern (43 bp):
TACATAACTTACATAAATTAAATAACTTACATAACTTACATTA
Found at i:57039662 original size:16 final size:16
Alignment explanation
Indices: 57039619--57039675 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 16
57039609 ATAACTTTCT
*
57039619 TACATAACTTACATTACT
1 TACATAACTTACA-TA-A
57039637 TACAGT-ACTTACATAA
1 TACA-TAACTTACATAA
57039653 TACATAACTTACATAA
1 TACATAACTTACATAA
57039669 TACATAA
1 TACATAA
57039676 AAATATATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 1 0.03
16 21 0.58
17 2 0.06
18 11 0.31
19 1 0.03
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:57045608 original size:41 final size:42
Alignment explanation
Indices: 57045543--57045747 Score: 295
Period size: 42 Copynumber: 4.8 Consensus size: 42
57045533 GCATTTTTGT
* *
57045543 AAAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
*
57045585 ACAAAAA-GCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTT-AG
* * ** * *
57045627 AAAAAAACGCCACTAAAGAACATGTTCTTTAGTAGCGTTTATA
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-G
57045670 AACAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 AA-AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
57045713 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGG
57045748 TGTTTTTTCT
Statistics
Matches: 143, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
41 30 0.21
42 48 0.34
43 31 0.22
44 34 0.24
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
Found at i:57045703 original size:87 final size:83
Alignment explanation
Indices: 57045543--57045745 Score: 307
Period size: 86 Copynumber: 2.4 Consensus size: 83
57045533 GCATTTTTGT
* * *
57045543 AAAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCGCTTAGACAAAAAGCCGCTAAAGACCATG
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCAGCGCTTAAACAAAAAGCCGCTAAAGACCATG
57045608 TTCTTTAGCGGCGCTTAAG
66 TTCTTTAGCGGCGCTT-AG
* * *
57045627 AAAAAAACGCCACTAAAGAACATGTTCTTTAGTAGCGTTTATAAACAAAAACGCCGCTAAAGACC
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCAGCG-CT-TAAACAAAAA-GCCGCTAAAGACC
57045692 ATGTTCTTTAGCGGCGCTTAG
63 ATGTTCTTTAGCGGCGCTTAG
*
57045713 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGC
1 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGC
57045746 GGTGTTTTTT
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
84 33 0.31
85 1 0.01
86 41 0.38
87 32 0.30
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (83 bp):
AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCAGCGCTTAAACAAAAAGCCGCTAAAGACCATG
TTCTTTAGCGGCGCTTAG
Found at i:57045766 original size:42 final size:42
Alignment explanation
Indices: 57045537--57045796 Score: 252
Period size: 42 Copynumber: 6.1 Consensus size: 42
57045527 ATAGTGGCAT
* *
57045537 TTTTGTAAAAAAACGCTGCTAAAGAACATGTTCTTTAGCGGCG
1 TTTT-TAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
* ** *
57045580 CTTAGACAAAAA-GCCGCTAAAGACCATGTTCTTTAGCGGCG
1 TTTTTAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
*** * * **
57045621 CTTAAGAAAAAAACGCCACTAAAGAACATGTTCTTTAGTAGCG
1 -TTTTTAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
*
57045664 TTTATAAACAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
1 TTT-TTAA-AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
* ** *
57045708 CTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGTG
1 TTTTTAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
**** * * *
57045750 TTTTTTCTTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCG
1 TTTTTAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
57045792 TTTTT
1 TTTTT
57045797 GTTTATAAAC
Statistics
Matches: 178, Mismatches: 35, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
41 27 0.15
42 87 0.49
43 31 0.17
44 33 0.19
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (42 bp):
TTTTTAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
Found at i:57046911 original size:21 final size:22
Alignment explanation
Indices: 57046873--57046915 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
57046863 AAAACAAGCT
57046873 TTTAGCGGCGCTTTTTTAGGCC
1 TTTAGCGGCGCTTTTTTAGGCC
57046895 TTTAGCGGCGC-TTTTTAGGCC
1 TTTAGCGGCGCTTTTTTAGGCC
57046916 GCAGATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.09, C:0.23, G:0.28, T:0.40
Consensus pattern (22 bp):
TTTAGCGGCGCTTTTTTAGGCC
Found at i:57047225 original size:86 final size:86
Alignment explanation
Indices: 57046994--57047403 Score: 332
Period size: 86 Copynumber: 4.8 Consensus size: 86
57046984 TTGCGGCATT
* *
57046994 TTTTTTCTCTAAACGCCGCTAAAGACCCTGATCTATAGCGGCGC-TTCTAGC-ACAAACGCCGCT
1 TTTTTTCAC-AAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTCT-CCTA-AAACGCCGCT
* * * *
57047057 GAAGACTAAGACCTTTAGCGGCGC
63 AAAGACCATGATCTTTAGCGGCGC
** ** * * * *
57047081 TTTAGT-GGAAGCGCCGCTAAAGACCCTGATCT-TCAGCGGCG-TTTGTGCTAGAAGCGCCGCTA
1 TTTTTTCACAAACGCCGCTAAAGACCCTGATCTAT-AGCGGCGCTTTCTCCTA-AAACGCCGCTA
* * * *
57047143 AAGATCAGGGTCTTTAGCGGCGT
64 AAGACCATGATCTTTAGCGGCGC
* *
57047166 TTTTTTCTCAAACGCCG-TAATAGACCCTGATCTATAGCGGCACTTTCTCCTAAAACGCCGC-AA
1 TTTTTTCACAAACGCCGCTAA-AGACCCTGATCTATAGCGGCGCTTTCTCCTAAAACGCCGCTAA
* *
57047229 TAGACCCTGATCTATAGCGGCGC
65 -AGACCATGATCTTTAGCGGCGC
**** * * * * *
57047252 TTCGACCACAAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTC-CCCAAAACGCCGCTAA
1 TTTTTTCAC-AAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTCTCCTAAAACGCCGCTAA
*
57047316 AGACCATGATCTTTAGTGGCGC
65 AGACCATGATCTTTAGCGGCGC
* * * * ** * *
57047338 TTTTTCCACAAATGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAA
1 TTTTTTCACAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTCTCCTAAAACGCCGCTAAA
57047403 G
66 G
57047404 GCCAACACCT
Statistics
Matches: 257, Mismatches: 54, Indels: 25
0.76 0.16 0.07
Matches are distributed among these distances:
84 3 0.01
85 102 0.40
86 106 0.41
87 43 0.17
88 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (86 bp):
TTTTTTCACAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTTCTCCTAAAACGCCGCTAAA
GACCATGATCTTTAGCGGCGC
Found at i:57047383 original size:43 final size:43
Alignment explanation
Indices: 57047004--57047403 Score: 296
Period size: 43 Copynumber: 9.3 Consensus size: 43
57046994 TTTTTTCTCT
* *
57047004 AAACGCCGCTAAAGACCCTGATCTATAGCGGCGC-TTCTAGCAC
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCT-CCAC
* *** * * **
57047047 AAACGCCGCTGAAGACTAAGACCTTTAGCGGCGCTTTAGT--GG
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTT-CTCCAC
* * * * *
57047089 AAGCGCCGCTAAAGACCCTGATCTTCAGCGGCG-TTTGTGCTAG
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCT-CCAC
* * ** * * * * *
57047132 AAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTTTCTC
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCTCCAC
* *
57047175 AAACGCCG-TAATAGACCCTGATCTATAGCGGCACTTTCTCCTA-
1 AAACGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTCTCC-AC
* *
57047218 AAACGCCGC-AATAGACCCTGATCTATAGCGGCGC-TTCGACCAC
1 AAACGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTC-TCCAC
* * * *
57047261 AAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCA-
1 -AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCTCCAC
* * *
57047304 AAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCTCCAC
* * ** *
57047347 AAATGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAA
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCTCCAC
*
57047390 AAACGCCACTAAAG
1 AAACGCCGCTAAAG
57047404 GCCAACACCT
Statistics
Matches: 281, Mismatches: 61, Indels: 30
0.76 0.16 0.08
Matches are distributed among these distances:
40 2 0.01
41 3 0.01
42 68 0.24
43 166 0.59
44 36 0.13
45 6 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCTCCAC
Found at i:57047427 original size:85 final size:84
Alignment explanation
Indices: 57047270--57047426 Score: 199
Period size: 85 Copynumber: 1.9 Consensus size: 84
57047260 CAAAACGCCA
* * * ** *
57047270 CTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCAAAACGCCGCTAAAGACCATGATCTTTAGTGG
1 CTAAAGAACCTAATCTTTAGCGGCGCTTTACCAAAAACGCCACTAAAGACCAACACCTTTAG-GG
57047335 CGCTTTTTCCACAAATGCCG
65 CGCTTTTTCCACAAATGCCG
* * *
57047355 CTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGGCCAACACCTTTA-GG
1 CTAAAGAACCTAATCTTTAGCGGCGCTTT-ACCAAAAACGCCACTAAAGACCAACACCTTTAGGG
*
57047419 CGTTTTTT
65 CGCTTTTT
57047427 TAAAAACGCC
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
84 9 0.15
85 27 0.44
86 25 0.41
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (84 bp):
CTAAAGAACCTAATCTTTAGCGGCGCTTTACCAAAAACGCCACTAAAGACCAACACCTTTAGGGC
GCTTTTTCCACAAATGCCG
Found at i:57047836 original size:21 final size:21
Alignment explanation
Indices: 57047743--57047835 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
57047733 CTTTTGACTG
57047743 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
57047764 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
57047785 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
57047806 CTGTACTTCTCTAGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
57047827 CTCTGCTTC
1 CTCTGCTTC
57047836 TTTTACTGCC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.05, C:0.44, G:0.17, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:57047914 original size:63 final size:63
Alignment explanation
Indices: 57047847--57047968 Score: 178
Period size: 63 Copynumber: 1.9 Consensus size: 63
57047837 TTTACTGCCG
57047847 ATCTGCTTT-AAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGCTG
1 ATCTGCTTTCAA-CTG-TAGCTGGAGTTCTTCATATCTTT-GTTGAACCTCAGCTTCTCTCGCTG
57047909 C
63 C
* *
57047910 ATCTGCTTTCAATTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCAGCTTCTCTCG
1 ATCTGCTTTCAACTGTAGCTGGAGTTCTTCATATCTTTGTTGAACCTCAGCTTCTCTCG
57047969 ATGTTGCCTC
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
62 1 0.02
63 47 0.87
64 6 0.11
ACGTcount: A:0.16, C:0.26, G:0.17, T:0.41
Consensus pattern (63 bp):
ATCTGCTTTCAACTGTAGCTGGAGTTCTTCATATCTTTGTTGAACCTCAGCTTCTCTCGCTGC
Found at i:57052714 original size:80 final size:81
Alignment explanation
Indices: 57052616--57052777 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
57052606 ACCCTCCCAA
57052616 ACATTTTAACTGGAAAAGACGAATGCAGAAA-GCATTTTTGAAAATTTCGATCCCTCATATAGTT
1 ACATTTTAACTGGAAAAGACGAATGCAGAAAGGCATTTTTGAAAATTTCGATCCCTCATATAGTT
57052680 CTTCATTCATCTCATT
66 CTTCATTCATCTCATT
57052696 ACATTTTAACTGGAAAAGACGAATGCAGAAAGGCATTTTTGAAAATTTCGATCCCTCATATAGTT
1 ACATTTTAACTGGAAAAGACGAATGCAGAAAGGCATTTTTGAAAATTTCGATCCCTCATATAGTT
57052761 CTTCATTCATCTCATT
66 CTTCATTCATCTCATT
57052777 A
1 A
57052778 AGTAGCGCGT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 31 0.38
81 50 0.62
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (81 bp):
ACATTTTAACTGGAAAAGACGAATGCAGAAAGGCATTTTTGAAAATTTCGATCCCTCATATAGTT
CTTCATTCATCTCATT
Found at i:57053308 original size:9 final size:9
Alignment explanation
Indices: 57053294--57053483 Score: 144
Period size: 9 Copynumber: 23.0 Consensus size: 9
57053284 AATTGCACGG
57053294 GTAAGTTAT
1 GTAAGTTAT
57053303 GTAAGTTAT
1 GTAAGTTAT
*
57053312 TTAAGTTAT
1 GTAAGTTAT
*
57053321 GTAAGTTGT
1 GTAAGTTAT
57053330 GT-A-TTAT
1 GTAAGTTAT
57053337 GTAAGTTAT
1 GTAAGTTAT
57053346 -T-A-TTAT
1 GTAAGTTAT
57053352 GTAAGTTAT
1 GTAAGTTAT
*
57053361 GTAAGTAAT
1 GTAAGTTAT
57053370 GT-A-TTAT
1 GTAAGTTAT
*
57053377 GTAAGTTGT
1 GTAAGTTAT
*
57053386 GT-A-TAAT
1 GTAAGTTAT
*
57053393 GTTAGTTAT
1 GTAAGTTAT
**
57053402 CAAAGTTA-
1 GTAAGTTAT
*
57053410 --CAG-TAT
1 GTAAGTTAT
57053416 GTAAGTTAT
1 GTAAGTTAT
*
57053425 TTAAGTTAT
1 GTAAGTTAT
*
57053434 GTAAGTTGT
1 GTAAGTTAT
57053443 GT-A-TTAT
1 GTAAGTTAT
57053450 GTAAGTTAT
1 GTAAGTTAT
*
57053459 GTAGGTTAT
1 GTAAGTTAT
*
57053468 GT-A-TAAT
1 GTAAGTTAT
57053475 GTAAGTTAT
1 GTAAGTTAT
57053484 TATGTTATTA
Statistics
Matches: 141, Mismatches: 23, Indels: 34
0.71 0.12 0.17
Matches are distributed among these distances:
5 2 0.01
6 6 0.04
7 26 0.18
8 13 0.09
9 94 0.67
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:57053338 original size:16 final size:16
Alignment explanation
Indices: 57053299--57053461 Score: 99
Period size: 16 Copynumber: 10.0 Consensus size: 16
57053289 CACGGGTAAG
*
57053299 TTATGTAAGTTATTTAA
1 TTATGTAAGTTATGT-A
*
57053316 GTTATGTAAGTTGTGTA
1 -TTATGTAAGTTATGTA
57053333 TTATGTAAGTTAT-TA
1 TTATGTAAGTTATGTA
57053348 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
57053364 --A-GT-A---ATGTA
1 TTATGTAAGTTATGTA
*
57053373 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
* *
57053389 TAATGTTAGTTATCAAAGTTACA
1 TTATGTAAGTTAT----G-T--A
* *
57053412 GTATGTAAGTTATTTAA
1 TTATGTAAGTTATGT-A
*
57053429 GTTATGTAAGTTGTGTA
1 -TTATGTAAGTTATGTA
57053446 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
57053462 GGTTATGTAT
Statistics
Matches: 113, Mismatches: 16, Indels: 34
0.69 0.10 0.21
Matches are distributed among these distances:
9 5 0.04
11 1 0.01
12 3 0.03
13 3 0.03
14 1 0.01
15 15 0.13
16 43 0.38
17 3 0.03
18 26 0.23
20 1 0.01
21 1 0.01
23 11 0.10
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:57053401 original size:25 final size:25
Alignment explanation
Indices: 57053299--57053483 Score: 134
Period size: 25 Copynumber: 7.5 Consensus size: 25
57053289 CACGGGTAAG
* *
57053299 TTATGTAAGTTATTTAAGTTATGTAA
1 TTATGTAAGTTATGTAAGTAATGT-A
* *
57053325 GTTGTGT-A-TTATGTAAGTTAT-TA
1 -TTATGTAAGTTATGTAAGTAATGTA
57053348 TTATGTAAGTTATGTAAGTAATGTA
1 TTATGTAAGTTATGTAAGTAATGTA
*
57053373 TTATGTAAGTTGTGT-A-TAATGTTA
1 TTATGTAAGTTATGTAAGTAATG-TA
** * *
57053397 GTTATCAAAGTTACAGTATGTAA-G--
1 -TTATGTAAGTTA-TGTAAGTAATGTA
* **
57053421 TTATTTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTAATGTA
* *
57053446 TTATGTAAGTTATGTAGGTTATGTA
1 TTATGTAAGTTATGTAAGTAATGTA
*
57053471 TAATGTAAGTTAT
1 TTATGTAAGTTAT
57053484 TATGTTATTA
Statistics
Matches: 127, Mismatches: 20, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
22 10 0.08
23 18 0.14
24 16 0.13
25 71 0.56
26 3 0.02
27 6 0.05
28 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTATGTAAGTAATGTA
Found at i:57053817 original size:43 final size:43
Alignment explanation
Indices: 57053715--57053803 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
57053705 ATTTATTGAC
*
57053715 AATAAAATTGTAATATAGGTTATATATCCATACCATATATATA
1 AATAAAATTGAAATATAGGTTATATATCCATACCATATATATA
57053758 AATAAAATTGAAATATAGGTTATATATCCATACCATATATATA
1 AATAAAATTGAAATATAGGTTATATATCCATACCATATATATA
57053801 AAT
1 AAT
57053804 TTTAAATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (43 bp):
AATAAAATTGAAATATAGGTTATATATCCATACCATATATATA
Found at i:57053849 original size:18 final size:18
Alignment explanation
Indices: 57053826--57053994 Score: 110
Period size: 18 Copynumber: 8.4 Consensus size: 18
57053816 TATATAAATA
57053826 TTAAGTAATGTAATATAT
1 TTAAGTAATGTAATATAT
*
57053844 TTAAGTAATGTAAGTTAAAAATTTT
1 TTAAGTAATGTAA--T----A-TAT
57053869 TGTAAGTAATGTAATA-ATT
1 T-TAAGTAATGTAATATA-T
57053888 TTAAGTAATGTAATATAT
1 TTAAGTAATGTAATATAT
57053906 TTAAGTAATATTGTAATATAT
1 TTAAGT-A-A-TGTAATATAT
*
57053927 TTAAGTAATGTAAGTTAAAAATTT
1 TTAAGTAATGTAA--T----ATAT
57053951 TGTAAGTAATGTAATA-ATT
1 T-TAAGTAATGTAATATA-T
*
57053970 TTAAGTAA-ATAATATAT
1 TTAAGTAATGTAATATAT
57053987 TTAAGTAA
1 TTAAGTAA
57053995 ATTTTAGTAA
Statistics
Matches: 124, Mismatches: 5, Indels: 45
0.71 0.03 0.26
Matches are distributed among these distances:
17 14 0.11
18 47 0.38
19 8 0.06
20 5 0.04
21 16 0.13
23 1 0.01
24 6 0.05
25 15 0.12
26 12 0.10
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (18 bp):
TTAAGTAATGTAATATAT
Found at i:57053873 original size:22 final size:23
Alignment explanation
Indices: 57053830--57053977 Score: 85
Period size: 21 Copynumber: 7.0 Consensus size: 23
57053820 TAAATATTAA
*
57053830 GTAATGT-AATATATTTAAGTAAT
1 GTAATGTAAAAAT-TTTAAGTAAT
*
57053853 GTAA-GTTAAAAATTTT-TGTAA-
1 GTAATG-TAAAAATTTTAAGTAAT
*
57053874 GTAATGTAATAATTTTAAGTAAT
1 GTAATGTAAAAATTTTAAGTAAT
*
57053897 GTAA--T--ATA-TTTAAGTAA-
1 GTAATGTAAAAATTTTAAGTAAT
* *
57053914 -TATTGT-AATATATTTAAGTAAT
1 GTAATGTAAAAAT-TTTAAGTAAT
57053936 GTAA-GTTAAAAATTTT--GTAA-
1 GTAATG-TAAAAATTTTAAGTAAT
*
57053956 GTAATGTAATAATTTTAAGTAA
1 GTAATGTAAAAATTTTAAGTAA
57053978 ATAATATATT
Statistics
Matches: 98, Mismatches: 10, Indels: 35
0.69 0.07 0.24
Matches are distributed among these distances:
16 2 0.02
18 10 0.10
19 4 0.04
20 13 0.13
21 28 0.29
22 15 0.15
23 18 0.18
24 8 0.08
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.43
Consensus pattern (23 bp):
GTAATGTAAAAATTTTAAGTAAT
Found at i:57053875 original size:44 final size:44
Alignment explanation
Indices: 57053827--57054038 Score: 198
Period size: 44 Copynumber: 5.0 Consensus size: 44
57053817 ATATAAATAT
57053827 TAAGTAATGTAATATATTTAAGTAATGTAAGTTAAAAATTTTTG
1 TAAGTAATGTAATATATTTAAGTAATGTAAGTTAAAAATTTTTG
* **
57053871 TAAGTAATGTAATA-ATTTTAAGTAATGTAA--T--ATATTTAAG
1 TAAGTAATGTAATATA-TTTAAGTAATGTAAGTTAAAAATTTTTG
*
57053911 TAA-TATTGTAATATATTTAAGTAATGTAAGTTAAAAA-TTTTG
1 TAAGTAATGTAATATATTTAAGTAATGTAAGTTAAAAATTTTTG
* *
57053953 TAAGTAATGTAATA-ATTTTAAGTAAATAATATATTTAAGTAAA--TTT-
1 TAAGTAATGTAATATA-TTTAAGT-AAT-GTA-AGTTAA--AAATTTTTG
* *
57053999 T-AGTAAT-TAATATATTTACGTAATGTAAGTTATAAATTTT
1 TAAGTAATGTAATATATTTAAGTAATGTAAGTTAAAAATTTT
57054039 AAATATATAT
Statistics
Matches: 138, Mismatches: 14, Indels: 35
0.74 0.07 0.19
Matches are distributed among these distances:
39 26 0.19
40 10 0.07
41 7 0.05
42 10 0.07
43 22 0.16
44 42 0.30
45 9 0.07
46 6 0.04
47 3 0.02
48 3 0.02
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (44 bp):
TAAGTAATGTAATATATTTAAGTAATGTAAGTTAAAAATTTTTG
Found at i:57053890 original size:83 final size:82
Alignment explanation
Indices: 57053801--57054038 Score: 286
Period size: 83 Copynumber: 2.8 Consensus size: 82
57053791 CATATATATA
57053801 AATTTTAAATATATATATATAAATATTAAGTAATGTAATATATTTAAGTAATGTAAGTTAAAAAT
1 AATTTTAAATATATATATATAAAT-TTAAGTAATGTAATATATTTAAGTAATGTAAGTTAAAAAT
57053866 TTTTGTAAGTAATGTAAT
65 TTTTGTAAGTAATGTAAT
* * *
57053884 AATTTTAAGTA-ATGTA-ATATATTTAAGTAATATTGTAATATATTTAAGTAATGTAAGTTAAAA
1 AATTTTAAATATATATATATAAATTTAAGT-A-A-TGTAATATATTTAAGTAATGTAAGTTAAAA
57053947 A-TTTTGTAAGTAATGTAAT
63 ATTTTTGTAAGTAATGTAAT
* * *
57053966 AATTTTAAGTAAATAATATATTTAAGTAAATTTTAGTAAT-TAATATATTTACGTAATGTAAGTT
1 AA-TTT---TAAAT-ATATATAT-A-TAAATTTAAGTAATGTAATATATTTAAGTAATGTAAGTT
*
57054030 ATAAATTTT
59 AAAAATTTT
57054039 AAATATATAT
Statistics
Matches: 132, Mismatches: 10, Indels: 21
0.81 0.06 0.13
Matches are distributed among these distances:
80 6 0.05
81 6 0.05
82 25 0.19
83 44 0.33
86 4 0.03
87 28 0.21
88 7 0.05
89 1 0.01
90 2 0.02
91 9 0.07
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (82 bp):
AATTTTAAATATATATATATAAATTTAAGTAATGTAATATATTTAAGTAATGTAAGTTAAAAATT
TTTGTAAGTAATGTAAT
Found at i:57053950 original size:62 final size:60
Alignment explanation
Indices: 57053821--57053994 Score: 171
Period size: 62 Copynumber: 2.9 Consensus size: 60
57053811 ATATATATAT
* * * **
57053821 AAATATTAAGTAATGTAATATATTTAAGTAATGTAAGTTAA-AAATTTTTGTAAGTAATGTAA
1 AAATTTTAAGTAATGTAATATATTTAAGTAA--TATG-TAATATATTTAAGTAAGTAATGTAA
*
57053883 TAATTTTAAGTAATGTAATATATTTAAGTAATATTGTAATATATTTAAGTAATGTAA-GTTAA
1 AAATTTTAAGTAATGTAATATATTTAAGTAATA-TGTAATATATTTAAGTAA-GTAATG-TAA
57053945 AAATTTTGTAAGTAATGTAATA-ATTTTAAGTAA-A--TAATATATTTAAGTAA
1 AAA-TTT-TAAGTAATGTAATATA-TTTAAGTAATATGTAATATATTTAAGTAA
57053995 ATTTTAGTAA
Statistics
Matches: 98, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
60 21 0.21
61 11 0.11
62 38 0.39
63 5 0.05
64 23 0.23
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (60 bp):
AAATTTTAAGTAATGTAATATATTTAAGTAATATGTAATATATTTAAGTAAGTAATGTAA
Found at i:57054009 original size:27 final size:28
Alignment explanation
Indices: 57053966--57054021 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
57053956 GTAATGTAAT
57053966 AATTTTAAGTAAATAATATATTTAAGTA
1 AATTTTAAGTAAATAATATATTTAAGTA
* *
57053994 AATTTT-AGTAATTAATATATTTACGTA
1 AATTTTAAGTAAATAATATATTTAAGTA
57054021 A
1 A
57054022 TGTAAGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (28 bp):
AATTTTAAGTAAATAATATATTTAAGTA
Found at i:57054092 original size:11 final size:11
Alignment explanation
Indices: 57054061--57054093 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
57054051 ATATATTAAT
57054061 AATTCATTGAC
1 AATTCATTGAC
57054072 -ATTCATTGAC
1 AATTCATTGAC
*
57054082 AATTCACTGAC
1 AATTCATTGAC
57054093 A
1 A
57054094 GTCAATCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (11 bp):
AATTCATTGAC
Found at i:57055169 original size:12 final size:12
Alignment explanation
Indices: 57055148--57055178 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57055138 AAATATCGCT
*
57055148 AAACAGACTAGA
1 AAACAAACTAGA
57055160 AAACAAACTAGA
1 AAACAAACTAGA
57055172 AAACAAA
1 AAACAAA
57055179 ACCCAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.16, G:0.10, T:0.06
Consensus pattern (12 bp):
AAACAAACTAGA
Found at i:57055672 original size:157 final size:157
Alignment explanation
Indices: 57055386--57055697 Score: 588
Period size: 157 Copynumber: 2.0 Consensus size: 157
57055376 CTTCATTATT
57055386 ATTTTGAGATTCAATTTACCTAGATTTTCCCTTTTGTGTCCTGCACTTAAAAAAGCCACTAACAA
1 ATTTTGAGATTCAATTTACCTAGATTTTCCCTTTTGTGTCCTGCACTTAAAAAAGCCACTAACAA
*
57055451 ACCCATCATTTTGCAACATATGCTAAGAAACAGTTTTCAATAAACATGAAATGATGATATTTTCT
66 ACCCATCATTTTGCAACATATGCTAAGAAACAGTTCTCAATAAACATGAAATGATGATATTTTCT
*
57055516 GCTGCAGATTAGCTAGAGGAATGGTTA
131 GCTGCAGATTAGCTAGACGAATGGTTA
* *
57055543 ATTTTGAGATTCAATTTAGCTAGATTTTCCCTTTTGTGTCCTGCACTTTAAAAAGCCACTAACAA
1 ATTTTGAGATTCAATTTACCTAGATTTTCCCTTTTGTGTCCTGCACTTAAAAAAGCCACTAACAA
57055608 ACCCATCATTTTGCAACATATGCTAAGAAACAGTTCTCAATAAACATGAAATGATGATATTTTCT
66 ACCCATCATTTTGCAACATATGCTAAGAAACAGTTCTCAATAAACATGAAATGATGATATTTTCT
57055673 GCTGCAGATTAGCTAGACGAATGGT
131 GCTGCAGATTAGCTAGACGAATGGT
57055698 CAAAGACATT
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 151 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (157 bp):
ATTTTGAGATTCAATTTACCTAGATTTTCCCTTTTGTGTCCTGCACTTAAAAAAGCCACTAACAA
ACCCATCATTTTGCAACATATGCTAAGAAACAGTTCTCAATAAACATGAAATGATGATATTTTCT
GCTGCAGATTAGCTAGACGAATGGTTA
Found at i:57055796 original size:32 final size:33
Alignment explanation
Indices: 57055749--57055812 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
57055739 GAAATTTGAG
57055749 TATACCAAAATAATTAGATACCAAAATAAGAAT
1 TATACCAAAATAATTAGATACCAAAATAAGAAT
57055782 TATACC-AAATAATTAGATACCAAAATAAGAA
1 TATACCAAAATAATTAGATACCAAAATAAGAA
57055813 AACAGGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.81
33 6 0.19
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.23
Consensus pattern (33 bp):
TATACCAAAATAATTAGATACCAAAATAAGAAT
Found at i:57055803 original size:15 final size:16
Alignment explanation
Indices: 57055750--57055809 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
57055740 AAATTTGAGT
57055750 ATACCAAAATAATTAG
1 ATACCAAAATAATTAG
** *
57055766 ATACCAAAATAAGAATT
1 ATACCAAAATAATTA-G
57055783 ATACC-AAATAATTAG
1 ATACCAAAATAATTAG
57055798 ATACCAAAATAA
1 ATACCAAAATAA
57055810 GAAAACAGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 5 0.14
16 26 0.72
17 5 0.14
ACGTcount: A:0.58, C:0.13, G:0.05, T:0.23
Consensus pattern (16 bp):
ATACCAAAATAATTAG
Found at i:57056169 original size:14 final size:14
Alignment explanation
Indices: 57056132--57056170 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
57056122 CTCCTCTGAT
*
57056132 TTTTTTTCTTTGTA
1 TTTTTTTCTTTCTA
**
57056146 TTTTGGTCTTTCTA
1 TTTTTTTCTTTCTA
57056160 TTTTTTTCTTT
1 TTTTTTTCTTT
57056171 TCCTTTCGAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.05, C:0.10, G:0.08, T:0.77
Consensus pattern (14 bp):
TTTTTTTCTTTCTA
Found at i:57057125 original size:7 final size:7
Alignment explanation
Indices: 57057102--57057139 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
57057092 ATATAATTCT
57057102 TAACCCC
1 TAACCCC
**
57057109 TAACGTC
1 TAACCCC
57057116 TAACCCC
1 TAACCCC
57057123 TAACCCC
1 TAACCCC
57057130 TAACCCC
1 TAACCCC
57057137 TAA
1 TAA
57057140 ACCTTAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.32, C:0.47, G:0.03, T:0.18
Consensus pattern (7 bp):
TAACCCC
Found at i:57057155 original size:21 final size:20
Alignment explanation
Indices: 57057131--57057171 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
57057121 CCTAACCCCT
*
57057131 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
57057152 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
57057172 TAGTCCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:57058162 original size:29 final size:28
Alignment explanation
Indices: 57058120--57058178 Score: 100
Period size: 29 Copynumber: 2.1 Consensus size: 28
57058110 AAATACCTCA
*
57058120 GCATTAGCGGCGCTTTTCCAGAAAACGCC
1 GCATTAGCGGCGCTTTTACA-AAAACGCC
57058149 GCATTAGCGGCGCTTTTACAAAAACGCC
1 GCATTAGCGGCGCTTTTACAAAAACGCC
57058177 GC
1 GC
57058179 TAAGAGCCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (28 bp):
GCATTAGCGGCGCTTTTACAAAAACGCC
Found at i:57058337 original size:39 final size:40
Alignment explanation
Indices: 57058262--57058376 Score: 121
Period size: 40 Copynumber: 2.9 Consensus size: 40
57058252 TTTGCTTTGG
* * * * *
57058262 CTATTTT-GCGGCGTTTTTATTAAAACCGCCGGTAATGGTT
1 CTATTTTAGCGGCG-TTTTCTTAAAAACGCCGCTAATGCTC
57058302 CT-TTTTAGCGGCGTGTTAT-TTAAAAA-GCCGCTAATGCTC
1 CTATTTTAGCGGCGT-TT-TCTTAAAAACGCCGCTAATGCTC
*
57058341 CTATTTTAGCGGCGTTTTCTTAAAAACACCGCTAAT
1 CTATTTTAGCGGCGTTTTCTTAAAAACGCCGCTAAT
57058377 TCTCGATTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
38 1 0.02
39 26 0.41
40 36 0.56
41 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (40 bp):
CTATTTTAGCGGCGTTTTCTTAAAAACGCCGCTAATGCTC
Found at i:57058386 original size:39 final size:40
Alignment explanation
Indices: 57058304--57058386 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
57058294 TAATGGTTCT
* *
57058304 TTTTAGCGGCGTGTTATTTAAAAAGCCGCTAATGCTCCTA
1 TTTTAGCGGCGTGTTATTTAAAAAACCGCTAATGCTCCGA
*
57058344 TTTTAGCGGCGT-TT-TCTTAAAAACACCGCTAATTCT-CGA
1 TTTTAGCGGCGTGTTAT-TTAAAAA-ACCGCTAATGCTCCGA
57058383 TTTT
1 TTTT
57058387 TTCCGGCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
38 1 0.03
39 15 0.39
40 22 0.58
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (40 bp):
TTTTAGCGGCGTGTTATTTAAAAAACCGCTAATGCTCCGA
Found at i:57066520 original size:40 final size:40
Alignment explanation
Indices: 57066472--57066564 Score: 127
Period size: 40 Copynumber: 2.3 Consensus size: 40
57066462 TTTGGATAAC
* * *
57066472 AAACGCCGCTAAAGATCGAGCA-TTAGCGGCGCT-TTCTGGA
1 AAACGCCGCTAAAGATCGAG-ATTTAGCGACGCTCTAC-GAA
57066512 AAACGCCGCTAAAGATCGAGATTTAGCGACGCTCTACGAA
1 AAACGCCGCTAAAGATCGAGATTTAGCGACGCTCTACGAA
57066552 AAACGCCGCTAAA
1 AAACGCCGCTAAA
57066565 AATAAGTACT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
39 1 0.02
40 45 0.94
41 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (40 bp):
AAACGCCGCTAAAGATCGAGATTTAGCGACGCTCTACGAA
Found at i:57066700 original size:41 final size:41
Alignment explanation
Indices: 57066638--57066956 Score: 352
Period size: 41 Copynumber: 7.8 Consensus size: 41
57066628 CTTTCGGGGA
* ** * ****
57066638 TTTAGTGGCGTTTTTAAGAAAGCGCCGCGAATATTTAGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCCCAGGGC
* * *
57066679 TTTAGCGGCGATTTTGGGAAAGCGCCGCTAAAGCCCTGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCCCAGGGC
* * *
57066720 ATTAGTGGCGTGTTTGGGAAAGCGCCGCTAATGCCCAGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCCCAGGGC
* * *
57066761 TTTAGCAGCGTGTTTT-GGAAAGCGCCACTAATGTCCAGGGC
1 TTTAGCGGCGT-TTTTGGGAAAGCGCCGCTAATGCCCAGGGC
* *
57066802 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGTCCATGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCCCAGGGC
* * *
57066843 TTTAGCGTCATTTTTGGGAAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCCCAGGGC
** * * * * *
57066884 TTTAGCGTTGTTTTTGAGAAAGCGCTGCTAACGCTCAGGGA
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCCCAGGGC
*
57066925 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAAT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAT
57066957 AATGCTCAGG
Statistics
Matches: 235, Mismatches: 41, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
40 4 0.02
41 228 0.97
42 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCCCAGGGC
Found at i:57068258 original size:19 final size:19
Alignment explanation
Indices: 57068234--57068271 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
57068224 GTAAAATTTT
*
57068234 TTATCATTTTGACTTTTAA
1 TTATCATTTTAACTTTTAA
57068253 TTATCATTTTAACTTTTAA
1 TTATCATTTTAACTTTTAA
57068272 CATTTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (19 bp):
TTATCATTTTAACTTTTAA
Found at i:57068538 original size:43 final size:43
Alignment explanation
Indices: 57068481--57068763 Score: 368
Period size: 43 Copynumber: 6.6 Consensus size: 43
57068471 AAAAATGCCA
* * * * *
57068481 CTAAAAGTCATGGTCTTTAGCAGCGTTTGTGGAAAAAGCCCCG
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCG
* * * * *
57068524 CTAAAGGTCGTGGTCTTTAGCGGTGTTTTTGGTAAAAGCGCCA
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCG
*
57068567 CTAAAGGTCTTGGTCTTTAGTGGCGTTTGTGGGAAAAGCGCCG
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCG
* * *
57068610 CTAAAGGTCATGGACTTTAGCGGCGTTTGTGAGAAAAGCGCCG
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCG
* * * *
57068653 CTAATGGTCTTGGTCTTTAGCGGCGTTTATGGGAAAGGCGTCG
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCG
*
57068696 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCAG
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCG
* * *
57068739 TTGAGGGTCTTGGTCTTTAGCGGCG
1 CTAAAGGTCTTGGTCTTTAGCGGCG
57068764 CTGTCATTAG
Statistics
Matches: 207, Mismatches: 33, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 207 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.29
Consensus pattern (43 bp):
CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCG
Found at i:57069440 original size:20 final size:20
Alignment explanation
Indices: 57069412--57069455 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
57069402 CTCGAGTATT
*
57069412 AAAATTATGAGAGAA-TATCA
1 AAAAGTATGAGA-AAGTATCA
57069432 AAAAGTATGAGAAAGTATCA
1 AAAAGTATGAGAAAGTATCA
57069452 AAAA
1 AAAA
57069456 AAATATAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAAGTATGAGAAAGTATCA
Found at i:57069558 original size:188 final size:192
Alignment explanation
Indices: 57069338--57069727 Score: 734
Period size: 188 Copynumber: 2.0 Consensus size: 192
57069328 GAAACAAAAC
57069338 ATATATATTTTTATATTCCCTCATTTTTTTTTGTACTTTTTTCATATATATTTTTTAATATTCTC
1 ATATATATTTTTATATTCCCTCATTTTTTTTTGTACTTTTTTCATATATATTTTTTAATATTCTC
57069403 TCGAGTATT-AAAATTATGAGAGAATATCAAAAAGTATGAGAAAGTATC-AAAAAAAATATAAGA
66 TCGAGTATTAAAAATTATGAGAGAATATCAAAAAGTATGAGAAAGTATCAAAAAAAAATATAAGA
57069466 GAAT-TGAAATATTAATTTATCTTATAAACTTTGCTTTATTTATTTA-TTTTAAATATTATT
131 GAATATGAAATATTAATTTATCTTATAAACTTTGCTTTATTTATTTATTTTTAAATATTATT
57069526 ATATATATTTTTATATTCCCTCATTTTTTTTTGTACTTTTTTCATATATATTTTTTAATATTCTC
1 ATATATATTTTTATATTCCCTCATTTTTTTTTGTACTTTTTTCATATATATTTTTTAATATTCTC
57069591 TCGAGTATTAAAAATTATGAGAGAATATCAAAAAGTATGAGAAAGTATCAAAAAAAAAATATAAG
66 TCGAGTATTAAAAATTATGAGAGAATATCAAAAAGTATGAGAAAGTATC-AAAAAAAAATATAAG
57069656 AGAATATGAAATATTAATTTATCTTATAAACTTTGCTTTATTTATTTATTTTTAAATATTATT
130 AGAATATGAAATATTAATTTATCTTATAAACTTTGCTTTATTTATTTATTTTTAAATATTATT
57069719 AGTATATAT
1 A-TATATAT
57069728 AAAAAATTTA
Statistics
Matches: 196, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
188 74 0.38
189 39 0.20
191 19 0.10
192 42 0.21
193 15 0.08
194 7 0.04
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (192 bp):
ATATATATTTTTATATTCCCTCATTTTTTTTTGTACTTTTTTCATATATATTTTTTAATATTCTC
TCGAGTATTAAAAATTATGAGAGAATATCAAAAAGTATGAGAAAGTATCAAAAAAAAATATAAGA
GAATATGAAATATTAATTTATCTTATAAACTTTGCTTTATTTATTTATTTTTAAATATTATT
Found at i:57069629 original size:20 final size:20
Alignment explanation
Indices: 57069594--57069644 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
57069584 TATTCTCTCG
* *
57069594 AGTATTAAAAATTATGAGAGA
1 AGTATCAAAAAGTATGAGA-A
57069615 A-TATCAAAAAGTATGAGAA
1 AGTATCAAAAAGTATGAGAA
57069634 AGTATCAAAAA
1 AGTATCAAAAA
57069645 AAAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.16, T:0.24
Consensus pattern (20 bp):
AGTATCAAAAAGTATGAGAA
Found at i:57069756 original size:20 final size:21
Alignment explanation
Indices: 57069709--57069756 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
57069699 ATTTATTTTT
*
57069709 AAATA-TTATTAGTATATATA
1 AAATATTTATTAGTATACATA
*
57069729 AAAAATTTATTAGTATACA-A
1 AAATATTTATTAGTATACATA
57069749 AAATATTT
1 AAATATTT
57069757 TTTTTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (21 bp):
AAATATTTATTAGTATACATA
Found at i:57070343 original size:9 final size:9
Alignment explanation
Indices: 57070329--57070376 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
57070319 TGATATAAAC
57070329 TTATAAAAA
1 TTATAAAAA
57070338 TTATAAAAAAA
1 TTAT--AAAAA
*
57070349 TTACAAAAA
1 TTATAAAAA
*
57070358 CTTATAAAAC
1 -TTATAAAAA
57070368 TTATAAAAA
1 TTATAAAAA
57070377 CTACCTAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 17 0.53
10 7 0.22
11 8 0.25
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (9 bp):
TTATAAAAA
Found at i:57070366 original size:10 final size:10
Alignment explanation
Indices: 57070325--57070378 Score: 67
Period size: 10 Copynumber: 5.5 Consensus size: 10
57070315 GAATTGATAT
57070325 AAACTTATAA
1 AAACTTATAA
57070335 AAA-TTATAAA
1 AAACTTAT-AA
* *
57070345 AAAATTACAA
1 AAACTTATAA
57070355 AAACTTAT-A
1 AAACTTATAA
57070364 AAACTTATAA
1 AAACTTATAA
57070374 AAACT
1 AAACT
57070379 ACCTAACAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
9 13 0.34
10 22 0.58
11 3 0.08
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (10 bp):
AAACTTATAA
Found at i:57070419 original size:24 final size:24
Alignment explanation
Indices: 57070389--57070436 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
57070379 ACCTAACAGA
57070389 AAGACTAGTTGGGGACCGACTGAG
1 AAGACTAGTTGGGGACCGACTGAG
57070413 AAGACTAGTTGGGGACCGACTGAG
1 AAGACTAGTTGGGGACCGACTGAG
57070437 GCTTTGAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.38, T:0.17
Consensus pattern (24 bp):
AAGACTAGTTGGGGACCGACTGAG
Found at i:57072104 original size:21 final size:21
Alignment explanation
Indices: 57072062--57072103 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
57072052 AATATTGTAG
57072062 ATAAAAATTTTAAAAATAAAA
1 ATAAAAATTTTAAAAATAAAA
*
57072083 ATAAAAA-TTTATAAATAAAA
1 ATAAAAATTTTAAAAATAAAA
57072103 A
1 A
57072104 AGAAGAGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
ATAAAAATTTTAAAAATAAAA
Found at i:57072344 original size:19 final size:20
Alignment explanation
Indices: 57072322--57072369 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
57072312 TTTTACATGA
*
57072322 TTTATATTTTTTTAT-AATT
1 TTTATATTTTTATATCAATT
**
57072341 TTTATAACTTTATATCAATT
1 TTTATATTTTTATATCAATT
*
57072361 TTAATATTT
1 TTTATATTT
57072370 AATAATTTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTATATTTTTATATCAATT
Found at i:57072395 original size:26 final size:27
Alignment explanation
Indices: 57072330--57072395 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 27
57072320 GATTTATATT
*
57072330 TTTTTATAATTTTTATAACTTTATATCAA
1 TTTTTAT-A-TTTAATAACTTTATATCAA
* *
57072359 TTTTAATATTTAATAA-TTTA-ATTAA
1 TTTTTATATTTAATAACTTTATATCAA
57072384 TTTTTATGATTT
1 TTTTTAT-ATTT
57072396 TTATGATTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 10 0.31
26 8 0.25
27 7 0.22
28 1 0.03
29 6 0.19
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTTATATTTAATAACTTTATATCAA
Found at i:57075041 original size:33 final size:33
Alignment explanation
Indices: 57074965--57075042 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
57074955 CCTTTCCAGG
* *
57074965 TCACCTTCACCATCATATTCTACCCCTACATCA
1 TCACCTTCCCCATCATATTCTACCCCTACAACA
* * *
57074998 TCACCCTCCCCATCA-ACTTCTATCCCTTCAACA
1 TCACCTTCCCCATCATA-TTCTACCCCTACAACA
57075031 TCACCTTCCCCA
1 TCACCTTCCCCA
57075043 ACAGTCAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 1 0.03
33 37 0.97
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.28
Consensus pattern (33 bp):
TCACCTTCCCCATCATATTCTACCCCTACAACA
Found at i:57076403 original size:12 final size:12
Alignment explanation
Indices: 57076364--57076403 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
57076354 CAATCCACAA
57076364 TCCACATTTCATTT
1 TCCA-ATTTCA-TT
*
57076378 TCCATTTTCATT
1 TCCAATTTCATT
57076390 TCCAATTTCATT
1 TCCAATTTCATT
57076402 TC
1 TC
57076404 TTATTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 15 0.62
13 5 0.21
14 4 0.17
ACGTcount: A:0.20, C:0.28, G:0.00, T:0.53
Consensus pattern (12 bp):
TCCAATTTCATT
Found at i:57080477 original size:12 final size:12
Alignment explanation
Indices: 57080460--57080484 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57080450 ATTTAGGTGA
57080460 AAAAATATTTTT
1 AAAAATATTTTT
57080472 AAAAATATTTTT
1 AAAAATATTTTT
57080484 A
1 A
57080485 TTAGGGGTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:57084070 original size:19 final size:19
Alignment explanation
Indices: 57084046--57084082 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57084036 CAACATATCA
57084046 TAATAAAACAAAATTTTAG
1 TAATAAAACAAAATTTTAG
* *
57084065 TAATAATACATAATTTTA
1 TAATAAAACAAAATTTTA
57084083 AAACAAGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (19 bp):
TAATAAAACAAAATTTTAG
Done.