Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 78 of 352
Found at i:24491707 original size:40 final size:40
Alignment explanation
Indices: 24491663--24491773 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
24491653 TGAGTTACCA
* *
24491663 TAGTGAATTAGGAACAAATCCTATCCACTTTATATAT-TTC
1 TAGTGAATCAGGAACAAATCCTATTCACTTTA-ATATCTTC
* * *
24491703 TAGTGAATCAGGAATAAATCCTATTCACTTTAATTTCTTT
1 TAGTGAATCAGGAACAAATCCTATTCACTTTAATATCTTC
*
24491743 TAGTGAATCAGGAATC-AATCTTATTCACTTT
1 TAGTGAATCAGGAA-CAAATCCTATTCACTTT
24491774 TAATTCTCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.05
40 59 0.95
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (40 bp):
TAGTGAATCAGGAACAAATCCTATTCACTTTAATATCTTC
Found at i:24492730 original size:13 final size:12
Alignment explanation
Indices: 24492640--24492731 Score: 58
Period size: 12 Copynumber: 7.0 Consensus size: 12
24492630 CAATTTCTCC
24492640 CTTTTCTTTCTTT
1 CTTTT-TTTCTTT
*
24492653 CCCTTTTTTCTTT
1 -CTTTTTTTCTTT
* **
24492666 CTTTCTTTCTCCC
1 CTTTTTTTCT-TT
24492679 CTATTTTTTCGTTT
1 CT-TTTTTTC-TTT
* *
24492693 CTATTCTGTTCTTC
1 CT-TT-TTTTCTTT
24492707 CTTTTTTTCTTT
1 CTTTTTTTCTTT
24492719 CTTTTGTTTCTTT
1 CTTTT-TTTCTTT
24492732 TGTTTATTAT
Statistics
Matches: 61, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
12 19 0.31
13 18 0.30
14 19 0.31
15 5 0.08
ACGTcount: A:0.02, C:0.25, G:0.03, T:0.70
Consensus pattern (12 bp):
CTTTTTTTCTTT
Found at i:24495927 original size:6 final size:6
Alignment explanation
Indices: 24495909--24495940 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
24495899 GTTACAGAGA
*
24495909 CTGGGT CTAGGT CTGGGT CTGGGT CTGGGT CT
1 CTGGGT CTGGGT CTGGGT CTGGGT CTGGGT CT
24495941 CATGACCGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.19, G:0.44, T:0.34
Consensus pattern (6 bp):
CTGGGT
Found at i:24507741 original size:39 final size:39
Alignment explanation
Indices: 24507683--24507906 Score: 281
Period size: 39 Copynumber: 5.7 Consensus size: 39
24507673 TTCCAACACA
24507683 AATGCCTTCGGGACTTAGCCCGAATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGAATATAACACCAGCACG
* * ** *
24507722 AATACCTTCAGGACTTAGCCCGGTTATAACACCAGTACG
1 AATGCCTTCGGGACTTAGCCCGAATATAACACCAGCACG
* * *
24507761 AATACCTTCAGAACTTAGCCC-AGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGA-ATATAACACCAGCACG
** *
24507800 AATGCCTTCGGGACTTTTCCCGGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGAATATAACACCAGCACG
* *
24507839 AATGCCTTCGGGACTTATCCC-AGACATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGA-ATATAACACCAGCACG
* *
24507878 AATGCCTTCGAGACTTAGCCCGGATATAA
1 AATGCCTTCGGGACTTAGCCCGAATATAA
24507907 ATCTCACACA
Statistics
Matches: 159, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
39 159 1.00
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGAATATAACACCAGCACG
Found at i:24507837 original size:117 final size:117
Alignment explanation
Indices: 24507683--24507906 Score: 324
Period size: 117 Copynumber: 1.9 Consensus size: 117
24507673 TTCCAACACA
* **
24507683 AATGCCTTCGGGACTTAGCCCGAATATAACACCAGCACGAATACCTTCAGGACTTAGCCCGGTTA
1 AATGCCTTCGGGACTTAGCCCGAATATAACACCAGCACGAATACCTTCAGGACTTAGCCCAGACA
*
24507748 TAACACCAGTACGAATACCTTC-AGAACTTAGCCCAGATATAACACCAGCACG
66 TAACACCAGCACGAATACCTTCGAG-ACTTAGCCCAGATATAACACCAGCACG
** * * * *
24507800 AATGCCTTCGGGACTTTTCCCGGATATAACACCAGCACGAATGCCTTCGGGACTTATCCCAGACA
1 AATGCCTTCGGGACTTAGCCCGAATATAACACCAGCACGAATACCTTCAGGACTTAGCCCAGACA
* *
24507865 TAACACCAGCACGAATGCCTTCGAGACTTAGCCCGGATATAA
66 TAACACCAGCACGAATACCTTCGAGACTTAGCCCAGATATAA
24507907 ATCTCACACA
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
117 92 0.98
118 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (117 bp):
AATGCCTTCGGGACTTAGCCCGAATATAACACCAGCACGAATACCTTCAGGACTTAGCCCAGACA
TAACACCAGCACGAATACCTTCGAGACTTAGCCCAGATATAACACCAGCACG
Found at i:24514773 original size:40 final size:41
Alignment explanation
Indices: 24514724--24514924 Score: 235
Period size: 40 Copynumber: 5.0 Consensus size: 41
24514714 TTATAAAATA
* * * *
24514724 CAGAGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAAA-
1 CAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAAC
* * * *
24514764 TAGAGCAATAGCGGCGCTTTCGGTAAAACACCGCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAAC
* * *
24514805 CAGCGCATTAGCGGCGCTTTCAATAAAACGCCTCTAAAAAC
1 CAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAAC
* *
24514846 CAGAGCATTAGCGGCACTTTCGATAAAACGTCGCTAAAAA-
1 CAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAAC
* * * *
24514886 CAGAGCATTAGCGACGCTTTTGCTAAAACGCCACTAAAA
1 CAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAA
24514925 GTCATATAAC
Statistics
Matches: 138, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
40 69 0.50
41 69 0.50
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
CAGAGCATTAGCGGCGCTTTCGATAAAACGCCGCTAAAAAC
Found at i:24514832 original size:41 final size:40
Alignment explanation
Indices: 24514717--24514924 Score: 236
Period size: 41 Copynumber: 5.1 Consensus size: 40
24514707 GCAAAAATTA
* * * *
24514717 TAAAATACAGAGCAATAGCGGCGTTTTTGGTAAAACGCCGC
1 TAAAA-ACAGAGCATTAGCGGCGCTTTCGATAAAACGCCGC
* * * *
24514758 TAAAAATAGAGCAATAGCGGCGCTTTCGGTAAAACACCGC
1 TAAAAACAGAGCATTAGCGGCGCTTTCGATAAAACGCCGC
* * *
24514798 TAAAAACCAGCGCATTAGCGGCGCTTTCAATAAAACGCCTC
1 TAAAAA-CAGAGCATTAGCGGCGCTTTCGATAAAACGCCGC
* *
24514839 TAAAAACCAGAGCATTAGCGGCACTTTCGATAAAACGTCGC
1 TAAAAA-CAGAGCATTAGCGGCGCTTTCGATAAAACGCCGC
* * * *
24514880 TAAAAACAGAGCATTAGCGACGCTTTTGCTAAAACGCCAC
1 TAAAAACAGAGCATTAGCGGCGCTTTCGATAAAACGCCGC
24514920 TAAAA
1 TAAAA
24514925 GTCATATAAC
Statistics
Matches: 144, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
40 70 0.49
41 74 0.51
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (40 bp):
TAAAAACAGAGCATTAGCGGCGCTTTCGATAAAACGCCGC
Found at i:24514894 original size:81 final size:80
Alignment explanation
Indices: 24514717--24514924 Score: 245
Period size: 81 Copynumber: 2.6 Consensus size: 80
24514707 GCAAAAATTA
* * * * * *
24514717 TAAAATACAGAGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAAATAGAGCAATAGCGGCGCT
1 TAAAA-ACAGAGCATTAGCGGCGCTTTTGATAAAACGCCACTAAAAACAGAGCAATAGCGGCACT
*
24514782 TTCGGTAAAACACCGC
65 TTCGATAAAACACCGC
* ** * *
24514798 TAAAAACCAGCGCATTAGCGGCGCTTTCAATAAAACGCCTCTAAAAACCAGAGCATTAGCGGCAC
1 TAAAAA-CAGAGCATTAGCGGCGCTTTTGATAAAACGCCACTAAAAA-CAGAGCAATAGCGGCAC
**
24514863 TTTCGATAAAACGTCGC
64 TTTCGATAAAACACCGC
* *
24514880 TAAAAACAGAGCATTAGCGACGCTTTTGCTAAAACGCCACTAAAA
1 TAAAAACAGAGCATTAGCGGCGCTTTTGATAAAACGCCACTAAAA
24514925 GTCATATAAC
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
80 1 0.01
81 71 0.67
82 34 0.32
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (80 bp):
TAAAAACAGAGCATTAGCGGCGCTTTTGATAAAACGCCACTAAAAACAGAGCAATAGCGGCACTT
TCGATAAAACACCGC
Found at i:24515106 original size:7 final size:7
Alignment explanation
Indices: 24515096--24515142 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
24515086 TATTATTATA
24515096 GTTTAAG
1 GTTTAAG
*
24515103 GTTTATG
1 GTTTAAG
24515110 GTTTAAG
1 GTTTAAG
* * *
24515117 ATATATG
1 GTTTAAG
24515124 GTTTAAG
1 GTTTAAG
24515131 GTTTAAG
1 GTTTAAG
24515138 GTTTA
1 GTTTA
24515143 GGAGTTAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (7 bp):
GTTTAAG
Found at i:24515113 original size:14 final size:14
Alignment explanation
Indices: 24515091--24515142 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
24515081 TTAATTATTA
*
24515091 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
24515105 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
*
24515119 ATATGGTTTAAGGT
1 TTATGGTTTAAGGT
*
24515133 TTAAGGTTTA
1 TTATGGTTTA
24515143 GGAGTTAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:24515209 original size:7 final size:7
Alignment explanation
Indices: 24515197--24515314 Score: 53
Period size: 7 Copynumber: 16.7 Consensus size: 7
24515187 GAGATTATGT
24515197 TTTAGGG
1 TTTAGGG
24515204 TTTA-GG
1 TTTAGGG
* *
24515210 ATTAGAG
1 TTTAGGG
*
24515217 TTTAAGG
1 TTTAGGG
*
24515224 TGTAAGGG
1 T-TTAGGG
*
24515232 TTTAGTG
1 TTTAGGG
*
24515239 TTAAGGG
1 TTTAGGG
* *
24515246 TTAAGGA
1 TTTAGGG
*
24515253 TTTAAGG
1 TTTAGGG
24515260 TTTAGGG
1 TTTAGGG
* *
24515267 TTAAGTG
1 TTTAGGG
*
24515274 TTTAGTG
1 TTTAGGG
24515281 TTTATGGG
1 TTTA-GGG
*
24515289 -ATAGGGG
1 TTTA-GGG
*
24515296 TTAAGAGG
1 TTTAG-GG
24515304 TTT-GGG
1 TTTAGGG
24515310 TTTAG
1 TTTAG
24515315 ATTAATTAGT
Statistics
Matches: 80, Mismatches: 25, Indels: 12
0.68 0.21 0.10
Matches are distributed among these distances:
6 10 0.12
7 58 0.73
8 12 0.15
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:24515249 original size:28 final size:28
Alignment explanation
Indices: 24515218--24515271 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
24515208 GGATTAGAGT
*
24515218 TTAAGG-TGTAAGGGTTTAGTGTTAAGGG
1 TTAAGGATGTAA-GGTTTAGGGTTAAGGG
*
24515246 TTAAGGATTTAAGGTTTAGGGTTAAG
1 TTAAGGATGTAAGGTTTAGGGTTAAG
24515272 TGTTTAGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (28 bp):
TTAAGGATGTAAGGTTTAGGGTTAAGGG
Found at i:24515283 original size:21 final size:20
Alignment explanation
Indices: 24515197--24515284 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 20
24515187 GAGATTATGT
* * *
24515197 TTTAGGGTTTAGGATTAGAG
1 TTTAGGGTTAAGGTTTAGTG
*
24515217 TTTAAGGTGTAAGGGTTTAGTG
1 TTTAGGGT-TAA-GGTTTAGTG
*
24515239 TTAAGGGTTAAGGATTTAAG-G
1 TTTAGGGTTAAGG-TTT-AGTG
24515260 TTTAGGGTTAAGTGTTTAGTG
1 TTTAGGGTTAAG-GTTTAGTG
24515281 TTTA
1 TTTA
24515285 TGGGATAGGG
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
20 11 0.20
21 28 0.51
22 16 0.29
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (20 bp):
TTTAGGGTTAAGGTTTAGTG
Found at i:24519779 original size:22 final size:22
Alignment explanation
Indices: 24519747--24519790 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24519737 GATTAATATT
*
24519747 TTATATTTAATATTTATAAATA
1 TTATATATAATATTTATAAATA
* *
24519769 TTATATATAATTTTTTTAAATA
1 TTATATATAATATTTATAAATA
24519791 ACAATAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATATATAATATTTATAAATA
Found at i:24526681 original size:10 final size:10
Alignment explanation
Indices: 24526654--24526713 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
24526644 TGAAATTTTA
24526654 AAAGATAAAT
1 AAAGATAAAT
*
24526664 ACAA-ATAATT
1 A-AAGATAAAT
*
24526674 AAAGATAACT
1 AAAGATAAAT
24526684 AAAGATAAAT
1 AAAGATAAAT
24526694 AAAGATAAAT
1 AAAGATAAAT
24526704 GAAA-ATAAAT
1 -AAAGATAAAT
24526714 CCTAGAATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.05
10 37 0.84
11 5 0.11
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:24527441 original size:40 final size:40
Alignment explanation
Indices: 24527397--24527477 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
24527387 GAAAGTGTGT
24527397 TCAGGGGTACAAAAGCACAAACAGGGGCACATATGTGCAA
1 TCAGGGGTACAAAAGCACAAACAGGGGCACATATGTGCAA
** * * *
24527437 TCAGGGGTACCGAAGTACAAATAGGGGCACTTATGTGCAA
1 TCAGGGGTACAAAAGCACAAACAGGGGCACATATGTGCAA
24527477 T
1 T
24527478 AATTCAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (40 bp):
TCAGGGGTACAAAAGCACAAACAGGGGCACATATGTGCAA
Found at i:24536271 original size:25 final size:25
Alignment explanation
Indices: 24536243--24536348 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
24536233 CAGCTCTTAT
* * *
24536243 GAGCTTCCCGTTATTTAGCTTGCAA
1 GAGCTTCCCATTATTCAGCTCGCAA
* * *
24536268 GAGCTTCCCATTATTTAGCTCGTAT
1 GAGCTTCCCATTATTCAGCTCGCAA
** * * *
24536293 GAGCTTCCTGTTATTCAACTTGCAT
1 GAGCTTCCCATTATTCAGCTCGCAA
* *
24536318 GAGCTTTCCATTATTCAGCTCGAAA
1 GAGCTTCCCATTATTCAGCTCGCAA
24536343 GAGCTT
1 GAGCTT
24536349 ACTATTTACA
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.37
Consensus pattern (25 bp):
GAGCTTCCCATTATTCAGCTCGCAA
Found at i:24536315 original size:50 final size:50
Alignment explanation
Indices: 24536233--24536348 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 50
24536223 GAACACACCA
* * *
24536233 CAGCTCTTATGAGCTTCCCGTTATTTAGCTTGCAAGAGCTTCCCATTATT
1 CAGCTCGTATGAGCTTCCCGTTATTCAACTTGCAAGAGCTTCCCATTATT
* * * *
24536283 TAGCTCGTATGAGCTTCCTGTTATTCAACTTGCATGAGCTTTCCATTATT
1 CAGCTCGTATGAGCTTCCCGTTATTCAACTTGCAAGAGCTTCCCATTATT
* *
24536333 CAGCTCGAAAGAGCTT
1 CAGCTCGTATGAGCTT
24536349 ACTATTTACA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (50 bp):
CAGCTCGTATGAGCTTCCCGTTATTCAACTTGCAAGAGCTTCCCATTATT
Found at i:24540185 original size:42 final size:43
Alignment explanation
Indices: 24540085--24540246 Score: 136
Period size: 44 Copynumber: 3.8 Consensus size: 43
24540075 AACGCCAACG
* *
24540085 TCCCAGACATGGTCTTACATGTAATCACATATCGATGCCACTT
1 TCCCAGACATGGTCTTACACGTAATCACATATCGATGCCACTA
* **
24540128 TCCCAGAAAAT-GTCTTACACG-AA-CTTATATACGATGCCGA-TA
1 TCCCAG-ACATGGTCTTACACGTAATCACATAT-CGATGCC-ACTA
* * *
24540170 TCCCAGACATGGTCTTACATGTAAATTACAAATCGATGCCAACT-
1 TCCCAGACATGGTCTTACACGT-AATCACATATCGATGCC-ACTA
* * * *
24540214 TCCTAGACATGGTCTTTCATGAAATCACATATC
1 TCCCAGACATGGTCTTACACGTAATCACATATC
24540247 AAAACCCTAT
Statistics
Matches: 94, Mismatches: 17, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
41 8 0.09
42 25 0.27
43 25 0.27
44 32 0.34
45 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATCACATATCGATGCCACTA
Found at i:24544702 original size:20 final size:21
Alignment explanation
Indices: 24544677--24544716 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
24544667 TACCTTCTGT
24544677 GGTATCACGATATCC-CCTTG
1 GGTATCACGATATCCACCTTG
*
24544697 GGTATCAGGATATCCACCTT
1 GGTATCACGATATCCACCTT
24544717 CTAAGGAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (21 bp):
GGTATCACGATATCCACCTTG
Found at i:24545461 original size:42 final size:41
Alignment explanation
Indices: 24545397--24545481 Score: 111
Period size: 41 Copynumber: 2.0 Consensus size: 41
24545387 TCAAAAAAAA
24545397 TTCAAAAATCCAAAAAATATTTTCCATCTTTGTTTTT-AATTT
1 TTCAAAAATCCAAAAAATATTTT-CATCTTT-TTTTTAAATTT
* *
24545439 TTCAAAAATCC-AAAATTAATTTTCTTCTTTTTTTTAAATTT
1 TTCAAAAATCCAAAAAAT-ATTTTCATCTTTTTTTTAAATTT
24545480 TT
1 TT
24545482 GTTATTACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
40 5 0.13
41 18 0.46
42 16 0.41
ACGTcount: A:0.34, C:0.13, G:0.01, T:0.52
Consensus pattern (41 bp):
TTCAAAAATCCAAAAAATATTTTCATCTTTTTTTTAAATTT
Found at i:24547198 original size:20 final size:21
Alignment explanation
Indices: 24547173--24547212 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
24547163 TACCTTCTAT
24547173 GGTATCACAATATCC-CCTTG
1 GGTATCACAATATCCACCTTG
*
24547193 GGTATCGCAATATCCACCTT
1 GGTATCACAATATCCACCTT
24547213 CCAAGAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (21 bp):
GGTATCACAATATCCACCTTG
Found at i:24550610 original size:55 final size:53
Alignment explanation
Indices: 24550484--24550680 Score: 151
Period size: 55 Copynumber: 3.7 Consensus size: 53
24550474 AGGGTTTAAG
* * * * * * * * * *
24550484 GATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCAAG
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGATAACTAC-ATAAGACAAA
* * *
24550538 GAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGACAAA
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGAT-AACTAC-ATAAGACAAA
* * * * * * * *
24550593 GATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGCAAA
1 GATACCATGTAAGACCATGTCAAGACATGGCAATGATAACTACATAAGACAAA
* * *
24550646 GATACCACGTAAGACCATGTAAAGACATGGAAATG
1 GATACCATGTAAGACCATGTCAAGACATGGCAATG
24550681 TTAAGTTTAA
Statistics
Matches: 114, Mismatches: 28, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 38 0.33
54 34 0.30
55 42 0.37
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (53 bp):
GATACCATGTAAGACCATGTCAAGACATGGCAATGATAACTACATAAGACAAA
Found at i:24550675 original size:53 final size:54
Alignment explanation
Indices: 24550484--24550687 Score: 203
Period size: 53 Copynumber: 3.8 Consensus size: 54
24550474 AGGGTTTAAG
* * * * *
24550484 GATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCTACAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGCAAA
* * * * * * * *
24550538 GAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGACAAA
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTCTATAAGGCAAA
* * *
24550593 GATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTC-ATAAGGCAAA
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGCAAA
* ** * *
24550646 GATACCACGTAAGACCATGTAAAGACATGGAAATGTTAAGTT
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
24550688 TAAAAAGGAA
Statistics
Matches: 119, Mismatches: 30, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
53 43 0.36
54 34 0.29
55 42 0.35
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (54 bp):
GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCTATAAGGCAAA
Found at i:24562269 original size:19 final size:19
Alignment explanation
Indices: 24562233--24562274 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
24562223 GTTCTTCAAA
*
24562233 AATAAATAAAAGACAAAAT
1 AATAAATAAAAGAAAAAAT
24562252 AATAAATAAAA-ATAAAAAT
1 AATAAATAAAAGA-AAAAAT
24562271 AATA
1 AATA
24562275 GTAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (19 bp):
AATAAATAAAAGAAAAAAT
Found at i:24567930 original size:13 final size:13
Alignment explanation
Indices: 24567912--24567936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24567902 CCTAATATCC
24567912 CTTGACTTATTCA
1 CTTGACTTATTCA
24567925 CTTGACTTATTC
1 CTTGACTTATTC
24567937 CATAGAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (13 bp):
CTTGACTTATTCA
Found at i:24568722 original size:30 final size:30
Alignment explanation
Indices: 24568687--24568744 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
24568677 CACGGTCATG
*
24568687 ACACACGGGCGTGTGG-TCTACCCGTGTGTC
1 ACACACGGGCCTGTGGATC-ACCCGTGTGTC
24568717 ACACACGGGCCTGTGGATCACCCGTGTG
1 ACACACGGGCCTGTGGATCACCCGTGTG
24568745 GAAGTGCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.16, C:0.31, G:0.33, T:0.21
Consensus pattern (30 bp):
ACACACGGGCCTGTGGATCACCCGTGTGTC
Found at i:24572459 original size:12 final size:12
Alignment explanation
Indices: 24572442--24572480 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
24572432 TGGTTTCCTC
24572442 AAAATGGAAATG
1 AAAATGGAAATG
* *
24572454 AAAATGAAAATA
1 AAAATGGAAATG
24572466 AAAATGGGAAATG
1 AAAAT-GGAAATG
24572479 AA
1 AA
24572481 TTGATTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:24574343 original size:26 final size:25
Alignment explanation
Indices: 24574293--24574351 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 25
24574283 ATTTTTCTTG
24574293 AAATTTTATCGGGGTAAAATCATCA
1 AAATTTTATCGGGGTAAAATCATCA
*
24574318 AAATTTTATTGAGGGTAAAA-CTATCA
1 AAATTTTATCG-GGGTAAAATC-ATCA
24574344 AAATTTTA
1 AAATTTTA
24574352 CTGGGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 11 0.35
26 20 0.65
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (25 bp):
AAATTTTATCGGGGTAAAATCATCA
Found at i:24576501 original size:22 final size:22
Alignment explanation
Indices: 24576459--24576501 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
24576449 AGTTCTAAAA
*
24576459 AAAATTATTCAATTTAAGTTAT
1 AAAATTATTCAATATAAGTTAT
*
24576481 AAAATCTATT-AATATATGTTA
1 AAAAT-TATTCAATATAAGTTA
24576502 AGGATGAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (22 bp):
AAAATTATTCAATATAAGTTAT
Found at i:24578881 original size:12 final size:12
Alignment explanation
Indices: 24578864--24578895 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
24578854 TAGTTAGAAA
24578864 AAGAAATTATTG
1 AAGAAATTATTG
24578876 AAGAAATTATTG
1 AAGAAATTATTG
24578888 AAGAAATT
1 AAGAAATT
24578896 GGGTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (12 bp):
AAGAAATTATTG
Found at i:24584506 original size:39 final size:39
Alignment explanation
Indices: 24584452--24584527 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
24584442 TCCTGTGGTT
24584452 GAGTGTTAATATACCATTAGGTTTACCCACATGAATTTA
1 GAGTGTTAATATACCATTAGGTTTACCCACATGAATTTA
24584491 GAGTGTTAATATACCATTAGGTTTACCCACATGAATT
1 GAGTGTTAATATACCATTAGGTTTACCCACATGAATT
24584528 CAGACTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (39 bp):
GAGTGTTAATATACCATTAGGTTTACCCACATGAATTTA
Found at i:24586212 original size:44 final size:44
Alignment explanation
Indices: 24586164--24586252 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
24586154 ATGGCCAAAT
24586164 CTTAAATAGGTGGCACTTTGGAATGAACACAGATTTTGTTCTTA
1 CTTAAATAGGTGGCACTTTGGAATGAACACAGATTTTGTTCTTA
* * *
24586208 CTTAAATAGGTGGCACTTTGGAATGAACCCAGGTTTTGTTTTTA
1 CTTAAATAGGTGGCACTTTGGAATGAACACAGATTTTGTTCTTA
24586252 C
1 C
24586253 ATAAGCATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (44 bp):
CTTAAATAGGTGGCACTTTGGAATGAACACAGATTTTGTTCTTA
Found at i:24592601 original size:22 final size:23
Alignment explanation
Indices: 24592576--24592621 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
24592566 CAATGCAACC
*
24592576 ATACATAAC-ATAAATTGAGAGA
1 ATACATAACAAGAAATTGAGAGA
* *
24592598 ATACCTAACAAGAAATTTAGAGA
1 ATACATAACAAGAAATTGAGAGA
24592621 A
1 A
24592622 AAAGTGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (23 bp):
ATACATAACAAGAAATTGAGAGA
Found at i:24597995 original size:11 final size:11
Alignment explanation
Indices: 24597979--24598013 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
24597969 CACGTCTTGT
24597979 TTTTCTTTTGA
1 TTTTCTTTTGA
*
24597990 TTTTCTTTTGT
1 TTTTCTTTTGA
24598001 TTTTCCTTTTGA
1 TTTT-CTTTTGA
24598013 T
1 T
24598014 CTTGACCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.06, C:0.11, G:0.09, T:0.74
Consensus pattern (11 bp):
TTTTCTTTTGA
Found at i:24603338 original size:60 final size:60
Alignment explanation
Indices: 24603245--24603366 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
24603235 ATCTCTTTAC
*
24603245 TTCTAAGGCAGTAGGTGAATGTGGTAGAATCTTCGAAAGTAGTCAACCTTGCATATTCGA
1 TTCTAAGGCAGTAGGTGAATGTCGTAGAATCTTCGAAAGTAGTCAACCTTGCATATTCGA
24603305 TTCTAAGGCAGTAGGTGAATGTCGTAGAATCTTCGAAAGTAGTCAACCTTGCATATTCGA
1 TTCTAAGGCAGTAGGTGAATGTCGTAGAATCTTCGAAAGTAGTCAACCTTGCATATTCGA
24603365 TT
1 TT
24603367 TTTTAAATGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (60 bp):
TTCTAAGGCAGTAGGTGAATGTCGTAGAATCTTCGAAAGTAGTCAACCTTGCATATTCGA
Found at i:24608222 original size:33 final size:33
Alignment explanation
Indices: 24608180--24608246 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
24608170 GCATTTGAAA
24608180 TAGTATATTGAGAGTGAGGAAAAATAATTTCAT
1 TAGTATATTGAGAGTGAGGAAAAATAATTTCAT
24608213 TAGTATATTGAGAGTGAGGAAAAATAATTTCAT
1 TAGTATATTGAGAGTGAGGAAAAATAATTTCAT
24608246 T
1 T
24608247 CACTGACTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (33 bp):
TAGTATATTGAGAGTGAGGAAAAATAATTTCAT
Found at i:24612105 original size:13 final size:13
Alignment explanation
Indices: 24612089--24612115 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24612079 TTTAAATCAA
24612089 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
24612102 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
24612115 A
1 A
24612116 TTGCCAAACT
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:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:24612700 original size:39 final size:41
Alignment explanation
Indices: 24612637--24612726 Score: 139
Period size: 39 Copynumber: 2.2 Consensus size: 41
24612627 TTGCAAATAT
*
24612637 TTATATTAAAAAAAACTATCATAAATATAATAAATATTTTA
1 TTATATTAAAAAAAACTATAATAAATATAATAAATATTTTA
*
24612678 TTATATTAAAAAATAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAAAACTATAATAAATATAATAAATATTTTA
*
24612717 TTGTATTAAA
1 TTATATTAAA
24612727 TATAATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 30 0.65
40 1 0.02
41 15 0.33
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (41 bp):
TTATATTAAAAAAAACTATAATAAATATAATAAATATTTTA
Found at i:24612867 original size:33 final size:32
Alignment explanation
Indices: 24612827--24612897 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 32
24612817 GTTAGTGATT
24612827 TAATATAAATATAATATATAATTATTATT-TAACA
1 TAATATAAAT-TAATATA-AA-TATTATTATAACA
*
24612861 T-ATAT-AATTAATATAAATATTTTTATAACA
1 TAATATAAATTAATATAAATATTATTATAACA
24612891 TAATATA
1 TAATATA
24612898 TTCGAGTCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
29 6 0.18
30 8 0.24
31 11 0.33
32 3 0.09
33 4 0.12
34 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (32 bp):
TAATATAAATTAATATAAATATTATTATAACA
Found at i:24612874 original size:29 final size:29
Alignment explanation
Indices: 24612834--24612897 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
24612824 ATTTAATATA
*
24612834 AATATAATATATAATTATTATT-TAACAT
1 AATATAATATATAAATATTATTATAACAT
*
24612862 -ATATAATTAATATAAATATTTTTATAACAT
1 AATATAA-T-ATATAAATATTATTATAACAT
24612892 AATATA
1 AATATA
24612898 TTCGAGTCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.20
28 1 0.03
29 12 0.40
30 6 0.20
31 5 0.17
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
AATATAATATATAAATATTATTATAACAT
Found at i:24638390 original size:40 final size:40
Alignment explanation
Indices: 24638346--24638573 Score: 370
Period size: 40 Copynumber: 5.7 Consensus size: 40
24638336 GCTACTAGCT
24638346 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
24638386 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
24638426 CAAATGCCTTGGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
24638466 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
24638506 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
24638545 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
24638574 CAATCCGAAT
Statistics
Matches: 176, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
38 1 0.01
39 34 0.19
40 140 0.80
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:24646571 original size:17 final size:17
Alignment explanation
Indices: 24646551--24646633 Score: 73
Period size: 17 Copynumber: 4.9 Consensus size: 17
24646541 TCTCCTCTTC
* *
24646551 CTCTTCTTATTTTTTTT
1 CTCTTCTTCTTCTTTTT
*
24646568 CTCTTTCTTCTTCTTCTT
1 CTC-TTCTTCTTCTTTTT
*
24646586 CTCTTGTTCTTCTTTTT
1 CTCTTCTTCTTCTTTTT
*
24646603 CT-TT-TTCTTC-TTTG
1 CTCTTCTTCTTCTTTTT
*
24646617 CTTCTTCTTTTTCTTTT
1 C-TCTTCTTCTTCTTTT
24646634 ATTGCCCAGC
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
14 4 0.07
15 7 0.13
16 4 0.07
17 22 0.41
18 17 0.31
ACGTcount: A:0.01, C:0.24, G:0.02, T:0.72
Consensus pattern (17 bp):
CTCTTCTTCTTCTTTTT
Found at i:24646578 original size:3 final size:3
Alignment explanation
Indices: 24646572--24646631 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
24646562 TTTTTTCTCT
* * * *
24646572 TTC TTC TTC TTC TTC -TC TTG TTC TTC TTT TTC TTT TTC TTC TT- TGC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
24646618 TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TT
24646632 TTATTGCCCA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:24646590 original size:35 final size:35
Alignment explanation
Indices: 24646538--24646624 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 35
24646528 AGAATTTTTC
* *
24646538 TCTTC-TCCTCTTCCTCTTCTTATTTTTTTTCTCTT
1 TCTTCTTCTTCTT-CTCTTCTTATTCTTTTTCTCTT
* * *
24646573 TCTTCTTCTTCTTCTCTTGTTCTTCTTTTTCTTTT
1 TCTTCTTCTTCTTCTCTTCTTATTCTTTTTCTCTT
24646608 TCTTCTTTGCTTCTTCT
1 TCTTC-TT-CTTCTTCT
24646625 TTTTCTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
35 28 0.64
36 8 0.18
37 8 0.18
ACGTcount: A:0.01, C:0.29, G:0.02, T:0.68
Consensus pattern (35 bp):
TCTTCTTCTTCTTCTCTTCTTATTCTTTTTCTCTT
Found at i:24646632 original size:6 final size:6
Alignment explanation
Indices: 24646554--24646633 Score: 56
Period size: 6 Copynumber: 13.2 Consensus size: 6
24646544 CCTCTTCCTC
* * * * * *
24646554 TTCTTAT TT-TTT TTCTCT TTCTTC TTCTTC TTC-TC TTGTTC TTCTTT
1 TTCTT-T TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
*
24646601 TTCTTT TTCTTCT TTGCTTC TTCTTT TTCTTT T
1 TTCTTT TTCTT-T TT-CTTT TTCTTT TTCTTT T
24646634 ATTGCCCAGC
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
5 7 0.11
6 44 0.72
7 7 0.11
8 3 0.05
ACGTcount: A:0.01, C:0.23, G:0.03, T:0.74
Consensus pattern (6 bp):
TTCTTT
Found at i:24646632 original size:26 final size:26
Alignment explanation
Indices: 24646569--24646633 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
24646559 ATTTTTTTTC
*
24646569 TCTTTCTTCTTCTTCTTCTCTTGTTCT
1 TCTTT-TTCTTTTTCTTCTCTTGTTCT
24646596 TCTTTTTCTTTTTCTTCT-TTGCTTCT
1 TCTTTTTCTTTTTCTTCTCTTG-TTCT
24646622 TCTTTTTCTTTT
1 TCTTTTTCTTTT
24646634 ATTGCCCAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
25 3 0.08
26 28 0.78
27 5 0.14
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (26 bp):
TCTTTTTCTTTTTCTTCTCTTGTTCT
Found at i:24648062 original size:29 final size:30
Alignment explanation
Indices: 24648030--24648108 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
24648020 ATATTAATAT
* *
24648030 AAAATTTAAATTTATTATTATA-CTTTTTG
1 AAAATTTATATTTATTATTATATATTTTTG
* *
24648059 AAAATATT-TATTTATTTTTATATATTTTTT
1 AAAAT-TTATATTTATTATTATATATTTTTG
*
24648089 AAATTTTATATATTATTATT
1 AAAATTTATAT-TTATTATT
24648109 TGTTGTGAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
29 19 0.47
30 14 0.35
31 7 0.17
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (30 bp):
AAAATTTATATTTATTATTATATATTTTTG
Found at i:24648094 original size:23 final size:23
Alignment explanation
Indices: 24648068--24648168 Score: 62
Period size: 25 Copynumber: 4.0 Consensus size: 23
24648058 GAAAATATTT
*
24648068 ATTTATTTTTATATATTTTTTAA
1 ATTTATTATTATATATTTTTTAA
24648091 ATTTTATATATTAT-TATTTGTTGTGAACAA
1 A-TTTAT-TATTATATATTT-TT-T----AA
*
24648121 CATTT-TTATTTTTATATGATTTTTAA
1 -ATTTATTA-TTATATAT--TTTTTAA
24648147 ATTTATTATTATATATTTTTTA
1 ATTTATTATTATATATTTTTTA
24648169 GAAAATATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 28
0.66 0.03 0.30
Matches are distributed among these distances:
23 7 0.11
24 10 0.16
25 18 0.30
26 6 0.10
28 2 0.03
29 4 0.07
30 9 0.15
31 3 0.05
32 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (23 bp):
ATTTATTATTATATATTTTTTAA
Found at i:24648189 original size:56 final size:53
Alignment explanation
Indices: 24648034--24648204 Score: 176
Period size: 55 Copynumber: 3.2 Consensus size: 53
24648024 TAATATAAAA
*
24648034 TTTAAATTTATTA-T-TATACTTTTTGAAAATATTTATTTATTTTTATATATTT
1 TTTAAATTTATTATTATATATTTTTTGAAAATATTTA-TTATTTTTATATATTT
*
24648086 TTTAAATTTTATATATTAT-TATTTGTTGTGAACAACATTT-TTATTTTTATATGA-TT
1 TTTAAA-TTTAT-TATTATATATTT-TT-TGAA-AATATTTATTATTTTTATAT-ATTT
24648142 TTTAAATTTATTATTATATATTTTTTAGAAAATATTTATGTATTTTT-TGA-ATTT
1 TTTAAATTTATTATTATATATTTTTT-GAAAATATTTAT-TATTTTTAT-ATATTT
24648196 TTTAGAATT
1 TTTA-AATT
24648205 GGGATCAAAT
Statistics
Matches: 101, Mismatches: 3, Indels: 27
0.77 0.02 0.21
Matches are distributed among these distances:
52 6 0.06
53 13 0.13
54 21 0.21
55 27 0.27
56 23 0.23
57 5 0.05
58 6 0.06
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (53 bp):
TTTAAATTTATTATTATATATTTTTTGAAAATATTTATTATTTTTATATATTT
Found at i:24649359 original size:53 final size:53
Alignment explanation
Indices: 24649292--24649393 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
24649282 TTTTCAATTG
24649292 GTAAGACACAATGTT-TCCGGTATTGAACAAAAGTGTTTAATTATTTTTTGTTT
1 GTAAGACACAATGTTCT-CGGTATTGAACAAAAGTGTTTAATTATTTTTTGTTT
* * * *
24649345 GTAATACACAATGTTCTCGGTCTTGAACAAAATTGTTTAATTTTTTTTT
1 GTAAGACACAATGTTCTCGGTATTGAACAAAAGTGTTTAATTATTTTTT
24649394 TCAGTATTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 43 0.98
54 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (53 bp):
GTAAGACACAATGTTCTCGGTATTGAACAAAAGTGTTTAATTATTTTTTGTTT
Found at i:24650804 original size:20 final size:20
Alignment explanation
Indices: 24650779--24650827 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
24650769 ATCGATTAAT
* *
24650779 TCAATTAATAGTAATTTGAG
1 TCAATTAACAGTAATTCGAG
*
24650799 TCAATTAACGGTAATTCGAG
1 TCAATTAACAGTAATTCGAG
24650819 TCAATTAAC
1 TCAATTAAC
24650828 CGATCAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (20 bp):
TCAATTAACAGTAATTCGAG
Found at i:24650836 original size:12 final size:12
Alignment explanation
Indices: 24650819--24650843 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24650809 GTAATTCGAG
24650819 TCAATTAACCGA
1 TCAATTAACCGA
24650831 TCAATTAACCGA
1 TCAATTAACCGA
24650843 T
1 T
24650844 TATACACGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (12 bp):
TCAATTAACCGA
Found at i:24651052 original size:22 final size:22
Alignment explanation
Indices: 24651027--24651068 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
24651017 AATAAATGAG
* *
24651027 AAAAATTATATTTTAATTTCTA
1 AAAAATTATAATTAAATTTCTA
24651049 AAAAATTATAATTAAATTTC
1 AAAAATTATAATTAAATTTC
24651069 GCAACAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAATTATAATTAAATTTCTA
Found at i:24651262 original size:28 final size:27
Alignment explanation
Indices: 24651228--24651280 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
24651218 CTTTTATATC
*
24651228 ATTATTTA-CTGAAATGGGCCTATTTTTT
1 ATTATTTACCGGAAAT-GGCC-ATTTTTT
24651256 ATTATTTACCGGAAATGGCCATTTT
1 ATTATTTACCGGAAATGGCCATTTT
24651281 CCCCGAAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 12 0.52
29 6 0.26
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.45
Consensus pattern (27 bp):
ATTATTTACCGGAAATGGCCATTTTTT
Found at i:24651460 original size:15 final size:16
Alignment explanation
Indices: 24651440--24651474 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
24651430 TTGTCCTGAT
24651440 TTTTTAGGG-TTAGGG
1 TTTTTAGGGTTTAGGG
24651455 TTTTTAGGGTTTAGGG
1 TTTTTAGGGTTTAGGG
24651471 TTTT
1 TTTT
24651475 AGTGTGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.54
Consensus pattern (16 bp):
TTTTTAGGGTTTAGGG
Found at i:24651855 original size:125 final size:124
Alignment explanation
Indices: 24651604--24651911 Score: 447
Period size: 125 Copynumber: 2.5 Consensus size: 124
24651594 ATTAGCTAAT
* *
24651604 AATTACGGAAAAAAGCTCCTATGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTT
1 AATTACGGAAAAAAGCTCC-ACGTGGACGCTTTTTTGCTACAGTAGTATCTG-AAAAATAATTTT
* * * *
24651669 GAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGGACTGTCTGCAA
64 GAGAAGATGTTTCTAAAAAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTATCAGCAA
* * *
24651730 AATTACGGAAAAAAACTCTCACATGGACGCTTTTTTGCTACAGTAGTATTTGAAAAATAATTTTG
1 AATTACGGAAAAAAGCTC-CACGTGGACGCTTTTTTGCTACAGTAGTATCTGAAAAATAATTTTG
*
24651795 AGAAGATGTTTCTGAAAAAAATAGTGTC-AAAACGCTTCAAGCAGGATGCACTATCAGCAA
65 AGAAGATGTTTCT-AAAAAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTATCAGCAA
* * *
24651855 AATTACGGAAAAAAGCTCCCACGTGGACGATTTATTGCTATAGTAGTATCTGAAAAA
1 AATTACGGAAAAAAGCT-CCACGTGGACGCTTTTTTGCTACAGTAGTATCTGAAAAA
24651912 GCCTTAGACT
Statistics
Matches: 163, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
125 103 0.63
126 59 0.36
127 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (124 bp):
AATTACGGAAAAAAGCTCCACGTGGACGCTTTTTTGCTACAGTAGTATCTGAAAAATAATTTTGA
GAAGATGTTTCTAAAAAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTATCAGCAA
Found at i:24653219 original size:16 final size:15
Alignment explanation
Indices: 24653198--24653227 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
24653188 GGTTTTTGAA
24653198 TAATATTGTTATTATG
1 TAATATTG-TATTATG
24653214 TAATATTGTATTAT
1 TAATATTGTATTAT
24653228 TTAACATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (15 bp):
TAATATTGTATTATG
Found at i:24655386 original size:10 final size:11
Alignment explanation
Indices: 24655358--24655389 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
24655348 AATTGAAAGT
24655358 ATATAAAAATA
1 ATATAAAAATA
24655369 ATATAAAAATA
1 ATATAAAAATA
24655380 ATA-AAAAATA
1 ATATAAAAATA
24655390 TTGGCTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:24655604 original size:132 final size:130
Alignment explanation
Indices: 24654998--24655826 Score: 1242
Period size: 132 Copynumber: 6.4 Consensus size: 130
24654988 TATTCTAATG
* * * * * * *
24654998 AAAATTATTGACTAATTTAAAAGAATATTTATTGTATTAAAATTTTAAAAAAAGTAAAATACAAT
1 AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAA-TTAAAAAAAAGTAAAGTACAAT
* *
24655063 TAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAATAGATATAAAAAT-AA
65 TAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAATAAATATAAAAATAAA
*
24655127 T
130 A
* *
24655128 AAAAATATTGGCTAATTTAAAAGAATATTTATTTTAATAAAATTAAAAAAAAGTAAAGTACGATT
1 AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTACAATT
* * * * * *
24655193 AAAGTATTAAAAATAACTTTTATTTTATTAATTGAAACTATAT-AATATATATATATAAAT-AAT
66 AAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAATAAATATAAAAATAAAA
*
24655256 AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATT--AAAAAAGTGAAGTACAATT
1 AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTACAATT
* * * *
24655319 AAAATATTAAAAATAAATTTTATTTTATTAATTGAAAGTATATAAAAAT-AATATAAAAATAATA
66 AAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAATAAATATAAAAATAAAA
*
24655383 AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAACT--AAAAAAGTAAAGTACAATT
1 AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTACAATT
*
24655446 AAAATATTGAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAATTAAATATAAAAATAAA
66 AAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAA-TAAATATAAAAATAAA
24655511 A
130 A
*
24655512 AAAAATATTGGTTAATTTAAAAGAACATTTATTTTTAATAAAATTAAAAAAAAGTAAAGTACAAT
1 AAAAATATTGGCTAATTTAAAAGAACATTTA-TTTTAATAAAATTAAAAAAAAGTAAAGTACAAT
*
24655577 TAAAATATTAAAAATAACTTTTATTTTATTAATTGAAACTATATAAAAATTAAATATAAAAATAA
65 TAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAA-TAAATATAAAAATAA
*
24655642 TA
129 AA
* * *
24655644 AAAAATATTGTCTAATTTAAAAGAATATTTATTTTAATAAAATTTAAAAAAAGTAAAGTACAATT
1 AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTACAATT
24655709 AAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAAAAATAA
66 AAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATAT-AAAAA-TAAATATAAAAATAA
*
24655774 TA
129 AA
* *
24655776 AAAAATATTGTCTAATTTAAAAGAACATTAATTTTAATAAAATTAAAAAAA
1 AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAA
24655827 GTCAATGTTG
Statistics
Matches: 647, Mismatches: 44, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
126 66 0.10
127 110 0.17
128 61 0.09
129 104 0.16
130 50 0.08
131 75 0.12
132 181 0.28
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (130 bp):
AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTACAATT
AAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAATAAATATAAAAATAAAA
Found at i:24655615 original size:385 final size:390
Alignment explanation
Indices: 24654993--24655825 Score: 1313
Period size: 385 Copynumber: 2.1 Consensus size: 390
24654983 ATATTTATTC
* * * * *
24654993 TAATGAAAATTATTGACTAATTTAAAAGAATATTTATTGTATTAAAATTTTAAAAAAAGTAAAAT
1 TAATAAAAAATATTGACTAATTTAAAAGAACATTTATTTTAATAAAA--TT-AAAAAAGTAAAAT
*
24655058 ACAATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAATAGATATAAAA
63 ACAATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAATAAATATAAAA
* *
24655123 ATAATAAAAATATTGGCTAATTTAAAAGAATATTTATTTTAATAAAATTAAAAAAAAGTAAAGTA
128 ATAAAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTA
* * * * *
24655188 CGATTAAAGTATTAAAAATAACTTTTATTTTATTAATTGAAACTATAT-AATA-TATATATATAA
193 CAATTAAAATATTAAAAATAACTTTTATTTTATTAATTGAAACTATATAAAAATTAAATATAAAA
*
24655251 ATAAT-AAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAA-TT-AAAAAAGTGAAGT
258 ATAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTTAAAAAAAGTAAAGT
* *
24655313 ACAATTAAAATATTAAAAATAAATTTTATTTTATTAATTGAAAGTATAT-AAAAA-T-AATATAA
323 ACAATTAAAATATTAAAAACAAATTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAA
24655375 AAA
388 AAA
* * *
24655378 TAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAACTAAAAAAGTAAAGTACA
1 TAATAAAAAATATTGACTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAGTAAAATACA
* *
24655443 ATTAAAATATTGAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAATTAAATATAAAAAT
66 ATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAA-TAAATATAAAAAT
*
24655508 AAAAAAAAATATTGGTTAATTTAAAAGAACATTTATTTTTAATAAAATTAAAAAAAAGTAAAGTA
130 -AAAAAAAATATTGGCTAATTTAAAAGAACATTTA-TTTTAATAAAATTAAAAAAAAGTAAAGTA
24655573 CAATTAAAATATTAAAAATAACTTTTATTTTATTAATTGAAACTATATAAAAATTAAATATAAAA
193 CAATTAAAATATTAAAAATAACTTTTATTTTATTAATTGAAACTATATAAAAATTAAATATAAAA
* *
24655638 ATAATAAAAAATATTGTCTAATTTAAAAGAATATTTATTTTAATAAAATTTAAAAAAAGTAAAGT
258 ATAATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTTAAAAAAAGTAAAGT
*
24655703 ACAATTAAAATATTAAAAACAACTTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAA
323 ACAATTAAAATATTAAAAACAAATTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAA
24655768 AAA
388 AAA
* *
24655771 TAATAAAAAATATTGTCTAATTTAAAAGAACATTAATTTTAATAAAATTAAAAAA
1 TAATAAAAAATATTGACTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAA
24655826 AGTCAATGTT
Statistics
Matches: 409, Mismatches: 28, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
382 64 0.16
383 13 0.03
384 31 0.08
385 116 0.28
386 3 0.01
387 14 0.03
388 40 0.10
389 2 0.00
390 58 0.14
391 5 0.01
392 1 0.00
393 62 0.15
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (390 bp):
TAATAAAAAATATTGACTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAGTAAAATACA
ATTAAAATATTAAAAACAACTTTTATTTTATTAATTAAAACTATATAAAAATAAATATAAAAATA
AAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTAAAAAAAAGTAAAGTACAA
TTAAAATATTAAAAATAACTTTTATTTTATTAATTGAAACTATATAAAAATTAAATATAAAAATA
ATAAAAAATATTGGCTAATTTAAAAGAACATTTATTTTAATAAAATTTAAAAAAAGTAAAGTACA
ATTAAAATATTAAAAACAAATTTTATTTTATTAATTGAAACTATATAAAAAATTAAATATAAAAA
Found at i:24656250 original size:18 final size:18
Alignment explanation
Indices: 24656209--24656251 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
24656199 GACTGGAAAA
* *
24656209 AGGAAACATAAAAGGGTT
1 AGGATACATAAAAGGGCT
* *
24656227 ACGATACATATAAGGGCT
1 AGGATACATAAAAGGGCT
24656245 AGGATAC
1 AGGATAC
24656252 GCACCTGGCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:24656339 original size:30 final size:30
Alignment explanation
Indices: 24656305--24656368 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
24656295 GTTGAAGTGT
* *
24656305 TGGGCCAGGTGGCTGTGTGGGCGCTGCTGA
1 TGGGCCAGGTGACTATGTGGGCGCTGCTGA
* *
24656335 TGGGCCCGGTGATTATGTGGGCGCTGCTGA
1 TGGGCCAGGTGACTATGTGGGCGCTGCTGA
24656365 TGGG
1 TGGG
24656369 TCCGCGTCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.08, C:0.19, G:0.48, T:0.25
Consensus pattern (30 bp):
TGGGCCAGGTGACTATGTGGGCGCTGCTGA
Found at i:24656880 original size:7 final size:7
Alignment explanation
Indices: 24656870--24656916 Score: 76
Period size: 7 Copynumber: 6.7 Consensus size: 7
24656860 TTATATACGT
24656870 AATACTA
1 AATACTA
24656877 AATACTA
1 AATACTA
*
24656884 AATAATA
1 AATACTA
24656891 AATACTA
1 AATACTA
24656898 AATACTA
1 AATACTA
*
24656905 AGTACTA
1 AATACTA
24656912 AATAC
1 AATAC
24656917 GAAACGACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:24658038 original size:21 final size:22
Alignment explanation
Indices: 24657993--24658039 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
24657983 ACAAAGCTTT
*
24657993 TTTG-CAAAAATTAAAGAGAGT
1 TTTGACAAAAATTAAAGAGAGA
24658014 TTTGACAAAAATTGAAAGA-A-A
1 TTTGACAAAAATT-AAAGAGAGA
24658035 TTTGA
1 TTTGA
24658040 GAGAATTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.49, C:0.04, G:0.17, T:0.30
Consensus pattern (22 bp):
TTTGACAAAAATTAAAGAGAGA
Found at i:24658044 original size:11 final size:11
Alignment explanation
Indices: 24658025--24658074 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 11
24658015 TTGACAAAAA
*
24658025 TTGAAAGAAAT
1 TTGAGAGAAAT
24658036 TTGAGAG-AAT
1 TTGAGAGAAAT
24658046 TTG-GAGAAAT
1 TTGAGAGAAAT
24658056 TT-AGAGAGAAT
1 TTGAGAGA-AAT
24658067 TGTGAGAG
1 T-TGAGAG
24658075 GACTATTGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 3 0.09
10 15 0.45
11 10 0.30
12 1 0.03
13 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (11 bp):
TTGAGAGAAAT
Found at i:24667533 original size:21 final size:19
Alignment explanation
Indices: 24667509--24667547 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
24667499 TAGACTATCG
*
24667509 AGAAAATATAAGTTACAACAA
1 AGAAAACAT-AGTTA-AACAA
24667530 AGAAAACATAGTTAAACA
1 AGAAAACATAGTTAAACA
24667548 GAGATTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (19 bp):
AGAAAACATAGTTAAACAA
Found at i:24669002 original size:12 final size:12
Alignment explanation
Indices: 24668985--24669009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24668975 AAATTTAAAA
24668985 ATTTTAAAAATT
1 ATTTTAAAAATT
24668997 ATTTTAAAAATT
1 ATTTTAAAAATT
24669009 A
1 A
24669010 AAATTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAAATT
Found at i:24675941 original size:23 final size:23
Alignment explanation
Indices: 24675915--24675958 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
24675905 CCTTTATCTA
24675915 TGTAATCCAACGAATATTTAACG
1 TGTAATCCAACGAATATTTAACG
24675938 TGTAATCCAACGAATATTTAA
1 TGTAATCCAACGAATATTTAA
24675959 GATGTGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (23 bp):
TGTAATCCAACGAATATTTAACG
Found at i:24676469 original size:21 final size:21
Alignment explanation
Indices: 24676443--24676494 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
24676433 CAATAAAAAA
24676443 TATATTTGATTTTTATA-ATTT
1 TATATTT-ATTTTTATATATTT
*
24676464 TATATTT-TTTATATATATTT
1 TATATTTATTTTTATATATTT
24676484 TA-ATTTATTTT
1 TATATTTATTTT
24676495 AGATTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 11 0.41
20 9 0.33
21 7 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATATTTATTTTTATATATTT
Found at i:24676495 original size:21 final size:19
Alignment explanation
Indices: 24676445--24676495 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
24676435 ATAAAAAATA
24676445 TATTTGATTTT-TATAATTT
1 TATTT-ATTTTATATAATTT
24676464 TATATT-TTTTATATATATTT
1 TAT-TTATTTTATATA-ATTT
24676484 TAATTTATTTTA
1 T-ATTTATTTTA
24676496 GATTTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 4 0.15
19 7 0.26
20 9 0.33
21 7 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TATTTATTTTATATAATTT
Found at i:24681691 original size:15 final size:15
Alignment explanation
Indices: 24681671--24681701 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
24681661 TTGACAACAT
24681671 TTTAGTATTTTAAGC
1 TTTAGTATTTTAAGC
24681686 TTTAGTATTTTAAGC
1 TTTAGTATTTTAAGC
24681701 T
1 T
24681702 ACCTCCCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (15 bp):
TTTAGTATTTTAAGC
Found at i:24686385 original size:25 final size:25
Alignment explanation
Indices: 24686351--24686398 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
24686341 TATTATGTTA
24686351 ATTTAGTCTTGATTTTAAAAAAACT
1 ATTTAGTCTTGATTTTAAAAAAACT
24686376 ATTTAGTCTTGATTTTAAAAAAA
1 ATTTAGTCTTGATTTTAAAAAAA
24686399 TCTAACCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (25 bp):
ATTTAGTCTTGATTTTAAAAAAACT
Found at i:24688789 original size:24 final size:26
Alignment explanation
Indices: 24688740--24688790 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
24688730 AATACAATAT
*
24688740 TAATATATATATATAAAATGTATACA
1 TAATATATATATATAAAATATATACA
*
24688766 TAATATA-ATAT-TAAAATATTTACA
1 TAATATATATATATAAAATATATACA
24688790 T
1 T
24688791 GGTATATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.52
25 4 0.17
26 7 0.30
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (26 bp):
TAATATATATATATAAAATATATACA
Found at i:24689400 original size:39 final size:38
Alignment explanation
Indices: 24689303--24689452 Score: 176
Period size: 39 Copynumber: 3.9 Consensus size: 38
24689293 ATTCCACTCC
* * * *
24689303 CCCCATGCTACTTTGTTTTATTATTAATCAAAAAC-ACT
1 CCCCATACTATTTTGTTTTATTATTAAT-TAAAACTATT
* * *
24689341 CCTCATGCTATTTTGTTTTATTGTTAATTAAAACTATTT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACTA-TT
* *
24689380 CCCCATACTATTTTGTTTTATTGTTAATTAAAATTACTT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACTA-TT
*
24689419 CCTCATACTATTTTGTTTTATTATTAATTAAAAC
1 CCCCATACTATTTTGTTTTATTATTAATTAAAAC
24689453 CATACTTTAT
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
37 5 0.05
38 26 0.27
39 67 0.68
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (38 bp):
CCCCATACTATTTTGTTTTATTATTAATTAAAACTATT
Found at i:24689440 original size:78 final size:77
Alignment explanation
Indices: 24689303--24689452 Score: 219
Period size: 78 Copynumber: 1.9 Consensus size: 77
24689293 ATTCCACTCC
* * *
24689303 CCCCATGCTACTTTGTTTTATTATTAATCAAAAACACTCCTCATGCTATTTTGTTTTATTGTTAA
1 CCCCATACTACTTTGTTTTATTATTAATCAAAAACACTCCTCATACTATTTTGTTTTATTATTAA
24689368 TTAAAACTATTT
66 TTAAAACTATTT
* * * **
24689380 CCCCATACTATTTTGTTTTATTGTTAATTAAAATTACTTCCTCATACTATTTTGTTTTATTATTA
1 CCCCATACTACTTTGTTTTATTATTAATCAAAAACAC-TCCTCATACTATTTTGTTTTATTATTA
24689445 ATTAAAAC
65 ATTAAAAC
24689453 CATACTTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
77 31 0.48
78 33 0.52
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (77 bp):
CCCCATACTACTTTGTTTTATTATTAATCAAAAACACTCCTCATACTATTTTGTTTTATTATTAA
TTAAAACTATTT
Found at i:24690738 original size:45 final size:45
Alignment explanation
Indices: 24690674--24690759 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
24690664 CGATATCTGC
* *
24690674 TATCTTTGATCTGCCCCCCGTCTACTACAGAGACGCCAAATCTAT
1 TATCTTCGATCTGCCCCCCGTCTAATACAGAGACGCCAAATCTAT
*
24690719 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAAT
1 TATCTTCGATCTGCCCCCCGTCTAATACAGAGACGCCAAAT
24690760 TTGCTTCTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.26, C:0.33, G:0.14, T:0.28
Consensus pattern (45 bp):
TATCTTCGATCTGCCCCCCGTCTAATACAGAGACGCCAAATCTAT
Found at i:24691265 original size:210 final size:209
Alignment explanation
Indices: 24690853--24691821 Score: 1201
Period size: 210 Copynumber: 4.7 Consensus size: 209
24690843 AAATCTGCTT
* * * * * * *
24690853 CTTCGATTTGTTCCCTGACAATACAGAGATGCCAAATCATCTTAGATTTGATTTGA-CGTAAGCA
1 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTG-CTTCATCGTAAACA
* * * ** * **
24690917 CGTGAAAGCCAAATCAACTATGA--TTCAATTTGCTCCTTGTAAGCATA-AG-GATGCCAA-A-C
65 CGTGAAAGCCAAATCAGCTAT-ATCTTCGATTTGCTCCCTG-CCGAATACAGAGA-GATAAGATC
* ** *
24690976 ---CATCTTGGATCCGCTTCAGCATAAACAT-TCGAAGGCGAGATCAGCTATGTGTCTGCTCTCC
127 TGTCATCTTGGATCTGCTTCAGCATAAACATCT-GAAGGTAAGATCTGCTATGTGTCTGCT-TCC
24691037 ATCAAAGTGAAGATGCCAAA
190 ATCAAAGTGAAGATGCCAAA
* *
24691057 CTTTGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGAAAACAC
1 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
*
24691122 GTGAAAGCCAAATCAGCTATATCTTCGATTTGTTCCCTGCCGAATACAGAGAGATAAGATCTGTC
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTCCCTGCCGAATACAGAGAGATAAGATCTGTC
** *
24691187 ATCTTGGATCTGCTTCAGTGTAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCCTTGCATCAA
131 ATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTG-CTTCCATCAA
24691252 AGTGGAA-ATGCCAAA
195 AGT-GAAGATGCCAAA
*
24691267 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
24691332 GTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCTGCCGAATACATAGAGATAAGATCTGTC
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTCCCTGCCGAATACAGAGAGATAAGATCTGTC
* *
24691397 ATCTTGGATTTGCTTCAGCGTAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCCTTCCATCAA
131 ATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTG-CTTCCATCAA
*
24691462 AGTGGAA-ATGCCAGA
195 AGT-GAAGATGCCAAA
* * *
24691477 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAACGTAAACAC
1 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * * * ** *
24691542 GTGAAAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTG-TAAACACA-AG-GATGCCAA-A-C-
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTCCCTGCCGAATACAGAGAGAT---AAGATCT
* * * *
24691601 --CATCTTGTATCCGCTTCAGCATAAACATCTGAAGGTCAGATCTGCTATGTGTCT-C-TCTATC
128 GTCATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCTTCCATC
24691662 AAAGTGAAGATGCCAAA
193 AAAGTGAAGATGCCAAA
24691679 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * ** *
24691744 GTGAAAGCCAAATCAACTATATCTTCGATATGCTCCCCACTGAATACAGAGAGATAAGATCTGTC
66 GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTCCCTGCCGAATACAGAGAGATAAGATCTGTC
*
24691809 ATCTTAGATCTGC
131 ATCTTGGATCTGC
24691822 CCCGATGAAG
Statistics
Matches: 672, Mismatches: 68, Indels: 47
0.85 0.09 0.06
Matches are distributed among these distances:
201 3 0.00
202 112 0.17
203 12 0.02
204 78 0.12
205 70 0.10
206 3 0.00
207 15 0.02
208 3 0.00
209 6 0.01
210 364 0.54
211 6 0.01
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (209 bp):
CTTCGATTCGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
GTGAAAGCCAAATCAGCTATATCTTCGATTTGCTCCCTGCCGAATACAGAGAGATAAGATCTGTC
ATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCTTCCATCAAA
GTGAAGATGCCAAA
Found at i:24820655 original size:26 final size:26
Alignment explanation
Indices: 24820620--24820670 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
24820610 AATGTGAAAG
*
24820620 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
24820646 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
24820671 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:24820708 original size:103 final size:103
Alignment explanation
Indices: 24820543--24820851 Score: 543
Period size: 103 Copynumber: 3.0 Consensus size: 103
24820533 TTGTATATAA
** * *
24820543 AGGGGTTGCTGTGTGCTGATTCCCCGATTCA-TGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
24820606 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
24820645 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
24820710 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
24820749 AGGGGTTGCTAAGTGCTGATTCCCC-GTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
24820813 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
24820851 A
1 A
24820852 TTCAGCGGTG
Statistics
Matches: 200, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
102 34 0.17
103 135 0.68
104 31 0.16
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:24828898 original size:15 final size:15
Alignment explanation
Indices: 24828878--24828907 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24828868 TCAAATCCTC
24828878 TCAAATCTCGAACAA
1 TCAAATCTCGAACAA
*
24828893 TCAAATTTCGAACAA
1 TCAAATCTCGAACAA
24828908 ACCTTACGCC
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:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (15 bp):
TCAAATCTCGAACAA
Found at i:24829726 original size:49 final size:49
Alignment explanation
Indices: 24829654--24829751 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
24829644 CTTTTTCATT
24829654 CACCTTTTGTTAAATGAAAAACGAATTGTAAGCTGAATGCAAATGAGAA
1 CACCTTTTGTTAAATGAAAAACGAATTGTAAGCTGAATGCAAATGAGAA
24829703 CACCTTTTGTTAAATGAAAAACGAATTGTAAGCTGAATGCAAATGAGAA
1 CACCTTTTGTTAAATGAAAAACGAATTGTAAGCTGAATGCAAATGAGAA
24829752 ATCAGAAGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (49 bp):
CACCTTTTGTTAAATGAAAAACGAATTGTAAGCTGAATGCAAATGAGAA
Found at i:24830829 original size:22 final size:23
Alignment explanation
Indices: 24830786--24830831 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
24830776 CTATTATAAA
*
24830786 TTTTTTTAAAAAAATTGTATATT
1 TTTTTTTAAAAAAATTGAATATT
*
24830809 TTTTTTTAAAATAA-TGAATATT
1 TTTTTTTAAAAAAATTGAATATT
24830831 T
1 T
24830832 ATATTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTTTTAAAAAAATTGAATATT
Found at i:24831112 original size:30 final size:29
Alignment explanation
Indices: 24831072--24831146 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
24831062 TTAAATTAGT
24831072 AAAA-ATAAAATTATATTTTAATCTCTTAA
1 AAAATATAAAATTATA-TTTAATCTCTTAA
* *
24831101 AAAATATAAAATTTTGATTTAATCTTTTAA
1 AAAATATAAAATTAT-ATTTAATCTCTTAA
* *
24831131 AAATTATAAAAATATA
1 AAAATATAAAATTATA
24831147 AACTATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 5 0.13
30 33 0.85
31 1 0.03
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (29 bp):
AAAATATAAAATTATATTTAATCTCTTAA
Found at i:24831973 original size:23 final size:23
Alignment explanation
Indices: 24831928--24831975 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
24831918 CAGCTCACCT
* *
24831928 TCTCCCACGTCCACAGCTTGCCA
1 TCTCCCACGTCCACAACTCGCCA
*
24831951 TCTCCCACGTCCATAACTCGCCA
1 TCTCCCACGTCCACAACTCGCCA
24831974 TC
1 TC
24831976 CCCTATTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.19, C:0.48, G:0.10, T:0.23
Consensus pattern (23 bp):
TCTCCCACGTCCACAACTCGCCA
Found at i:24837500 original size:15 final size:15
Alignment explanation
Indices: 24837482--24837512 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24837472 TAATATTAAA
*
24837482 TTATTTTTTATTTTT
1 TTATTTTTAATTTTT
24837497 TTATTTTTAATTTTT
1 TTATTTTTAATTTTT
24837512 T
1 T
24837513 AAGTAACTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTATTTTTAATTTTT
Found at i:24840124 original size:24 final size:23
Alignment explanation
Indices: 24840096--24840144 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 23
24840086 GTATAAAATG
24840096 TCACTAACTTTGAGTATGGGATTC
1 TCACT-ACTTTGAGTATGGGATTC
24840120 T--C-ACTTTGAGTATGGGATTC
1 TCACTACTTTGAGTATGGGATTC
24840140 TCACT
1 TCACT
24840145 GGATGCCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
20 19 0.86
22 2 0.09
24 1 0.05
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (23 bp):
TCACTACTTTGAGTATGGGATTC
Found at i:24840127 original size:20 final size:20
Alignment explanation
Indices: 24840102--24840144 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
24840092 AATGTCACTA
24840102 ACTTTGAGTATGGGATTCTC
1 ACTTTGAGTATGGGATTCTC
24840122 ACTTTGAGTATGGGATTCTC
1 ACTTTGAGTATGGGATTCTC
24840142 ACT
1 ACT
24840145 GGATGCCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (20 bp):
ACTTTGAGTATGGGATTCTC
Found at i:24840519 original size:37 final size:35
Alignment explanation
Indices: 24840478--24840550 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 35
24840468 CCGACGATAA
* *
24840478 TAATTATAAGCCTAGCTCTAGTTGGATAAACCAACAG
1 TAATTAT--GCCTAGCGCTAGTCGGATAAACCAACAG
* * *
24840515 TAATTGTGCCTAGCGCTAGTCGGATTAACCGACAG
1 TAATTATGCCTAGCGCTAGTCGGATAAACCAACAG
24840550 T
1 T
24840551 TATGTGCCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 25 0.81
37 6 0.19
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (35 bp):
TAATTATGCCTAGCGCTAGTCGGATAAACCAACAG
Found at i:24840526 original size:35 final size:34
Alignment explanation
Indices: 24840487--24840558 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 34
24840477 ATAATTATAA
* *
24840487 GCCTAGCTCTAGTTGGATAAACCAACAGTAATTGT
1 GCCTAGCGCTAGTCGGATAAACCAACAGTAA-TGT
* * *
24840522 GCCTAGCGCTAGTCGGATTAACCGACAGTTATGT
1 GCCTAGCGCTAGTCGGATAAACCAACAGTAATGT
24840556 GCC
1 GCC
24840559 CAGCAATAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
34 6 0.19
35 26 0.81
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (34 bp):
GCCTAGCGCTAGTCGGATAAACCAACAGTAATGT
Found at i:24841516 original size:14 final size:13
Alignment explanation
Indices: 24841497--24841530 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
24841487 TCCTACTAAC
*
24841497 TCTTTTATTTCTTT
1 TCTTTTATTT-ATT
24841511 TCTTTTATTTATT
1 TCTTTTATTTATT
24841524 TCTTTTA
1 TCTTTTA
24841531 CTAACTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTTTTATTTATT
Found at i:24861536 original size:146 final size:145
Alignment explanation
Indices: 24861272--24861553 Score: 352
Period size: 146 Copynumber: 1.9 Consensus size: 145
24861262 TACCAGAAAA
* * * *
24861272 ACTTTCCTTTAATAGAGATTGCCACTAAGATGTTTCCTTTCAAAGATTTTCTACAAAAGCGTTCT
1 ACTTTCCTTTAACAGAGATCGCCACAAAGATGTTTCCTTTCAAAGATTTAC-ACAAAAGCGTTCT
** * *
24861337 TAAACAAAGGTTGCCACAAGGACTTACCTTTCCAAAGTTCTGCCATAAAGGCATCATTTACATCC
65 TAAACAAACATTGCCACAAGGACTTACCTTTCCAAAGTTCTGCCACAAAGGCATCACTTACATCC
24861402 AGTACTTGCCACAAAG
130 AGTACTTGCCACAAAG
* * *
24861418 ACTTTCTTTTAACAGAGATCGTCACAAAGATGTTT-CTTCTCAGAGATTTAC-CATAAAGACGTT
1 ACTTTCCTTTAACAGAGATCGCCACAAAGATGTTTCCTT-TCAAAGATTTACACA-AAAG-CGTT
* * * * * *
24861481 CTTAAACAGACATTGCCATAAGGGCTTACCTTTCCAGAGTTTTGCCACAAAGGCATCCCTTACAT
63 CTTAAACAAACATTGCCACAAGGACTTACCTTTCCAAAGTTCTGCCACAAAGGCATCACTTACAT
*
24861546 CTAGTACT
128 CCAGTACT
24861554 CGCTACAGAG
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
144 2 0.02
145 7 0.06
146 106 0.92
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (145 bp):
ACTTTCCTTTAACAGAGATCGCCACAAAGATGTTTCCTTTCAAAGATTTACACAAAAGCGTTCTT
AAACAAACATTGCCACAAGGACTTACCTTTCCAAAGTTCTGCCACAAAGGCATCACTTACATCCA
GTACTTGCCACAAAG
Found at i:24861684 original size:61 final size:60
Alignment explanation
Indices: 24861523--24861688 Score: 181
Period size: 61 Copynumber: 2.7 Consensus size: 60
24861513 TCCAGAGTTT
* * * * * *
24861523 TGCCACAAAGGCATCCCTTACATCTAGTACTCGCTACAGAGGTTTTCCTATCTAGAGTTG
1 TGCCACAAAGGTATCCTTTACATCTAGTACTCGCTACAAAGGCTTTCCTATCTAGAATTA
* * * * * *
24861583 TGCCACAAAAGCTATCATTTACATCCAATACTAG-TCACAAAGGCTTTCCTGTCTAGAATTA
1 TGCCAC-AAAGGTATCCTTTACATCTAGTACTCGCT-ACAAAGGCTTTCCTATCTAGAATTA
*
24861644 TGCCACAAAGGTTGTCCTTTACATCTAGTACTCGCTACAAAGGCT
1 TGCCACAAAGG-TATCCTTTACATCTAGTACTCGCTACAAAGGCT
24861689 ATCATTTACA
Statistics
Matches: 84, Mismatches: 18, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
60 11 0.13
61 72 0.86
62 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (60 bp):
TGCCACAAAGGTATCCTTTACATCTAGTACTCGCTACAAAGGCTTTCCTATCTAGAATTA
Found at i:24861744 original size:31 final size:32
Alignment explanation
Indices: 24861584--24861755 Score: 122
Period size: 32 Copynumber: 5.5 Consensus size: 32
24861574 CTAGAGTTGT
* * * *
24861584 GCCACAAAAGCTATCATTTACATCCAATACTA
1 GCCACAAAGGCTTTCCTTTACATCCAATACTC
* * **
24861616 GTCACAAAGGCTTTCCTGT-C-TAGAATTA-T-
1 GCCACAAAGGCTTTCCTTTACATCCAA-TACTC
* *
24861645 GCCACAAAGG-TTGTCCTTTACATCTAGTACTC
1 GCCACAAAGGCTT-TCCTTTACATCCAATACTC
* * * * *
24861677 GCTACAAAGGCTATCATTTACATGCAATACTA
1 GCCACAAAGGCTTTCCTTTACATCCAATACTC
* *
24861709 GCCAC-AAGGCTTTCCTTTACAACCACTACTC
1 GCCACAAAGGCTTTCCTTTACATCCAATACTC
24861740 GCCACAAAGGCCTTTC
1 GCCACAAAGG-CTTTC
24861756 TGTCCAGAGT
Statistics
Matches: 105, Mismatches: 26, Indels: 17
0.71 0.18 0.11
Matches are distributed among these distances:
28 2 0.02
29 14 0.13
30 7 0.07
31 31 0.30
32 45 0.43
33 6 0.06
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (32 bp):
GCCACAAAGGCTTTCCTTTACATCCAATACTC
Found at i:24862047 original size:53 final size:53
Alignment explanation
Indices: 24861902--24862050 Score: 199
Period size: 53 Copynumber: 2.8 Consensus size: 53
24861892 TTATTATTTT
* *
24861902 CCATATGATGCCATAACTTACCAGTTACGGTCTTACATAATATAGTCTTCTCC
1 CCATATGATGCCATAACTTACCAGTTACGGTCTTATACAATATAGTCTTCTCC
* * *
24861955 CCATATGATGCCATAACTTACCAATTGCGGTCTTATACAATATAGTCTTTTCC
1 CCATATGATGCCATAACTTACCAGTTACGGTCTTATACAATATAGTCTTCTCC
* ** ** *
24862008 CCATATAATGCCATAACCCACCAGTTACAATCTTGTACAATAT
1 CCATATGATGCCATAACTTACCAGTTACGGTCTTATACAATAT
24862051 TGTCCTTTAA
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 83 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (53 bp):
CCATATGATGCCATAACTTACCAGTTACGGTCTTATACAATATAGTCTTCTCC
Found at i:24867846 original size:34 final size:30
Alignment explanation
Indices: 24867808--24867874 Score: 80
Period size: 34 Copynumber: 2.1 Consensus size: 30
24867798 TATATTATTT
24867808 TAATAAAATTATATATTTATTATTTTATAAAAAG
1 TAATAAAATTA-ATA--TATTATTTT-TAAAAAG
* *
24867842 TAATAATATTAATATATTATTTTTAAATAG
1 TAATAAAATTAATATATTATTTTTAAAAAG
24867872 TAA
1 TAA
24867875 CTGTCGAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 9 0.29
31 9 0.29
33 3 0.10
34 10 0.32
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
TAATAAAATTAATATATTATTTTTAAAAAG
Found at i:24868728 original size:23 final size:25
Alignment explanation
Indices: 24868683--24868733 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
24868673 GAGCTAATTA
**
24868683 TAAAAGAAAATTAATAAGTAAAAAC
1 TAAAAGAAAATTAATAAAAAAAAAC
*
24868708 TAAAA-AAAA-TAATAAAAAAAATC
1 TAAAAGAAAATTAATAAAAAAAAAC
24868731 TAA
1 TAA
24868734 TAGTAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 14 0.61
24 4 0.17
25 5 0.22
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.20
Consensus pattern (25 bp):
TAAAAGAAAATTAATAAAAAAAAAC
Found at i:24868788 original size:3 final size:3
Alignment explanation
Indices: 24868780--24868836 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
24868770 AGTTTAAAAT
* * * *
24868780 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAT TAA TAA TAA TGA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
24868828 TAA CTAA TA
1 TAA -TAA TA
24868837 GAATACCTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:24868886 original size:21 final size:22
Alignment explanation
Indices: 24868860--24868903 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
24868850 TTGAAATTAT
24868860 ATAAAAGG-ATATAAATAA-ATA
1 ATAAAAGGAATA-AAATAAGATA
*
24868881 ATAAAATGAATAAAATAAGATA
1 ATAAAAGGAATAAAATAAGATA
24868903 A
1 A
24868904 ATGTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (22 bp):
ATAAAAGGAATAAAATAAGATA
Found at i:24868988 original size:18 final size:18
Alignment explanation
Indices: 24868950--24868984 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24868940 AAAAAATAAA
24868950 AATAATACTAATATTAAT
1 AATAATACTAATATTAAT
*
24868968 AATAATGCTAA-ATTAAT
1 AATAATACTAATATTAAT
24868985 TAATTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (18 bp):
AATAATACTAATATTAAT
Found at i:24869798 original size:25 final size:25
Alignment explanation
Indices: 24869740--24869803 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
24869730 ACTTGCTTTC
*
24869740 TCTGTTTTTTTGTTTGGATTCGATTG
1 TCTGTTTTTTT-TTTGGATTCAATTG
*
24869766 TCTTTTTTTTTTTTGGATTCAATCT-
1 TCTGTTTTTTTTTTGGATTCAAT-TG
*
24869791 TGTGTTTTTTTTT
1 TCTGTTTTTTTTT
24869804 ATTCAAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 22 0.67
26 11 0.33
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.69
Consensus pattern (25 bp):
TCTGTTTTTTTTTTGGATTCAATTG
Found at i:24870603 original size:133 final size:133
Alignment explanation
Indices: 24870407--24870695 Score: 340
Period size: 133 Copynumber: 2.2 Consensus size: 133
24870397 TTAATCCGAC
*
24870407 CTACTGCAAGTTCAGAG-G-TATAGGATTTG-TCA-CTTTAATCCGCTCCACTGCAACTTCAGGG
1 CTACTGCAACTTCAGAGAGATA-AGG-TTTGCT-ATCTTTAATCCGCTCCACTGCAACTTCAGGG
* * *
24870468 AGATAAGATT-GAT-ATTTTCAGTCTGCTCTATTGCAACTTCA-AGGAGATAAGACTTGTAATTT
63 AGATAAGATTCG-TGA-CTTCAATCTGCTCTACTGCAACTTCAGA-GAGATAAGACTTGTAATTT
24870530 CAACCTGCT
125 CAACCTGCT
* * * * *
24870539 CTACTGCAACTTTAGAGAGATAAGGTTTGCTATCTTTAATCTGCTTCACTGTAACTTTAGGGAGA
1 CTACTGCAACTTCAGAGAGATAAGGTTTGCTATCTTTAATCCGCTCCACTGCAACTTCAGGGAGA
* * * *
24870604 TAAGATTCGTGACTTCAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTAGTTTTAATCT
66 TAAGATTCGTGACTTCAATCTGCTCTACTGCAACTTCAGAGAGATAAGACTTGTAATTTCAACCT
24870669 GCT
131 GCT
* *
24870672 TTACTTCAACTTCAGAGAGATAAG
1 CTACTGCAACTTCAGAGAGATAAG
24870696 ATTGCCATAA
Statistics
Matches: 134, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
132 20 0.15
133 109 0.81
134 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (133 bp):
CTACTGCAACTTCAGAGAGATAAGGTTTGCTATCTTTAATCCGCTCCACTGCAACTTCAGGGAGA
TAAGATTCGTGACTTCAATCTGCTCTACTGCAACTTCAGAGAGATAAGACTTGTAATTTCAACCT
GCT
Found at i:24870605 original size:89 final size:88
Alignment explanation
Indices: 24870448--24870698 Score: 273
Period size: 89 Copynumber: 2.8 Consensus size: 88
24870438 ACTTTAATCC
* * *
24870448 GCTCCACTGCAACTTCAGGGAGATAAGA-TTGATA-TTTTCAGTCTGC-TCTA-TTGCAACTTCA
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTG-TAGTTTT-AATCTGCTTC-ACTT-CAACTTCA
* *
24870509 AGGAGATAAGACTT-GTAATTTCAACCT
62 GGGAGATAAGA-TTCGTAACTTCAACCT
* * *
24870536 GCTCTACTGCAACTTTAGAGAGATAAGGTTTGCTA-TCTTTAATCTGCTTCACTGT-AACTTTAG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTG-TAGT-TTTAATCTGCTTCACT-TCAACTTCAG
* *
24870599 GGAGATAAGATTCGTGACTTCAATCT
63 GGAGATAAGATTCGTAACTTCAACCT
* *
24870625 GCTCTACTGCAACTTCAGAGAGATAAGATTTGTAGTTTTAATCTGCTTTACTTCAACTTCAGAGA
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGTAGTTTTAATCTGCTTCACTTCAACTTCAGGGA
24870690 GATAAGATT
66 GATAAGATT
24870699 GCCATAATAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
87 1 0.01
88 61 0.44
89 70 0.50
90 6 0.04
91 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (88 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATTTGTAGTTTTAATCTGCTTCACTTCAACTTCAGGGA
GATAAGATTCGTAACTTCAACCT
Found at i:24870792 original size:44 final size:44
Alignment explanation
Indices: 24870430--24871170 Score: 312
Period size: 44 Copynumber: 16.1 Consensus size: 44
24870420 AGAGGTATAG
* *
24870430 GATTTGTCACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAA
1 GATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
24870474 GA-TTG-ATATTTTCAGTCTGCTCTATTGCAACTTCAAGGAGATAA
1 GATTTGTA-ACTTT-AATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
24870518 GACTTGTAA-TTTCAACCTGCTCTACTGCAACTTTAGAGAGATAA
1 GATTTGTAACTTT-AATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
24870562 GGTTTGCTATCTTTAATCTGCTTCACTGTAACTTTAGGGAGATAA
1 GATTTG-TAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
24870607 GATTCGTGACTTCAATCTGCTCTACTGCAACTTCAGAGAGATAA
1 GATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
** ** * *
24870651 GATTTGTAGTTTTAATCTGCTTTACTTCAACTTCAGAGAGATAA
1 GATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
24870695 GATTGCCATAATAACTTCAATC--CATCCCATTGCAAACTTTAGGG-GTATGA
1 GATT----T-GTAACTTTAATCTGC-T-CCACTGC-AACTTCAGGGAG-ATAA
* *
24870745 GATTTGTAACTTTAATCTACTCCACTGCAACTTTAGGGAGATAA
1 GATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* ** * *
24870789 GATTTTTTATTTTTAA-CTTGCTCCACTGCAACTTCAAGGAAATAA
1 GA-TTTGTAACTTTAATC-TGCTCCACTGCAACTTCAGGGAGATAA
* * * * * * * *
24870834 GGTTTGCAATTTGTAGCTTTATTTTGATCTACTGCAACTTTAGGAAAATAA
1 -----G--ATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
** * * *
24870885 GATTCACT-ATTTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGA
1 GATT-TGTAACTTT-AATCTGCTCCACTGCAACTTCAGGGAGAT-A-A
* *** * *
24870932 TTTGCAATTTGTAGCTTTAATCTGCTCTGTTGCAACTTCAGGGAGTTTA
1 ---G--ATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
** * * *
24870981 GATTTGTGATTTTTAACCTTCTCCACTGTAACTTCAGGGAGATAA
1 GATTTGT-AACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* * ** *
24871026 GGTTTGAACTTCGATAGCTTTAATCTGTTCCACAACAACCTT-AGGGAAATAA
1 GATTTG----T--A-A-CTTTAATCTGCTCCACTGCAA-CTTCAGGGAGATAA
* * * * * *
24871078 GATTTTCTATCTTTTACCTGCTCCACTACAACTTCAGGAAGATAA
1 GA-TTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
* ** * * *
24871123 GGTTTGTGGCTTTAATCTACTCCACTGCAACTTTAGAGAGATAA
1 GATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
24871167 GATT
1 GATT
24871171 CGCCATAACA
Statistics
Matches: 516, Mismatches: 132, Indels: 98
0.69 0.18 0.13
Matches are distributed among these distances:
43 7 0.01
44 200 0.39
45 168 0.33
46 9 0.02
47 4 0.01
48 2 0.00
49 15 0.03
50 19 0.04
51 55 0.11
52 31 0.06
53 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (44 bp):
GATTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
Found at i:24870813 original size:45 final size:44
Alignment explanation
Indices: 24870764--24870934 Score: 117
Period size: 45 Copynumber: 3.7 Consensus size: 44
24870754 CTTTAATCTA
*
24870764 CTCCACTGCAACTTTAGGGAGATAAGATTTTTTATTTTTAACTTG
1 CTCCACTGCAACTTTAGGGAAATAAGATTTTTTA-TTTTAACTTG
* * * * **
24870809 CTCCACTGCAACTTCAAGGAAATAAGGTTTGCAATTTGTAGCTTTATTTTG
1 CTCCACTGCAACTTTAGGGAAATAA-GATT----TTT-TA-TTTTAACTTG
* * * *** * *
24870860 ATCTACTGCAACTTTAGGAAAATAAGATTCACTATTTTCAGTCTG
1 CTCCACTGCAACTTTAGGGAAATAAGATTTTTTATTTTAACT-TG
*
24870905 CTCCACTGCAACTTTAGGGAGATAAGATTT
1 CTCCACTGCAACTTTAGGGAAATAAGATTT
24870935 GCAATTTGTA
Statistics
Matches: 93, Mismatches: 26, Indels: 14
0.70 0.20 0.11
Matches are distributed among these distances:
44 4 0.04
45 51 0.55
46 3 0.03
50 6 0.06
51 29 0.31
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (44 bp):
CTCCACTGCAACTTTAGGGAAATAAGATTTTTTATTTTAACTTG
Found at i:24870868 original size:96 final size:96
Alignment explanation
Indices: 24870746--24871128 Score: 339
Period size: 96 Copynumber: 4.0 Consensus size: 96
24870736 GGGGTATGAG
* * * *
24870746 ATTTGTAACTTTAATCT-ACTCCACTGCAACTTTAGGGAGATAAGATTTTTTATTTTTAACTTGC
1 ATTTGTAGCTTTAATCTGA-TCTACTGCAACTTTAGGGAAATAAGATTTTCTATTTTTAACTTGC
24870810 TCCACTGCAACTTCAAGGAAATAAGGTTTGCA
65 TCCACTGCAACTTCAAGGAAATAAGGTTTGCA
* * * ** * *
24870842 ATTTGTAGCTTTATTTTGATCTACTGCAACTTTAGGAAAATAAGATTCACTA-TTTTCAGTCTGC
1 ATTTGTAGCTTTAATCTGATCTACTGCAACTTTAGGGAAATAAGATTTTCTATTTTTAACT-TGC
* * * *
24870906 TCCACTGCAACTTTAGGGAGATAAGATTTGCA
65 TCCACTGCAACTTCAAGGAAATAAGGTTTGCA
* ** * ** * *
24870938 ATTTGTAGCTTTAATCTGCTCTGTTGCAACTTCAGGGAGTTTAGATTTGT-GATTTTTAACCTT-
1 ATTTGTAGCTTTAATCTGATCTACTGCAACTTTAGGGAAATAAGATTT-TCTATTTTTAA-CTTG
* * *
24871001 CTCCACTGTAACTTCAGGGAGATAAGGTTTG-A
64 CTCCACTGCAACTTCAAGGAAATAAGGTTTGCA
* * * ** * *
24871033 ACTTCGATAGCTTTAATCTGTTCCACAACAACCTTAGGGAAATAAGATTTTCTATCTTTT-ACCT
1 A-TTTG-TAGCTTTAATCTGATCTACTGCAACTTTAGGGAAATAAGATTTTCTAT-TTTTAACTT
*
24871097 GCTCCACTACAACTTC-AGGAAGATAAGGTTTG
63 GCTCCACTGCAACTTCAAGGAA-ATAAGGTTTG
24871129 TGGCTTTAAT
Statistics
Matches: 225, Mismatches: 51, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
95 8 0.04
96 147 0.65
97 65 0.29
98 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (96 bp):
ATTTGTAGCTTTAATCTGATCTACTGCAACTTTAGGGAAATAAGATTTTCTATTTTTAACTTGCT
CCACTGCAACTTCAAGGAAATAAGGTTTGCA
Found at i:24876233 original size:20 final size:20
Alignment explanation
Indices: 24876210--24876276 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
24876200 TCTCACGAAC
24876210 TCGGACTCAACTCAACGAGT
1 TCGGACTCAACTCAACGAGT
* * **
24876230 TCGGACAT-TACATCCACGAAC
1 TCGGAC-TCAAC-TCAACGAGT
24876251 TCGGACTCAACTCAACGAGT
1 TCGGACTCAACTCAACGAGT
24876271 TCGGAC
1 TCGGAC
24876277 ATTGCATCCA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGGACTCAACTCAACGAGT
Found at i:24876254 original size:21 final size:20
Alignment explanation
Indices: 24876195--24876257 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
24876185 TCGGATCCAG
24876195 TTACATCTCACGAACTCGGAC
1 TTACATC-CACGAACTCGGAC
* * **
24876216 TCA-ACTCAACGAGTTCGGAC
1 TTACA-TCCACGAACTCGGAC
24876236 ATTACATCCACGAACTCGGAC
1 -TTACATCCACGAACTCGGAC
24876257 T
1 T
24876258 CAACTCAACG
Statistics
Matches: 31, Mismatches: 8, Indels: 7
0.67 0.17 0.15
Matches are distributed among these distances:
20 12 0.39
21 18 0.58
22 1 0.03
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (20 bp):
TTACATCCACGAACTCGGAC
Found at i:24876260 original size:41 final size:43
Alignment explanation
Indices: 24876115--24876320 Score: 240
Period size: 45 Copynumber: 4.7 Consensus size: 43
24876105 GCCCATAAGT
* * * * *
24876115 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATT-ACATCCA--AGC
24876161 GAACTCGGACTCAACTCAACGAGTTCGGATCCAGTTACATCTC-A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGA--CA-TTACATC-CAAGC
24876206 GAACTCGGACTCAACTCAACGAGTTCGGACATTACATCC-A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTACATCCAAGC
* *
24876247 GAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTACATCC--AAGC
24876292 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
24876321 TGCCCAAATA
Statistics
Matches: 145, Mismatches: 7, Indels: 17
0.86 0.04 0.10
Matches are distributed among these distances:
41 41 0.28
42 7 0.05
43 2 0.01
44 1 0.01
45 58 0.40
46 28 0.19
48 5 0.03
49 3 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (43 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTACATCCAAGC
Found at i:24876269 original size:86 final size:89
Alignment explanation
Indices: 24876107--24876320 Score: 260
Period size: 86 Copynumber: 2.4 Consensus size: 89
24876097 TGTAACCCGC
* * * * * *
24876107 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCA--AGCGAACTCGGACT
24876172 CAACTCAACGAGTTCGGATCCAGTTACAT
64 CAACTCAACGAGTTCGGA--CA-TTACAT
*
24876201 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATT-ACATCC-A-CGAACTCGGACTCA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCAAGCGAACTCGGACTCA
*
24876260 ACTCAACGAGTTCGGACATTGCAT
66 ACTCAACGAGTTCGGACATTACAT
*
24876284 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
24876321 TGCCCAAATA
Statistics
Matches: 107, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
83 5 0.05
84 3 0.03
85 2 0.02
86 58 0.54
87 1 0.01
90 5 0.05
91 30 0.28
92 2 0.02
93 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (89 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCAAGCGAACTCGGACTCA
ACTCAACGAGTTCGGACATTACAT
Found at i:24890675 original size:28 final size:27
Alignment explanation
Indices: 24890617--24890678 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
24890607 GCTTTCTCTA
* * *
24890617 TTTTTTTTGTTTGGATTCGATTTTATT
1 TTTTTTTTGTTTGGATTCAATCTTATG
* *
24890644 TTTTTCTTTTTTTGGATTCAATCTTGTG
1 TTTTT-TTTGTTTGGATTCAATCTTATG
24890672 TTTTTTT
1 TTTTTTT
24890679 GTATTCAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.10, C:0.06, G:0.13, T:0.71
Consensus pattern (27 bp):
TTTTTTTTGTTTGGATTCAATCTTATG
Found at i:24895847 original size:20 final size:20
Alignment explanation
Indices: 24895796--24895847 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 20
24895786 CTCGATTCTT
*
24895796 TTTGTTGTTTGAATCAATTC
1 TTTGTTGTTTAAATCAATTC
* * * **
24895816 ATTATTGCTTAAATTGATTC
1 TTTGTTGTTTAAATCAATTC
24895836 TTTGTTGTTTAA
1 TTTGTTGTTTAA
24895848 CCCAATTCAA
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.08, G:0.13, T:0.56
Consensus pattern (20 bp):
TTTGTTGTTTAAATCAATTC
Found at i:24895995 original size:21 final size:22
Alignment explanation
Indices: 24895971--24896028 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
24895961 CTTTGCTTAT
*
24895971 TTGAATC-GTTCATTTTGTTGA
1 TTGAATCAATTCATTTTGTTGA
* * *
24895992 TTGACTCAATTCTTTTTGTTGT
1 TTGAATCAATTCATTTTGTTGA
24896014 TTGAATCAATTCATT
1 TTGAATCAATTCATT
24896029 ATTGCTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (22 bp):
TTGAATCAATTCATTTTGTTGA
Found at i:24896057 original size:20 final size:20
Alignment explanation
Indices: 24896006--24896057 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
24895996 CTCAATTCTT
*
24896006 TTTGTTGTTTGAATCAATTC
1 TTTGTTGTTTAAATCAATTC
* * *
24896026 ATTATTGCTTAAATCAATTC
1 TTTGTTGTTTAAATCAATTC
24896046 TTTGTTGTTTAA
1 TTTGTTGTTTAA
24896058 CTCGATTCAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.54
Consensus pattern (20 bp):
TTTGTTGTTTAAATCAATTC
Found at i:24896812 original size:27 final size:26
Alignment explanation
Indices: 24896752--24896812 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
24896742 TTAAATATAA
* *
24896752 TAATAT-ATTATATTTAAAAATAATT
1 TAATATAATGATATATAAAAATAATT
24896777 TAATATAATGATATATAAAATATAATT
1 TAATATAATGATATATAAAA-ATAATT
*
24896804 TAATTTAAT
1 TAATATAAT
24896813 TTTTTTATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 6 0.19
26 11 0.35
27 14 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
TAATATAATGATATATAAAAATAATT
Found at i:24902336 original size:12 final size:12
Alignment explanation
Indices: 24902319--24902345 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
24902309 TTTTGAGCAT
24902319 ACACCCCGAAAG
1 ACACCCCGAAAG
24902331 ACACCCCGAAAG
1 ACACCCCGAAAG
24902343 ACA
1 ACA
24902346 AACGAAACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.41, G:0.15, T:0.00
Consensus pattern (12 bp):
ACACCCCGAAAG
Found at i:24905396 original size:30 final size:31
Alignment explanation
Indices: 24905362--24905420 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
24905352 TTTAATTTGA
* *
24905362 TCAATTTTAAT-CTTGTATTTTTTGAATTGG
1 TCAATTTTAATCCATGTACTTTTTGAATTGG
*
24905392 TCAATTTTAGTCCATGTACTTTTTGAATT
1 TCAATTTTAATCCATGTACTTTTTGAATT
24905421 TTGAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (31 bp):
TCAATTTTAATCCATGTACTTTTTGAATTGG
Found at i:24906461 original size:9 final size:9
Alignment explanation
Indices: 24906439--24906478 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
24906429 GTTTTTTGTC
24906439 TTTATTTA-
1 TTTATTTAT
24906447 TTTATTTAT
1 TTTATTTAT
24906456 TTTATTTAT
1 TTTATTTAT
*
24906465 TATTATTAAT
1 T-TTATTTAT
24906475 TTTA
1 TTTA
24906479 AAAATTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 8 0.28
9 13 0.45
10 8 0.28
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTATTTAT
Found at i:24906567 original size:21 final size:23
Alignment explanation
Indices: 24906541--24906597 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
24906531 TTTTAAATAT
*
24906541 ATATTTTGAA-ATTACTTTTTTA
1 ATATTTTAAATATTACTTTTTTA
*
24906563 A-ATTTTAAATATTATTTTTTTA
1 ATATTTTAAATATTACTTTTTTA
24906585 ATA-TTTAAATATT
1 ATATTTTAAATATT
24906598 TTAAACTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 7 0.23
22 23 0.74
23 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
ATATTTTAAATATTACTTTTTTA
Found at i:24907252 original size:31 final size:30
Alignment explanation
Indices: 24907208--24907292 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
24907198 CCGAATATCT
24907208 TTAAAAATAATTTAAAATATTATAAAACAAA
1 TTAAAAAT-ATTTAAAATATTATAAAACAAA
*
24907239 TTAAATAATATTTAAACAT-TTATAAAACTAA
1 TTAAA-AATATTTAAA-ATATTATAAAACAAA
*
24907270 -TAACAA-ATTTAAAATATT-TAAAA
1 TTAAAAATATTTAAAATATTATAAAA
24907293 TATTTAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
27 7 0.14
28 9 0.18
29 2 0.04
30 3 0.06
31 23 0.47
32 5 0.10
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (30 bp):
TTAAAAATATTTAAAATATTATAAAACAAA
Done.