Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 1 of 279
Found at i:2219 original size:104 final size:103
Alignment explanation
Indices: 2038--2245 Score: 337
Period size: 104 Copynumber: 2.0 Consensus size: 103
2028 GACCACACCC
* *
2038 CCTAACCAAGCCTCATTACAACCTTCTAAAGACCTTTTGATTGATGTATCATCTTAAATTACAGT
1 CCTAACCAAGCCTCACTACAACCCTCTAAAGACCTTTTGATTGATGTATCATCTTAAATTACAGT
2103 GGTGGAGATTTGATTTTCAT-ACAAGCCTATGGTAATGA
66 GGTGGAGATTTGATTTTCATGA-AAGCCTATGGTAATGA
* * * *
2141 CNCTAACCAAGCGTTACTACAACCCTCTAAAGACCTTTTGATTGATGTATCATCTTAAATTATAT
1 C-CTAACCAAGCCTCACTACAACCCTCTAAAGACCTTTTGATTGATGTATCATCTTAAATTACAG
2206 TGGTGGAGATTTGATTTTCATGAAAGCCTATGGTAATGA
65 TGGTGGAGATTTGATTTTCATGAAAGCCTATGGTAATGA
2245 C
1 C
2246 ATTTCATTAT
Statistics
Matches: 97, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
103 1 0.01
104 95 0.98
105 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (103 bp):
CCTAACCAAGCCTCACTACAACCCTCTAAAGACCTTTTGATTGATGTATCATCTTAAATTACAGT
GGTGGAGATTTGATTTTCATGAAAGCCTATGGTAATGA
Found at i:21786 original size:46 final size:46
Alignment explanation
Indices: 21736--21908 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
21726 TGGTTGAGCA
21736 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
21782 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
21827 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
21875 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
21909 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:21892 original size:93 final size:93
Alignment explanation
Indices: 21733--21903 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
21723 GGATGGTTGA
* *
21733 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
21798 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
21826 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
21891 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
21904 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:24010 original size:15 final size:16
Alignment explanation
Indices: 23982--24011 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23972 ACATATCATT
23982 TATTTCATTATACCAA
1 TATTTCATTATACCAA
23998 TATTTCA-TATACCA
1 TATTTCATTATACCA
24012 TCGTTTCCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTTCATTATACCAA
Found at i:34126 original size:53 final size:54
Alignment explanation
Indices: 34044--34155 Score: 172
Period size: 53 Copynumber: 2.1 Consensus size: 54
34034 GGCCGAAATG
* * *
34044 ATGACCAACATACCCTCATAGGGTAAAATGACTAAAATACTCCCATAGGGTAAA
1 ATGACCAAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAA
* *
34098 ATGACCAAAATACCC-CATAGGGTAAAATGACCGAAATACCCCCATAGGGTATA
1 ATGACCAAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAA
34151 ATGAC
1 ATGAC
34156 TGTAATACCC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 39 0.74
54 14 0.26
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (54 bp):
ATGACCAAAATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGGTAAA
Found at i:34166 original size:27 final size:27
Alignment explanation
Indices: 34044--34155 Score: 163
Period size: 27 Copynumber: 4.2 Consensus size: 27
34034 GGCCGAAATG
* *
34044 ATGACCAACATACCCTCATAGGGTAAA
1 ATGACCAAAATACCCCCATAGGGTAAA
* *
34071 ATGACTAAAATACTCCCATAGGGTAAA
1 ATGACCAAAATACCCCCATAGGGTAAA
34098 ATGACCAAAATA-CCCCATAGGGTAAA
1 ATGACCAAAATACCCCCATAGGGTAAA
* *
34124 ATGACCGAAATACCCCCATAGGGTATA
1 ATGACCAAAATACCCCCATAGGGTAAA
34151 ATGAC
1 ATGAC
34156 TGTAATACCC
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
26 24 0.32
27 52 0.68
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (27 bp):
ATGACCAAAATACCCCCATAGGGTAAA
Found at i:34175 original size:27 final size:27
Alignment explanation
Indices: 34065--34210 Score: 107
Period size: 27 Copynumber: 5.4 Consensus size: 27
34055 ACCCTCATAG
** * *
34065 GGTAAAATGACTAAAATACTCCC-ATAG
1 GGTAAAATGACTGTAATAC-CCCTGTAA
*** * *
34092 GGTAAAATGACCAAAATACCCC-ATAG
1 GGTAAAATGACTGTAATACCCCTGTAA
* * ** *
34118 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACTGTAATACCCCTGTAA
*
34145 GGTATAATGACTGTAATACCCCTGTAA
1 GGTAAAATGACTGTAATACCCCTGTAA
** *
34172 GGTAAAGCGACTGTAACACCCCTGTAA
1 GGTAAAATGACTGTAATACCCCTGTAA
34199 GGTAAAATGACT
1 GGTAAAATGACT
34211 ATTTTGCCTT
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
26 28 0.27
27 76 0.73
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACTGTAATACCCCTGTAA
Found at i:34231 original size:27 final size:27
Alignment explanation
Indices: 34199--34407 Score: 149
Period size: 27 Copynumber: 7.7 Consensus size: 27
34189 ACCCCTGTAA
*
34199 GGTAAAATGACTATTTTGCCTTTGTGT
1 GGTAAAATGACTATTTTGCCTTTATGT
* * * *
34226 GTTAAAATGA-TGGTTTTGCCCTTATGC
1 GGTAAAATGACT-ATTTTGCCTTTATGT
* * * * *
34253 GATAAAAT-AATGGTTGTT-CATTTATAT
1 GGTAAAATGACT-ATT-TTGCCTTTATGT
*
34280 GGTAAAATGACTATTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCTTTATGT
* * * *
34307 GTTAAATTGACGATTTTG-CTCTTATAT
1 GGTAAAATGACTATTTTGCCT-TTATGT
*
34334 GGTAAAATGA-TGATTTTGCCTTTATGA
1 GGTAAAATGACT-ATTTTGCCTTTATGT
* *
34361 GGTAAAATGACTATTTTGCCCTTATAT
1 GGTAAAATGACTATTTTGCCTTTATGT
** *
34388 GGTAGGATGACTGTTTTGCC
1 GGTAAAATGACTATTTTGCC
34408 CCTATGTGAT
Statistics
Matches: 141, Mismatches: 32, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
26 5 0.04
27 129 0.91
28 7 0.05
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.42
Consensus pattern (27 bp):
GGTAAAATGACTATTTTGCCTTTATGT
Found at i:34308 original size:81 final size:81
Alignment explanation
Indices: 34198--34385 Score: 236
Period size: 81 Copynumber: 2.3 Consensus size: 81
34188 CACCCCTGTA
* * * * *
34198 AGGTAAAATGACTATTTTGCCTTTGTGTGTTAAAATGATGGTTTTGCCCTTATGCGATAAAATAA
1 AGGTAAAATGACTATTTTGCCCTTATGTGTTAAAATGACGATTTTGCCCTTATACGATAAAATAA
*
34263 TGGTTGTT-CATTTAT-
66 TGATT-TTGCATTTATG
* * * * *
34278 ATGGTAAAATGACTATTTTGCCCTTATGTGTTAAATTGACGATTTTGCTCTTATATGGTAAAATG
1 A-GGTAAAATGACTATTTTGCCCTTATGTGTTAAAATGACGATTTTGCCCTTATACGATAAAATA
*
34343 ATGATTTTGCCTTTATG
65 ATGATTTTGCATTTATG
34360 AGGTAAAATGACTATTTTGCCCTTAT
1 AGGTAAAATGACTATTTTGCCCTTAT
34386 ATGGTAGGAT
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
80 3 0.03
81 89 0.96
82 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.43
Consensus pattern (81 bp):
AGGTAAAATGACTATTTTGCCCTTATGTGTTAAAATGACGATTTTGCCCTTATACGATAAAATAA
TGATTTTGCATTTATG
Found at i:34332 original size:54 final size:54
Alignment explanation
Indices: 34199--34415 Score: 179
Period size: 54 Copynumber: 4.0 Consensus size: 54
34189 ACCCCTGTAA
* * * * * * *
34199 GGTAAAATGACTATTTTGCCTTTGTGTGTTAAAATGA-TGGTTTTGCCCTTATGC
1 GGTAAAATGACGATTTTGCCCTTATATGGTAAAATGACT-ATTTTGCCCTTATGT
* * * * **
34253 GATAAAATAATGGTTGTT-CATTTATATGGTAAAATGACTATTTTGCCCTTATGT
1 GGTAAAATGACGATT-TTGCCCTTATATGGTAAAATGACTATTTTGCCCTTATGT
* * * * *
34307 GTTAAATTGACGATTTTGCTCTTATATGGTAAAATGA-TGATTTTGCCTTTATGA
1 GGTAAAATGACGATTTTGCCCTTATATGGTAAAATGACT-ATTTTGCCCTTATGT
* ** * *
34361 GGTAAAATGACTATTTTGCCCTTATATGGTAGGATGACTGTTTTGCCCCTATGT
1 GGTAAAATGACGATTTTGCCCTTATATGGTAAAATGACTATTTTGCCCTTATGT
34415 G
1 G
34416 ATGTATGTTT
Statistics
Matches: 128, Mismatches: 30, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
53 3 0.02
54 121 0.95
55 4 0.03
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (54 bp):
GGTAAAATGACGATTTTGCCCTTATATGGTAAAATGACTATTTTGCCCTTATGT
Found at i:34760 original size:18 final size:18
Alignment explanation
Indices: 34734--34786 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
34724 GGACTTGCAT
*
34734 ACTGCTTACTGTTACTGC
1 ACTGATTACTGTTACTGC
*
34752 ACTGATTACTGTTATTGC
1 ACTGATTACTGTTACTGC
* * *
34770 ATTGTTTACTCTTACTG
1 ACTGATTACTGTTACTG
34787 TAATGGGCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (18 bp):
ACTGATTACTGTTACTGC
Found at i:35460 original size:24 final size:26
Alignment explanation
Indices: 35428--35493 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 26
35418 CTACAAAATC
35428 AGTAAGCTCATACGAGCTGAGA-A-T
1 AGTAAGCTCATACGAGCTGAGATATT
* * *
35452 AGTAAGCTCTTATGAGCTGATATATT
1 AGTAAGCTCATACGAGCTGAGATATT
*
35478 GGTAAGCTCATACGAG
1 AGTAAGCTCATACGAG
35494 TTGTGGTGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 19 0.56
25 1 0.03
26 14 0.41
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (26 bp):
AGTAAGCTCATACGAGCTGAGATATT
Found at i:40791 original size:48 final size:48
Alignment explanation
Indices: 40724--40869 Score: 172
Period size: 48 Copynumber: 3.0 Consensus size: 48
40714 GGTTATGTGT
40724 GATCCCATGTAAGACCATGTCTGAGACTTGGCATTGGCATC-ATTATGA
1 GATCCCATGTAAGACCATGTCTGAGACTTGGCATTGGCATCGA-TATGA
* * * * * * *
40772 GATCCCATGTAAGATCATGTTTGGGACATGGCATTAGCATCGACATGT
1 GATCCCATGTAAGACCATGTCTGAGACTTGGCATTGGCATCGATATGA
*
40820 GATCCCATGTAAGACCATATCT-AGGA-TATGGCATTGGCATCGATATGA
1 GATCCCATGTAAGACCATGTCTGA-GACT-TGGCATTGGCATCGATATGA
40868 GA
1 GA
40870 CATCGTGTAA
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
48 79 0.99
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGAGACTTGGCATTGGCATCGATATGA
Found at i:43862 original size:31 final size:31
Alignment explanation
Indices: 43824--43887 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
43814 CCTTTTCATA
43824 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
43855 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
43886 TT
1 TT
43888 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:44129 original size:25 final size:25
Alignment explanation
Indices: 44101--44177 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 25
44091 GCCTAGCCTC
44101 TTTTAATAACTGGGGCAAAGCCCTT
1 TTTTAATAACTGGGGCAAAGCCCTT
44126 TTTTAATAACTGGGGCATAAGCCC--
1 TTTTAATAACTGGGGCA-AAGCCCTT
*
44150 -TTTAATAACTGGGGCGTAAGCCCTT
1 TTTTAATAACTGGGGC-AAAGCCCTT
44175 TTT
1 TTT
44178 CACTTCCCCC
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
23 21 0.46
25 17 0.37
26 8 0.17
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (25 bp):
TTTTAATAACTGGGGCAAAGCCCTT
Found at i:44251 original size:20 final size:20
Alignment explanation
Indices: 44226--44292 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
44216 TTATGATTAC
44226 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
44246 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
44266 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
44286 ACCATGT
1 ATCATGT
44293 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:44257 original size:11 final size:11
Alignment explanation
Indices: 44226--44281 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
44216 TTATGATTAC
44226 ATCATGTGCAT
1 ATCATGTGCAT
*
44237 ATCA--TACAT
1 ATCATGTGCAT
44246 ATCATGTGCAT
1 ATCATGTGCAT
*
44257 ATCA--TACAT
1 ATCATGTGCAT
*
44266 GTCATGTGCAT
1 ATCATGTGCAT
44277 ATCAT
1 ATCAT
44282 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:44361 original size:25 final size:25
Alignment explanation
Indices: 44329--44376 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
44319 ATATTTAAAC
* *
44329 CCTAGGGGCATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
44354 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
44377 CATGTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:46705 original size:11 final size:11
Alignment explanation
Indices: 46678--46711 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
46668 TTTTTTTCCA
*
46678 TATAATAATAAT
1 TATAATAAT-TT
46690 TATAATAATTT
1 TATAATAATTT
46701 TATAATAATTT
1 TATAATAATTT
46712 CAAATATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATAATAATTT
Found at i:46817 original size:19 final size:18
Alignment explanation
Indices: 46780--46823 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
46770 ATACTTACAG
46780 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
46797 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
46816 TACTAATT
1 TAATAATT
46824 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:56047 original size:499 final size:498
Alignment explanation
Indices: 55109--56106 Score: 1933
Period size: 499 Copynumber: 2.0 Consensus size: 498
55099 AGGACCCACC
55109 ATCCTAGCCACCACCACCCTCTCATCCAGTTCATGTGGCGGCTTTATATGCTGACATCTCTGAGT
1 ATCCTAGCCACCACCACCCTCTCATCCAGTTCATGTGGCGGCTTTATATGCTGACATCTCTGAGT
55174 GCCTCACTCGATTCGAGCAATAGTGTTTTCAACGATTTGACAACATTGATGCTACTCTACAGTAG
66 GCCTCACTCGATTCGAGCAATAGTGTTTTCAACGATTTGACAACATTGATGCTACTCTACAGTAG
55239 ATTTGTCAGCACCTTCACATCTCATCCCCAGTCCCACCTCACGAACCATCCAGCGATGAAAATGT
131 ATTTGTCAGCACCTTCACATCTCATCCCCAGTCCCACCTCACGAACCATCCAGCGATGAAAATGT
55304 TTAAAAATATTTATTTATTATTTTATGTTTTTAATTTTTATTAAAAATACTTTTTATTTTGATTA
196 TTAAAAATATTTATTTATTATTTTATGTTTTTAATTTTTATTAAAAATACTTTTTATTTTGATTA
55369 GATTTTAGAATTTTATTTTTAATTATCAATTTCAGTTATTTCTTTATGAATAATTATTCTCCCTA
261 GATTTTAGAATTTTATTTTTAATTATCAATTTCAGTTATTTCTTTATGAATAATTATTCTCCCTA
55434 ATATCCCCTAAAAAGTTCTTGATCTTATCACAGTTATATAGAGCTCTTAAAGCTAATCATCGCAT
326 ATATCCCCTAAAAAGTTCTTGATCTTATCACAGTTATATAGAGCTCTTAAAGCTAATCATCGCAT
55499 AGGAACTAAAAACTCCACCGAGAAAGGTTCTCCATGACTGCCATGTCCTAATGGACCACGACCAT
391 AGGAACTAAAAACTCCACCGAGAAAGGTTCTCCATGACTGCCATGTCCTAATGGACCACGACCAT
55564 AGCTACCACTAGATATAATATTCTTTTGGTGTAGGACTTATGG
456 AGCTACCACTAGATATAATATTCTTTTGGTGTAGGACTTATGG
*
55607 NATCCTAGCCACCACCACCCTCTCGTCCAGTTCATGTGGCGGCTTTATATGCTGACATCTCTGAG
1 -ATCCTAGCCACCACCACCCTCTCATCCAGTTCATGTGGCGGCTTTATATGCTGACATCTCTGAG
55672 TGCCTCACTCGATTCGAGCAATAGTGTTTTCAACGATTTGACAACATTGATGCTACTCTACAGTA
65 TGCCTCACTCGATTCGAGCAATAGTGTTTTCAACGATTTGACAACATTGATGCTACTCTACAGTA
55737 GATTTGTCAGCACCTTCACATCTCATCCCCAGTCCCACCTCACGAACCATCCAGCGATGAAAATG
130 GATTTGTCAGCACCTTCACATCTCATCCCCAGTCCCACCTCACGAACCATCCAGCGATGAAAATG
* *
55802 TTTAAAAATATTTATTTATTATTTTATGTTTTTAATTTTTATTAAAACTACTTTTTATTTTTATT
195 TTTAAAAATATTTATTTATTATTTTATGTTTTTAATTTTTATTAAAAATACTTTTTATTTTGATT
* * *
55867 AGATTTTAGAATTTTATTTTTAATTATCAATTTCGGTTATTTCTTTATGAGTAATTATTCTTCCT
260 AGATTTTAGAATTTTATTTTTAATTATCAATTTCAGTTATTTCTTTATGAATAATTATTCTCCCT
55932 AATATCCCCTAAAAAGTTCTTGATCTTATCACAGTTATATAGAGCTCTTAAAGCTAATCATCGCA
325 AATATCCCCTAAAAAGTTCTTGATCTTATCACAGTTATATAGAGCTCTTAAAGCTAATCATCGCA
55997 TAGGAACTAAAAACTCCACCGAGAAAGGTTCTCCATGACTGCCATGTCCTAATGGACCACGACCA
390 TAGGAACTAAAAACTCCACCGAGAAAGGTTCTCCATGACTGCCATGTCCTAATGGACCACGACCA
56062 TAGCTACCACTAGATATAATATTCTTTTGGTGTAGGACTTATGG
455 TAGCTACCACTAGATATAATATTCTTTTGGTGTAGGACTTATGG
56106 A
1 A
56107 CTAATGAACC
Statistics
Matches: 493, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
498 1 0.00
499 492 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (498 bp):
ATCCTAGCCACCACCACCCTCTCATCCAGTTCATGTGGCGGCTTTATATGCTGACATCTCTGAGT
GCCTCACTCGATTCGAGCAATAGTGTTTTCAACGATTTGACAACATTGATGCTACTCTACAGTAG
ATTTGTCAGCACCTTCACATCTCATCCCCAGTCCCACCTCACGAACCATCCAGCGATGAAAATGT
TTAAAAATATTTATTTATTATTTTATGTTTTTAATTTTTATTAAAAATACTTTTTATTTTGATTA
GATTTTAGAATTTTATTTTTAATTATCAATTTCAGTTATTTCTTTATGAATAATTATTCTCCCTA
ATATCCCCTAAAAAGTTCTTGATCTTATCACAGTTATATAGAGCTCTTAAAGCTAATCATCGCAT
AGGAACTAAAAACTCCACCGAGAAAGGTTCTCCATGACTGCCATGTCCTAATGGACCACGACCAT
AGCTACCACTAGATATAATATTCTTTTGGTGTAGGACTTATGG
Found at i:61387 original size:27 final size:26
Alignment explanation
Indices: 61347--61458 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
61337 AGGAAGTGCC
*
61347 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
61374 CTGGTGGCTCTGCCACGTATT-TCTGTT
1 CTGGTGGCTCTGCCAC--ATTATCTGAT
61401 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
61429 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
61455 CTGG
1 CTGG
61459 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 8 0.11
27 48 0.65
28 18 0.24
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:61453 original size:54 final size:53
Alignment explanation
Indices: 61347--61458 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 53
61337 AGGAAGTGCC
*
61347 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACGTATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACG-ATTTCTGTT
* * *
61401 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACGATT-TCTGTT
61455 CTGG
1 CTGG
61459 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
53 3 0.06
54 33 0.63
55 16 0.31
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.38
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACGATTTCTGTT
Found at i:63905 original size:45 final size:46
Alignment explanation
Indices: 63820--63938 Score: 213
Period size: 45 Copynumber: 2.6 Consensus size: 46
63810 ACATTTAGCC
63820 GATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCT
63866 GATGCATGTCCCAGACATGT-TTACACTGGCTTACGTCTCGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCT
* *
63911 GATACATGTCCTAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
63939 AGAACTCGAC
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
45 43 0.61
46 27 0.39
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCT
Found at i:66588 original size:17 final size:18
Alignment explanation
Indices: 66562--66595 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
66552 TTTTTGTATA
66562 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
66579 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
66596 ATATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:71800 original size:15 final size:15
Alignment explanation
Indices: 71780--71809 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
71770 CAACATTTGT
71780 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
71795 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
71810 AATACATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Found at i:78858 original size:16 final size:16
Alignment explanation
Indices: 78839--78869 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
78829 CTTCTTCACT
78839 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
78855 TACTTACTTACTTAA
1 TACTCACTTACTTAA
78870 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:78875 original size:20 final size:20
Alignment explanation
Indices: 78836--78875 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
78826 AAACTTCTTC
* *
78836 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
78856 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
78876 TTATTAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:79190 original size:53 final size:54
Alignment explanation
Indices: 79061--79315 Score: 265
Period size: 55 Copynumber: 4.8 Consensus size: 54
79051 ACACGGGTAC
* * * *
79061 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * *
79110 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * *
79163 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
* * * *
79218 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
79271 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACACGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
79316 AAACCCTAAT
Statistics
Matches: 172, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
52 2 0.01
53 49 0.28
54 10 0.06
55 71 0.41
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.35
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:79252 original size:108 final size:110
Alignment explanation
Indices: 79108--79305 Score: 312
Period size: 108 Copynumber: 1.8 Consensus size: 110
79098 ATCCTTTTGA
* *
79108 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTAGCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTA-GAAACCTCACCAA
79171 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* ** *
79216 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTAGAAACCTCACCAAT
79281 TGCCATGCCTTGGCATGGTCTTACA
66 TGCCATGCCTTGGCATGGTCTTACA
79306 CGGTATCCTT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.59
109 7 0.09
110 25 0.31
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATAGCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:81972 original size:11 final size:11
Alignment explanation
Indices: 81940--81973 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
81930 TTGGTCATGA
*
81940 GAGTTTGAATA
1 GAGTTTGAATG
81951 GAGTTTGAATG
1 GAGTTTGAATG
81962 GAGTTTGAATG
1 GAGTTTGAATG
81973 G
1 G
81974 GATGTTGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (11 bp):
GAGTTTGAATG
Found at i:87037 original size:27 final size:27
Alignment explanation
Indices: 87007--87184 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
86997 ATATTGAGTC
* * * *
87007 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
87034 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
87061 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
87089 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
87116 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
87143 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
87170 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
87185 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:87146 original size:82 final size:81
Alignment explanation
Indices: 87028--87183 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
87018 TGCTATATAA
* *
87028 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
87093 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
87110 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
87174 CACTTAGTGC
65 CACTTAGTGC
87184 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:90235 original size:20 final size:21
Alignment explanation
Indices: 90199--90246 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
90189 ATTTTGATAT
*
90199 ACATGATTTGATATGATATGC
1 ACATGATATGATATGATATGC
90220 ACATGATATG-TATGATATGC
1 ACATGATATGATATGATATGC
90240 ACATGAT
1 ACATGAT
90247 GTATTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (21 bp):
ACATGATATGATATGATATGC
Found at i:90340 original size:24 final size:25
Alignment explanation
Indices: 90294--90345 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
90284 GAGGAAGTGC
90294 AAAAGGGCTTTGCCCCAGATTATCA
1 AAAAGGGCTTTGCCCCAGATTATCA
*
90319 AAAAGGGCTTTGCCCCAG-TTATTA
1 AAAAGGGCTTTGCCCCAGATTATCA
90343 AAA
1 AAA
90346 GAGGCTAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGATTATCA
Found at i:90351 original size:24 final size:24
Alignment explanation
Indices: 90293--90365 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 24
90283 GGAGGAAGTG
90293 CAAAAG-GGCTTTGCCCCAGATTAT
1 CAAAAGAGGCTTTGCCCCAG-TTAT
90317 CAAAA-AGGGCTTTGCCCCAGTTAT
1 CAAAAGA-GGCTTTGCCCCAGTTAT
* **
90341 TAAAAGAGGCTAGGCCTCCAGTTAT
1 CAAAAGAGGCTTTGCC-CCAGTTAT
90366 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 20 0.48
25 22 0.52
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (24 bp):
CAAAAGAGGCTTTGCCCCAGTTAT
Found at i:96736 original size:20 final size:21
Alignment explanation
Indices: 96700--96747 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
96690 ATTTTGATAT
*
96700 ACATGATTTGATATGATATGC
1 ACATGATATGATATGATATGC
96721 ACATGATATG-TATGATATGC
1 ACATGATATGATATGATATGC
96741 ACATGAT
1 ACATGAT
96748 GTATTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (21 bp):
ACATGATATGATATGATATGC
Found at i:96829 original size:25 final size:25
Alignment explanation
Indices: 96795--96864 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
96785 GAGGAAGTGC
* *
96795 AAAAGGGCTTTGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
96820 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
96845 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
96865 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:96877 original size:24 final size:24
Alignment explanation
Indices: 96794--96891 Score: 85
Period size: 25 Copynumber: 4.0 Consensus size: 24
96784 GGAGGAAGTG
* *
96794 CAAAAG-GGCTTTGCCCTAGTTTAC
1 CAAAAGAGGCTTTGCCCCAG-TTAT
96818 CGAAAAG-GGCTTTGCCCCAGTTTAT
1 C-AAAAGAGGCTTTGCCCCAG-TTAT
96843 CAAAA-AGGGCTTTGCCCCAGTTAT
1 CAAAAGA-GGCTTTGCCCCAGTTAT
* **
96867 TAAAAGAGGCTAGGCCTCCAGTTAT
1 CAAAAGAGGCTTTGCC-CCAGTTAT
96892 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
24 20 0.31
25 44 0.69
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (24 bp):
CAAAAGAGGCTTTGCCCCAGTTAT
Found at i:96888 original size:50 final size:50
Alignment explanation
Indices: 96795--96889 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
96785 GAGGAAGTGC
* **
96795 AAAAGGGCTTTGCCCTAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
**
96845 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
96890 ATATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 23 0.61
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (50 bp):
AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:103056 original size:22 final size:22
Alignment explanation
Indices: 103031--103117 Score: 95
Period size: 22 Copynumber: 3.8 Consensus size: 22
103021 TCATGATCGA
103031 TAAGCTCATACGAGCTGAACAG
1 TAAGCTCATACGAGCTGAACAG
*
103053 TAAGCTCATACGAGCTGAATCGG
1 TAAGCTCATACGAGCTGAA-CAG
* *
103076 TAAGCTC-TAATGAGCTGAAAACAA
1 TAAGCTCAT-ACGAGCTG--AACAG
*
103100 TAAGCTCTTACGAGCTGA
1 TAAGCTCATACGAGCTGA
103118 TATATAGGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 21 0.38
23 16 0.29
24 15 0.27
25 3 0.05
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (22 bp):
TAAGCTCATACGAGCTGAACAG
Found at i:103115 original size:47 final size:49
Alignment explanation
Indices: 103031--103144 Score: 132
Period size: 47 Copynumber: 2.4 Consensus size: 49
103021 TCATGATCGA
* *
103031 TAAGCTC-ATACGAGCTG--AACAGTAAGCTCATACGAGCTG-A-ATCGG
1 TAAGCTCTAT-CGAGCTGAAAACAATAAGCTCATACGAGCTGAATATAGG
*
103076 TAAGCTCTAAT-GAGCTGAAAACAATAAGCTCTTACGAGCTGATATATAGG
1 TAAGCTCT-ATCGAGCTGAAAACAATAAGCTCATACGAGCTGA-ATATAGG
103126 TAAGCTCTATCGAGCTGAA
1 TAAGCTCTATCGAGCTGAA
103145 TTGGTAAGCT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
45 13 0.22
47 22 0.38
49 3 0.05
50 20 0.34
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (49 bp):
TAAGCTCTATCGAGCTGAAAACAATAAGCTCATACGAGCTGAATATAGG
Found at i:103132 original size:26 final size:24
Alignment explanation
Indices: 103031--103212 Score: 113
Period size: 23 Copynumber: 7.6 Consensus size: 24
103021 TCATGATCGA
* *
103031 TAAGCTCATACGAGCTG-A-ACAG
1 TAAGCTCTTACGAGCTGAATATAG
* **
103053 TAAGCTCATACGAGCTGAAT-CGG
1 TAAGCTCTTACGAGCTGAATATAG
* * * * *
103076 TAAGCTCTAATGAGCTGAAAACAA
1 TAAGCTCTTACGAGCTGAATATAG
103100 TAAGCTCTTACGAGCTGATATATAGG
1 TAAGCTCTTACGAGCTGA-ATATA-G
*
103126 TAAGCTC-TATCGAGCTGAAT-TGG
1 TAAGCTCTTA-CGAGCTGAATATAG
** * * *
103149 TAAGCTCCAATGAGCTGAAAACAG
1 TAAGCTCTTACGAGCTGAATATAG
* *
103173 TAAACTCTCACGAGCTGACATATCAG
1 TAAGCTCTTACGAGCTGA-ATAT-AG
*
103199 TAAGCTCATACGAG
1 TAAGCTCTTACGAG
103213 TTGTGGTGAG
Statistics
Matches: 123, Mismatches: 27, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
22 17 0.14
23 35 0.28
24 34 0.28
25 9 0.07
26 28 0.23
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (24 bp):
TAAGCTCTTACGAGCTGAATATAG
Found at i:103151 original size:73 final size:73
Alignment explanation
Indices: 103050--103212 Score: 240
Period size: 73 Copynumber: 2.2 Consensus size: 73
103040 ACGAGCTGAA
* * *
103050 CAGTAAGCTCATACGAGCTGAATCGGTAAGCTCTAATGAGCTGAAAACAATAAGCTCTTACGAGC
1 CAGTAAGCTCATACGAGCTGAATCGGTAAGCTCCAATGAGCTGAAAACAATAAACTCTCACGAGC
*
103115 TGATATAT
66 TGACATAT
* *
103123 -AGGTAAGCTC-TATCGAGCTGAATTGGTAAGCTCCAATGAGCTGAAAACAGTAAACTCTCACGA
1 CA-GTAAGCTCATA-CGAGCTGAATCGGTAAGCTCCAATGAGCTGAAAACAATAAACTCTCACGA
103186 GCTGACATAT
64 GCTGACATAT
103196 CAGTAAGCTCATACGAG
1 CAGTAAGCTCATACGAG
103213 TTGTGGTGAG
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
72 3 0.04
73 74 0.93
74 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (73 bp):
CAGTAAGCTCATACGAGCTGAATCGGTAAGCTCCAATGAGCTGAAAACAATAAACTCTCACGAGC
TGACATAT
Found at i:108993 original size:44 final size:44
Alignment explanation
Indices: 108939--109083 Score: 195
Period size: 44 Copynumber: 3.3 Consensus size: 44
108929 TGGCTTAAAT
108939 CTACTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTTAGC
1 CTACTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTTAGC
* * * * * *
108983 CTACTTCACTACTGCTTAGGGACACAAGAT-TCGCCATC-TTCGAT
1 CTACTCCACTACTGCTTAGGGAGACAAGATCT-ACAATCTTTAG-C
*
109027 CTGCTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTTAGC
1 CTACTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTTAGC
109071 CTACTCCACTACT
1 CTACTCCACTACT
109084 ATAGGGAGAT
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
43 4 0.05
44 75 0.90
45 4 0.05
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (44 bp):
CTACTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTTAGC
Found at i:110337 original size:8 final size:8
Alignment explanation
Indices: 110326--110401 Score: 55
Period size: 8 Copynumber: 8.5 Consensus size: 8
110316 TCTTTCTTCC
110326 TTTTTTAT
1 TTTTTTAT
110334 TTTTTTATT
1 TTTTTTA-T
110343 TTTTATTGAT
1 TTTT-TT-AT
110353 TTTTTTAT
1 TTTTTTAT
110361 TTTTGATTGA-
1 TTTT--TT-AT
110371 TTTTTTAT
1 TTTTTTAT
*
110379 TATTATCATAT
1 T-TT-T-TTAT
110390 TTTTTTAT
1 TTTTTTAT
110398 TTTT
1 TTTT
110402 GATTGTTTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 20
0.72 0.03 0.26
Matches are distributed among these distances:
7 1 0.02
8 23 0.41
9 10 0.18
10 16 0.29
11 6 0.11
ACGTcount: A:0.17, C:0.01, G:0.04, T:0.78
Consensus pattern (8 bp):
TTTTTTAT
Found at i:110356 original size:11 final size:11
Alignment explanation
Indices: 110340--110379 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
110330 TTATTTTTTT
110340 ATTTTTTATTG
1 ATTTTTTATTG
110351 A-TTTTT-TT-
1 ATTTTTTATTG
*
110359 ATTTTTGATTG
1 ATTTTTTATTG
110370 ATTTTTTATT
1 ATTTTTTATT
110380 ATTATCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
8 1 0.04
9 6 0.25
10 7 0.29
11 10 0.42
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.75
Consensus pattern (11 bp):
ATTTTTTATTG
Found at i:110357 original size:18 final size:19
Alignment explanation
Indices: 110332--110410 Score: 94
Period size: 19 Copynumber: 4.3 Consensus size: 19
110322 TTCCTTTTTT
*
110332 ATTTTTTTATTTTTTATTG
1 ATTTTTTTATTTTTGATTG
110351 ATTTTTTTATTTTTGATTG
1 ATTTTTTTATTTTTGATTG
*
110370 A-TTTTTTATTATT-ATCAT-
1 ATTTTTTTATTTTTGAT--TG
110388 ATTTTTTTATTTTTGATTG
1 ATTTTTTTATTTTTGATTG
110407 -TTTT
1 ATTTT
110411 GGTCTTAAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
17 2 0.04
18 17 0.33
19 31 0.60
20 2 0.04
ACGTcount: A:0.18, C:0.01, G:0.06, T:0.75
Consensus pattern (19 bp):
ATTTTTTTATTTTTGATTG
Found at i:110375 original size:37 final size:35
Alignment explanation
Indices: 110334--110410 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 35
110324 CCTTTTTTAT
*
110334 TTTTTTATT-TTTTATTGATTTTTTTATTTTTGATTG
1 TTTTTTATTATTATA-T-ATTTTTTTATTTTTGATTG
110370 ATTTTTTATTATTATCATATTTTTTTATTTTTGATTG
1 -TTTTTTATTATTAT-ATATTTTTTTATTTTTGATTG
110407 TTTT
1 TTTT
110411 GGTCTTAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 4 0.11
37 28 0.76
38 4 0.11
39 1 0.03
ACGTcount: A:0.17, C:0.01, G:0.06, T:0.75
Consensus pattern (35 bp):
TTTTTTATTATTATATATTTTTTTATTTTTGATTG
Found at i:113558 original size:12 final size:12
Alignment explanation
Indices: 113541--113571 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
113531 ACCAGTTGCT
113541 CTTGCATTTGTG
1 CTTGCATTTGTG
*
113553 CTTGCATTTGTT
1 CTTGCATTTGTG
113565 CTTGCAT
1 CTTGCAT
113572 CTCCTTCTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (12 bp):
CTTGCATTTGTG
Found at i:113746 original size:19 final size:20
Alignment explanation
Indices: 113722--113766 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
113712 TTGTGACATC
*
113722 CAATGCATATG-ATAAAATG
1 CAATGCAGATGCATAAAATG
*
113741 CAATGCAGATGCATGAAATG
1 CAATGCAGATGCATAAAATG
113761 -AATGCA
1 CAATGCA
113767 AAAAGAGACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.22
Consensus pattern (20 bp):
CAATGCAGATGCATAAAATG
Found at i:116361 original size:26 final size:26
Alignment explanation
Indices: 116305--116422 Score: 130
Period size: 26 Copynumber: 4.5 Consensus size: 26
116295 GAATGATCCA
* *
116305 AAATAAACAATATATGAAAA-ATATTTG
1 AAATAAATAATATAT-AAAACA-ATTTC
*
116332 AAATAAATAAAATATAAAACAATTTC
1 AAATAAATAATATATAAAACAATTTC
116358 AAATAAAATAATATATAAAACAATTTC
1 AAAT-AAATAATATATAAAACAATTTC
* * * * *
116385 AAATATATAATATGTAAAATAAATTA
1 AAATAAATAATATATAAAACAATTTC
116411 AAATAAATAATA
1 AAATAAATAATA
116423 CACAAAGTAA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
26 40 0.51
27 39 0.49
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.30
Consensus pattern (26 bp):
AAATAAATAATATATAAAACAATTTC
Found at i:116365 original size:15 final size:15
Alignment explanation
Indices: 116345--116389 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
116335 TAAATAAAAT
116345 ATAAAACAATTTCAA
1 ATAAAACAATTTCAA
* *
116360 ATAAAATAA--T-AT
1 ATAAAACAATTTCAA
116372 ATAAAACAATTTCAA
1 ATAAAACAATTTCAA
116387 ATA
1 ATA
116390 TATAATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 6
0.70 0.12 0.18
Matches are distributed among these distances:
12 9 0.39
13 1 0.04
14 1 0.04
15 12 0.52
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAAAACAATTTCAA
Found at i:116388 original size:22 final size:23
Alignment explanation
Indices: 116336--116387 Score: 59
Period size: 27 Copynumber: 2.1 Consensus size: 23
116326 TATTTGAAAT
*
116336 AAATAAAATATAAAACAATTTCAAATA
1 AAATAATATATAAAACAATTTC----A
116363 AAATAATATATAAAACAATTTCA
1 AAATAATATATAAAACAATTTCA
116386 AA
1 AA
116388 TATATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.12
27 21 0.88
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATAATATATAAAACAATTTCA
Found at i:116389 original size:53 final size:53
Alignment explanation
Indices: 116304--116422 Score: 134
Period size: 53 Copynumber: 2.2 Consensus size: 53
116294 AGAATGATCC
* * *
116304 AAAATAAACAATATATGAAAAATATTTGAAATAAATAAAATATAAAACAATTT
1 AAAATAAATAATATATGAAAAATATTTCAAATAAATAAAATATAAAACAAATT
* * * * *
116357 CAAATAAAATAATATAT-AAAACA-ATTTCAAATATATAATATGTAAAATAAATT
1 AAAAT-AAATAATATATGAAAA-ATATTTCAAATAAATAAAATATAAAACAAATT
116410 AAAATAAATAATA
1 AAAATAAATAATA
116423 CACAAAGTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
52 8 0.15
53 36 0.65
54 11 0.20
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (53 bp):
AAAATAAATAATATATGAAAAATATTTCAAATAAATAAAATATAAAACAAATT
Found at i:116600 original size:19 final size:19
Alignment explanation
Indices: 116574--116635 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
116564 AAAGTAACAT
116574 ATATATATATAAATGTTTAAG
1 ATATATATAT-AA-GTTTAAG
*
116595 ATATATATATAAGCTTAAG
1 ATATATATATAAGTTTAAG
116614 ATATATATATAAGTTTAAG
1 ATATATATATAAGTTTAAG
116633 ATA
1 ATA
116636 AGGAGTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 27 0.69
20 2 0.05
21 10 0.26
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (19 bp):
ATATATATATAAGTTTAAG
Found at i:116783 original size:26 final size:25
Alignment explanation
Indices: 116742--116878 Score: 98
Period size: 26 Copynumber: 5.3 Consensus size: 25
116732 AGTATAACTA
* *
116742 AATAACATATACAAAATTTTAAAAT
1 AATAATATATATAAAATTTTAAAAT
*
116767 ACATATTATATATAAAATAATTTAAAAT
1 A-ATAATATATATAAAAT--TTTAAAAT
* * *
116795 AA-AAGGTATATAAAAAACTTCAAAAT
1 AATAA--TATATATAAAATTTTAAAAT
* ** *
116821 AATAATATGTATAGTAGTTTAAAAT
1 AATAATATATATAAAATTTTAAAAT
*
116846 AAACAATATATATAAAA-TTTAAAAT
1 -AATAATATATATAAAATTTTAAAAT
116871 AAATAATA
1 -AATAATA
116879 GTTCAAAAAT
Statistics
Matches: 87, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
25 30 0.34
26 35 0.40
27 3 0.03
28 19 0.22
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (25 bp):
AATAATATATATAAAATTTTAAAAT
Found at i:116847 original size:25 final size:25
Alignment explanation
Indices: 116740--116878 Score: 102
Period size: 25 Copynumber: 5.4 Consensus size: 25
116730 CTAGTATAAC
* *
116740 TAAATAACATATACAAAATTTTAAAA
1 TAAATAATATATATAAAA-TTTAAAA
* *
116766 TACATATTATATATAAAATAATTTAAAA
1 TA-A-ATAATATATATAA-AATTTAAAA
* * *
116794 TAAA-AGGTATATAAAAAACTTCAAAA
1 TAAATA-ATATATATAAAA-TTTAAAA
* * *
116820 T-AATAATATGTATAGTAGTTTAAAA
1 TAAATAATATATATA-AAATTTAAAA
*
116845 TAAACAATATATATAAAATTTAAAA
1 TAAATAATATATATAAAATTTAAAA
116870 TAAATAATA
1 TAAATAATA
116879 GTTCAAAAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
25 33 0.38
26 32 0.36
27 2 0.02
28 19 0.22
29 2 0.02
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (25 bp):
TAAATAATATATATAAAATTTAAAA
Found at i:121363 original size:27 final size:27
Alignment explanation
Indices: 121330--121553 Score: 152
Period size: 27 Copynumber: 8.3 Consensus size: 27
121320 CAAAACAGTC
* * * *
121330 ATTTTACCCTACAGGGGTATGTCGATC
1 ATTTTACACTACAAGGGTATTTCGATA
* *
121357 ATTTTACACTACAATGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATTTCGATA
121384 ATTTTACACTACAAGGGTATTTCGATA
1 ATTTTACACTACAAGGGTATTTCGATA
* * * *
121411 ATTTTACA-AATCGAGGGTGTTTCGGTA
1 ATTTTACACTA-CAAGGGTATTTCGATA
* ** * *
121438 ATTTTACA-AATTGAGGGTATTTTGGTA
1 ATTTTACACTA-CAAGGGTATTTCGATA
* *
121465 ATTTTACA-AATCGAGGGTATTTCGATA
1 ATTTTACACTA-CAAGGGTATTTCGATA
* * *
121492 ATTTTACA-AATCGAGGGTATTTTGATA
1 ATTTTACACTA-CAAGGGTATTTCGATA
* * * *
121519 ATTTTACA-AATTAAGGGTGTTTCGGTA
1 ATTTTACACTA-CAAGGGTATTTCGATA
121546 ATTTTACA
1 ATTTTACA
121554 AGTCGAGGGT
Statistics
Matches: 172, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 1 0.01
27 171 0.99
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTATTTCGATA
Found at i:121396 original size:54 final size:54
Alignment explanation
Indices: 121330--121553 Score: 202
Period size: 54 Copynumber: 4.1 Consensus size: 54
121320 CAAAACAGTC
* * * * *
121330 ATTTTACCCTACAGGGGTATGTCGATCATTTTAC-ACTACAATGGTATTTCGGTA
1 ATTTTACACTACAAGGGTATGTCGATAATTTTACAAAT-CAAGGGTATTTCGGTA
* * *
121384 ATTTTACACTACAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCGGTA
1 ATTTTACACTACAAGGGTATGTCGATAATTTTACAAATCAAGGGTATTTCGGTA
* ** * * * * *
121438 ATTTTACA-AATTGAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGATA
1 ATTTTACACTA-CAAGGGTATGTCGATAATTTTACAAATCAAGGGTATTTCGGTA
* * * * * *
121492 ATTTTACA-AATCGAGGGTATTTTGATAATTTTACAAATTAAGGGTGTTTCGGTA
1 ATTTTACACTA-CAAGGGTATGTCGATAATTTTACAAATCAAGGGTATTTCGGTA
121546 ATTTTACA
1 ATTTTACA
121554 AGTCGAGGGT
Statistics
Matches: 147, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 144 0.98
55 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (54 bp):
ATTTTACACTACAAGGGTATGTCGATAATTTTACAAATCAAGGGTATTTCGGTA
Found at i:121457 original size:81 final size:81
Alignment explanation
Indices: 121372--121709 Score: 375
Period size: 81 Copynumber: 4.2 Consensus size: 81
121362 ACACTACAAT
* * **
121372 GGTATTTCGGTAATTTTAC-ACTACAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCGG
1 GGTATTTCGGTAATTTTACAAAT-CAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTAG
121436 TAATTTTACAAATTGAG
65 TAATTTTACAAATTGAG
* *
121453 GGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTT-GA
1 GGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTAG-
*
121517 TAATTTTACAAATTAAG
65 TAATTTTACAAATTGAG
* * * * * * *
121534 GGTGTTTCGGTAATTTTACAAGTCGAGGGTGTTT-TAGTAATTTCACAAAT-TAGGGGTATTTTA
1 GGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGA-TAATTTTACAAATCGA-GGGTATTTTA
*
121597 GTAATTTTAAAAATT-AGG
64 GTAATTTTACAAATTGA-G
* * * * *
121615 GGTGTTTCGGTAATTTCACAAATTAGGGGTATTTCGATAATTTTACAAATCGAAGGTATTTTAGT
1 GGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTAGT
* *
121680 -ATTTCAC-AATCGAG
66 AATTTTACAAATTGAG
*
121694 GGTATTTCAGTAATTT
1 GGTATTTCGGTAATTT
121710 CTCTTTATTA
Statistics
Matches: 219, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
79 18 0.08
80 10 0.05
81 186 0.85
82 5 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (81 bp):
GGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTAGT
AATTTTACAAATTGAG
Found at i:121554 original size:27 final size:27
Alignment explanation
Indices: 121372--121709 Score: 297
Period size: 27 Copynumber: 12.6 Consensus size: 27
121362 ACACTACAAT
*
121372 GGTATTTCGGTAATTTTAC-ACTACAAG
1 GGTATTTCGGTAATTTTACAAAT-CAAG
* *
121399 GGTATTTCGATAATTTTACAAATCGAG
1 GGTATTTCGGTAATTTTACAAATCAAG
* **
121426 GGTGTTTCGGTAATTTTACAAATTGAG
1 GGTATTTCGGTAATTTTACAAATCAAG
* *
121453 GGTATTTTGGTAATTTTACAAATCGAG
1 GGTATTTCGGTAATTTTACAAATCAAG
* *
121480 GGTATTTCGATAATTTTACAAATCGAG
1 GGTATTTCGGTAATTTTACAAATCAAG
* * *
121507 GGTATTTTGATAATTTTACAAATTAAG
1 GGTATTTCGGTAATTTTACAAATCAAG
* * *
121534 GGTGTTTCGGTAATTTTACAAGTCGAG
1 GGTATTTCGGTAATTTTACAAATCAAG
* ** * * *
121561 GGTGTTTTAGTAATTTCACAAATTAGG
1 GGTATTTCGGTAATTTTACAAATCAAG
** * * *
121588 GGTATTTTAGTAATTTTAAAAATTAGG
1 GGTATTTCGGTAATTTTACAAATCAAG
* * * *
121615 GGTGTTTCGGTAATTTCACAAATTAGG
1 GGTATTTCGGTAATTTTACAAATCAAG
*
121642 GGTATTTCGATAATTTTACAAATCGAA-
1 GGTATTTCGGTAATTTTACAAATC-AAG
** * *
121669 GGTATTTTAGT-ATTTCAC-AATCGAG
1 GGTATTTCGGTAATTTTACAAATCAAG
*
121694 GGTATTTCAGTAATTT
1 GGTATTTCGGTAATTT
121710 CTCTTTATTA
Statistics
Matches: 261, Mismatches: 46, Indels: 9
0.83 0.15 0.03
Matches are distributed among these distances:
24 1 0.00
25 14 0.05
26 10 0.04
27 233 0.89
28 3 0.01
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
GGTATTTCGGTAATTTTACAAATCAAG
Found at i:121697 original size:25 final size:26
Alignment explanation
Indices: 121642--121710 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
121632 ACAAATTAGG
*
121642 GGTATTTC-GATAATTTTACAAATCGAA
1 GGTATTTCAG-TAATTTCAC-AATCGAA
* *
121669 GGTATTTTAGT-ATTTCACAATCGAG
1 GGTATTTCAGTAATTTCACAATCGAA
121694 GGTATTTCAGTAATTTC
1 GGTATTTCAGTAATTTC
121711 TCTTTATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 16 0.44
26 11 0.31
27 8 0.22
28 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (26 bp):
GGTATTTCAGTAATTTCACAATCGAA
Found at i:131450 original size:49 final size:49
Alignment explanation
Indices: 131331--131633 Score: 485
Period size: 49 Copynumber: 6.3 Consensus size: 49
131321 NNNNNNNNNN
*
131331 TATATATGTGATAAGGTCTAATGGCCGATGTGATGAATGTGAAAGTG--
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
131378 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
131427 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
131476 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
131525 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
* * * * * *
131572 TATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTA
1 TATATATGTGATAAG-GCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
131621 TA-A-ATGTGATAAG
1 TATATATGTGATAAG
131634 TCCCGAAGGG
Statistics
Matches: 242, Mismatches: 8, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
46 2 0.01
47 90 0.37
48 3 0.01
49 147 0.61
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
Found at i:134191 original size:13 final size:14
Alignment explanation
Indices: 134173--134205 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
134163 AATAAAAAAT
*
134173 AAACATATCAATA-
1 AAACATATAAATAC
134186 AAACATATAAATAC
1 AAACATATAAATAC
134200 AAACAT
1 AAACAT
134206 GGTCGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACATATAAATAC
Found at i:135560 original size:43 final size:43
Alignment explanation
Indices: 135502--136603 Score: 1915
Period size: 43 Copynumber: 25.6 Consensus size: 43
135492 ATCCTAGATA
* * * ** *
135502 TGGTCATACATGTAATCACATATTGATGCCATTGTCTCAGACAG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGAC-G
135546 -GGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
135588 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
135631 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
135674 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
135717 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
135760 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
135803 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
135846 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
135889 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
135932 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
135975 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
136018 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
136061 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
136104 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
136147 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
136190 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
136233 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
136276 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* * *
136319 TGGTCTTACACGTAATCACATATCGATGTCAATGTCCCAGACA
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* * *
136362 TGGTCTTACACGTAATCACATATTGATGCCAACATCCGAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* * *
136405 TGGTCTTACATGTAATCACATATCGATGCC-ACTGTCCTAGATAG
1 TGGTCTTACACGTAATCACATATCGATGCCAAC-GTCCCAGA-CG
* * *
136449 -GGTCTTACACGTAATCACATGTTGATGCCAACATCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
* * * * *
136491 TGGTCTTACACATAATCATATATCGATGCC-ACTATCCTAGACA
1 TGGTCTTACACGTAATCACATATCGATGCCAAC-GTCCCAGACG
* *
136534 AGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
136577 TGGTCTTACACGTAATCACATATCGAT
1 TGGTCTTACACGTAATCACATATCGAT
136604 ATCACATATC
Statistics
Matches: 1011, Mismatches: 40, Indels: 15
0.95 0.04 0.01
Matches are distributed among these distances:
42 6 0.01
43 1001 0.99
44 4 0.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (43 bp):
TGGTCTTACACGTAATCACATATCGATGCCAACGTCCCAGACG
Found at i:144051 original size:40 final size:39
Alignment explanation
Indices: 144004--144110 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 39
143994 TACTAGCTCA
* * *
144004 AAGCCTGCGGAACTTTAAGTCTGGATATACA-ACCAGCACT
1 AAGCCTGCGGAA-TTTAA-CCCGGATATACATACCAGCACG
* *
144044 AAGCCTGCGGGATTTAACCCGGATATATATTACCAGCACG
1 AAGCCTGCGGAATTTAACCCGGATATACA-TACCAGCACG
*
144084 AAGCCTGCGGGATTTAACCCGGATATA
1 AAGCCTGCGGAATTTAACCCGGATATA
144111 TATTATATCG
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 9 0.15
39 5 0.08
40 46 0.77
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (39 bp):
AAGCCTGCGGAATTTAACCCGGATATACATACCAGCACG
Found at i:144111 original size:40 final size:40
Alignment explanation
Indices: 144035--144115 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
144025 TGGATATACA
*
144035 ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATATT
144075 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATATT
144115 A
1 A
144116 TATCGAGAGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (40 bp):
ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATATT
Found at i:154220 original size:28 final size:28
Alignment explanation
Indices: 154161--154252 Score: 103
Period size: 28 Copynumber: 3.2 Consensus size: 28
154151 ATCCACACTT
* * *
154161 ATTCATTTGGCCCCTTTAGGCCCAATCTC
1 ATTCATATGG-CCCATTAGGCCCAATCAC
*
154190 ATTCATATGGCCCATTAGGCTCAATCAC
1 ATTCATATGGCCCATTAGGCCCAATCAC
* * * *
154218 ATTCATATGGCCCGTCAAGCCCAATCAA
1 ATTCATATGGCCCATTAGGCCCAATCAC
154246 ATTCATA
1 ATTCATA
154253 GTCATGGAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 45 0.83
29 9 0.17
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.29
Consensus pattern (28 bp):
ATTCATATGGCCCATTAGGCCCAATCAC
Found at i:161823 original size:28 final size:28
Alignment explanation
Indices: 161764--161855 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
161754 ATCCACACTT
* * *
161764 ATTCATTTGGCCCCTTTAGGCCCAATCTC
1 ATTCATATGG-CCCATTAGGCCCAATCAC
*
161793 ATTCATATGGCCCATTAGGCTCAATCAC
1 ATTCATATGGCCCATTAGGCCCAATCAC
* * *
161821 ATTCATATGGCCCGTCAAGCCCAATCAC
1 ATTCATATGGCCCATTAGGCCCAATCAC
161849 ATTCATA
1 ATTCATA
161856 GTCATGCAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 46 0.84
29 9 0.16
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (28 bp):
ATTCATATGGCCCATTAGGCCCAATCAC
Found at i:161937 original size:17 final size:18
Alignment explanation
Indices: 161915--161948 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
161905 TGCCTATTAT
161915 GGGCCC-TATAGCCCATC
1 GGGCCCATATAGCCCATC
*
161932 GGGCCCATTTAGCCCAT
1 GGGCCCATATAGCCCAT
161949 TCTTGCCCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.38, G:0.24, T:0.21
Consensus pattern (18 bp):
GGGCCCATATAGCCCATC
Found at i:165137 original size:30 final size:30
Alignment explanation
Indices: 165077--165138 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
165067 AAATTAACTA
* *
165077 TATAAAAACAATTTAAAAATAAATTGTATG
1 TATAAAAACAATTTAAAAATAAAATATATG
165107 TATAAAAA-AATTT-AAAATAAGTAATATATG
1 TATAAAAACAATTTAAAAATAA--AATATATG
165137 TA
1 TA
165139 AAAGTTTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.25
29 5 0.18
30 16 0.57
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (30 bp):
TATAAAAACAATTTAAAAATAAAATATATG
Found at i:165470 original size:13 final size:13
Alignment explanation
Indices: 165444--165478 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
165434 AAAACAATTC
165444 AAAACTATACAAAA
1 AAAACTA-ACAAAA
*
165458 GAAACTAACAAAA
1 AAAACTAACAAAA
165471 AAAACTAA
1 AAAACTAA
165479 AACAATGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.71, C:0.14, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAACTAACAAAA
Found at i:167334 original size:41 final size:41
Alignment explanation
Indices: 167245--167391 Score: 141
Period size: 41 Copynumber: 3.4 Consensus size: 41
167235 TCAAAATCAG
* *
167245 CTGGGACATTGGCATTGATAAATGTGGTTACGTGTAACACCATGT
1 CTGGGACATTGGCATTG-T--ATGTGATT-CGTGTAAGACCATGT
* * *
167290 CTGGGACATTGGCATTGTATTTGATTCATGTAAGACCATAT
1 CTGGGACATTGGCATTGTATGTGATTCGTGTAAGACCATGT
* ** * * *
167331 CTGGGACAGTGGCATCAATATGAGATAGCGTGTAAGACCACGT
1 CTGGGACATTGGCAT-TGTATGTGAT-TCGTGTAAGACCATGT
167374 CTGGGACATTGGCATTGT
1 CTGGGACATTGGCATTGT
167392 TCGATATATG
Statistics
Matches: 83, Mismatches: 17, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
41 26 0.31
42 13 0.16
43 26 0.31
44 1 0.01
45 17 0.20
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (41 bp):
CTGGGACATTGGCATTGTATGTGATTCGTGTAAGACCATGT
Found at i:175381 original size:28 final size:27
Alignment explanation
Indices: 175339--175440 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 27
175329 ACTGATCGAT
*
175339 CTCGCACATATAGTGCTCGGTTGAAGAA
1 CTCGCACACATAGTGCTCGGTT-AAGAA
* ** * *
175367 CTCGCACACACAGTGCCTCAATTACCGAT
1 CTCGCACACATAGTG-CTCGGTTA-AGAA
175396 CTCGCACACATAGTGCTCGGTTAAAGGAA
1 CTCGCACACATAGTGCTCGGTT-AA-GAA
* *
175425 TTTGCACACATAGTGC
1 CTCGCACACATAGTGC
175441 CTCTAATCAT
Statistics
Matches: 57, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
28 19 0.33
29 38 0.67
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (27 bp):
CTCGCACACATAGTGCTCGGTTAAGAA
Found at i:175402 original size:57 final size:58
Alignment explanation
Indices: 175335--175443 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 58
175325 GCCCACTGAT
* *
175335 CGATCTCGCACATATAGTGCTCGGTTGAA-GAACTCGCACACACAGTGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTCAATTAC
* * *
175392 CGATCTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACATAGTGCCTC
1 CGATCTCGCACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTC
175444 TAATCATTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 27 0.59
58 19 0.41
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (58 bp):
CGATCTCGCACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTCAATTAC
Found at i:175658 original size:43 final size:43
Alignment explanation
Indices: 175609--175772 Score: 213
Period size: 43 Copynumber: 3.8 Consensus size: 43
175599 CACCAGCATT
* * * *
175609 AAGCCTGCTAGACAAGAAGACCCGAATACAGATCACCGGCACA
1 AAGCCTGCTAGACACGAAGGCCCGAATACACATCACCGGCACG
*
175652 AAGCCTGCTA-AGCACGAAGGCCTGAATACACATCACCGGCACG
1 AAGCCTGCTAGA-CACGAAGGCCCGAATACACATCACCGGCACG
* * * * *
175695 AAGCATTCTAGGCACGAAGGCCCAAATACACATCACCGGCATG
1 AAGCCTGCTAGACACGAAGGCCCGAATACACATCACCGGCACG
*
175738 AAGCCTGCTAGGCACGAAGGCCCGAATACACATCA
1 AAGCCTGCTAGACACGAAGGCCCGAATACACATCA
175773 TCGAGTTTCA
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
42 1 0.01
43 104 0.99
ACGTcount: A:0.35, C:0.31, G:0.22, T:0.12
Consensus pattern (43 bp):
AAGCCTGCTAGACACGAAGGCCCGAATACACATCACCGGCACG
Found at i:178433 original size:28 final size:28
Alignment explanation
Indices: 178401--178465 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
178391 ATTTACTAGA
* *
178401 ATACCCCTATGTATGCCAAATTACCAT-T
1 ATACCCCTATGTATGCAAAATGACC-TCT
178429 ATACCCCTATGTATGCAAAATGACCTCT
1 ATACCCCTATGTATGCAAAATGACCTCT
178457 ATACCCCTA
1 ATACCCCTA
178466 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.32, C:0.31, G:0.08, T:0.29
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCTCT
Found at i:178629 original size:27 final size:27
Alignment explanation
Indices: 178571--178660 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 27
178561 AGGAAGCGTC
178571 CTGGTGG-CTATGCCACAAATTATCTGTT
1 CTGGTGGCCT-TGCCACAAA-TATCTGTT
*
178599 CTGGTGGCCTTGCCACATATATCTGTT
1 CTGGTGGCCTTGCCACAAATATCTGTT
178626 CTGGTGGCAC-TGCCACAAAATATCTGTAT
1 CTGGTGGC-CTTGCCAC-AAATATCTGT-T
178655 CTGGTG
1 CTGGTG
178661 ACTCTGTCAC
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
27 22 0.39
28 25 0.45
29 9 0.16
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCCTTGCCACAAATATCTGTT
Found at i:178679 original size:55 final size:56
Alignment explanation
Indices: 178571--178685 Score: 139
Period size: 55 Copynumber: 2.1 Consensus size: 56
178561 AGGAAGCGTC
* *
178571 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCTTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCTTGCCACATATATCTGTAT
* *
178626 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGA-CTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCT-TGCCACATATATCTGTAT
178682 CTGG
1 CTGG
178686 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
54 1 0.02
55 32 0.62
56 19 0.37
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCTTGCCACATATATCTGTAT
Found at i:179779 original size:11 final size:10
Alignment explanation
Indices: 179751--179784 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
179741 AGCCTGTAAG
179751 TATTCTGAAT
1 TATTCTGAAT
*
179761 TTTTCTGAAT
1 TATTCTGAAT
179771 ATATTCTGAAT
1 -TATTCTGAAT
179782 TAT
1 TAT
179785 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:184910 original size:18 final size:18
Alignment explanation
Indices: 184864--184910 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
184854 TGAGAATTAT
*
184864 TATATTTAAATTTAACTA
1 TATATTTAATTTTAACTA
*
184882 TAGATTATAATTTTAA-TA
1 TATATT-TAATTTTAACTA
184900 GTATATTTAAT
1 -TATATTTAAT
184911 CATACATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (18 bp):
TATATTTAATTTTAACTA
Found at i:191724 original size:28 final size:28
Alignment explanation
Indices: 191661--191811 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
191651 ATATTAAGTC
*
191661 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
191688 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
191716 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
191744 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
191772 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
191801 CGCACACTTAG
1 CGCACACTTAG
191812 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.19
28 76 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:197111 original size:28 final size:28
Alignment explanation
Indices: 197063--197127 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
197053 ATTTACTAGA
* * *
197063 ATACCCCTATGTATGCCAAATTACCAGT
1 ATACCCCTATGTATGCAAAATGACCACT
* *
197091 ATACCCCTATGTATGTAAAATGACCTCT
1 ATACCCCTATGTATGCAAAATGACCACT
197119 ATACCCCTA
1 ATACCCCTA
197128 GGGTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.29
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCACT
Found at i:197272 original size:27 final size:29
Alignment explanation
Indices: 197233--197294 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 29
197223 AGGAAGCGTC
* *
197233 CTGGTGGCCCTGCCAC-ATATATCTGT-T
1 CTGGTGGCACTGCCACAAAATATCTGTAT
197260 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGTAT
197289 CTGGTG
1 CTGGTG
197295 ACTCTGTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 15 0.48
28 9 0.29
29 7 0.23
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (29 bp):
CTGGTGGCACTGCCACAAAATATCTGTAT
Found at i:197305 original size:29 final size:28
Alignment explanation
Indices: 197233--197305 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
197223 AGGAAGCGTC
* * *
197233 CTGGTGGCCCTGCCAC-ATATATCTGTT
1 CTGGTGACACTGCCACAAAATATCTGTT
*
197260 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGACACTGCCACAAAATATCTGT-T
* *
197289 CTGGTGACTCTGTCACA
1 CTGGTGACACTGCCACA
197306 TTTTCTGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 15 0.38
28 9 0.23
29 15 0.38
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (28 bp):
CTGGTGACACTGCCACAAAATATCTGTT
Found at i:199380 original size:40 final size:40
Alignment explanation
Indices: 199313--199516 Score: 263
Period size: 40 Copynumber: 5.2 Consensus size: 40
199303 CCTTTGGAAT
* *
199313 TTAG-CCGGATATAGCT-ACTTGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
* * * *
199352 TTAGCCCGGTTATAGTAACTCGCACAAATGACTACGAGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
199392 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
199432 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG-C
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* * * **
199471 TTAGCCC-GAAATTAGTCACTAGCACAAATGCCTTCGAAAC
1 TTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGAC
199511 TTAGCC
1 TTAGCC
199517 AGTTATCATC
Statistics
Matches: 146, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
38 3 0.02
39 35 0.24
40 108 0.74
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:205652 original size:21 final size:21
Alignment explanation
Indices: 205627--205675 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
205617 ATGATATGAT
* *
205627 ATGATATGATATAATATGCGC
1 ATGATATGATATAAGATGCAC
* *
205648 ATGATATGTTATGAGATGCAC
1 ATGATATGATATAAGATGCAC
205669 ATGATAT
1 ATGATAT
205676 ACTCATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (21 bp):
ATGATATGATATAAGATGCAC
Found at i:205757 original size:25 final size:26
Alignment explanation
Indices: 205721--205792 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 26
205711 GGAGGAAGTG
* *
205721 CAAAAAGAGCTTTGG-CCTAGTTTA-
1 CAAAAAGGGCTTTGGCCCCAGTTTAT
*
205745 CTGAAAAGGGC-TTGGCCCCAGTTTAT
1 C-AAAAAGGGCTTTGGCCCCAGTTTAT
205771 CAAAAAGGGCTTT-GCCCCAGTT
1 CAAAAAGGGCTTTGGCCCCAGTT
205793 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 5 0.12
25 32 0.80
26 3 0.08
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (26 bp):
CAAAAAGGGCTTTGGCCCCAGTTTAT
Found at i:205775 original size:24 final size:24
Alignment explanation
Indices: 205739--205805 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
205729 GCTTTGGCCT
*
205739 AGTTTACTGAAAAGGGCTTGGCCCC
1 AGTTTA-TCAAAAGGGCTTGGCCCC
*
205764 AGTTTATCAAAAAGGGCTTTGCCCC
1 AGTTTATC-AAAAGGGCTTGGCCCC
*
205789 AG-TTATTAAAAGAGGCT
1 AGTTTATCAAAAG-GGCT
205806 AAGCCTCCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.14
24 9 0.24
25 23 0.62
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (24 bp):
AGTTTATCAAAAGGGCTTGGCCCC
Found at i:210501 original size:30 final size:30
Alignment explanation
Indices: 210467--210527 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
210457 TTCCTGAGCC
210467 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * * *
210497 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
210527 T
1 T
210528 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Found at i:211337 original size:64 final size:64
Alignment explanation
Indices: 211257--211440 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
211247 AGACATTATG
* * *
211257 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGTCAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGTCAAGAGAGCTACGAGATAA
* * * * * * *
211321 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGTTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGTCAAGAGAGCTACGAGAT
211386 AA
63 AA
* * *
211388 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAGT-CAAGAGAGC
211441 CGAACTATAT
Statistics
Matches: 95, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
62 1 0.01
63 17 0.18
64 25 0.26
66 21 0.22
67 31 0.33
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGTCAAGAGAGCTACGAGATAA
Found at i:216864 original size:21 final size:21
Alignment explanation
Indices: 216837--216887 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
216827 CTTTTGATAT
* *
216837 ACATGATATGATATGATATGC
1 ACATGATATGATATCAGATGC
* *
216858 GCATGATATGTTATCAGATGC
1 ACATGATATGATATCAGATGC
216879 ACATGATAT
1 ACATGATAT
216888 ACTCATTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (21 bp):
ACATGATATGATATCAGATGC
Found at i:216969 original size:25 final size:25
Alignment explanation
Indices: 216933--217004 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 25
216923 AGAGGAAGTG
* *
216933 CAAAAAGAGCTTTGCCCCAGTTTAC
1 CAAAAAGGGCTTTGCCCTAGTTTAC
* *
216958 CGAAAAGGGCTTTGCCCTAGTTTAT
1 CAAAAAGGGCTTTGCCCTAGTTTAC
216983 CAAAAAGGGCTTTGCCCTAGTT
1 CAAAAAGGGCTTTGCCCTAGTT
217005 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (25 bp):
CAAAAAGGGCTTTGCCCTAGTTTAC
Found at i:217017 original size:24 final size:25
Alignment explanation
Indices: 216935--217017 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
216925 AGGAAGTGCA
* *
216935 AAAAGA-GCTTTGCCCCAGTTTACC
1 AAAAGAGGCTTTGCCCTAGTTTATC
216959 GAAAAG-GGCTTTGCCCTAGTTTATC
1 -AAAAGAGGCTTTGCCCTAGTTTATC
*
216984 AAAA-AGGGCTTTGCCCTAG-TTATT
1 AAAAGA-GGCTTTGCCCTAGTTTATC
217008 AAAAGAGGCT
1 AAAAGAGGCT
217018 AGGCCTCCAG
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
24 16 0.31
25 35 0.69
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (25 bp):
AAAAGAGGCTTTGCCCTAGTTTATC
Found at i:227495 original size:34 final size:32
Alignment explanation
Indices: 227402--227480 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
227392 CCCATCATAG
* * * * *
227402 TATCAATTGTGCCTAGCCCATCTTAGAATCAC
1 TATCAGTTGGGCCTAGCCCATATCAGAATCAA
*
227434 TATCAGTTGGGTCTAGCCCATATCAGAATCAA
1 TATCAGTTGGGCCTAGCCCATATCAGAATCAA
227466 TATCAGTTAGGGCCT
1 TATCAGTT-GGGCCT
227481 TGGCCCATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 34 0.87
33 5 0.13
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (32 bp):
TATCAGTTGGGCCTAGCCCATATCAGAATCAA
Found at i:227900 original size:27 final size:27
Alignment explanation
Indices: 227841--227908 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
227831 ATAAATATAC
227841 ATCACATAAGGGCAAAACAGTCATCCT
1 ATCACATAAGGGCAAAACAGTCATCCT
* **
227868 ACCACATAAGGGCAAAACAGTCATTTT
1 ATCACATAAGGGCAAAACAGTCATCCT
*
227895 ATCACATAATGGCA
1 ATCACATAAGGGCA
227909 GAATCACCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.21
Consensus pattern (27 bp):
ATCACATAAGGGCAAAACAGTCATCCT
Found at i:227947 original size:27 final size:27
Alignment explanation
Indices: 227917--227974 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
227907 CAGAATCACC
* *
227917 ATTTCACCATATAGGGGTATTACAGTA
1 ATTTCACCATACAGGGGCATTACAGTA
* * **
227944 ATTTTACCCTACAGGGGCATTATGGTA
1 ATTTCACCATACAGGGGCATTACAGTA
227971 ATTT
1 ATTT
227975 TACATCACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (27 bp):
ATTTCACCATACAGGGGCATTACAGTA
Found at i:231965 original size:42 final size:42
Alignment explanation
Indices: 231914--231999 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
231904 TTCAGGAGAG
*
231914 TAGGACTAAAGGAAGATAGGGAGACTTCCGTTGAGTTAAGTA
1 TAGGACTAAAGGAAGATAGGGAGACTTCCCTTGAGTTAAGTA
*
231956 TAGGGCTAAAGGAAGATAGGGAGACTTCCCTTGAGTTAAGTA
1 TAGGACTAAAGGAAGATAGGGAGACTTCCCTTGAGTTAAGTA
231998 TA
1 TA
232000 AGGTCTGATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.35, C:0.10, G:0.30, T:0.24
Consensus pattern (42 bp):
TAGGACTAAAGGAAGATAGGGAGACTTCCCTTGAGTTAAGTA
Found at i:239412 original size:56 final size:55
Alignment explanation
Indices: 239326--239431 Score: 167
Period size: 56 Copynumber: 1.9 Consensus size: 55
239316 GCCATGGCAA
239326 GAGAAGACCATATAGTGTAAGGCCTAGCCATATTAATAAGGCATCATATGGGGAAT
1 GAGAAGACCATATAGTGTAAGGCCTAGCCAT-TTAATAAGGCATCATATGGGGAAT
* ** *
239382 GAGAAGTCCATATAGTGTAAGGCCTAGCCATTTGCTATGGCATCATATGG
1 GAGAAGACCATATAGTGTAAGGCCTAGCCATTTAATAAGGCATCATATGG
239432 CATATGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 16 0.35
56 30 0.65
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (55 bp):
GAGAAGACCATATAGTGTAAGGCCTAGCCATTTAATAAGGCATCATATGGGGAAT
Found at i:244124 original size:23 final size:23
Alignment explanation
Indices: 244098--244148 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
244088 TGAGTGTAAG
244098 CATTCAGGTATTCTATCCTTTTT
1 CATTCAGGTATTCTATCCTTTTT
244121 CATTCAGGTATTCTATCCTTTTT
1 CATTCAGGTATTCTATCCTTTTT
244144 CATTC
1 CATTC
244149 TTTCGGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.18, C:0.24, G:0.08, T:0.51
Consensus pattern (23 bp):
CATTCAGGTATTCTATCCTTTTT
Found at i:252015 original size:40 final size:40
Alignment explanation
Indices: 251812--252015 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
251802 CGGAATTTAA
** *
251812 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
251852 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
251892 CCAGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
251931 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCCTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
251971 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
252011 CCGGA
1 CCGGA
252016 CATCATTCAA
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.24
40 89 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:256232 original size:43 final size:42
Alignment explanation
Indices: 256152--256272 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 42
256142 GTTGAGGTTA
* * *
256152 CGTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTT
1 CGTGTAAGACCATAGCTGAGATATGGCATCGATATGAGATCT
* *
256194 CGTGTAAGACCATAGCTGAGCTATTGGCATTGATATGAGATCT
1 CGTGTAAGACCATAGCTGAGATA-TGGCATCGATATGAGATCT
* * * * *
256237 CATGTCAGACCATATCT-AGGACATGGCATTGATATG
1 CGTGTAAGACCATAGCTGA-GATATGGCATCGATATG
256273 GCACTATGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 34 0.51
43 33 0.49
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCATAGCTGAGATATGGCATCGATATGAGATCT
Found at i:260570 original size:22 final size:20
Alignment explanation
Indices: 260518--260569 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
260508 CAGGCTGAGG
260518 ACACGGGTGTGTCCCAAGCC
1 ACACGGGTGTGTCCCAAGCC
260538 ACACGGGTGTGTCCCAAGCC
1 ACACGGGTGTGTCCCAAGCC
260558 ACACGGGTGTGT
1 ACACGGGTGTGT
260570 GTGACTACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17
Consensus pattern (20 bp):
ACACGGGTGTGTCCCAAGCC
Found at i:265681 original size:33 final size:33
Alignment explanation
Indices: 265578--265681 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
265568 TTGCATATTG
* * *
265578 TACTGATT-CTGTAATGGGCTTAGGCCCCACTAA
1 TACTG-TTACTGTAATGGGCTAAGGCCCAACTGA
* * *
265611 TACTGTTACTGT-CTGGGCTCAGGCCCAGACTGC
1 TACTGTTACTGTAATGGGCTAAGGCCCA-ACTGA
* *
265644 TACTGTTACTGTAATGGGCTAAGGCCTAACTGT
1 TACTGTTACTGTAATGGGCTAAGGCCCAACTGA
265677 TACTG
1 TACTG
265682 GACTGTTTCT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 14 0.24
33 33 0.56
34 12 0.20
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (33 bp):
TACTGTTACTGTAATGGGCTAAGGCCCAACTGA
Found at i:285018 original size:43 final size:45
Alignment explanation
Indices: 284960--285092 Score: 126
Period size: 51 Copynumber: 2.9 Consensus size: 45
284950 AGATATGTGG
* * *
284960 CATCCAAGTTCGTTGAGAGGTCCGAGTTCATTATGGATGC-G-AG
1 CATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCAGTAA
* * * *
285003 CATCTGAGCTCGTTGAGTGGTCTGAGTTCATAATAGATGGGATTCATGTAA
1 CATCCGAGCTCGTTGAGAGGTCCGAGTTCAT--T--AT-GGATGCA-GTAA
*
285054 CATCCGAGCTCGTTGAGAGGTCCAAGTTCATTATGGATG
1 CATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
285093 TGTTACATGT
Statistics
Matches: 70, Mismatches: 12, Indels: 13
0.74 0.13 0.14
Matches are distributed among these distances:
43 26 0.37
45 1 0.01
46 4 0.06
47 4 0.06
48 5 0.07
49 1 0.01
50 1 0.01
51 28 0.40
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (45 bp):
CATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCAGTAA
Found at i:288890 original size:17 final size:18
Alignment explanation
Indices: 288868--288902 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
288858 TCACATTGAA
288868 GTGTTTT-AGTGAAAACC
1 GTGTTTTCAGTGAAAACC
*
288885 GTGTTTTCATTGAAAACC
1 GTGTTTTCAGTGAAAACC
288903 CTTCTTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACC
Found at i:290022 original size:28 final size:29
Alignment explanation
Indices: 289986--290093 Score: 114
Period size: 29 Copynumber: 3.8 Consensus size: 29
289976 GTATCTGCCT
* *
289986 ATTAAGCCC-AATCATATTCATATGGCCC
1 ATTAGGCCCAAATCACATTCATATGGCCC
* *
290014 ATTAGGCCCAAATCACCTGT-ATATGGCCT
1 ATTAGGCCCAAATCACAT-TCATATGGCCC
* * *
290043 ATTCGGCCCAAATCACATTTATATGGACC
1 ATTAGGCCCAAATCACATTCATATGGCCC
*
290072 ATTAGGCCC-AGTCACATTCATA
1 ATTAGGCCCAAATCACATTCATA
290094 GTCATGCTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
28 20 0.30
29 45 0.68
30 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (29 bp):
ATTAGGCCCAAATCACATTCATATGGCCC
Found at i:290074 original size:58 final size:56
Alignment explanation
Indices: 289972--290081 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 56
289962 AATTTCACAT
* * *
289972 ACCTGTATCTGCCTATTAAGCCCAATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGCCTATTAAGCCCAATCACATTCATATGGACCATTAGGCCCAAATC
** *
290028 ACCTGTATATGGCCTATTCGGCCCAAATCACATTTATATGGACCATTAGGCCCA
1 ACCTGTATAT-GCCTATTAAGCCC-AATCACATTCATATGGACCATTAGGCCCA
290082 GTCACATTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
56 9 0.20
57 11 0.24
58 26 0.57
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (56 bp):
ACCTGTATATGCCTATTAAGCCCAATCACATTCATATGGACCATTAGGCCCAAATC
Found at i:291515 original size:6 final size:6
Alignment explanation
Indices: 291494--291584 Score: 78
Period size: 6 Copynumber: 14.8 Consensus size: 6
291484 TACCAGAACT
* * * *
291494 AGAATC AAAATG AGAATC AGAATC AGAATC AG-GTGAC AGAATC AGAATT
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* *
291543 AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC AGAAT
1 AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAAT
291585 GTGAATGCAA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
5 2 0.03
6 58 0.87
7 5 0.07
8 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:291535 original size:37 final size:37
Alignment explanation
Indices: 291494--291584 Score: 146
Period size: 37 Copynumber: 2.5 Consensus size: 37
291484 TACCAGAACT
* *
291494 AGAATCAAAATGAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGAATCAGGTGAC
* *
291531 AGAATCAGAATTAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGAATCAGGTGAC
291568 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
291585 GTGAATGCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (37 bp):
AGAATCAGAATCAGAATCAGAATCAGAATCAGGTGAC
Found at i:291987 original size:22 final size:22
Alignment explanation
Indices: 291939--291997 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
291929 GTAAATACGT
*
291939 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
291961 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
291983 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
291998 CAATTACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:292144 original size:27 final size:27
Alignment explanation
Indices: 292105--292215 Score: 154
Period size: 27 Copynumber: 4.1 Consensus size: 27
292095 TCGATCGGTC
* *
292105 AACAGATA-TTGTGACAGAGTCACCAG
1 AACAGATATTTGTGGCAGAGCCACCAG
292131 ATACAGATA-TTGTGGCAGAGCCACCAG
1 A-ACAGATATTTGTGGCAGAGCCACCAG
*
292158 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATATTTGTGGCAGAGCCACCAG
*
292185 AAACAGATATTTGTGGCATAGCCACCAG
1 -AACAGATATTTGTGGCAGAGCCACCAG
292213 AAC
1 AAC
292216 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
26 8 0.10
27 44 0.56
28 27 0.34
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (27 bp):
AACAGATATTTGTGGCAGAGCCACCAG
Found at i:292470 original size:27 final size:27
Alignment explanation
Indices: 292440--292529 Score: 135
Period size: 27 Copynumber: 3.3 Consensus size: 27
292430 GGGCAAAATG
* * * * *
292440 GTAATTTTACCCCACAAGGGTATCTCA
1 GTAATTCTACCCTACAGGGGTATTTTA
292467 GTAATTCTACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTTA
292494 GTAATTCTACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTTA
292521 GTAATTCTA
1 GTAATTCTA
292530 TAAATTGAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTTA
Found at i:292864 original size:27 final size:27
Alignment explanation
Indices: 292521--292866 Score: 395
Period size: 27 Copynumber: 12.8 Consensus size: 27
292511 GGGTATTTTA
* * * *
292521 GTAATTCTATAAATTGAAGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
292548 ATAATTCTGTAAATTGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * * *
292575 GTAATTCTGTAAACCGAAGGTGAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
292602 GTAATTTTGTAAATCGAGAGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
292629 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
292656 ATAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
292683 GTAATTCTGTAAATCGAGGATAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * * *
292710 ATAATTCTATAAATCGAGGATAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
292737 ATAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
292764 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * * *
292791 GTAATTTTATAAATTGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
292818 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
292845 GTAATTCTATAAATCAAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
292867 CTTTGGTAAT
Statistics
Matches: 271, Mismatches: 48, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 271 1.00
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:293110 original size:17 final size:17
Alignment explanation
Indices: 293077--293110 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
293067 AACTTATCCA
*
293077 ATTGGGCCCATAGGCCC
1 ATTGGGCCCACAGGCCC
*
293094 ATTGGGCCCACATGCCC
1 ATTGGGCCCACAGGCCC
293111 CTTTCGGCCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.38, G:0.26, T:0.18
Consensus pattern (17 bp):
ATTGGGCCCACAGGCCC
Found at i:294607 original size:16 final size:17
Alignment explanation
Indices: 294564--294610 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 17
294554 ACAAAGAAAG
294564 TTCGGGA-TTTTGGGAT
1 TTCGGGATTTTTGGGAT
*
294580 TTCAGGATTTTTGGG-T
1 TTCGGGATTTTTGGGAT
294596 TTCGGGATTTTTGGG
1 TTCGGGATTTTTGGG
294611 GCGTTACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 21 0.75
17 7 0.25
ACGTcount: A:0.11, C:0.06, G:0.36, T:0.47
Consensus pattern (17 bp):
TTCGGGATTTTTGGGAT
Found at i:298066 original size:46 final size:47
Alignment explanation
Indices: 297975--298193 Score: 218
Period size: 46 Copynumber: 4.7 Consensus size: 47
297965 AACCCGCCCT
* * **
297975 TAAGCGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCGTTCACATCCA
* *
298021 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGA-CGTTCATATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCGTTCACATCCA
* * *
298067 TAAGTAAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C--GTTCACATCCA
* * * * *
298115 TCA-CGAACTCGAACTCAACTCAACGAGTTCGGA-TGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCGTTCACATCCA
*
298160 TAAGTGAACTCGGACTCAATTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
298194 TGCTCAAATA
Statistics
Matches: 140, Mismatches: 23, Indels: 20
0.77 0.13 0.11
Matches are distributed among these distances:
42 3 0.02
43 3 0.02
44 1 0.01
45 2 0.01
46 94 0.67
47 27 0.19
48 2 0.01
49 2 0.01
50 3 0.02
51 3 0.02
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCGTTCACATCCA
Found at i:298145 original size:93 final size:93
Alignment explanation
Indices: 298026--298196 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
298016 ATCCATAAGT
* * *
298026 GAACTCGGACTCAACTCAATGAGTTCGGACGTTCATATCCATAAGTAAACTCAGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACGTTCACATCCATAAGTAAACTCAGACTCAACTCAA
298091 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* * * * *
298119 GAACTCGAACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGTGAACTCGGACTCAATTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACGTTCACATCCATAAGTAAACTCAGACTCAACTCAA
*
298184 CGAGTTCGGATGC
66 CGAGCTCGGATGC
298197 TCAAATATTT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGTTCGGACGTTCACATCCATAAGTAAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:300968 original size:30 final size:29
Alignment explanation
Indices: 300925--300981 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
300915 AAAGATAACA
*
300925 AGAAAACCAAATAAAGAAATCCAAGATTG
1 AGAAAACCAAATAAAGAAACCCAAGATTG
* *
300954 AGAAACCCAGAATAAATAAACCCAAGAT
1 AGAAAACCA-AATAAAGAAACCCAAGAT
300982 ACAATACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (29 bp):
AGAAAACCAAATAAAGAAACCCAAGATTG
Done.