Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 56 of 64
Found at i:11339030 original size:20 final size:20
Alignment explanation
Indices: 11338968--11339161 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
11338958 CGATTTTCCA
* ** *
11338968 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
11338988 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
11339008 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
11339028 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
11339048 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
11339068 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
11339088 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
11339108 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
11339128 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
11339149 AAATCGCAACGCG
1 AAATCGCAACGCG
11339162 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:11339052 original size:60 final size:60
Alignment explanation
Indices: 11338968--11339161 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
11338958 CGATTTTCCA
* ** * *
11338968 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
11339028 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
11339088 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
11339149 AAATCGCAACGCG
1 AAATCGCAACGCG
11339162 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:11339334 original size:21 final size:22
Alignment explanation
Indices: 11339308--11339361 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
11339298 CTCTCTACGG
11339308 CGAAGAAATCCGT-CCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
11339329 CGAAGATTTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
11339351 CGGCGAAATCC
1 CGAAGAAATCC
11339362 CTCACAACCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:11339581 original size:33 final size:33
Alignment explanation
Indices: 11339542--11339612 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
11339532 TTCACTTAGA
*
11339542 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
11339575 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
11339608 TTTCA
1 TTTCA
11339613 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:11339797 original size:33 final size:32
Alignment explanation
Indices: 11339731--11339800 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
11339721 AGAATGACTG
***
11339731 TCGCAACGAGAGATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGATCGCAACGCGAAACCAAAA
11339763 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAG-ATCGCAACGCGAAACCAAAA
11339796 TCGCA
1 TCGCA
11339801 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.35
33 22 0.65
ACGTcount: A:0.41, C:0.26, G:0.24, T:0.09
Consensus pattern (32 bp):
TCGCAACGAGAGATCGCAACGCGAAACCAAAA
Found at i:11339818 original size:19 final size:19
Alignment explanation
Indices: 11339796--11339893 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
11339786 GAAACCAAAA
*
11339796 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
11339815 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
11339829 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
11339848 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
11339862 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
11339881 TCGCGTTGCGATT
1 TCGCGTTGCGATT
11339894 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:11339837 original size:14 final size:14
Alignment explanation
Indices: 11339818--11339907 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
11339808 TTTCATTTCG
11339818 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
11339832 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
11339851 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
11339865 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
11339882 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
11339898 CGTTGCGATT
1 CGTTGCGATT
11339908 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:11339843 original size:33 final size:33
Alignment explanation
Indices: 11339801--11339915 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
11339791 CAAAATCGCA
11339801 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
11339834 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
11339867 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
11339900 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
11339916 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:11341827 original size:92 final size:93
Alignment explanation
Indices: 11341611--11341897 Score: 567
Period size: 93 Copynumber: 3.1 Consensus size: 93
11341601 TAGATTGCTT
11341611 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
11341676 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
11341704 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
11341768 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
11341796 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
11341861 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
11341889 AGTAAATTT
1 AGTAAATTT
11341898 ATCCATTCAA
Statistics
Matches: 193, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.48
93 101 0.52
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:11341981 original size:19 final size:19
Alignment explanation
Indices: 11341941--11342069 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
11341931 TAGTTTACTT
* *
11341941 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
11341961 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
11341980 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
11341999 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
11342013 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
11342032 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
11342046 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
11342065 TCGCA
1 TCGCA
11342070 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:11342020 original size:33 final size:32
Alignment explanation
Indices: 11341977--11342069 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
11341967 CGCGAAACCA
**
11341977 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
11342009 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
11342042 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
11342070 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:11342067 original size:52 final size:52
Alignment explanation
Indices: 11341941--11342069 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
11341931 TAGTTTACTT
**
11341941 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
11341993 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
11342046 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
11342070 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:11342087 original size:19 final size:19
Alignment explanation
Indices: 11342065--11342199 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
11342055 GAAACCAAAA
*
11342065 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
11342084 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
11342100 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
11342117 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
11342133 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
11342150 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
11342169 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
11342189 TCGTGTTGCGA
1 TCGCGTTGCGA
11342200 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:11342106 original size:14 final size:14
Alignment explanation
Indices: 11342087--11342143 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
11342077 TTTCATTTCG
11342087 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
11342101 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
11342118 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
11342134 CGTTGCGATT
1 CGTTGCGATT
11342144 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:11342112 original size:33 final size:33
Alignment explanation
Indices: 11342070--11342162 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
11342060 CAAAATCGCA
*
11342070 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
11342103 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
11342136 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
11342163 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:11344009 original size:12 final size:12
Alignment explanation
Indices: 11343994--11344029 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
11343984 TGATTCAATA
11343994 GTTTAATTGATT
1 GTTTAATTGATT
**
11344006 GTTTTTTTGATT
1 GTTTAATTGATT
11344018 GTTTAATTGATT
1 GTTTAATTGATT
11344030 TGTAAAAGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (12 bp):
GTTTAATTGATT
Found at i:11344115 original size:14 final size:14
Alignment explanation
Indices: 11344096--11344131 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
11344086 ATTGTTTAAT
11344096 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
11344110 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
11344124 TGATTTGT
1 TGATTTGT
11344132 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:11344254 original size:19 final size:18
Alignment explanation
Indices: 11344238--11344337 Score: 136
Period size: 19 Copynumber: 5.6 Consensus size: 18
11344228 AAAAATGACT
11344238 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
11344257 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
11344276 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
11344290 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
11344308 ATCGCAATGCGGAAATGAA
1 ATCGCAATGC-GAAATGAA
11344327 ATCGCAATGCG
1 ATCGCAATGCG
11344338 TTTATAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 8 0.11
16 5 0.07
17 5 0.07
18 12 0.16
19 44 0.59
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:11344390 original size:19 final size:19
Alignment explanation
Indices: 11344366--11344672 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
11344356 GATTATCTCG
11344366 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
11344385 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
11344404 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
11344418 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
11344437 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
11344456 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
11344475 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
11344494 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
11344509 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
11344527 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
11344546 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
11344560 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
11344579 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
11344598 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
11344612 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
11344632 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
11344646 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
11344665 TTGCGATT
1 TTGCGATT
11344673 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.12
17 28 0.11
18 5 0.02
19 139 0.56
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:11344441 original size:71 final size:71
Alignment explanation
Indices: 11344366--11344605 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
11344356 GATTATCTCG
11344366 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
11344431 TTCGCA
66 TTCGCA
* *
11344437 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
* *
11344500 TT-ATGTCG-G
61 TTCATTTCGCA
*
11344509 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
11344573 TTCGCA
66 TTCGCA
11344579 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
11344606 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 6 0.04
68 6 0.04
69 7 0.05
70 2 0.01
71 107 0.71
72 2 0.01
73 7 0.05
74 7 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:11344515 original size:142 final size:136
Alignment explanation
Indices: 11344334--11344672 Score: 504
Period size: 142 Copynumber: 2.4 Consensus size: 136
11344324 GAAATCGCAA
11344334 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTAT-TCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
11344398 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-
*
11344463 TTTCATTTCGTAT
128 -TTC-TCTCG--T
11344476 TGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTAT-TC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
11344540 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
11344605 TCTCTCGT
129 TCTCTCGT
* * *
11344613 TGCGATTTTCATTTCCGCATTGCGATT-TTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATTC--GTTGCGATTTTCATTTCGCATTGCGATT
11344673 GTATTTTCCG
Statistics
Matches: 185, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 34 0.18
139 4 0.02
140 3 0.02
142 118 0.64
143 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (136 bp):
TGCGATTTTAATTTCGCATTGCGATTATTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTC
TCTCGT
Found at i:11344611 original size:52 final size:52
Alignment explanation
Indices: 11344366--11344644 Score: 354
Period size: 52 Copynumber: 5.2 Consensus size: 52
11344356 GATTATCTCG
*
11344366 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
11344418 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
11344475 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
11344527 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
11344579 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
11344632 TTGCGATTTTCAT
1 TTGCGATTTTCAT
11344645 GTTGGGATTT
Statistics
Matches: 212, Mismatches: 7, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
51 3 0.01
52 152 0.72
53 19 0.09
54 6 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:11345407 original size:20 final size:20
Alignment explanation
Indices: 11345379--11345747 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
11345369 AAATTTCAGT
* * * *
11345379 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
11345399 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
11345419 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
11345439 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
11345459 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
11345479 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
11345499 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
11345519 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
11345539 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
11345559 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
11345579 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
11345599 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
11345619 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* * **
11345639 ATTACGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
11345659 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
11345679 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
11345699 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
11345719 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
11345739 GTTGCGATT
1 GTTGCGATT
11345748 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 34, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 5 0.02
20 297 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:11346314 original size:38 final size:37
Alignment explanation
Indices: 11346270--11346341 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
11346260 TTGGCCATTG
* * *
11346270 GTTCGAAGGCCGCGGAGTGGCATTTTATTTTCTCCTTT
1 GTTCGAA-GCCACAGAGTAGCATTTTATTTTCTCCTTT
*
11346308 GTTCGAAGCCACATAGTAGCATTTTATTTTCTCC
1 GTTCGAAGCCACAGAGTAGCATTTTATTTTCTCC
11346342 AATTGTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 23 0.77
38 7 0.23
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (37 bp):
GTTCGAAGCCACAGAGTAGCATTTTATTTTCTCCTTT
Found at i:11346369 original size:20 final size:20
Alignment explanation
Indices: 11346344--11346384 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
11346334 TTTTCTCCAA
11346344 TTGTTTTCCTTTAATAAAAG
1 TTGTTTTCCTTTAATAAAAG
11346364 TTGTTTTCCTTTAATAAAAG
1 TTGTTTTCCTTTAATAAAAG
11346384 T
1 T
11346385 AGTGACACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (20 bp):
TTGTTTTCCTTTAATAAAAG
Found at i:11346529 original size:17 final size:17
Alignment explanation
Indices: 11346507--11346546 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
11346497 ATTTATTTAA
*
11346507 TTAAATTAAAATAATAT
1 TTAAATTAAAAGAATAT
*
11346524 TTAAATTAATAGAATAT
1 TTAAATTAAAAGAATAT
*
11346541 ATAAAT
1 TTAAAT
11346547 ATTAAGAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
TTAAATTAAAAGAATAT
Found at i:11346697 original size:13 final size:13
Alignment explanation
Indices: 11346679--11346714 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
11346669 TTTGATGGAT
11346679 AAATTAATTTTTG
1 AAATTAATTTTTG
11346692 AAATTAATTTTTG
1 AAATTAATTTTTG
11346705 AAATTAATTT
1 AAATTAATTT
11346715 ACCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
AAATTAATTTTTG
Found at i:11349816 original size:36 final size:36
Alignment explanation
Indices: 11349761--11349848 Score: 151
Period size: 36 Copynumber: 2.5 Consensus size: 36
11349751 TTTTTATTAT
*
11349761 TTCGGGTC-GGTCGGGTTGGATTTCTAATTCATATA
1 TTCGGGTCGGGTCGGATTGGATTTCTAATTCATATA
*
11349796 TTCGGATCGGGTCGGATTGGATTTCTAATTCATATA
1 TTCGGGTCGGGTCGGATTGGATTTCTAATTCATATA
11349832 TTCGGGTCGGGTCGGAT
1 TTCGGGTCGGGTCGGAT
11349849 GAAACTTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 7 0.14
36 42 0.86
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.38
Consensus pattern (36 bp):
TTCGGGTCGGGTCGGATTGGATTTCTAATTCATATA
Found at i:11349931 original size:38 final size:38
Alignment explanation
Indices: 11349868--11349957 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
11349858 TTTTGTTCGG
*
11349868 GTCGGGTCGGG-ATTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
* *
11349905 GTCGGGTCGGGTTTTTTTACGTGTGATATTCGGGTCGG
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
11349943 GTCGGGTTCGGGTTT
1 GTCGGG-TCGGGTTT
11349958 AGGGTGAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
37 11 0.23
38 29 0.60
39 8 0.17
ACGTcount: A:0.10, C:0.12, G:0.40, T:0.38
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:11350150 original size:27 final size:28
Alignment explanation
Indices: 11350118--11350180 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
11350108 TTTGTTCGGG
11350118 TCGGGTCGAG-TTTTTTAAGTGTAATAT
1 TCGGGTCGAGTTTTTTTAAGTGTAATAT
* *
11350145 TGGGGTCGAGTTTTTTTAAGTGTGATAT
1 TCGGGTCGAGTTTTTTTAAGTGTAATAT
11350173 TCGGGTCG
1 TCGGGTCG
11350181 TGTTCGGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.17, C:0.08, G:0.32, T:0.43
Consensus pattern (28 bp):
TCGGGTCGAGTTTTTTTAAGTGTAATAT
Found at i:11351179 original size:2 final size:2
Alignment explanation
Indices: 11351172--11351308 Score: 81
Period size: 2 Copynumber: 73.5 Consensus size: 2
11351162 ACATTATTAT
11351172 TA TA TA TA TA GTA TA TA T- TA T- TA T- TA T- TA T- TA TA TA GTA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
11351211 TA TA GTA TA TA T- TA TA TA TA TA T- TA TA T- TA TA T- TA TA AA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
11351250 GT- TCA TA TA T- TA TA T- TT TCA TA T- TA TA TA TA TA TA TA TA
1 -TA T-A TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
*
11351289 T- TA TA TT TA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
11351309 TTAGATCTAA
Statistics
Matches: 108, Mismatches: 5, Indels: 44
0.69 0.03 0.28
Matches are distributed among these distances:
1 16 0.15
2 84 0.78
3 8 0.07
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (2 bp):
TA
Found at i:11351188 original size:7 final size:7
Alignment explanation
Indices: 11351166--11351308 Score: 111
Period size: 7 Copynumber: 20.1 Consensus size: 7
11351156 TATGATACAT
11351166 TATTAT-
1 TATTATA
11351172 TATATATA
1 TAT-TATA
*
11351180 TAGTATA
1 TATTATA
11351187 TATTAT-
1 TATTATA
11351193 TATTAT-
1 TATTATA
11351199 TATTATA
1 TATTATA
*
11351206 TAGTATA
1 TATTATA
*
11351213 TAGTATA
1 TATTATA
11351220 TATTATA
1 TATTATA
11351227 TA-TATA
1 TATTATA
11351233 T-TATATTA
1 TAT-TA-TA
11351241 TATTATA
1 TATTATA
*
11351248 AAGTTCATA
1 TA-TT-ATA
11351257 TATTATA
1 TATTATA
*
11351264 TTTTCATA
1 TATT-ATA
11351272 T-TATATA
1 TAT-TATA
11351279 TATATATA
1 TAT-TATA
11351287 TATTATA
1 TATTATA
11351294 T-TTATTA
1 TATTA-TA
11351301 TATTATA
1 TATTATA
11351308 T
1 T
11351309 TTAGATCTAA
Statistics
Matches: 116, Mismatches: 7, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
6 23 0.20
7 60 0.52
8 28 0.24
9 5 0.04
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (7 bp):
TATTATA
Found at i:11351192 original size:21 final size:21
Alignment explanation
Indices: 11351166--11351309 Score: 124
Period size: 21 Copynumber: 6.9 Consensus size: 21
11351156 TATGATACAT
*
11351166 TATTATTATATATATAGTATA
1 TATTATTATATATATATTATA
11351187 TATTATTAT-TAT-TATTATA
1 TATTATTATATATATATTATA
*
11351206 TAGTA-TATAGTATATATTATA
1 TATTATTATA-TATATATTATA
11351227 TATATATTATAT-TATATTATA
1 TAT-TATTATATATATATTATA
* *
11351248 AAGTTCA-TATAT-TATATTTTCA
1 TA-TT-ATTATATATATATTAT-A
11351270 TATTA-TATATATATATATATTA
1 TATTATTATATATATAT-TA-TA
11351292 TATTTATTATAT-TATATT
1 TA-TTATTATATATATATT
11351310 TAGATCTAAA
Statistics
Matches: 103, Mismatches: 7, Indels: 25
0.76 0.05 0.19
Matches are distributed among these distances:
18 3 0.03
19 10 0.10
20 12 0.12
21 48 0.47
22 12 0.12
23 13 0.13
24 5 0.05
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (21 bp):
TATTATTATATATATATTATA
Found at i:11351232 original size:51 final size:49
Alignment explanation
Indices: 11351169--11351301 Score: 155
Period size: 51 Copynumber: 2.6 Consensus size: 49
11351159 GATACATTAT
11351169 TATTATATATATAGTATATATTATTATTATTATT-ATATAGTATATAGTAT-A
1 TATTATATATATA-TATATATTA-TATTATTATTCATATA-T-TATAGTATCA
* * *
11351220 TATTATATATATAT-TATATTATATTATAAAGTTCATATATTATATTTTCA
1 TATTATATATATATATATATTATATTAT-TA-TTCATATATTATAGTATCA
11351270 TATTATATATATATATATATTATATTTATTAT
1 TATTATATATATATATATATTATA-TTATTAT
11351302 ATTATATTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
48 6 0.08
49 14 0.19
50 20 0.28
51 28 0.39
52 4 0.06
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (49 bp):
TATTATATATATATATATATTATATTATTATTCATATATTATAGTATCA
Found at i:11351930 original size:17 final size:17
Alignment explanation
Indices: 11351883--11351936 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
11351873 CGAAAACCAT
11351883 AAAAAAACCAACCAAG-
1 AAAAAAACCAACCAAGC
* * * *
11351899 TAAAATA-CGAGCAAGC
1 AAAAAAACCAACCAAGC
11351915 AAAAAAACCAACCAAGC
1 AAAAAAACCAACCAAGC
11351932 AAAAA
1 AAAAA
11351937 TCAAGGAGAA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
15 6 0.21
16 10 0.36
17 12 0.43
ACGTcount: A:0.65, C:0.22, G:0.09, T:0.04
Consensus pattern (17 bp):
AAAAAAACCAACCAAGC
Found at i:11352454 original size:36 final size:36
Alignment explanation
Indices: 11352375--11352457 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
11352365 ACTGAATTAA
* *
11352375 ACGGGGACGAGGAAAAACCATTTATGCTAAACGGGG
1 ACGGGGATGGGGAAAAACCATTTATGCTAAACGGGG
* * * *
11352411 ACGGGGATGGGGAAAAATCGTTTATGTTAAATGGGG
1 ACGGGGATGGGGAAAAACCATTTATGCTAAACGGGG
11352447 ACGGGGATGGG
1 ACGGGGATGGG
11352458 TTTAGTAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.31, C:0.11, G:0.40, T:0.18
Consensus pattern (36 bp):
ACGGGGATGGGGAAAAACCATTTATGCTAAACGGGG
Found at i:11352550 original size:33 final size:32
Alignment explanation
Indices: 11352512--11352589 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
11352502 ATATTAAAAA
*
11352512 TAATTATTATATATATTATATATAAATTTAATT
1 TAATTA-TATATATAATATATATAAATTTAATT
* * *
11352545 TAATTAAAATATATAATATTTATATATTTAATT
1 TAATT-ATATATATAATATATATAAATTTAATT
*
11352578 TAAATATATATA
1 TAATTATATATA
11352590 CATGGCCCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 6 0.16
33 31 0.82
34 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TAATTATATATATAATATATATAAATTTAATT
Found at i:11352559 original size:28 final size:29
Alignment explanation
Indices: 11352528--11352589 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
11352518 TTATATATAT
11352528 TATATATA-AATT-TA-ATTTAATTAAAA
1 TATATATATAATTATATATTTAATTAAAA
* *
11352554 TATATA-ATATTTATATATTTAATTTAAA
1 TATATATATAATTATATATTTAATTAAAA
11352582 TATATATA
1 TATATATA
11352590 CATGGCCCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 9 0.30
27 2 0.07
28 17 0.57
29 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TATATATATAATTATATATTTAATTAAAA
Found at i:11353085 original size:9 final size:9
Alignment explanation
Indices: 11353060--11353140 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 9
11353050 ATTTAATCCT
11353060 TTTATTTTA
1 TTTATTTTA
*
11353069 GATT-TTTTA
1 -TTTATTTTA
11353078 TTTATTTTA
1 TTTATTTTA
*
11353087 TTTATTTAATT
1 TTTATTT--TA
*
11353098 TTTATTTAA
1 TTTATTTTA
11353107 TTT-TTTTA
1 TTTATTTTA
* *
11353115 TCTACTTTA
1 TTTATTTTA
11353124 CTCTTATTTTA
1 -T-TTATTTTA
11353135 -TTATTT
1 TTTATTT
11353141 AACATTATTT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
8 14 0.25
9 24 0.44
10 3 0.05
11 14 0.25
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (9 bp):
TTTATTTTA
Found at i:11361017 original size:2 final size:2
Alignment explanation
Indices: 11361000--11361334 Score: 203
Period size: 2 Copynumber: 176.5 Consensus size: 2
11360990 TTTTGTTTTT
*
11361000 TA TA TGA TA TA GTA TA TA TA TA TA T- TA TA TT TA TA TA T- TA TA
1 TA TA T-A TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11361042 TA -A TA TA TA TA T- TA TA TA TA TA TA TA T- TA T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
11361079 T- TA TA T- TA TA TT TA TA TT TA TA TA T- TA TA GTG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
11361119 TT TA GTA TA TA T- TA TA TA T- TA TA TT TA TA TA GTA TA TA GTA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
11361160 TA TA TA T- TA T- TA T- TA TA TA TA TA TA CT- TA GTA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA
* * *
11361199 -A TT TA TA -A TA TA TA T- TA TA TT TA TA TA T- TA TA TGG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* *
11361238 TA T- TA TA T- TT TA TA TA GTA TA TA GTA TA TA TA T- TA T- TA TT
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* *
11361278 TA TA T- TA TA AA CT- TCA TA TA T- TA TA T- TT TCA TA T- TA TA
1 TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA T-A TA TA TA TA
11361316 T- TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
11361335 TGTTATTATT
Statistics
Matches: 263, Mismatches: 24, Indels: 92
0.69 0.06 0.24
Matches are distributed among these distances:
1 32 0.12
2 210 0.80
3 21 0.08
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.55
Consensus pattern (2 bp):
TA
Found at i:11361102 original size:66 final size:66
Alignment explanation
Indices: 11361012--11361368 Score: 326
Period size: 66 Copynumber: 5.2 Consensus size: 66
11361002 TATGATATAG
*
11361012 TATATATATATATTATATTTATATATTATATA-ATATATATATTATATATATATATATTATTATT
1 TATATATATATATTATATTTATATATTATATATATATATATAGTATATAT-TAT-TATTA-TATT
11361076 ATAT
63 ATAT
*
11361080 TATAT-TATAT-TTATATTTATATATTATAGTGTATATATATTTAGTATATATTATATATTATAT
1 TATATATATATATTATATTTATATATTATA---TATATATATATAGTATATATTAT-TATTATAT
11361143 T-TA-
62 TATAT
*
11361146 TATAGTATATAGTA-TATATATTAT-TATTATATATATATACT-TAGTATATATTAAT-TTATAA
1 TATA-TATATA-TATTATAT-TTATATATTATATATATATA-TATAGTATATATTATTATTAT-A
11361207 TATATAT
61 T-TATAT
* *
11361214 TATATTTATATATTATATGGTATATATTATATTTTATATAGTATATAGTATATA-TATTATTAT-
1 TATATATATATATTATAT-TTATATATTATA---TATATA-TATATAGTATATATTATTATTATA
11361277 TTATAT
61 TTATAT
* * *
11361283 TATAAACTTCATATATTATATTT-TCATATTATATTATATATATATATTATATTGTTATTATTAT
1 TATATA--T-ATATATTATATTTAT-ATATTATA-TATATATATATAGTATA-TATTATTATTAT
11361347 ATTATAT
60 ATTATAT
*
11361354 TATATACATAT-TTAT
1 TATATATATATATTAT
11361369 TTAATTTAAT
Statistics
Matches: 246, Mismatches: 14, Indels: 59
0.77 0.04 0.18
Matches are distributed among these distances:
64 4 0.02
65 3 0.01
66 45 0.18
67 28 0.11
68 38 0.15
69 41 0.17
70 30 0.12
71 31 0.13
72 26 0.11
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (66 bp):
TATATATATATATTATATTTATATATTATATATATATATATAGTATATATTATTATTATATTATA
T
Found at i:11361136 original size:7 final size:7
Alignment explanation
Indices: 11361000--11361348 Score: 265
Period size: 7 Copynumber: 50.4 Consensus size: 7
11360990 TTTTGTTTTT
*
11361000 TATATGA
1 TATATTA
*
11361007 TATAGTA
1 TATATTA
11361014 TATA-TA
1 TATATTA
11361020 TATATTA
1 TATATTA
11361027 TAT-TTA
1 TATATTA
11361033 TATATTA
1 TATATTA
11361040 TATAATATA
1 TAT-AT-TA
11361049 TATATTA
1 TATATTA
11361056 TATATATA
1 TATAT-TA
11361064 TATATTA
1 TATATTA
11361071 T-TATTA
1 TATATTA
11361077 TAT-TATA
1 TATAT-TA
11361084 TTATATT-
1 -TATATTA
11361091 TATATTTA
1 TATA-TTA
11361099 TATATTA
1 TATATTA
*
11361106 TAGT-GTA
1 TA-TATTA
11361113 TATA-TA
1 TATATTA
* *
11361119 TTTAGTA
1 TATATTA
11361126 TATATTA
1 TATATTA
11361133 TATATTA
1 TATATTA
11361140 TAT-TTA
1 TATATTA
*
11361146 TATAGTA
1 TATATTA
11361153 TATAGTATA
1 TATA-T-TA
11361162 TATATTA
1 TATATTA
11361169 T-TATTA
1 TATATTA
11361175 TATA-TA
1 TATATTA
11361181 TATACTTA
1 TATA-TTA
11361189 GTATA-TA
1 -TATATTA
11361196 T-TAATT-
1 TAT-ATTA
*
11361202 TATAATA
1 TATATTA
11361209 TATATTA
1 TATATTA
11361216 TAT-TTA
1 TATATTA
11361222 TATATTA
1 TATATTA
**
11361229 TATGGTA
1 TATATTA
11361236 TATATTA
1 TATATTA
*
11361243 TATTTTA
1 TATATTA
*
11361250 TATAGTA
1 TATATTA
11361257 TATAGTATA
1 TATA-T-TA
11361266 TATATTA
1 TATATTA
11361273 T-TATT-
1 TATATTA
11361278 TATATTA
1 TATATTA
*
11361285 TAAACTTCA
1 TATA-TT-A
11361294 TATATTA
1 TATATTA
11361301 TAT-TT-
1 TATATTA
11361306 TCATA-T-
1 T-ATATTA
11361312 TATATTA
1 TATATTA
11361319 TATA-TA
1 TATATTA
11361325 TATATTA
1 TATATTA
*
11361332 TATTGTTA
1 TA-TATTA
11361340 T-TATTA
1 TATATTA
11361346 TAT
1 TAT
11361349 TATATTATAT
Statistics
Matches: 281, Mismatches: 22, Indels: 78
0.74 0.06 0.20
Matches are distributed among these distances:
5 6 0.02
6 84 0.30
7 132 0.47
8 33 0.12
9 26 0.09
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (7 bp):
TATATTA
Found at i:11363385 original size:22 final size:21
Alignment explanation
Indices: 11363359--11363399 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
11363349 GGAGGGGAGC
11363359 AGAGGTGGCAGTGGTCTCCTGG
1 AGAGGTGGCAGTGGT-TCCTGG
11363381 AGAGGTGGCAGTGGTTCCT
1 AGAGGTGGCAGTGGTTCCT
11363400 TGTGCATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.15, C:0.17, G:0.44, T:0.24
Consensus pattern (21 bp):
AGAGGTGGCAGTGGTTCCTGG
Found at i:11374278 original size:18 final size:18
Alignment explanation
Indices: 11374255--11374293 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
11374245 TTCATGGGGT
* *
11374255 AATCAAGGAAACAATAAC
1 AATCAAGCAAAAAATAAC
*
11374273 AATCAAGCAAAAAATTAC
1 AATCAAGCAAAAAATAAC
11374291 AAT
1 AAT
11374294 AGGCCATAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (18 bp):
AATCAAGCAAAAAATAAC
Found at i:11386317 original size:24 final size:21
Alignment explanation
Indices: 11386272--11386320 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 21
11386262 GGAGCAGAGG
*
11386272 TGGCAGTGGTCCCTGGGCAGC
1 TGGCAGTGGTCCCTGGGAAGC
11386293 TGGCAGTGGTCCATCCTGGGAAGC
1 TGGCAGTGGT-C--CCTGGGAAGC
11386317 TGGC
1 TGGC
11386321 TGAGTACCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 10 0.42
22 1 0.04
24 13 0.54
ACGTcount: A:0.12, C:0.27, G:0.41, T:0.20
Consensus pattern (21 bp):
TGGCAGTGGTCCCTGGGAAGC
Found at i:11387445 original size:15 final size:16
Alignment explanation
Indices: 11387425--11387463 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
11387415 CTTTTATTTC
11387425 TTTTATTTAA-TTAAT
1 TTTTATTTAACTTAAT
*
11387440 TTTTATTTAACTTTAT
1 TTTTATTTAACTTAAT
*
11387456 TTTAATTT
1 TTTTATTT
11387464 TTTACTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTATTTAACTTAAT
Found at i:11394389 original size:20 final size:21
Alignment explanation
Indices: 11394350--11394389 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11394340 CCCCCTTTGA
*
11394350 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
11394371 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
11394390 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:11396986 original size:23 final size:23
Alignment explanation
Indices: 11396960--11397021 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
11396950 TTGCTCAGAG
11396960 GGAACCGATTCCCCCCCATAGGA
1 GGAACCGATTCCCCCCCATAGGA
11396983 GGAACCGATTCCCCCCCATAGGA
1 GGAACCGATTCCCCCCCATAGGA
11397006 GGAACCGATTCCCCCC
1 GGAACCGATTCCCCCC
11397022 TGAATGGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.24, C:0.42, G:0.21, T:0.13
Consensus pattern (23 bp):
GGAACCGATTCCCCCCCATAGGA
Found at i:11399944 original size:32 final size:32
Alignment explanation
Indices: 11399908--11399981 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
11399898 ATGTCTTAAA
11399908 GGTTTAGTCCTTATTCGCTATAGGGTCTTGAT
1 GGTTTAGTCCTTATTCGCTATAGGGTCTTGAT
11399940 GGTTTAGTCCTTATTCGCTATAGGGTCTTGAT
1 GGTTTAGTCCTTATTCGCTATAGGGTCTTGAT
11399972 GGTTTAGTCC
1 GGTTTAGTCC
11399982 CAAATTGAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.15, C:0.16, G:0.26, T:0.43
Consensus pattern (32 bp):
GGTTTAGTCCTTATTCGCTATAGGGTCTTGAT
Found at i:11401920 original size:2 final size:2
Alignment explanation
Indices: 11401909--11401976 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
11401899 CTCTTAATAC
11401909 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11401950 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11401977 GGTTCTATTA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11409010 original size:30 final size:28
Alignment explanation
Indices: 11408976--11409041 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
11408966 TATTTATCTA
11408976 ATATCTGATTTACTGTGTATTTCTG-ATATG
1 ATATCTGA-TTA-T-TGTATTTCTGTATATG
*
11409006 ATATCTGATTATTGTATTTTTGTATATG
1 ATATCTGATTATTGTATTTCTGTATATG
*
11409034 ATTTCTGA
1 ATATCTGA
11409042 GTATGGAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 9 0.27
28 13 0.39
29 3 0.09
30 8 0.24
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (28 bp):
ATATCTGATTATTGTATTTCTGTATATG
Found at i:11412091 original size:2 final size:2
Alignment explanation
Indices: 11412084--11412115 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11412074 TTATTATTTA
11412084 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11412116 GTGACTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11412135 original size:11 final size:10
Alignment explanation
Indices: 11412121--11412179 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
11412111 TATATGTGAC
11412121 TAATATGAAAA
1 TAATAT-AAAA
11412132 TAATAATAAAA
1 TAAT-ATAAAA
11412143 TAATATAAAA
1 TAATATAAAA
*
11412153 TTAATAACAAAA
1 -TAAT-ATAAAA
*
11412165 TAATAAATAAA
1 TAATATA-AAA
11412176 TAAT
1 TAAT
11412180 GATTAAAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.19
11 27 0.64
12 7 0.17
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (10 bp):
TAATATAAAA
Found at i:11412179 original size:22 final size:22
Alignment explanation
Indices: 11412121--11412179 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
11412111 TATATGTGAC
* *
11412121 TAATATGAAAATAATAATAAAA
1 TAATATAAAAATAATAACAAAA
*
11412143 TAATATAAAATTAATAACAAAA
1 TAATATAAAAATAATAACAAAA
11412165 TAATA-AATAAATAAT
1 TAATATAA-AAATAAT
11412180 GATTAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
TAATATAAAAATAATAACAAAA
Found at i:11412960 original size:13 final size:13
Alignment explanation
Indices: 11412942--11412968 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11412932 TTCTTTCCTC
11412942 TCTTCTCTTCTCT
1 TCTTCTCTTCTCT
11412955 TCTTCTCTTCTCT
1 TCTTCTCTTCTCT
11412968 T
1 T
11412969 TTCCTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTCTCTTCTCT
Found at i:11413509 original size:3 final size:3
Alignment explanation
Indices: 11413501--11413551 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
11413491 ATTTATTTAT
* *
11413501 ATA ATA ATA ATA ATA ATA ATA TATA TTA ACA ATA ATA ATA A-A ATTA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA
11413547 ATA AT
1 ATA AT
11413552 TTTAATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.83
4 5 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:11413523 original size:22 final size:22
Alignment explanation
Indices: 11413498--11413551 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
11413488 GTAATTTATT
11413498 TATATAATAATAATAATAATAA
1 TATATAATAATAATAATAATAA
* *
11413520 TATATATTAACAATAATAATAA
1 TATATAATAATAATAATAATAA
*
11413542 AAT-TAATAAT
1 TATATAATAAT
11413552 TTTAATTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TATATAATAATAATAATAATAA
Found at i:11414583 original size:76 final size:76
Alignment explanation
Indices: 11413690--11414556 Score: 1563
Period size: 76 Copynumber: 11.4 Consensus size: 76
11413680 GAAATGTTGA
** * * *
11413690 AAACATCATGCACTAAAGGGCATACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11413755 AGGCTTTTTGG
66 AGGCTTTTTGG
*
11413766 AAACATCATGCACTGCAGGACTTACAGATGACTCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11413831 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
11413842 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
11413907 AGGCTTTTTTG
66 AGGCTTTTTGG
11413918 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11413983 AGGCTTTTTGG
66 AGGCTTTTTGG
11413994 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
11414059 ATGCTTTTTGG
66 AGGCTTTTTGG
* *
11414070 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11414135 AGGCTTTTTGG
66 AGGCTTTTTGG
*
11414146 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11414211 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
11414222 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCTCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11414287 AGGCTTTTTGG
66 AGGCTTTTTGG
*
11414298 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11414363 AGGCTTTTTTGG
66 AGGC-TTTTTGG
* *
11414375 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11414440 AGGCTTTTTGG
66 AGGCTTTTTGG
11414451 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
11414516 AGGCTTTTTGG
66 AGGCTTTTTGG
11414527 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
11414557 TGGGAAATAG
Statistics
Matches: 765, Mismatches: 25, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
76 690 0.90
77 75 0.10
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:11414847 original size:166 final size:166
Alignment explanation
Indices: 11414553--11414883 Score: 565
Period size: 166 Copynumber: 2.0 Consensus size: 166
11414543 AGGACTTACA
*
11414553 GATGTGGGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATTGTTTTCTTACTTTTCAACAATTT
1 GATGTGGGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTT
**
11414618 CATTTCTAGAAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACA
66 CATTTCTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACA
* *
11414683 TGTTGATTGGGTAACATGCCCCAATCTTAAGATAAG
131 TGTTGATTGGGTAACATGACCCAATCTCAAGATAAG
*
11414719 GATGTTGGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTT
1 GATGTGGGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTT
* **
11414784 CATTT-TAGAAAAGATAAAATGAGAAACTATGGAAATTGTTTTCTCATTATTTTTTTGAAATAAC
66 CATTTCTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTA-TTTTTCAAAATAAC
11414848 ATGTTGATTGGGTAACATGACCCAATCTCAAGATAA
130 ATGTTGATTGGGTAACATGACCCAATCTCAAGATAA
11414884 TGTTCTTTCT
Statistics
Matches: 155, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
165 41 0.26
166 114 0.74
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (166 bp):
GATGTGGGAAATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTT
CATTTCTAGAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACA
TGTTGATTGGGTAACATGACCCAATCTCAAGATAAG
Found at i:11415422 original size:22 final size:22
Alignment explanation
Indices: 11415394--11415448 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
11415384 CATAAAGCTT
*
11415394 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAACCTA
*
11415416 TCATCTTTAAAAAGAGAACCTA
1 TCATCTTTGAAAAGAGAACCTA
11415438 TCATCTTTGAA
1 TCATCTTTGAA
11415449 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAACCTA
Found at i:11418035 original size:114 final size:114
Alignment explanation
Indices: 11417830--11418044 Score: 340
Period size: 114 Copynumber: 1.9 Consensus size: 114
11417820 GCTCAAATGG
* ** * *
11417830 CTTTTAAATCCAATGATTGGTTTTGGGGTTCTTACCGAACCAGATCAGATAACTCAAAGAACACT
1 CTTTCAAATCCAATGATTGGTTTAAGGGTTCTTACCAAACCAAATCAGATAACTCAAAGAACACT
* * **
11417895 TCCAGAAGATGCTATTGGGTTTCCTTATTTCTACTATGAGCAAATTCAT
66 TCCAGAAAATACTATTGGGCCTCCTTATTTCTACTATGAGCAAATTCAT
*
11417944 CTTTCAAATCCAATGATTGGTTTAAGGGTTCTTATCAAACCAAATCAGATAACTCAAAGAACACT
1 CTTTCAAATCCAATGATTGGTTTAAGGGTTCTTACCAAACCAAATCAGATAACTCAAAGAACACT
11418009 TCCAGAAAATACTATTGGGCCTCCTTATTTCTACTA
66 TCCAGAAAATACTATTGGGCCTCCTTATTTCTACTA
11418045 CGAGAACATG
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 91 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Consensus pattern (114 bp):
CTTTCAAATCCAATGATTGGTTTAAGGGTTCTTACCAAACCAAATCAGATAACTCAAAGAACACT
TCCAGAAAATACTATTGGGCCTCCTTATTTCTACTATGAGCAAATTCAT
Found at i:11420200 original size:10 final size:9
Alignment explanation
Indices: 11420163--11420225 Score: 60
Period size: 9 Copynumber: 7.2 Consensus size: 9
11420153 ATTTCTCCCC
11420163 TTTT-TCTT
1 TTTTCTCTT
* *
11420171 TTTCCTTTT
1 TTTTCTCTT
*
11420180 TTTTTTCTT
1 TTTTCTCTT
*
11420189 TTTTCTCAT
1 TTTTCTCTT
11420198 TTTTC-CTT
1 TTTTCTCTT
11420206 TTTTCTCCTT
1 TTTTCT-CTT
11420216 TTTTC-CTT
1 TTTTCTCTT
11420224 TT
1 TT
11420226 GTTGTTTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 15 0.34
9 21 0.48
10 8 0.18
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:11420200 original size:18 final size:18
Alignment explanation
Indices: 11420179--11420225 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
11420169 TTTTTCCTTT
*
11420179 TTTTTTTCTTTTTTCTCA
1 TTTTTTCCTTTTTTCTCA
*
11420197 -TTTTTCCTTTTTTCTCC
1 TTTTTTCCTTTTTTCTCA
11420214 TTTTTTCCTTTT
1 TTTTTTCCTTTT
11420226 GTTGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTCCTTTTTTCTCA
Found at i:11423116 original size:36 final size:36
Alignment explanation
Indices: 11423031--11423128 Score: 101
Period size: 36 Copynumber: 2.7 Consensus size: 36
11423021 AATGTAATGT
*
11423031 AAATGTGAAAATGCATAA-ATGCAAAAATAAGAATGCA
1 AAATGTG-AAATGCA-AAGATGCAAAAATAAGAATACA
* * *
11423068 AACTGTGTAATGCAAAGATGTAAAAAGTAAGAATACA
1 AAATGTGAAATGCAAAGATGCAAAAA-TAAGAATACA
* *
11423105 AAATG-GAAATGCACAGATACAAAA
1 AAATGTGAAATGCAAAGATGCAAAA
11423129 TGTAAATGCA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
35 2 0.04
36 29 0.58
37 19 0.38
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.18
Consensus pattern (36 bp):
AAATGTGAAATGCAAAGATGCAAAAATAAGAATACA
Found at i:11425478 original size:12 final size:12
Alignment explanation
Indices: 11425451--11425496 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
11425441 ATACCTGAAT
11425451 AAAATAAATAAATA
1 AAAAT-AAT-AATA
*
11425465 AAAATATTAAT-
1 AAAATAATAATA
11425476 AAAATAAT-ATA
1 AAAATAATAATA
11425487 AAAATAATAA
1 AAAATAATAA
11425497 GTTATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 2 0.07
11 15 0.54
12 4 0.14
13 2 0.07
14 5 0.18
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:11426293 original size:22 final size:23
Alignment explanation
Indices: 11426268--11426317 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
11426258 TTTATGTGAC
*
11426268 TAATATGAAAA-TAATAA-TAAAA
1 TAATAT-AAAAGTAATAACAAAAA
11426290 TAATATAAAAGTAATAACAAAAA
1 TAATATAAAAGTAATAACAAAAA
11426313 TAATA
1 TAATA
11426318 AATAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 12 0.48
23 9 0.36
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (23 bp):
TAATATAAAAGTAATAACAAAAA
Found at i:11427665 original size:3 final size:3
Alignment explanation
Indices: 11427657--11427711 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
11427647 ATTTATTTAT
*
11427657 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA TTA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11427703 ATTA ATA AT
1 A-TA ATA AT
11427712 TTTAATTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 41 0.87
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:11427716 original size:9 final size:9
Alignment explanation
Indices: 11427661--11427717 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
11427651 ATTTATATAA
*
11427661 TAATAATAA
1 TAATAATAT
*
11427670 TAATAATAA
1 TAATAATAT
11427679 TAAT-ATAT
1 TAATAATAT
*
11427687 TAATAATAA
1 TAATAATAT
*
11427696 TAATAAAAT
1 TAATAATAT
*
11427705 TAATAATTT
1 TAATAATAT
11427714 TAAT
1 TAAT
11427718 TTTAATGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
8 7 0.17
9 34 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TAATAATAT
Found at i:11429871 original size:202 final size:202
Alignment explanation
Indices: 11429525--11429929 Score: 751
Period size: 202 Copynumber: 2.0 Consensus size: 202
11429515 TATATTTTGG
11429525 AAAAATAAATCATGATTTATTCTATACAAATTTTCGATATTAACTCTTTTTTAATTAATTCGAAG
1 AAAAATAAATCATGATTTATTCTATACAAATTTTCGATATTAACTCTTTTTTAATTAATTCGAAG
* *
11429590 ATAAAATATTCTTTTACGAATGAGAAATAGACGAGATAGTCTTCCCATTGGAGGATGTGCAAATC
66 ATAAAATATTCTTTTACGAATGAGAAATAGACGAGATAGTCTTCCCATGGGAGGATGTACAAATC
11429655 TGGTGATTTATTCTCGAATAAAGGAATGTTCCCTAATAAATAATTCAAGGCAAATTAATTAATCT
131 TGGTGATTTATTCTCGAATAAAGGAATGTTCCCTAATAAATAATTCAAGGCAAATTAATTAATCT
11429720 TTAATAA
196 TTAATAA
*
11429727 AAAAATAAATCATGATTTATTTTATACAAATTTTCGATATTAACTCTTTTTTAATTAATTCGAAG
1 AAAAATAAATCATGATTTATTCTATACAAATTTTCGATATTAACTCTTTTTTAATTAATTCGAAG
11429792 ATAAAATATTCTTTTACGAATGAG-AA-AGACGATAGATAGTCTTCCCATGGGAGGATGTACAAA
66 ATAAAATATTCTTTTACGAATGAGAAATAGACG--AGATAGTCTTCCCATGGGAGGATGTACAAA
11429855 TCTGGTGATTTATTCTCGAATAAAGGAATGTTCCCTAATAAATAATTCAAGGCAAATTAATTAAT
129 TCTGGTGATTTATTCTCGAATAAAGGAATGTTCCCTAATAAATAATTCAAGGCAAATTAATTAAT
11429920 CTTTAATAA
194 CTTTAATAA
11429929 A
1 A
11429930 TGGATCATAT
Statistics
Matches: 198, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
200 5 0.03
201 2 0.01
202 191 0.96
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (202 bp):
AAAAATAAATCATGATTTATTCTATACAAATTTTCGATATTAACTCTTTTTTAATTAATTCGAAG
ATAAAATATTCTTTTACGAATGAGAAATAGACGAGATAGTCTTCCCATGGGAGGATGTACAAATC
TGGTGATTTATTCTCGAATAAAGGAATGTTCCCTAATAAATAATTCAAGGCAAATTAATTAATCT
TTAATAA
Found at i:11430117 original size:16 final size:17
Alignment explanation
Indices: 11430088--11430119 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11430078 AAACGCATAC
11430088 CAATTTTGTCTTAAAAA
1 CAATTTTGTCTTAAAAA
11430105 CAATTTT-TCTTAAAA
1 CAATTTTGTCTTAAAA
11430120 TTGTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (17 bp):
CAATTTTGTCTTAAAAA
Found at i:11431481 original size:69 final size:69
Alignment explanation
Indices: 11431393--11431610 Score: 282
Period size: 69 Copynumber: 3.1 Consensus size: 69
11431383 TGTGGTGAAA
*
11431393 GAACTTAAACCGAACAAAAGGCAACACCATGCATA-AAGATCCATACTTCT-TACCCAAAATAAG
1 GAACTTAAATCGAACAAAAGGCAACACCATGCATAGAA-ATCCATACTT-TATACCCAAAATAAG
11431456 TACATT
64 TACATT
* * * *
11431462 GAACTTAAATTGAACAAAA-GCAAACACCGTGAATAGAAATCCATACTTTCTACCCTAAAATAAG
1 GAACTTAAATCGAACAAAAGGC-AACACCATGCATAGAAATCCATACTTTATACCC-AAAATAAG
11431526 TACATT
64 TACATT
* * *
11431532 GAACTTAAATCGAACAAAAGCCAACACCCTGCATAGAAATCCATAATTTATA-CCATAAATAAGT
1 GAACTTAAATCGAACAAAAGGCAACACCATGCATAGAAATCCATACTTTATACCCA-AAATAAGT
11431596 ACATT
65 ACATT
*
11431601 GAACTAAAAT
1 GAACTTAAAT
11431611 ATCAGAAACA
Statistics
Matches: 132, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
68 4 0.03
69 67 0.51
70 60 0.45
71 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.22
Consensus pattern (69 bp):
GAACTTAAATCGAACAAAAGGCAACACCATGCATAGAAATCCATACTTTATACCCAAAATAAGTA
CATT
Found at i:11431548 original size:70 final size:69
Alignment explanation
Indices: 11431393--11431610 Score: 282
Period size: 70 Copynumber: 3.1 Consensus size: 69
11431383 TGTGGTGAAA
*
11431393 GAACTTAAACCGAACAAAAGGCAACACCATGCATA-AAGATCCATAC-TTCTTACCC-AAAATAA
1 GAACTTAAATCGAACAAAA-GCAACACCATGCATAGAA-ATCCATACTTTC-TACCCTAAAATAA
11431455 GTACATT
63 GTACATT
* * *
11431462 GAACTTAAATTGAACAAAAGCAAACACCGTGAATAGAAATCCATACTTTCTACCCTAAAATAAGT
1 GAACTTAAATCGAACAAAAGC-AACACCATGCATAGAAATCCATACTTTCTACCCTAAAATAAGT
11431527 ACATT
65 ACATT
* * * *
11431532 GAACTTAAATCGAACAAAAGCCAACACCCTGCATAGAAATCCATAATTTATACCAT-AAATAAGT
1 GAACTTAAATCGAACAAAAG-CAACACCATGCATAGAAATCCATACTTTCTACCCTAAAATAAGT
11431596 ACATT
65 ACATT
*
11431601 GAACTAAAAT
1 GAACTTAAAT
11431611 ATCAGAAACA
Statistics
Matches: 133, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
68 2 0.02
69 63 0.47
70 67 0.50
71 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.22
Consensus pattern (69 bp):
GAACTTAAATCGAACAAAAGCAACACCATGCATAGAAATCCATACTTTCTACCCTAAAATAAGTA
CATT
Found at i:11436044 original size:14 final size:14
Alignment explanation
Indices: 11436027--11436053 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11436017 AAATTAAAAC
11436027 ATAAAAAAACAATA
1 ATAAAAAAACAATA
11436041 ATAAAAAAACAAT
1 ATAAAAAAACAAT
11436054 TAGAGAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (14 bp):
ATAAAAAAACAATA
Found at i:11436253 original size:15 final size:16
Alignment explanation
Indices: 11436223--11436255 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
11436213 AATATTATTT
11436223 TAAATAAAGGACTAAAA
1 TAAATAAA-GACTAAAA
11436240 TAAATAAA-ACTAAAA
1 TAAATAAAGACTAAAA
11436255 T
1 T
11436256 TTAGAGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (16 bp):
TAAATAAAGACTAAAA
Found at i:11437278 original size:3 final size:3
Alignment explanation
Indices: 11437261--11437303 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
11437251 TAATATTTAT
* *
11437261 TAA TAG TAA -AA TAA TAA TAA TAA TAA TAA TAA T-A TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11437304 AAAAAATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:11437911 original size:112 final size:113
Alignment explanation
Indices: 11437519--11438151 Score: 753
Period size: 113 Copynumber: 5.7 Consensus size: 113
11437509 TAGAGTCATT
* * *
11437519 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTC-T-CTTCTTCAGATGAGTTCTTTTCA
1 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
11437580 TTATGAACTTTCTCTGTAAAGGTTGATCCATTAAGTGATGAATTTGAA-
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAA-TTCAAG
* * * * * * *
11437628 TAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTTTTCAGATGAGTTATTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**** * * * * **
11437693 TTATGAACTCAAACTGGAAAAGCTGATCCATCAAGTGGTGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAG
* * * *
11437741 CAAAAGGTTGAAAAAATTCTTATCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ****
11437806 TTATGAACTTTCTTTGGCGCTGTTGATCCATCAAATGATGAATTCAAG
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAG
11437854 CAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ***
11437918 TTATGAACTTTCTTTGGCGCTA-TTGATCCATCAAATGATGAATTCAAG
66 TTATGAACTTTCTCTGG-AAAAGTTGATCCATCAAATGATGAATTCAAG
* * *
11437966 -AAAAGGGTTAAACAAGTTCTTCGTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAA-GGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
**** * *
11438030 ATTATGAACTCAAACTGGAAAAGCTAATCCATCAAATGATGAATTCAAG
65 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAG
11438079 CAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
11438143 TTATGAACT
66 TTATGAACT
11438152 CTAACTGGGA
Statistics
Matches: 445, Mismatches: 69, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
109 27 0.06
110 1 0.00
111 7 0.02
112 168 0.38
113 238 0.53
114 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAG
Found at i:11437920 original size:225 final size:223
Alignment explanation
Indices: 11437519--11438182 Score: 775
Period size: 225 Copynumber: 3.0 Consensus size: 223
11437509 TAGAGTCATT
* * * *
11437519 CAAAAGGTTGAATAAGCTCTTCTTATTATGAAC-T-TTC-T-CTTCTTCAGATGAGTTCTTTTCA
1 CAAAAGGTTGAAAAAGTTCTT-ATATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * * * *
11437580 TTATGAACTTTCTCTGTAAAGGTTGATCCATTAAGTGATGAATTTGAA-TAAAGGGTTAAACAAG
65 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAA-TTCAAGCAAA-AGTTGAACAAG
* * * * *
11437644 TTCTTCTCATTATGAACTTTTTCTTCCTTTTTCAGATGAGTTATTCTCATTATGAACTCAAACTG
128 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
* * * **
11437709 GAAAAGCTGATCCATCAAGTGGTGGATTTGAG
193 GAAAA-CTGATCCATCAAATGATGAATTCAAG
*
11437741 CAAAAGGTTGAAAAAATTCTTATCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAAAAAGTTCTTAT-ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ****
11437806 TTATGAACTTTCTTTGGCGCTGTTGATCCATCAAATGATGAATTCAAGCAAAAGTTGAACAAGTT
65 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGTTGAACAAGTT
* ***
11437871 CTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGGC
130 CTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGG-
*** *
11437936 GCTATTGATCCATCAAATGATGAATTCAAG
194 AAAACTGATCCATCAAATGATGAATTCAAG
* *
11437966 -AAAAGGGTT-AAACAAGTTCTTCGTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCT
1 CAAAA-GGTTGAAA-AAGTTCTT-ATATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
**** * *
11438029 CATTATGAACTCAAACTGGAAAAGCTAATCCATCAAATGATGAATTCAAGCAAAAGTTGAACAAG
63 CATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGTTGAACAAG
11438094 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
128 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT-
**
11438159 GGAAAACTGATCCATTGAATGATG
192 GGAAAACTGATCCATCAAATGATG
11438183 GATTTGAATT
Statistics
Matches: 372, Mismatches: 59, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
221 1 0.00
222 27 0.07
223 1 0.00
224 10 0.03
225 270 0.73
226 63 0.17
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (223 bp):
CAAAAGGTTGAAAAAGTTCTTATATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGTTGAACAAGTTC
TTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGAA
AACTGATCCATCAAATGATGAATTCAAG
Found at i:11439024 original size:93 final size:93
Alignment explanation
Indices: 11438877--11439227 Score: 573
Period size: 93 Copynumber: 3.8 Consensus size: 93
11438867 TTCATCTTTT
* *
11438877 AATTCCAATGATTGG-TTCT-GTGGTTCCTACCAAA-CAGATCAGATAACTCAAAGAACACTTCC
1 AATT-CAATGATTGGTTTTTAG-GGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCC
11438939 AGAAGATGCTATGAGCACATTCATCTTCCA
64 AGAAGATGCTATGAGCACATTCATCTTCCA
11438969 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
11439034 AAGATGCTATGAGCACATTCATCTTCCA
66 AAGATGCTATGAGCACATTCATCTTCCA
* * * *
11439062 AATTTAATGATTGGTTTTTAGGGTTCATACCAAACCAGATTAGATAACTAAAAGAACACTTCCAA
1 AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
*
11439127 AAGATGCTATGAGCATATTCATCTTCCA
66 AAGATGCTATGAGCACATTCATCTTCCA
*
11439155 AATTCAAATGATTGGTTTTTTAGGGTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCC
1 AATTC-AATGATTGG-TTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCC
11439220 AGAAGATG
64 AGAAGATG
11439228 TTATTGGGTC
Statistics
Matches: 242, Mismatches: 12, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
91 10 0.04
92 19 0.08
93 151 0.62
94 9 0.04
95 53 0.22
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (93 bp):
AATTCAATGATTGGTTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
AAGATGCTATGAGCACATTCATCTTCCA
Found at i:11439739 original size:17 final size:19
Alignment explanation
Indices: 11439700--11439746 Score: 71
Period size: 17 Copynumber: 2.6 Consensus size: 19
11439690 TCCATAAAAG
*
11439700 AATAAATTGAATTTTCGAA
1 AATAAATTGAATTCTCGAA
11439719 AATAAATTGAA-TCTC-AA
1 AATAAATTGAATTCTCGAA
11439736 AATAAATTGAA
1 AATAAATTGAA
11439747 CTTGAAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 13 0.48
18 3 0.11
19 11 0.41
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (19 bp):
AATAAATTGAATTCTCGAA
Found at i:11440086 original size:7 final size:7
Alignment explanation
Indices: 11440074--11440119 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
11440064 CCTTGACCCC
11440074 CTTTTTT
1 CTTTTTT
11440081 CTTTTTT
1 CTTTTTT
11440088 CTTTTTT
1 CTTTTTT
11440095 -TTTCTTT
1 CTTT-TTT
11440102 -TTTTTT
1 CTTTTTT
*
11440108 CTTCTTT
1 CTTTTTT
11440115 CTTTT
1 CTTTT
11440120 CTTTTTCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:11440095 original size:17 final size:17
Alignment explanation
Indices: 11440074--11440127 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
11440064 CCTTGACCCC
11440074 CTTTTTTCTTTTTTCTTT
1 CTTTTTTCTTTTTT-TTT
11440092 -TTTTTTCTTTTTTTTT
1 CTTTTTTCTTTTTTTTT
*
11440108 CTTCTTTCTTTTCTTTTT
1 CTTTTTTCTTTT-TTTTT
11440126 CT
1 CT
11440128 CTTCAAGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 3 0.09
17 23 0.70
18 7 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
CTTTTTTCTTTTTTTTT
Found at i:11440097 original size:10 final size:10
Alignment explanation
Indices: 11440082--11440125 Score: 70
Period size: 10 Copynumber: 4.2 Consensus size: 10
11440072 CCCTTTTTTC
11440082 TTTTTTCTTT
1 TTTTTTCTTT
11440092 TTTTTTCTTT
1 TTTTTTCTTT
11440102 TTTTTTCTTCT
1 TTTTTTCTT-T
11440113 TTCTTTTCTTT
1 TT-TTTTCTTT
11440124 TT
1 TT
11440126 CTCTTCAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 19 0.59
11 6 0.19
12 7 0.22
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:11440115 original size:27 final size:28
Alignment explanation
Indices: 11440075--11440127 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
11440065 CTTGACCCCC
*
11440075 TTTTTTCTTTTTTCTTTT-TTTTTCTTT
1 TTTTTTCTTCTTTCTTTTCTTTTTCTTT
11440102 TTTTTTCTTCTTTCTTTTCTTTTTCT
1 TTTTTTCTTCTTTCTTTTCTTTTTCT
11440128 CTTCAAGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (28 bp):
TTTTTTCTTCTTTCTTTTCTTTTTCTTT
Found at i:11440130 original size:20 final size:18
Alignment explanation
Indices: 11440075--11440131 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 18
11440065 CTTGACCCCC
11440075 TTTTTTCTTTTTTCTT-T
1 TTTTTTCTTTTTTCTTCT
11440092 TTTTTTCTTTTTTTTTCTTCT
1 TTTTTTC---TTTTTTCTTCT
11440113 TTCTTTTCTTTTTCTCTTC
1 TT-TTTTCTTTTT-TCTTC
11440132 AAGCATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.21
19 5 0.15
20 14 0.41
21 3 0.09
22 5 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTCTTTTTTCTTCT
Found at i:11448272 original size:286 final size:285
Alignment explanation
Indices: 11447761--11448335 Score: 1107
Period size: 286 Copynumber: 2.0 Consensus size: 285
11447751 TCATTACTTC
11447761 TTTGAGATCATTAGGTCCTAGACGAACCTTTTCTTGAAATAATGATTCTTCAAGTTGCAAATGTA
1 TTTGAGATCATTAGGTCCTAGACGAACCTTTTCTTGAAATAATGATTCTTCAAGTTGCAAATGTA
11447826 AGCATTAAACTCTGAGTTTTGTTTCTAGACTGATCCAGATCTTCTTCAAGTTTTGTTCGTGCTTC
66 AGCATTAAACTCTGAGTTTTGTTTCTAGACTGATCCAGATCTTCTTCAAGTTTTGTTCGTGCTTC
11447891 TTGCGTTCTTTGATTAATCTTCTGGATTTGAACATTCTTGTTTCTGCATCTTTGCATCCAATTGC
131 TTGCGTTCTTTGATTAATCTTCTGGATTTGAACATTCTTGTTTCTGCATCTTTGCATCCAATTGC
*
11447956 TAGCCACTTCTTTCTCTACCTCAATTTTGGTGTTGAAATTCTTTCTTTCCAACTCCCATTTTTCT
196 TAGCCACTTCTTGCTCTACCTCAATTTTGGTGTTGAAATTCTTTCTTTCCAACTCCCATTTTTCT
11448021 TTTTCAATATTGAACTCTTCAATCT
261 TTTTCAATATTGAACTCTTCAATCT
11448046 TTTGAGATCATTAGGTCCTAGACGAACCTTTTCTTGAAATAATGA-TCTTCAAGTTGCAAAATGT
1 TTTGAGATCATTAGGTCCTAGACGAACCTTTTCTTGAAATAATGATTCTTCAAGTTGC-AAATGT
*
11448110 AAGCGTTAAACTCTGAGTTTTTGTTTCTAGACTGATCCAGATCTTCTTCAAGTTTTGTTCGTGCT
65 AAGCATTAAACTCTGAG-TTTTGTTTCTAGACTGATCCAGATCTTCTTCAAGTTTTGTTCGTGCT
11448175 TCTTGCGTTCTTTGATTAATCTTCTGGATTTGAACATTCTTGTTTCTGCATCTTTGCATCCAATT
129 TCTTGCGTTCTTTGATTAATCTTCTGGATTTGAACATTCTTGTTTCTGCATCTTTGCATCCAATT
11448240 GCTAGCCACTTCTTGCTCTACCTCAATTTTGGTGTTGAAATTCTTTCTTTCCAACTCCCATTTTT
194 GCTAGCCACTTCTTGCTCTACCTCAATTTTGGTGTTGAAATTCTTTCTTTCCAACTCCCATTTTT
11448305 CTTTTTCAATATTGAACTCTTCAATCT
259 CTTTTTCAATATTGAACTCTTCAATCT
11448332 TTTG
1 TTTG
11448336 GCCCCTGGTT
Statistics
Matches: 286, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
284 12 0.04
285 67 0.23
286 207 0.72
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.44
Consensus pattern (285 bp):
TTTGAGATCATTAGGTCCTAGACGAACCTTTTCTTGAAATAATGATTCTTCAAGTTGCAAATGTA
AGCATTAAACTCTGAGTTTTGTTTCTAGACTGATCCAGATCTTCTTCAAGTTTTGTTCGTGCTTC
TTGCGTTCTTTGATTAATCTTCTGGATTTGAACATTCTTGTTTCTGCATCTTTGCATCCAATTGC
TAGCCACTTCTTGCTCTACCTCAATTTTGGTGTTGAAATTCTTTCTTTCCAACTCCCATTTTTCT
TTTTCAATATTGAACTCTTCAATCT
Found at i:11452749 original size:3 final size:3
Alignment explanation
Indices: 11452741--11452803 Score: 69
Period size: 3 Copynumber: 21.3 Consensus size: 3
11452731 ATTTGGGCCT
* *
11452741 ATA ATA ATA TTTA TTA ATA ATA A-A ATA ATA A-A ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11452785 ATA ATA AT- ATAA ATA ATA A
1 ATA ATA ATA AT-A ATA ATA A
11452804 AAAAATGAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 6 0.11
3 43 0.81
4 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:11452799 original size:32 final size:32
Alignment explanation
Indices: 11452741--11452805 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
11452731 ATTTGGGCCT
* *
11452741 ATAATAATATTTATTAATAATAAAATAATAAA
1 ATAATAATATATAATAATAATAAAATAATAAA
11452773 ATAATAATA-ATAATAATAATATAAATAATAAA
1 ATAATAATATATAATAATAATA-AAATAATAAA
11452805 A
1 A
11452806 AAATGAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (32 bp):
ATAATAATATATAATAATAATAAAATAATAAA
Found at i:11457873 original size:24 final size:24
Alignment explanation
Indices: 11457838--11457887 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
11457828 TGGGAGATAA
*
11457838 TATTTTTTTAATAATTTAATATTT
1 TATTTTTATAATAATTTAATATTT
* *
11457862 TATTTTTATAATATTTTTATATTT
1 TATTTTTATAATAATTTAATATTT
11457886 TA
1 TA
11457888 AATTTAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TATTTTTATAATAATTTAATATTT
Found at i:11457903 original size:24 final size:24
Alignment explanation
Indices: 11457846--11457902 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
11457836 AATATTTTTT
* * **
11457846 TAATAATTTAATATTTTATTTTTA
1 TAATATTTTTATATTTTAAATTTA
11457870 TAATATTTTTATATTTTAAATTTA
1 TAATATTTTTATATTTTAAATTTA
11457894 -AATATTTTT
1 TAATATTTTT
11457903 TTATAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TAATATTTTTATATTTTAAATTTA
Found at i:11458074 original size:2 final size:2
Alignment explanation
Indices: 11458067--11458131 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
11458057 CGTTGCTGGT
11458067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11458109 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
11458132 TTCATTACAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11459918 original size:3 final size:3
Alignment explanation
Indices: 11459910--11459954 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
11459900 CTAAATATAG
11459910 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11459955 TCATTCTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11463990 original size:13 final size:12
Alignment explanation
Indices: 11463959--11463995 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
11463949 TTTTAATATT
11463959 TATCGGGTCGGG
1 TATCGGGTCGGG
*
11463971 TATCGGGGCGGG
1 TATCGGGTCGGG
11463983 TAATCGGGTCGGG
1 T-ATCGGGTCGGG
11463996 GATTACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.11, C:0.16, G:0.51, T:0.22
Consensus pattern (12 bp):
TATCGGGTCGGG
Found at i:11464612 original size:26 final size:26
Alignment explanation
Indices: 11464566--11464617 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
11464556 GGTCATCTTA
*
11464566 GAGTTCAAGGTATTCTAATTCTTTTG
1 GAGTTCAAGGTATTCTAATTCATTTG
* *
11464592 GAGTTCATGGGTATT-TCATTCATTTG
1 GAGTTCA-AGGTATTCTAATTCATTTG
11464618 AATATTGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (26 bp):
GAGTTCAAGGTATTCTAATTCATTTG
Found at i:11466716 original size:24 final size:25
Alignment explanation
Indices: 11466689--11466743 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
11466679 CGATAAATGT
* *
11466689 TTGTTAT-TGAAATTACATACTATA
1 TTGTTATATCAAATTACATAATATA
*
11466713 TTGTTATATCAAATTGCATAATATA
1 TTGTTATATCAAATTACATAATATA
*
11466738 TGGTTA
1 TTGTTA
11466744 GATAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (25 bp):
TTGTTATATCAAATTACATAATATA
Found at i:11475545 original size:3 final size:3
Alignment explanation
Indices: 11475537--11475593 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
11475527 TACTAAATTT
11475537 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11475585 ATA ATA ATA
1 ATA ATA ATA
11475594 TATCTTTCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11477683 original size:20 final size:20
Alignment explanation
Indices: 11477660--11477723 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
11477650 TAGTATTTAG
11477660 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
11477680 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
11477700 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
11477719 TTAAA
1 ATAAA
11477724 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:11477693 original size:19 final size:20
Alignment explanation
Indices: 11477669--11477718 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
11477659 GATAAATTTA
*
11477669 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
11477688 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
11477709 TT-ATAATTTT
1 TTAATAATTTT
11477719 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:11477721 original size:31 final size:30
Alignment explanation
Indices: 11477636--11477722 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
11477626 TTCGATAATA
* *
11477636 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
11477667 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
11477698 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
11477723 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:11478473 original size:31 final size:30
Alignment explanation
Indices: 11478438--11478524 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
11478428 TCAATAAAGT
11478438 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
11478469 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
11478500 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
11478525 TATTATCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:11478500 original size:20 final size:20
Alignment explanation
Indices: 11478433--11478500 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
11478423 TTTCGTCAAT
*
11478433 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
11478451 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
11478472 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
11478491 ATAA-ATTTAT
1 A-AAGATTTAT
11478501 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:11479521 original size:16 final size:16
Alignment explanation
Indices: 11479502--11479573 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
11479492 ACTTTAGTTA
*
11479502 AAATAATTAAAACAAC
1 AAATAATAAAAACAAC
*
11479518 AAATAATAAAAACAATAA
1 AAATAATAAAAAC-A-AC
*
11479536 AAACAATAAAAAACAAC
1 AAATAAT-AAAAACAAC
*
11479553 ATAA-AATAAAAATAA-
1 A-AATAATAAAAACAAC
11479568 AAATAA
1 AAATAA
11479574 ATATAAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.04
15 3 0.07
16 19 0.41
17 6 0.13
18 10 0.22
19 6 0.13
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.15
Consensus pattern (16 bp):
AAATAATAAAAACAAC
Found at i:11479546 original size:8 final size:9
Alignment explanation
Indices: 11479522--11479547 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
11479512 AACAACAAAT
11479522 AATAAAAAC
1 AATAAAAAC
11479531 AATAAAAAC
1 AATAAAAAC
11479540 AATAAAAA
1 AATAAAAA
11479548 ACAACATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
AATAAAAAC
Found at i:11479556 original size:21 final size:21
Alignment explanation
Indices: 11479519--11479558 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11479509 TAAAACAACA
*
11479519 AATAATAAAAACAATAAAAAC
1 AATAAAAAAAACAATAAAAAC
11479540 AATAAAAAACAAC-ATAAAA
1 AATAAAAAA-AACAATAAAA
11479559 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (21 bp):
AATAAAAAAAACAATAAAAAC
Found at i:11479570 original size:23 final size:23
Alignment explanation
Indices: 11479540--11479584 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
11479530 CAATAAAAAC
11479540 AATAAAAA-ACAACATAAAATAAA
1 AATAAAAATA-AACATAAAATAAA
*
11479563 AATAAAAATAAATATAAAATAA
1 AATAAAAATAAACATAAAATAA
11479585 GTACAAGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (23 bp):
AATAAAAATAAACATAAAATAAA
Found at i:11480863 original size:91 final size:91
Alignment explanation
Indices: 11480708--11481215 Score: 732
Period size: 91 Copynumber: 5.6 Consensus size: 91
11480698 ATCGAACAAA
* * * * * *
11480708 GTTGAACAATTTCTTCTCATTATGAACTTCTTATCTCTTGTCGGATGAGTTTTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * * *
11480773 CTTTTCATTGGAAATGTTGAGTCAAT
66 CTCTCCATTGGAAATGTTGAGCCAAG
* *
11480799 GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* *
11480864 CTCTCTATTGGAAATG-TGAAGCCAAT
66 CTCTCCATTGGAAATGTTG-AGCCAAG
* *
11480890 GTTGAACAAGTTCTTCTAATTATGAACTTCTTCTCCCTCGTTGGACGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* *
11480955 CTCTCCACTGGAACTGTTGAGCCAAG
66 CTCTCCATTGGAAATGTTGAGCCAAG
* * * *
11480981 GTTGAACAAGTTCTTCTCATTATGAACTTTTTCTACCTCATCGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* *
11481046 CTCTCCATCGAAAATGTTGAGCCAAG
66 CTCTCCATTGGAAATGTTGAGCCAAG
* *
11481072 GTTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCGTTAGATGAGTTCTTCTCATT-TGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
**
11481136 CTCTCCATTGGAAATGTTGATTCAAG
66 CTCTCCATTGGAAATGTTGAGCCAAG
*
11481162 GTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTCTT
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTT
11481216 TTGTAACAAC
Statistics
Matches: 374, Mismatches: 41, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
90 79 0.21
91 293 0.78
92 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (91 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
CTCTCCATTGGAAATGTTGAGCCAAG
Found at i:11482016 original size:17 final size:18
Alignment explanation
Indices: 11481983--11482020 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
11481973 ACTGGTTATA
*
11481983 ACCCGACCCGACTCGTTG
1 ACCCGACCCGACCCGTTG
11482001 ACCCGA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
11482018 ACC
1 ACC
11482021 ATTGACCGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:11482075 original size:29 final size:29
Alignment explanation
Indices: 11482033--11482154 Score: 190
Period size: 29 Copynumber: 4.2 Consensus size: 29
11482023 TGACCGGTTT
*
11482033 CTATTTTAGTAATTAATTCGAAATGGGTG
1 CTATTTTAGTAATTAATTCAAAATGGGTG
*
11482062 CTATTTTAGTAATTAATTCAAAATAGGTG
1 CTATTTTAGTAATTAATTCAAAATGGGTG
11482091 CTATTTTAGTAATTAATTCAAAATGGGTG
1 CTATTTTAGTAATTAATTCAAAATGGGTG
* * *
11482120 CTATTTTAGTAATTATTTTAAAAAGGGTG
1 CTATTTTAGTAATTAATTCAAAATGGGTG
*
11482149 TTATTT
1 CTATTT
11482155 CTGTAAAATA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 86 1.00
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (29 bp):
CTATTTTAGTAATTAATTCAAAATGGGTG
Found at i:11483292 original size:117 final size:117
Alignment explanation
Indices: 11483081--11483372 Score: 435
Period size: 117 Copynumber: 2.5 Consensus size: 117
11483071 GGAAGTATTT
* * * *
11483081 CAGGCTCCTTTGATGTGTGCTCAGGGTAAGTCCTTACTGGTATACATGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAAGTGGGTGTATGGTTCTGG
* *
11483146 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACTG
66 GGAACCTACACATTGTACTGATTGGAGTGACTGGATGGAGAAGTTATTACTG
* *
11483198 CATGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAAGTGGGTGTATGGTTCTGG
*
11483263 GGAACCTACACATTGTACTGA-TGGAAGTGACTGGATGGAGACGTTATTACTG
66 GGAACCTACACATTGTACTGATTGG-AGTGACTGGATGGAGAAGTTATTACTG
* ** *
11483315 TAGGCTCCTCGGCT-TCGTGCTTAGGGTAAGTCCTTACTGGTGTGCAAGTGGGTGTATG
1 CAGGCTCCTTTGCTGT-GTGCTCAGGGTAAGTCCTTACTGGTGTGCAAGTGGGTGTATG
11483373 TTTCGGGAAA
Statistics
Matches: 159, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
116 4 0.03
117 155 0.97
ACGTcount: A:0.18, C:0.16, G:0.33, T:0.32
Consensus pattern (117 bp):
CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAAGTGGGTGTATGGTTCTGG
GGAACCTACACATTGTACTGATTGGAGTGACTGGATGGAGAAGTTATTACTG
Found at i:11489350 original size:13 final size:13
Alignment explanation
Indices: 11489329--11489358 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11489319 GTTACAACCC
11489329 GACCCGACCCGTT
1 GACCCGACCCGTT
*
11489342 GACCTGACCCGTT
1 GACCCGACCCGTT
11489355 GACC
1 GACC
11489359 GGGTGTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:11489560 original size:29 final size:29
Alignment explanation
Indices: 11489359--11489572 Score: 284
Period size: 29 Copynumber: 7.4 Consensus size: 29
11489349 CCCGTTGACC
* *
11489359 GGGTGTTATTTTAGTAATTAATTCGAAAT
1 GGGTGCTATTTTAGTAATTAATTCAAAAT
** * *
11489388 ATGTGTTATTTTAGTAATTAATTCGAAAT
1 GGGTGCTATTTTAGTAATTAATTCAAAAT
* * *
11489417 AGGTACTATTTTAGTAATTAATTCGAAAT
1 GGGTGCTATTTTAGTAATTAATTCAAAAT
11489446 GGGTGCTATTTTAGTAATTAATTCAAAAT
1 GGGTGCTATTTTAGTAATTAATTCAAAAT
*
11489475 GGGTGCTATTTTAGTAATTAATTTAAAAT
1 GGGTGCTATTTTAGTAATTAATTCAAAAT
* *
11489504 AGGTGCAATTTTAGTAATTAATTCAAAAT
1 GGGTGCTATTTTAGTAATTAATTCAAAAT
* * *
11489533 GGGTGCTATTTTAGTAATTATTTTAAAAA
1 GGGTGCTATTTTAGTAATTAATTCAAAAT
*
11489562 GGGTTCTATTT
1 GGGTGCTATTT
11489573 ATGTAAAATG
Statistics
Matches: 167, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 167 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (29 bp):
GGGTGCTATTTTAGTAATTAATTCAAAAT
Found at i:11490715 original size:117 final size:116
Alignment explanation
Indices: 11490504--11490798 Score: 459
Period size: 117 Copynumber: 2.5 Consensus size: 116
11490494 GGAAGTATTT
* *
11490504 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGAGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTAT-GTTTTGG
* *
11490569 GGAACCTACACATAGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTACTG
65 GGAACCTACACATAGTAGTGATTGGAGTGACTGGATGGAGAAGTTATTACTA
11490621 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATAGTTTTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTAT-GTTTTGG
* *
11490686 GGAACCTACACATTGTAGTGA-TGGAAGTGACTGGATGGAGACGTTATTACTA
65 GGAACCTACACATAGTAGTGATTGG-AGTGACTGGATGGAGAAGTTATTACTA
** *
11490738 CAGGCTCCTCGGCT-TCGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGTTT
1 CAGGCTCCTTTGCTGT-GTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGTTT
11490799 CGGGAAAATA
Statistics
Matches: 166, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
116 8 0.05
117 158 0.95
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (116 bp):
CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGTTTTGGG
GAACCTACACATAGTAGTGATTGGAGTGACTGGATGGAGAAGTTATTACTA
Found at i:11492481 original size:42 final size:41
Alignment explanation
Indices: 11492358--11492481 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 41
11492348 AAAACATCCA
* * * *
11492358 GCTCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTT
1 GCTCGAAAGACTTATAGATGGCCCGAAGGACTTATCATCAT
* * * *
11492399 GCTCGAAAGACTTATAGATGACCCAAAGGATTTAAGCATCAT
1 GCTCGAAAGACTTATAGATGGCCCGAAGGACTT-ATCATCAT
11492441 GCTCGAAAGACTTACT-GATGGCCCGAAGGACTTACTCATCA
1 GCTCGAAAGACTTA-TAGATGGCCCGAAGGACTTA-TCATCA
11492482 AGAAACCCTT
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
41 28 0.41
42 39 0.57
43 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (41 bp):
GCTCGAAAGACTTATAGATGGCCCGAAGGACTTATCATCAT
Found at i:11492754 original size:42 final size:41
Alignment explanation
Indices: 11492641--11492754 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
11492631 GCCCGAAGGT
* * * **
11492641 CTTATGGATGGCCTGAAGAACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCACGCTCGAAAGA
* * * *
11492682 CTTATAGATGACCCGAAGGATTTAAGCATCACGCTTGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCACGCTCGAAAGA
11492724 CTTACT-GATGGCCCGAAGGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCA
11492755 AGAAACCCTT
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
41 19 0.33
42 38 0.66
43 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCACGCTCGAAAGA
Found at i:11492775 original size:273 final size:275
Alignment explanation
Indices: 11492243--11492908 Score: 1020
Period size: 273 Copynumber: 2.4 Consensus size: 275
11492233 TTCAGTTTTC
* * *
11492243 ATCAAGGAACCCCTAAAAATTAGGCTTATCTT-CTTTTATAAATTCTTTGGAGATAATCATCAAG
1 ATCAAGGAACCCCTAAAAATTAGGCTTAGCTTCCTTTTAAAAATTCTTTGGAGAAAATCATCAAG
* *
11492307 AAACCCCTGAAAATAAGGCTTAGTTTCTAAAAACTCATTTGAAAACATCCAGCTCGAAGGTCTTA
66 AAACCCCTGAAAATCA-GCTTAGTTTCTAAAAACTCATTTGAAAACATCCAGCCCGAAGGTCTTA
*
11492372 TGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCAAAGGATTTAAGCA
130 TGGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGACTTATAGATGACCCAAAGGATTTAAGCA
*
11492437 TCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAATCAAG
195 TCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAATCAAG
11492502 CTTAGTTTCTTAGTTG
260 CTTAGTTTCTTAGTTG
* *
11492518 -TCAAGGAACCCCTAAAAATTAGGCTTAGCTTCCTTTTAAAAACTCTTTGGAGAAAATAATCAAG
1 ATCAAGGAACCCCTAAAAATTAGGCTTAGCTTCCTTTTAAAAATTCTTTGGAGAAAATCATCAAG
* *
11492582 AAACCCCTGAAAATCATGCTTAGTTTCTAAAAGCTCA-TTG-AAACATCCTGCCCGAAGGTCTTA
66 AAACCCCTGAAAATCA-GCTTAGTTTCTAAAAACTCATTTGAAAACATCCAGCCCGAAGGTCTTA
* *
11492645 TGGATGGCCTGAAGAACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGCA
130 TGGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGACTTATAGATGACCCAAAGGATTTAAGCA
*
11492710 TCACGCTTGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAATCAAG
195 TCACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAATCAAG
*
11492775 CTTAGTTTCTTATTTG
260 CTTAGTTTCTTAGTTG
* * *
11492791 TCATCAAGGAACCCCTAAAAATTAGGCTTAGATTCATTTTAAAAAATTCATT-GA-AAATCATCA
1 --ATCAAGGAACCCCTAAAAATTAGGCTTAGCTTCCTTTT-AAAAATTCTTTGGAGAAA--ATCA
* * *
11492854 TCAAGAAACCCCTAAAAAATCAGACTTAGTTTATAAAAACTAATTTGAAAACATC
61 TCAAGAAACCCCT-GAAAATCAG-CTTAGTTTCTAAAAACTCATTTGAAAACATC
11492909 AAGAAACCTA
Statistics
Matches: 355, Mismatches: 25, Indels: 17
0.89 0.06 0.04
Matches are distributed among these distances:
273 161 0.45
274 33 0.09
275 65 0.18
276 37 0.10
277 26 0.07
278 23 0.06
279 3 0.01
280 7 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (275 bp):
ATCAAGGAACCCCTAAAAATTAGGCTTAGCTTCCTTTTAAAAATTCTTTGGAGAAAATCATCAAG
AAACCCCTGAAAATCAGCTTAGTTTCTAAAAACTCATTTGAAAACATCCAGCCCGAAGGTCTTAT
GGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGACTTATAGATGACCCAAAGGATTTAAGCAT
CACGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTCATCAAGAAACCCTTGAAAATCAAGC
TTAGTTTCTTAGTTG
Found at i:11492944 original size:53 final size:55
Alignment explanation
Indices: 11492791--11492944 Score: 131
Period size: 53 Copynumber: 2.7 Consensus size: 55
11492781 TTCTTATTTG
* * *
11492791 TCATCAAGGAACCCCTAAAAATTAGGCTTAGATTCATTTTAAAAAATTCATTGAAAATCA
1 TCATCAA-GAAACCCTAAAAATTAGGCTTAG-TTC-TTTT-AAAAACTAATTGAAAA-CA
* * *
11492851 TCATCAAGAAACCCCTAAAAAATCAGACTTAG-T-TTATAAAAACTAATTTG-AAA-A
1 TCATCAAGAAA-CCCT-AAAAATTAGGCTTAGTTCTTTTAAAAACTAA-TTGAAAACA
11492905 -CATCAAGAAA-CCTAAAAATTAGGCTTAGCTTCTTTTAAAA
1 TCATCAAGAAACCCTAAAAATTAGGCTTAG-TTCTTTTAAAA
11492945 CTTTCTTTGA
Statistics
Matches: 79, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
50 13 0.16
51 3 0.04
52 1 0.01
53 17 0.22
54 1 0.01
56 10 0.13
57 6 0.08
59 4 0.05
60 11 0.14
61 13 0.16
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.29
Consensus pattern (55 bp):
TCATCAAGAAACCCTAAAAATTAGGCTTAGTTCTTTTAAAAACTAATTGAAAACA
Found at i:11492954 original size:53 final size:52
Alignment explanation
Indices: 11492792--11492962 Score: 130
Period size: 53 Copynumber: 3.1 Consensus size: 52
11492782 TCTTATTTGT
* * *
11492792 CATCAAGGAACCCCTAAAAATTAGGCTTAGATTCATTTTAAAAAATTCATTGAAAATCA
1 CATCAA-GAAACCCTAAAAATTAGGCTTAG-TTC-TTTT-AAAACTTCTTTG-AAA--A
* * * * **
11492851 TCATCAAGAAACCCCTAAAAAATCAGACTTAGTT-TATAAAAACTAATTTGAAAA
1 -CATCAAGAAA-CCCT-AAAAATTAGGCTTAGTTCTTTTAAAACTTCTTTGAAAA
11492905 CATCAAGAAA-CCTAAAAATTAGGCTTAGCTTCTTTTAAAACTTTCTTTGAAAA
1 CATCAAGAAACCCTAAAAATTAGGCTTAG-TTCTTTTAAAAC-TTCTTTGAAAA
*
11492958 TATCA
1 CATCA
11492963 TTGGCTTGAG
Statistics
Matches: 90, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
50 13 0.14
51 5 0.06
52 7 0.08
53 23 0.26
54 1 0.01
56 3 0.03
57 8 0.09
58 2 0.02
59 3 0.03
60 12 0.13
61 13 0.14
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (52 bp):
CATCAAGAAACCCTAAAAATTAGGCTTAGTTCTTTTAAAACTTCTTTGAAAA
Found at i:11493541 original size:6 final size:6
Alignment explanation
Indices: 11493525--11494928 Score: 1969
Period size: 6 Copynumber: 244.0 Consensus size: 6
11493515 TGGGCATGCA
11493525 AAATA- AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT -AATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11493571 AAATAT AAATAT AAAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
1 AAATAT AAATAT -AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
*
11493620 -AA-AT AAATAT AAATAT AAATAT AAATAT -AATAT -AATAT AAATGT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
*
11493664 AAATAT AAAGAT AAATA- AAATAT AAATAT AAATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11493711 AAATAT AAAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
1 AAATAT -AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11493760 -AATAT AAATAT AAATAT -AA-AT AAATAT AAATAT AAATAT -AA-AT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
*
11493803 AAATAT AAATAT AAATAT AAATAT AAATAT -AA-AT AAATAT -AATAA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
*
11493848 AAATAT AAATAT -AATAT AAATAT -AATAT AAATAT AAATAT AAATAA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11493894 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT -AATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11493941 AAATAT -AA-AT AAATAT AAATA- AAATAT AAATAT AAATA- AAATA-
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11493984 AATATAT ATAATAT AAATAT -AATAT -AA-AT AAATAT AAATAT AAATAT
1 AA-ATAT A-AATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
*
11494031 AAATAA ATAATAT AAATAT AAATAT AAATAT --A-AT AAATAT AAATAT
1 AAATAT A-AATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11494077 -AATAT AAATAT AAATAT AAATA- AAATAT AAATAT -AATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11494122 -AA-AT AAATAT -AA-AT AAATAT AAATAT AAATAT -AATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11494165 -AA-AT AAATAT AAATAT -AATAT AAATAT AAATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11494210 AAATAT -AA-AT -AATAT AAATAT AAATAT AAATAT -AATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
*
11494254 AAATAT AAATAT -AATAT -AATAT AAATAT AAATAT AAATAT ATAAAAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT A-AATAT
*
11494301 ATAA-AT AAATAT AAATAT AAATAT -AATAT AAAAAT AAATAT AAATAT
1 A-AATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11494348 AAATAT -AA-AT AAATAT AAATAT -AA-AT -AATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11494391 -AATAT AAATAT -AATAT AAATAT AAATAT AAATAT AAATATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT -AA-ATAT AAATAT
*
11494439 AAATAT AAATAT AAAAATAT AAATAT AAATAT AATATAA AAATAT AAATAT
1 AAATAT AAATAT --AAATAT AAATAT AAATAT AA-ATAT AAATAT AAATAT
11494490 AAATAT AAATAT AAATAT AAATAT AAATAT AAA-AT AAATAT -AA-AT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11494535 AAATAT -AATAT AAATAT AAATAT AAA-AT ATAA-AT AAA-AT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT A-AATAT AAATAT AAATAT
*
11494580 AAATAT AAATAT AAATAT AAATAT AAATA- AATAAAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AA-ATAT AAATAT AAATAT
11494628 AAATAT AAATAT AAATAT AAATAT AAAATAT AAATAT -AA-AT AAATAT
1 AAATAT AAATAT AAATAT AAATAT -AAATAT AAATAT AAATAT AAATAT
11494675 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT -AA-AT AAATA-
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11494720 AAATA- AAATAT AAA-ATT AAA-AT AAATAT -AATAT -AATAT AAATAT
1 AAATAT AAATAT AAATA-T AAATAT AAATAT AAATAT AAATAT AAATAT
11494764 AAATAT -AATAT AAATAT AAATATAT AAATAT AAATAT AAAT-T AAATAT
1 AAATAT AAATAT AAATAT -AA-ATAT AAATAT AAATAT AAATAT AAATAT
11494812 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
* *
11494860 AAATAT AAATAT ATATATAT AAATAT AAA-AT AAATAT -ACTAT -GATAT
1 AAATAT AAATAT A-A-ATAT AAATAT AAATAT AAATAT AAATAT AAATAT
11494907 AAATAT AAATA- AAAT-T AAATAT
1 AAATAT AAATAT AAATAT AAATAT
11494929 CTGAACCTGA
Statistics
Matches: 1291, Mismatches: 21, Indels: 173
0.87 0.01 0.12
Matches are distributed among these distances:
3 2 0.00
4 35 0.03
5 261 0.20
6 919 0.71
7 54 0.04
8 20 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATAT
Found at i:11494938 original size:6 final size:6
Alignment explanation
Indices: 11494929--11494991 Score: 94
Period size: 6 Copynumber: 10.8 Consensus size: 6
11494919 AATTAAATAT
*
11494929 CTGAAC CTGAAC CTGAAC CTGAAC CTGAAC CTGAAC C--AAT CTGAAC
1 CTGAAC CTGAAC CTGAAC CTGAAC CTGAAC CTGAAC CTGAAC CTGAAC
*
11494975 CTGAAC CTGAAC ATGAA
1 CTGAAC CTGAAC CTGAA
11494992 TCTCAATCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
4 3 0.06
6 49 0.94
ACGTcount: A:0.37, C:0.30, G:0.16, T:0.17
Consensus pattern (6 bp):
CTGAAC
Found at i:11494975 original size:28 final size:30
Alignment explanation
Indices: 11494941--11495000 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 30
11494931 GAACCTGAAC
*
11494941 CTGAACCTGAACCTGAACCTGAA-C-CAAT
1 CTGAACCTGAACCTGAACATGAATCTCAAT
11494969 CTGAACCTGAACCTGAACATGAATCTCAAT
1 CTGAACCTGAACCTGAACATGAATCTCAAT
11494999 CT
1 CT
11495001 CAATCTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 22 0.76
29 1 0.03
30 6 0.21
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (30 bp):
CTGAACCTGAACCTGAACATGAATCTCAAT
Found at i:11494999 original size:6 final size:6
Alignment explanation
Indices: 11494990--11495160 Score: 236
Period size: 6 Copynumber: 28.7 Consensus size: 6
11494980 CCTGAACATG
* *
11494990 AATCTC AATCTC AATCTC AATCTC AATCTC AATCTA AATCTC AATCTA
1 AATCTC AATCTC AATCTC AATCTC AATCTC AATCTC AATCTC AATCTC
* * * *
11495038 AATCTA AATCTC AATCTC AATCTC AATCTA AATCTA AATCTA AATCTC
1 AATCTC AATCTC AATCTC AATCTC AATCTC AATCTC AATCTC AATCTC
* * * * *
11495086 AATCTA AATCTA AATCTC AATCTA AATCTC AATCTC AATCTA AATCTA
1 AATCTC AATCTC AATCTC AATCTC AATCTC AATCTC AATCTC AATCTC
11495134 AATCTC AATCTC AATCT- AATCTC AATC
1 AATCTC AATCTC AATCTC AATCTC AATC
11495161 ATAAATAACA
Statistics
Matches: 152, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
5 5 0.03
6 147 0.97
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.33
Consensus pattern (6 bp):
AATCTC
Done.