Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 122 of 226
Found at i:41320425 original size:20 final size:20
Alignment explanation
Indices: 41320388--41320425 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41320378 TTTATTTTTA
*
41320388 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
41320408 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
41320426 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:41321469 original size:11 final size:11
Alignment explanation
Indices: 41321455--41321527 Score: 73
Period size: 11 Copynumber: 6.5 Consensus size: 11
41321445 TTAAATATGG
41321455 ATTTGAGAGAA
1 ATTTGAGAGAA
41321466 ATTTG-GAAGAA
1 ATTTGAG-AGAA
41321477 ATTTGAGAGCAA
1 ATTTGAGAG-AA
41321489 A-TTGAGAGGAA
1 ATTTGAGA-GAA
41321500 ATTT-AGAGCAA
1 ATTTGAGAG-AA
41321511 A-TTGAGAGGAA
1 ATTTGAGA-GAA
41321522 ATTTGA
1 ATTTGA
41321528 AAGAGGATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
10 4 0.08
11 37 0.70
12 12 0.23
ACGTcount: A:0.44, C:0.03, G:0.27, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:41321480 original size:22 final size:23
Alignment explanation
Indices: 41321455--41321527 Score: 107
Period size: 22 Copynumber: 3.3 Consensus size: 23
41321445 TTAAATATGG
*
41321455 ATTTGAGAG-AAATTTG-GAAGAA
1 ATTTGAGAGCAAA-TTGAGAGGAA
41321477 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAGCAAATTGAGAGGAA
41321500 ATTT-AGAGCAAATTGAGAGGAA
1 ATTTGAGAGCAAATTGAGAGGAA
41321522 ATTTGA
1 ATTTGA
41321528 AAGAGGATTA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
22 34 0.72
23 13 0.28
ACGTcount: A:0.44, C:0.03, G:0.27, T:0.26
Consensus pattern (23 bp):
ATTTGAGAGCAAATTGAGAGGAA
Found at i:41321516 original size:33 final size:33
Alignment explanation
Indices: 41321457--41321524 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
41321447 AAATATGGAT
*
41321457 TTGAGAGAAATTTGGAAGAAATTTGAGAGCAAA
1 TTGAGAGAAATTTAGAAGAAATTTGAGAGCAAA
*
41321490 TTGAGAGGAAATTTAG-AGCAAA-TTGAGAGGAAA
1 TTGAGA-GAAATTTAGAAG-AAATTTGAGAGCAAA
41321523 TT
1 TT
41321525 TGAAAGAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 20 0.65
34 11 0.35
ACGTcount: A:0.44, C:0.03, G:0.28, T:0.25
Consensus pattern (33 bp):
TTGAGAGAAATTTAGAAGAAATTTGAGAGCAAA
Found at i:41334188 original size:43 final size:42
Alignment explanation
Indices: 41334135--41334395 Score: 251
Period size: 42 Copynumber: 6.0 Consensus size: 42
41334125 CGTTTACAGA
*
41334135 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* **
41334177 AAATAAACGCCGCTAAAGATCATGTTCTTTAGTGGCGCTTATT
1 AAA-AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* * *
41334220 AAAAAACGCCGTTAAATATCATGTTCTTTAGCGGCGTTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
41334262 AAAAACGCCGCTAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
1 --AAA-------AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* * * *
41334313 AAGAAAATGCCACTAAA-AGTAATGTTCTATAGCGGCGCTT-GG
1 AA-AAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAGG
*
41334355 TCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 -AAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
41334396 TTTCACAAAC
Statistics
Matches: 183, Mismatches: 21, Indels: 29
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
42 71 0.39
43 69 0.38
44 3 0.02
49 2 0.01
50 1 0.01
51 36 0.20
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.26
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
Found at i:41334227 original size:85 final size:84
Alignment explanation
Indices: 41334135--41334397 Score: 255
Period size: 85 Copynumber: 3.0 Consensus size: 84
41334125 CGTTTACAGA
41334135 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGG-AAATAAACGCCGCTAAAGATCA
1 AAAAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCGCT-AGGAAAATAAACGCCGCTAAAGATCA
*
41334199 TGTTCTTTAGTGGCGCTTATT
64 TGTTCTTTAGCGGCGCTTATT
* *
41334220 AAAAAACGCCGTTAAATATCATGTTCTTTAGCGGCGTTTAGGAAAAACGCCGCTAAACGCCGCTA
1 AAAAAACGCCGCTAAA-ATCATGTTCTTTAGCGGCG-CTAGG-AAAA------TAAACGCCGCTA
**
41334285 AAGATCATGTTCTTTAGCGGCGCTTAGG
57 AAGATCATGTTCTTTAGCGGCGCTTATT
* * * * * **
41334313 AAGAAAATGCCACTAAAAGTAATGTTCTATAGCGGCGCTTGGTCAA-AAACGCCGCTAAA-AGT-
1 AA-AAAACGCCGCTAAAA-TCATGTTCTTTAGCGGCGCTAGGAAAATAAACGCCGCTAAAGA-TC
41334375 AGTGTTCTTTAGCGGCGCTTATT
63 A-TGTTCTTTAGCGGCGCTTATT
41334398 TCACAAACGC
Statistics
Matches: 148, Mismatches: 17, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
84 2 0.01
85 70 0.47
86 1 0.01
87 3 0.02
92 2 0.01
93 43 0.29
94 27 0.18
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (84 bp):
AAAAAACGCCGCTAAAATCATGTTCTTTAGCGGCGCTAGGAAAATAAACGCCGCTAAAGATCATG
TTCTTTAGCGGCGCTTATT
Found at i:41334296 original size:136 final size:136
Alignment explanation
Indices: 41334138--41334391 Score: 354
Period size: 136 Copynumber: 1.9 Consensus size: 136
41334128 TTACAGAAAA
* *
41334138 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGGAA-ATAAACGCCGCT-AAAGATCATG
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAGA-AAACGCCACTAAAAG-TAATG
* * * *
41334201 TTCTTTAGTGGCGCTTATTAAAAAACGCCGTTAAATA-TCA-TGTTCTTTAGCGGCGTTTAGGAA
64 TTCTATAGCGGCGCTTAGTAAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGTTTAGGAA
41334264 AAACGCCGCT
127 AAACGCCGCT
* *
41334274 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGAAAATGCCACTAAAAGTAATGTT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAGAAAACGCCACTAAAAGTAATGTT
* *
41334339 CTATAGCGGCGCTTGGTCAAAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCG
66 CTATAGCGGCGCTTAGTAAAAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCG
41334392 CTTATTTCAC
Statistics
Matches: 104, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
135 2 0.02
136 97 0.93
137 5 0.05
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (136 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAGAAAACGCCACTAAAAGTAATGTT
CTATAGCGGCGCTTAGTAAAAAACGCCGCTAAAAGTAGTGTTCTTTAGCGGCGTTTAGGAAAAAC
GCCGCT
Found at i:41334863 original size:21 final size:21
Alignment explanation
Indices: 41334839--41334907 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
41334829 GCTTTTATCG
*
41334839 CTGCTTCTCTTGCTGCGACCT
1 CTGCTTCTCTCGCTGCGACCT
*
41334860 CTGCTTCTCTCGCTG-TAGCCT
1 CTGCTTCTCTCGCTGCGA-CCT
*
41334881 CTGCTTCCCTCGCTGCCG-CCT
1 CTGCTTCTCTCGCTG-CGACCT
41334902 CTGCTT
1 CTGCTT
41334908 TAAGTTGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.02
21 40 0.98
ACGTcount: A:0.03, C:0.42, G:0.19, T:0.36
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCGACCT
Found at i:41337089 original size:25 final size:25
Alignment explanation
Indices: 41337058--41337296 Score: 128
Period size: 25 Copynumber: 8.9 Consensus size: 25
41337048 ATTTTTCTCA
41337058 ATGTAAGTTATGTATTAAGTAAATT
1 ATGTAAGTTATGTATTAAGTAAATT
*
41337083 ATGTAAGTTATGTA-TATAGTATAAAAGAT
1 ATGTAAGTTATGTATTA-AG--T-AAA-TT
* *
41337112 ATGTAAGTTATGTATTATGTAAGTT
1 ATGTAAGTTATGTATTAAGTAAATT
**
41337137 ATGTAAGTTATGTAGGTTATTA-TAAGCT
1 ATGTAAGTTATGTA--TTA--AGTAAATT
41337165 ATGTAAGTTATTATGTAAGTTAAGATATAATAT
1 ATGTAAG---TTATGT-A-TTAAG-TA-AAT-T
*
41337198 ATGT-TGATTATGTATTAAGTAAATT
1 ATGTAAG-TTATGTATTAAGTAAATT
* * * *
41337223 ATGTAAGTTATGGAGTATGTAAGTT
1 ATGTAAGTTATGTATTAAGTAAATT
* **
41337248 ATATAAGTTATGTAAGTTATA-TAAGCT
1 ATGTAAGTTATGT-A-TTA-AGTAAATT
41337275 ATGTAAGTTAT-TATGTAAGTAA
1 ATGTAAGTTATGTAT-TAAGTAA
41337297 TGTATTAAAT
Statistics
Matches: 170, Mismatches: 20, Indels: 48
0.71 0.08 0.20
Matches are distributed among these distances:
24 4 0.02
25 67 0.39
26 8 0.05
27 24 0.14
28 20 0.12
29 18 0.11
30 9 0.05
31 12 0.07
32 3 0.02
33 5 0.03
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (25 bp):
ATGTAAGTTATGTATTAAGTAAATT
Found at i:41337093 original size:9 final size:9
Alignment explanation
Indices: 41337058--41337410 Score: 173
Period size: 9 Copynumber: 39.3 Consensus size: 9
41337048 ATTTTTCTCA
41337058 ATGTAAGTT
1 ATGTAAGTT
41337067 ATGT-A-TT
1 ATGTAAGTT
* *
41337074 AAGTAAATT
1 ATGTAAGTT
41337083 ATGTAAGTT
1 ATGTAAGTT
41337092 ATGTATA-TAGT
1 ATGTA-AGT--T
** *
41337103 ATAAAAGAT
1 ATGTAAGTT
41337112 ATGTAAGTT
1 ATGTAAGTT
41337121 ATGT-A-TT
1 ATGTAAGTT
41337128 ATGTAAGTT
1 ATGTAAGTT
41337137 ATGTAAGTT
1 ATGTAAGTT
*
41337146 ATGTAGGTT
1 ATGTAAGTT
* *
41337155 ATTATAAGCT
1 A-TGTAAGTT
41337165 ATGTAAGTTATT
1 ATGTAAG---TT
41337177 ATGTAAGTT
1 ATGTAAGTT
* *
41337186 AAGATATAATAT
1 ATG-TA-AGT-T
*
41337198 ATGT-TGATT
1 ATGTAAG-TT
41337207 ATGT-A-TT
1 ATGTAAGTT
* *
41337214 AAGTAAATT
1 ATGTAAGTT
41337223 ATGTAAGTT
1 ATGTAAGTT
*
41337232 ATG-GAG-T
1 ATGTAAGTT
41337239 ATGTAAGTT
1 ATGTAAGTT
*
41337248 ATATAAGTT
1 ATGTAAGTT
41337257 ATGTAAGTT
1 ATGTAAGTT
* *
41337266 ATATAAGCT
1 ATGTAAGTT
41337275 ATGTAAGTTATT
1 ATGTAAG---TT
*
41337287 ATGTAAGTA
1 ATGTAAGTT
41337296 ATGT-A-TT
1 ATGTAAGTT
**
41337303 AAATAAGTT
1 ATGTAAGTT
*
41337312 ATGT-ATTT
1 ATGTAAGTT
*
41337320 ATTTAAGTT
1 ATGTAAGTT
41337329 ATGT-A-TT
1 ATGTAAGTT
41337336 ATGTAAGTT
1 ATGTAAGTT
* *
41337345 ATATAAGCT
1 ATGTAAGTT
*
41337354 ATGTACCATTT
1 ATGTA--AGTT
41337365 AT-TAAGTT
1 ATGTAAGTT
*
41337373 ATGTATG-T
1 ATGTAAGTT
* *
41337381 ATGTGACTT
1 ATGTAAGTT
*
41337390 TTGTAAGTT
1 ATGTAAGTT
*
41337399 ATGTGAGTT
1 ATGTAAGTT
41337408 ATG
1 ATG
41337411 NNNNNNNNNN
Statistics
Matches: 255, Mismatches: 57, Indels: 64
0.68 0.15 0.17
Matches are distributed among these distances:
7 29 0.11
8 29 0.11
9 154 0.60
10 13 0.05
11 11 0.04
12 19 0.07
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:41337117 original size:29 final size:25
Alignment explanation
Indices: 41337058--41337358 Score: 125
Period size: 25 Copynumber: 11.2 Consensus size: 25
41337048 ATTTTTCTCA
41337058 ATGTAAGTTATGTATTA-AGTAA-ATT
1 ATGTAAGTTATGTATTATA-TAAGA-T
41337083 ATGTAAGTTATGTATATAGTATAAAAGAT
1 ATGTAAGTTATGTAT-TA-TAT--AAGAT
* *
41337112 ATGTAAGTTATGTATTATGTAAGTT
1 ATGTAAGTTATGTATTATATAAGAT
*
41337137 ATGTAAGTTATGTAGGTTATTATAAGCT
1 ATGTAAGTTATGTA--TTA-TATAAGAT
*
41337165 ATGTAAGTTATTATGTAAGTTAAGATATAATAT
1 ATGTAAG---TTATGT-A-TT---ATATAAGAT
*
41337198 ATGT-TGATTATGTATTA-AGTAA-ATT
1 ATGTAAG-TTATGTATTATA-TAAGA-T
* * * *
41337223 ATGTAAGTTATGGAGTATGTAAGTT
1 ATGTAAGTTATGTATTATATAAGAT
* *
41337248 ATATAAGTTATGTAAGTTATATAAGCT
1 ATGTAAGTTATGT-A-TTATATAAGAT
41337275 ATGTAAGTTAT-TATGTA-AGTAATGTATT
1 ATGTAAGTTATGTAT-TATA-TAA-G-A-T
** * *
41337303 AAATAAGTTATGTATTTATTTAAGTT
1 ATGTAAGTTATGTA-TTATATAAGAT
*
41337329 ATGT-A-TTATGTAAGTTATATAAGCT
1 ATGTAAGTTATGT-A-TTATATAAGAT
41337354 ATGTA
1 ATGTA
41337359 CCATTTATTA
Statistics
Matches: 215, Mismatches: 28, Indels: 65
0.70 0.09 0.21
Matches are distributed among these distances:
24 10 0.05
25 86 0.40
26 9 0.04
27 24 0.11
28 29 0.13
29 26 0.12
30 9 0.04
31 9 0.04
32 2 0.01
33 10 0.05
34 1 0.00
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.44
Consensus pattern (25 bp):
ATGTAAGTTATGTATTATATAAGAT
Found at i:41337167 original size:19 final size:19
Alignment explanation
Indices: 41337127--41337178 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
41337117 AGTTATGTAT
* *
41337127 TATGTAAGTTA-TGTAAGT
1 TATGTAAGTTATTATAAGC
*
41337145 TATGTAGGTTATTATAAGC
1 TATGTAAGTTATTATAAGC
41337164 TATGTAAGTTATTAT
1 TATGTAAGTTATTAT
41337179 GTAAGTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 10 0.34
19 19 0.66
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (19 bp):
TATGTAAGTTATTATAAGC
Found at i:41337328 original size:17 final size:16
Alignment explanation
Indices: 41337111--41337346 Score: 118
Period size: 16 Copynumber: 14.8 Consensus size: 16
41337101 GTATAAAAGA
41337111 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
41337127 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
*
41337145 TATGTAGGTTAT-TA-
1 TATGTAAGTTATGTAT
* * *
41337159 TAAGCTATG-TAAGTTAT
1 TATG-TAAGTTATG-TAT
*
41337176 TATGTAAGTTAAGATAT
1 TATGTAAGTTATG-TAT
* * *
41337193 AATATATGTTGAT-TAT
1 TATGTAAGTT-ATGTAT
*
41337209 GTAT-TAAG-TA--AAT
1 -TATGTAAGTTATGTAT
* *
41337222 TATGTAAGTTATGGAG
1 TATGTAAGTTATGTAT
*
41337238 TATGTAAGTTATATAAGT
1 TATGTAAGTTATGT-A-T
* *
41337256 TATGTAAGTTATATAAGC
1 TATGTAAGTTATGT-A-T
41337274 TATGTAAG---T-TAT
1 TATGTAAGTTATGTAT
*
41337286 TATGTAAGTAATGTAT
1 TATGTAAGTTATGTAT
**
41337302 TAAATAAGTTATGTATT
1 TATGTAAGTTATGTA-T
*
41337319 TATTTAAGTTATGTAT
1 TATGTAAGTTATGTAT
41337335 TATGTAAGTTAT
1 TATGTAAGTTAT
41337347 ATAAGCTATG
Statistics
Matches: 173, Mismatches: 27, Indels: 40
0.72 0.11 0.17
Matches are distributed among these distances:
12 11 0.06
13 7 0.04
14 9 0.05
15 6 0.03
16 66 0.38
17 36 0.21
18 38 0.22
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.45
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:41340585 original size:14 final size:15
Alignment explanation
Indices: 41340569--41340620 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
41340559 TCCTAAACCC
41340569 TAAACCTAAAACTC-
1 TAAACCTAAAACTCG
41340583 TAAA-CTATAAA-TCG
1 TAAACCTA-AAACTCG
41340597 TAAACCCT-AAAC-CG
1 TAAA-CCTAAAACTCG
41340611 TAAACCTAAA
1 TAAACCTAAA
41340621 CCATATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 8 0.25
14 22 0.69
16 2 0.06
ACGTcount: A:0.50, C:0.25, G:0.04, T:0.21
Consensus pattern (15 bp):
TAAACCTAAAACTCG
Found at i:41340586 original size:21 final size:21
Alignment explanation
Indices: 41340560--41340620 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
41340550 TTCTAAATAT
*
41340560 CCTAAACCCTAAACCTAAAAC
1 CCTAAACCATAAACCTAAAAC
* * *
41340581 TCTAAACTATAAATCGT-AAAC
1 CCTAAACCATAAA-CCTAAAAC
*
41340602 CCTAAACCGTAAACCTAAA
1 CCTAAACCATAAACCTAAA
41340621 CCATATTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.48, C:0.30, G:0.03, T:0.20
Consensus pattern (21 bp):
CCTAAACCATAAACCTAAAAC
Found at i:41340776 original size:20 final size:21
Alignment explanation
Indices: 41340738--41340787 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
41340728 TCTTCTATTT
41340738 CCAAACT-AAACCTTAAAACC
1 CCAAACTCAAACCTTAAAACC
*
41340758 CTAAACTCAAACCTT-AAACC
1 CCAAACTCAAACCTTAAAACC
41340778 CCAAACTCAA
1 CCAAACTCAA
41340788 TCTCTAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (21 bp):
CCAAACTCAAACCTTAAAACC
Found at i:41341056 original size:7 final size:7
Alignment explanation
Indices: 41341032--41341092 Score: 68
Period size: 7 Copynumber: 8.4 Consensus size: 7
41341022 ACCCTAACTG
41341032 TAACCCC
1 TAACCCC
41341039 TAAATCCCC
1 T-AA-CCCC
41341048 TAACCCC
1 TAACCCC
41341055 TAACCCC
1 TAACCCC
41341062 TAACCCC
1 TAACCCC
** *
41341069 TAAAGCA
1 TAACCCC
*
41341076 TAACACC
1 TAACCCC
41341083 TAACCCC
1 TAACCCC
41341090 TAA
1 TAA
41341093 ACTTTAAATC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
7 36 0.80
8 4 0.09
9 5 0.11
ACGTcount: A:0.36, C:0.46, G:0.02, T:0.16
Consensus pattern (7 bp):
TAACCCC
Found at i:41341587 original size:75 final size:77
Alignment explanation
Indices: 41341449--41341592 Score: 204
Period size: 75 Copynumber: 1.9 Consensus size: 77
41341439 CCGCTAAAGG
* *
41341449 AAGCATTAGCGGCGCTTTCTTAGAAAACGCCGCTAAATCCACTGAAAGTTAAGAAAACGGTGCCG
1 AAGCATTAGCGGCGCTTTCTTAGAAAACGCCGCTAAAGCCACTGAAAGATAAGAAAACGGTGCCG
41341514 TTGGGCACCCCC
66 TTGGGCACCCCC
* * **
41341526 AAGCATTAGCGGCGC-TTCATTA-AAAACGCCGCTAAGGCCTC-GAAAGATCTGAAAACGGTGCC
1 AAGCATTAGCGGCGCTTTC-TTAGAAAACGCCGCTAAAGCCACTGAAAGATAAGAAAACGGTGCC
41341588 GTTGG
65 GTTGG
41341593 ACATATGTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
75 23 0.38
76 19 0.32
77 18 0.30
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (77 bp):
AAGCATTAGCGGCGCTTTCTTAGAAAACGCCGCTAAAGCCACTGAAAGATAAGAAAACGGTGCCG
TTGGGCACCCCC
Found at i:41341776 original size:72 final size:71
Alignment explanation
Indices: 41341692--41341871 Score: 193
Period size: 72 Copynumber: 2.5 Consensus size: 71
41341682 AAAGTTGAGA
*
41341692 AAACGACACCGTTTGGCTTAGGTTTTTTAGCGGCGCTTCACCAAAAACGCCATTAAAT-CCCAAA
1 AAACGACACCGTTTGGCTTAGG-TTTTTAGCGGCGCTTCACCAAAAACGCCACTAAATCCCCAAA
*
41341756 AACTACGG
65 AACT-CAG
* * * ** * *
41341764 AAACGACACCGTTTGGCTTAGGATTATTAGTGGCGCTTGATTAAAAACGTCGCTAAATCCCCAAA
1 AAACGACACCGTTTGGCTTAGG-TTTTTAGCGGCGCTTCACCAAAAACGCCACTAAATCCCCAAA
*
41341829 AGCTCAG
65 AACTCAG
* * * *
41341836 AAACGGCATCGTTGGGCTTTGGTTTTT-GCGGCGCTT
1 AAACGACACCGTTTGGCTTAGGTTTTTAGCGGCGCTT
41341872 TCTGGAAAAC
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
70 8 0.09
71 4 0.04
72 69 0.77
73 9 0.10
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (71 bp):
AAACGACACCGTTTGGCTTAGGTTTTTAGCGGCGCTTCACCAAAAACGCCACTAAATCCCCAAAA
ACTCAG
Found at i:41347952 original size:53 final size:53
Alignment explanation
Indices: 41347889--41347996 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
41347879 AAAAGAAGAT
41347889 AGAACAAATGGAGGAAGAGAAGATGAACTTAAGATTAGACATAGACGTTCAGA
1 AGAACAAATGGAGGAAGAGAAGATGAACTTAAGATTAGACATAGACGTTCAGA
41347942 AGAACAAATGGAGGAAGAGAAGATGAACTTAAGATTAGACATAGACGTTCAGA
1 AGAACAAATGGAGGAAGAGAAGATGAACTTAAGATTAGACATAGACGTTCAGA
41347995 AG
1 AG
41347997 CTTGAAACTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.47, C:0.09, G:0.27, T:0.17
Consensus pattern (53 bp):
AGAACAAATGGAGGAAGAGAAGATGAACTTAAGATTAGACATAGACGTTCAGA
Found at i:41349309 original size:14 final size:13
Alignment explanation
Indices: 41349277--41349319 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
41349267 ATTATTATTT
*
41349277 TATTATATT-GTA
1 TATTATATTAATA
*
41349289 AATTATATTAATTA
1 TATTATATTAA-TA
41349303 TATTATATTAATA
1 TATTATATTAATA
41349316 TATT
1 TATT
41349320 TCAAATAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 8 0.31
13 6 0.23
14 12 0.46
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TATTATATTAATA
Found at i:41349547 original size:20 final size:19
Alignment explanation
Indices: 41349524--41349586 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
41349514 ATAGGCAAAC
41349524 AAAACAGAGAAGGAAAGAAG
1 AAAA-AGAGAAGGAAAGAAG
* * *
41349544 AAAAGGA-AAGAAAAAGAAA
1 AAAAAGAGAAG-GAAAGAAG
*
41349563 AAAAAGGGAAGGAAAGGAAG
1 AAAAAGAGAAGGAAA-GAAG
41349583 AAAA
1 AAAA
41349587 TTTGGGATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 3 0.09
19 16 0.48
20 14 0.42
ACGTcount: A:0.70, C:0.02, G:0.29, T:0.00
Consensus pattern (19 bp):
AAAAAGAGAAGGAAAGAAG
Found at i:41360254 original size:44 final size:44
Alignment explanation
Indices: 41360190--41360337 Score: 206
Period size: 44 Copynumber: 3.4 Consensus size: 44
41360180 GGTGAAACTT
* *
41360190 AAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT
1 AAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGC
*
41360234 AAGTCCTATCTCCCTAGTCAGTAGTGGAATAGGTTGAAGATTGC
1 AAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGC
* * ** *
41360278 AAGTCCTATCTCCCTGGGCAGCAAAGGAATAGGTTGAAGATTAC
1 AAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGC
* *
41360322 AAATCTTATCTCCCTA
1 AAGTCCTATCTCCCTA
41360338 AGCAGTAGTG
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 92 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
AAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGC
Found at i:41360361 original size:88 final size:87
Alignment explanation
Indices: 41360190--41360523 Score: 269
Period size: 88 Copynumber: 3.8 Consensus size: 87
41360180 GGTGAAACTT
* ** ** * *
41360190 AAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCT-AGTCA
1 AAGTCCTATCTCCCTGGGCAGCAAAGGAATAGGTTGAAGATTACAAATCTTATCTCCCTAAG-CA
** * * **
41360254 GTAGTGGAATAGGTTGAAGATTGC
65 GTAGTGGAGCAGATCGAAGA-CCC
41360278 AAGTCCTATCTCCCTGGGCAGCAAAGGAATAGGTTGAAGATTACAAATCTTATCTCCCTAAGCAG
1 AAGTCCTATCTCCCTGGGCAGCAAAGGAATAGGTTGAAGATTACAAATCTTATCTCCCTAAGCAG
41360343 TAGTGGAGCAGATCGAAGACCC
66 TAGTGGAGCAGATCGAAGACCC
* * ** * * * *
41360365 CAG-CCTTGTCTCCCTAAGCAGTAGTA-GAGTAGGTTGAAGATTACAGATCTTATCTCCCTAAGC
1 AAGTCC-TATCTCCCTGGGCAGCA-AAGGAATAGGTTGAAGATTACAAATCTTATCTCCCTAAGC
* *
41360428 AGTAGTGGAGCATATCGAAGTCCC
64 AGTAGTGGAGCAGATCGAAGACCC
* * ** * ** ** * * * * *
41360452 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATCTTATATCCCTAAGCA
1 AAG-TCCTATCTCCCTGGGCAGCAAAGGAATAGGTTGAAGATTACAAATCTTATCTCCCTAAGCA
41360517 GTAGTGG
65 GTAGTGG
41360524 TACAGATTAA
Statistics
Matches: 208, Mismatches: 32, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
86 2 0.01
87 76 0.37
88 127 0.61
89 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (87 bp):
AAGTCCTATCTCCCTGGGCAGCAAAGGAATAGGTTGAAGATTACAAATCTTATCTCCCTAAGCAG
TAGTGGAGCAGATCGAAGACCC
Found at i:41360415 original size:87 final size:88
Alignment explanation
Indices: 41360307--41360523 Score: 328
Period size: 88 Copynumber: 2.5 Consensus size: 88
41360297 AGCAAAGGAA
*
41360307 TAGGTTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAG-CCT
1 TAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGACCT
*
41360371 TGTCTCCCTAAGCAGTAGTAGAG
66 TATCTCCCTAAGCAGTAGTAGAG
* * *
41360394 TAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCGAAGTCCCCAGATCT
1 TAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGACCT
*
41360459 TATCTCCCTAAGCAGTAGTGGAG
66 TATCTCCCTAAGCAGTAGTAGAG
* * * * *
41360482 CAGATCGAAGATGACAGATCTTATATCCCTAAGCAGTAGTGG
1 TAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
41360524 TACAGATTAA
Statistics
Matches: 118, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 58 0.49
88 60 0.51
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (88 bp):
TAGGTTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACCCCAGACCT
TATCTCCCTAAGCAGTAGTAGAG
Found at i:41360530 original size:44 final size:44
Alignment explanation
Indices: 41360313--41360523 Score: 264
Period size: 44 Copynumber: 4.8 Consensus size: 44
41360303 GGAATAGGTT
* *
41360313 GAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
1 GAAGATCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
* * * * * * * *
41360357 GAAGACCCCAG-CCTTGTCTCCCTAAGCAGTAGTAGAGTAGGTT
1 GAAGATCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
* *
41360400 GAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATC
1 GAAGATCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
*
41360444 GAAG-TCCCCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
1 GAAGAT-CACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
* *
41360488 GAAGATGACAGATCTTATATCCCTAAGCAGTAGTGG
1 GAAGATCACAGATCTTATCTCCCTAAGCAGTAGTGG
41360524 TACAGATTAA
Statistics
Matches: 138, Mismatches: 26, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
43 35 0.25
44 102 0.74
45 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (44 bp):
GAAGATCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
Found at i:41360704 original size:216 final size:216
Alignment explanation
Indices: 41360456--41361092 Score: 836
Period size: 216 Copynumber: 2.9 Consensus size: 216
41360446 AGTCCCCAGA
* * * * *
41360456 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATGACAGATCTTATATCCCTAAGCAGTA
1 TCTTATCCCCCTGAAGTAGCAGTGG-GCAGATCGAAGATGACAGATCTTATCTCCCTAAGTAGTA
*
41360520 GTGGTA-CAGATTAAAGCCAATAATCCTATCTCCCTGAGGTTACAGTGGAGCGGATTAAAATAAT
65 GTGG-AGCAGATTAAAGCCAATAATCCTATCTCCCTGAGGTTACAGTGGAGCGGATTAAAATAAC
*
41360584 AGATCTTATCTCTCTGAAGTGGCAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTATA
129 AGATCTTATCTCTCTGAAGTGGCAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTACA
*
41360649 GTGGAGCAGACTGAGTAAGCAGG
194 GTGGAGCAGACTGAATAAGCAGG
**
41360672 TCTTATCCCCCTGAAGTAGCAGTGGGCAGATCGAAGATGGTAGATCTTATCTCCCTAAGTAGTAG
1 TCTTATCCCCCTGAAGTAGCAGTGGGCAGATCGAAGATGACAGATCTTATCTCCCTAAGTAGTAG
* ** * *
41360737 TGGATCTA-ATTAAAGCCAATAATCCTATCTCCCTGAGGTTACAACGGAGCAGATTAAAAAAACA
66 TGGAGC-AGATTAAAGCCAATAATCCTATCTCCCTGAGGTTACAGTGGAGCGGATTAAAATAACA
* *
41360801 GATCTTATCTCTCTGAAGTGGCAGTAGAGTAAATCGCATCAAGTCTTATCTCCCTAAGGTTACAG
130 GATCTTATCTCTCTGAAGTGGCAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAG
41360866 TGGAGCAGACTGAATAAGCAGG
195 TGGAGCAGACTGAATAAGCAGG
* * * * * * *
41360888 TCTTATCCTCCGGAAGTTGCAGTTGGGCAGACCCAAAATGAC-GAATCTTATCTCCCTGAAGTTG
1 TCTTATCCCCCTGAAGTAGCAG-TGGGCAGATCGAAGATGACAG-ATCTTATCTCCCT-AAGTAG
* * * * * * *
41360952 CAGTGGAGCAGATTTAAGCCTATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATCA
63 TAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAGGTTACAGTGGAGCGGATTAAAATAA
* * * * * * *
41361017 CAGATCTTAGCTCTCTGAAGTTGCA-AAGAGCAGATCTCATCTAGTCTTATCTCCCTGAGGTTGC
128 CAGATCTTATCTCTCTGAAGTGGCAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTAC
41361081 AGTGG-GCAGACT
193 AGTGGAGCAGACT
41361093 CAAAATGACG
Statistics
Matches: 368, Mismatches: 46, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
215 1 0.00
216 212 0.58
217 76 0.21
218 79 0.21
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (216 bp):
TCTTATCCCCCTGAAGTAGCAGTGGGCAGATCGAAGATGACAGATCTTATCTCCCTAAGTAGTAG
TGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAGGTTACAGTGGAGCGGATTAAAATAACAG
ATCTTATCTCTCTGAAGTGGCAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGT
GGAGCAGACTGAATAAGCAGG
Found at i:41361108 original size:84 final size:86
Alignment explanation
Indices: 41360900--41361109 Score: 221
Period size: 84 Copynumber: 2.4 Consensus size: 86
41360890 TTATCCTCCG
* * **
41360900 GAAGTTGCAGTTGGGCAGACCCAAAATGACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
1 GAAGTTGCAG-TGGGCAGACTCAAAATGACGAATCTTAGCTCCCTGAAGTTGCAGAAGAGCAGAT
* *
41360965 TTAAGCCTATAATCCTATCTCCCT
65 CT-A-CATATAATCCTATCTCCCT
* * * *
41360989 GAAGTTGCAGTGGAGC-GAATTAAAATCAC-AGATCTTAGCTCTCTGAAGTTGCA-AAGAGCAGA
1 GAAGTTGCAGTGG-GCAGACTCAAAATGACGA-ATCTTAGCTCCCTGAAGTTGCAGAAGAGCAGA
* * *
41361051 TCT-CATCTAGTCTTATCTCCCT
64 TCTACATATAATCCTATCTCCCT
*
41361073 GAGGTTGCAGTGGGCAGACTCAAAATGACGAATCTTA
1 GAAGTTGCAGTGGGCAGACTCAAAATGACGAATCTTA
41361110 TTTCCAGTGG
Statistics
Matches: 100, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
83 2 0.02
84 43 0.43
85 1 0.01
87 10 0.10
88 32 0.32
89 12 0.12
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (86 bp):
GAAGTTGCAGTGGGCAGACTCAAAATGACGAATCTTAGCTCCCTGAAGTTGCAGAAGAGCAGATC
TACATATAATCCTATCTCCCT
Found at i:41369657 original size:44 final size:45
Alignment explanation
Indices: 41369595--41369726 Score: 137
Period size: 44 Copynumber: 3.0 Consensus size: 45
41369585 TTAAGTTACA
*
41369595 CATTTCCG-GTTTAGTGCCATGGTATCTTTCAACTATGGTCTTAT-T
1 CATTT-CGAGTTTAATGCCATGGTATCTTTCAACTATGGTCTT-TCT
** * *
41369640 CA-TTCTTGTTTAATGCCATAGTATCTTTCAACTATAGTCTTTCT
1 CATTTCGAGTTTAATGCCATGGTATCTTTCAACTATGGTCTTTCT
** *
41369684 CATTTCGAGTAAAATGCCATGATATCTTTCAA-TCATGGTCTTT
1 CATTTCGAGTTTAATGCCATGGTATCTTTCAACT-ATGGTCTTT
41369727 ATCGTTTCTC
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
43 2 0.03
44 37 0.51
45 33 0.46
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.44
Consensus pattern (45 bp):
CATTTCGAGTTTAATGCCATGGTATCTTTCAACTATGGTCTTTCT
Found at i:41369725 original size:45 final size:43
Alignment explanation
Indices: 41369609--41369726 Score: 123
Period size: 45 Copynumber: 2.7 Consensus size: 43
41369599 TCCGGTTTAG
* ** **
41369609 TGCCATGGTATCTTTCAACTATGGTCTTATTCATTCTTGTTTAA
1 TGCCATGATATCTTTCAACTATGGTCTT-TTCATTCGAGTAAAA
*
41369653 TGCCAT-AGTATCTTTCAACTATAGTCTTTCTCATTTCGAGTAAAA
1 TGCCATGA-TATCTTTCAACTATGGTCTTT-TCA-TTCGAGTAAAA
41369698 TGCCATGATATCTTTCAA-TCATGGTCTTT
1 TGCCATGATATCTTTCAACT-ATGGTCTTT
41369727 ATCGTTTCTC
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.02
44 29 0.47
45 31 0.50
46 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (43 bp):
TGCCATGATATCTTTCAACTATGGTCTTTTCATTCGAGTAAAA
Found at i:41370124 original size:109 final size:109
Alignment explanation
Indices: 41369933--41370136 Score: 399
Period size: 109 Copynumber: 1.9 Consensus size: 109
41369923 TAGGTAATAC
*
41369933 ATTTCTTTCAATTAAACCATTCAAATAACTTAAAATAATTAACTCAAACTTATAACCCTTATCAA
1 ATTTCATTCAATTAAACCATTCAAATAACTTAAAATAATTAACTCAAACTTATAACCCTTATCAA
41369998 TATGAATTTACAAAATTACCTCCACATTTTTACCTAGATAATGA
66 TATGAATTTACAAAATTACCTCCACATTTTTACCTAGATAATGA
41370042 ATTTCATTCAATTAAACCATTCAAATAACTTAAAATAATTAACTCAAACTTATAACCCTTATCAA
1 ATTTCATTCAATTAAACCATTCAAATAACTTAAAATAATTAACTCAAACTTATAACCCTTATCAA
41370107 TATGAATTTACAAAATTACCTCCACATTTT
66 TATGAATTTACAAAATTACCTCCACATTTT
41370137 AACCATTATG
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 94 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.36
Consensus pattern (109 bp):
ATTTCATTCAATTAAACCATTCAAATAACTTAAAATAATTAACTCAAACTTATAACCCTTATCAA
TATGAATTTACAAAATTACCTCCACATTTTTACCTAGATAATGA
Found at i:41378165 original size:13 final size:13
Alignment explanation
Indices: 41378129--41378166 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
41378119 TCCACAGTTA
41378129 ATATATCAAATAAT
1 ATATAT-AAATAAT
*
41378143 -TATCTAAATAAT
1 ATATATAAATAAT
41378155 ATATATAAATAA
1 ATATATAAATAA
41378167 ATCATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATATAAATAAT
Found at i:41383192 original size:482 final size:484
Alignment explanation
Indices: 41382239--41383197 Score: 1690
Period size: 482 Copynumber: 2.0 Consensus size: 484
41382229 ATTGACACTA
* * * *
41382239 ACAAGAAATCATCGCCGCTTTCATTAGCCAAATTAGCACCAGCTGCATCTTCCTCGTTACTCTCA
1 ACAAGAAATCATCACCACTTTCATCAGCCAAATTAGCACCAGCTACATCTTCCTCGTTACTCTCA
* * * *
41382304 GTAGCTCTTTTATTTCGCAGTTTATAACAATTTGCTTTGACGTGACCTAACTTTTTACAATAGAG
66 GCAGCTCTTTTATTTCGCAGTTTATAACAATCTACTTTGACATGACCTAACTTTTTACAATAGAG
*
41382369 ATACCTTTTGTCTCGTTTCTTTAATGCTACCAAAACGAAAGCTTGCCTACCTGCCTTGCTATCCA
131 ACACCTTTTGTCTCGTTTCTTTAATGCTACCAAAACGAAAGCTTGCCTACCTGCCTTGCTATCCA
41382434 AACCAAACTCATTGTCCAGTTTGTCTCTACTCAACAAATGACCCTTCACATATTCGAACGAGAGT
196 AACCAAACTCATTGTCCAGTTTGTCTCTACTCAACAAATGACCCTTCACATATTCGAACGAGAGT
* *
41382499 TTGTCTCTACCATAAATTAGGGTCTCCCTAAAAGACTTGTATGAAGGGGGTAAAGAGCACAATAA
261 TTGTCTCTACCATAAATCAAGGTCTCCCTAAAAGACTTGTATGAAGGGGGTAAAGAGCACAATAA
* *
41382564 TAGTGTAGCCTGATCTTCATCGTCAATATGAACCTCAACATTCTTTAAATCATTTAAAAGAGTAA
326 TAGCGTAGCCTGATCTTCATCGTCAATATAAACCTCAACATTCTTTAAATCATTTAAAAGAGTAA
*
41382629 TGAAATGACTGATGTGATCTCTAAGAAGCTCACATTCGTTCATGCGAAACGTAAATAGATGTTGT
391 TGAAATGACTGATGTCATCTCTAAGAAGCTCACATTCGTTCATGCGAAACGTAAATAGATGTTGT
41382694 TTCAACACTAAACGGTTAGCCTGAGACTT
456 TTCAACACTAAACGGTTAGCCTGAGACTT
*
41382723 ACAAGAAATCATCACCACTTTCATCGGCCAAATTAGCACCAGCTACATCTTCCTCGTTACTCTCA
1 ACAAGAAATCATCACCACTTTCATCAGCCAAATTAGCACCAGCTACATCTTCCTCGTTACTCTCA
* *
41382788 GCAGCTCTTTTATTTTGCAGTTTATAACAATCTACTTTGACATGACCTAACTTTTTACAATAGCG
66 GCAGCTCTTTTATTTCGCAGTTTATAACAATCTACTTTGACATGACCTAACTTTTTACAATAGAG
*
41382853 ACACCTTTTGTCTCGTTTCTTTGATGCTACCAAAACGAAAGCTTGCCTACCTGCCTTGCTATCCA
131 ACACCTTTTGTCTCGTTTCTTTAATGCTACCAAAACGAAAGCTTGCCTACCTGCCTTGCTATCCA
*
41382918 AACCAAACTCATTGTCCAGTTTGTCTCTACTCAA-AAATGACCC-TCACATCTTCGAACGAGAGT
196 AACCAAACTCATTGTCCAGTTTGTCTCTACTCAACAAATGACCCTTCACATATTCGAACGAGAGT
*
41382981 TTGTCTCTGCCATAAATCAAGGTCTCCCTAAAAGACTTGTATGAAGGGGGTAAAGAGCACAATAA
261 TTGTCTCTACCATAAATCAAGGTCTCCCTAAAAGACTTGTATGAAGGGGGTAAAGAGCACAATAA
*
41383046 TAGCGTAGCCTGATCTTCATCGTCAATATAAACTTCAACATTCTTTAAATCATTTAAAAGAGTAA
326 TAGCGTAGCCTGATCTTCATCGTCAATATAAACCTCAACATTCTTTAAATCATTTAAAAGAGTAA
*
41383111 TGAATTGACTGATGTCATCTCTAAGAAGCTCATC-TTCGTTCATGCGAAACGTAAATAGATGTTG
391 TGAAATGACTGATGTCATCTCTAAGAAGCTCA-CATTCGTTCATGCGAAACGTAAATAGATGTTG
41383175 TTTCAACACTAAACGGTTAGCCT
455 TTTCAACACTAAACGGTTAGCCT
41383198 AAGATTTAGA
Statistics
Matches: 452, Mismatches: 22, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
482 226 0.50
483 10 0.02
484 216 0.48
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (484 bp):
ACAAGAAATCATCACCACTTTCATCAGCCAAATTAGCACCAGCTACATCTTCCTCGTTACTCTCA
GCAGCTCTTTTATTTCGCAGTTTATAACAATCTACTTTGACATGACCTAACTTTTTACAATAGAG
ACACCTTTTGTCTCGTTTCTTTAATGCTACCAAAACGAAAGCTTGCCTACCTGCCTTGCTATCCA
AACCAAACTCATTGTCCAGTTTGTCTCTACTCAACAAATGACCCTTCACATATTCGAACGAGAGT
TTGTCTCTACCATAAATCAAGGTCTCCCTAAAAGACTTGTATGAAGGGGGTAAAGAGCACAATAA
TAGCGTAGCCTGATCTTCATCGTCAATATAAACCTCAACATTCTTTAAATCATTTAAAAGAGTAA
TGAAATGACTGATGTCATCTCTAAGAAGCTCACATTCGTTCATGCGAAACGTAAATAGATGTTGT
TTCAACACTAAACGGTTAGCCTGAGACTT
Found at i:41387273 original size:16 final size:16
Alignment explanation
Indices: 41387252--41387289 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
41387242 ACAACATAAT
41387252 TGTTATCGATTCAACA
1 TGTTATCGATTCAACA
41387268 TGTTATCGATTCAACA
1 TGTTATCGATTCAACA
*
41387284 TTTTAT
1 TGTTAT
41387290 ATTCACTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (16 bp):
TGTTATCGATTCAACA
Found at i:41388438 original size:29 final size:29
Alignment explanation
Indices: 41388405--41388503 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 29
41388395 AGAAAGTACA
41388405 CAAATTAGTAATTATTACAATTAGGAGAT
1 CAAATTAGTAATTATTACAATTAGGAGAT
*
41388434 CAAATT-G--ATTAGTTA-ATAGTTGAGGATAAAGT
1 CAAATTAGTAATTA-TTACA-A-TT-AGG--AGA-T
41388466 ACAAAAATTAGTAATTATTACAATTAGGAGAT
1 -C--AAATTAGTAATTATTACAATTAGGAGAT
41388498 CAAATT
1 CAAATT
41388504 GATTAGTTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 28
0.64 0.02 0.33
Matches are distributed among these distances:
26 5 0.09
27 4 0.07
28 3 0.06
29 14 0.26
31 3 0.06
32 2 0.04
33 3 0.06
35 8 0.15
36 3 0.06
37 4 0.07
38 5 0.09
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (29 bp):
CAAATTAGTAATTATTACAATTAGGAGAT
Found at i:41388446 original size:33 final size:33
Alignment explanation
Indices: 41388408--41388510 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
41388398 AAGTACACAA
41388408 ATTAGTAATTATTACAATTAGGAGATCAAATTG
1 ATTAGTAATTATTACAATTAGGAGATCAAATTG
** * *
41388441 ATTAGTTAA-TAGTTGAGGA-TA-AAG-TACAAA--A
1 ATTAG-TAATTA-TT-ACAATTAGGAGAT-CAAATTG
41388472 ATTAGTAATTATTACAATTAGGAGATCAAATTG
1 ATTAGTAATTATTACAATTAGGAGATCAAATTG
41388505 ATTAGT
1 ATTAGT
41388511 TAATAGTTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
29 2 0.04
30 7 0.13
31 13 0.25
32 2 0.04
33 19 0.37
34 7 0.13
35 2 0.04
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.35
Consensus pattern (33 bp):
ATTAGTAATTATTACAATTAGGAGATCAAATTG
Found at i:41388498 original size:64 final size:64
Alignment explanation
Indices: 41388397--41388524 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
41388387 TTGTAAAAAG
*
41388397 AAAGTACACAAATTAGTAATTATTACAATTAGGAGATCAAATTGATTAGTTAATAGTTGAGGAT
1 AAAGTACAAAAATTAGTAATTATTACAATTAGGAGATCAAATTGATTAGTTAATAGTTGAGGAT
41388461 AAAGTACAAAAATTAGTAATTATTACAATTAGGAGATCAAATTGATTAGTTAATAGTTGAGGAT
1 AAAGTACAAAAATTAGTAATTATTACAATTAGGAGATCAAATTGATTAGTTAATAGTTGAGGAT
41388525 GGACTTAAGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (64 bp):
AAAGTACAAAAATTAGTAATTATTACAATTAGGAGATCAAATTGATTAGTTAATAGTTGAGGAT
Found at i:41389625 original size:35 final size:35
Alignment explanation
Indices: 41389573--41389801 Score: 235
Period size: 35 Copynumber: 6.5 Consensus size: 35
41389563 TACTCCTTGT
* *
41389573 TTGGCGTGTTTCTGTTGGATTAGCTCTTATGAGCA
1 TTGGCGTGTTACAGTTGGATTAGCTCTTATGAGCA
* * *
41389608 TTGGCGTGCTATAGTTGGATTAGCTCATATGAGCA
1 TTGGCGTGTTACAGTTGGATTAGCTCTTATGAGCA
* * * *
41389643 TTGGCGTGTAACAATTGGATTAGATCTTATGAGAA
1 TTGGCGTGTTACAGTTGGATTAGCTCTTATGAGCA
*
41389678 TTGTCGTGTTACAGTTGGATTAGCTCTTATGAGCA
1 TTGGCGTGTTACAGTTGGATTAGCTCTTATGAGCA
* * * * * *
41389713 TTGGCATGTTACGGTTGGGTTTGCTCTTATAAGTA
1 TTGGCGTGTTACAGTTGGATTAGCTCTTATGAGCA
* * * *
41389748 CTGGCGTGTTTC-GATTGGGTTAGATCTTATGAGCA
1 TTGGCGTGTTACAG-TTGGATTAGCTCTTATGAGCA
* * *
41389783 TCGGTGTGTTATAGTTGGA
1 TTGGCGTGTTACAGTTGGA
41389802 CTTACGATGT
Statistics
Matches: 155, Mismatches: 37, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
34 1 0.01
35 153 0.99
36 1 0.01
ACGTcount: A:0.20, C:0.12, G:0.29, T:0.39
Consensus pattern (35 bp):
TTGGCGTGTTACAGTTGGATTAGCTCTTATGAGCA
Found at i:41389765 original size:105 final size:105
Alignment explanation
Indices: 41389577--41389780 Score: 264
Period size: 105 Copynumber: 1.9 Consensus size: 105
41389567 CCTTGTTTGG
* * * * *
41389577 CGTGTTTCTGTTGGATTAGCTCTTATGAGCATTGGCGTGCTATAGTTGGATTAGCTCATATGAGC
1 CGTGTTACAGTTGGATTAGCTCTTATGAGCATTGGCATGCTACAGTTGGATTAGCTCATATAAGC
*
41389642 ATTGGCGTGTAACAATTGGATTAGATCTTATGAGAATTGT
66 ACTGGCGTGTAACAATTGGATTAGATCTTATGAGAATTGT
* * * * * *
41389682 CGTGTTACAGTTGGATTAGCTCTTATGAGCATTGGCATGTTACGGTTGGGTTTGCTCTTATAAGT
1 CGTGTTACAGTTGGATTAGCTCTTATGAGCATTGGCATGCTACAGTTGGATTAGCTCATATAAGC
** * *
41389747 ACTGGCGTGTTTCGATTGGGTTAGATCTTATGAG
66 ACTGGCGTGTAACAATTGGATTAGATCTTATGAG
41389781 CATCGGTGTG
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
105 83 1.00
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.39
Consensus pattern (105 bp):
CGTGTTACAGTTGGATTAGCTCTTATGAGCATTGGCATGCTACAGTTGGATTAGCTCATATAAGC
ACTGGCGTGTAACAATTGGATTAGATCTTATGAGAATTGT
Found at i:41397321 original size:35 final size:35
Alignment explanation
Indices: 41397265--41397520 Score: 287
Period size: 35 Copynumber: 7.3 Consensus size: 35
41397255 TACTCCCTGT
* * *
41397265 TTGGTGTGTTTCGGTTGGATTAACTCTTATGAGGA
1 TTGGCGTGTTACGGTTGGATTAACTCTTATGAGCA
* *
41397300 TTGGCGTGTTACGGTTAGATTAGCTCTTATGAGCA
1 TTGGCGTGTTACGGTTGGATTAACTCTTATGAGCA
* * * * *
41397335 TTGGTGTGTTATGGTCGAATTAGCTCTTATGAGCA
1 TTGGCGTGTTACGGTTGGATTAACTCTTATGAGCA
* *
41397370 TTGGCATGTTACGGTTGGATTAGCTCTTATGAGCA
1 TTGGCGTGTTACGGTTGGATTAACTCTTATGAGCA
* * **
41397405 TTGCCGTGTTACGATTGGATTAACTCTTATGAGTT
1 TTGGCGTGTTACGGTTGGATTAACTCTTATGAGCA
*
41397440 TTGGCATGTTACGGTTGGATTAACTCTTATGAGCA
1 TTGGCGTGTTACGGTTGGATTAACTCTTATGAGCA
* * * * * *
41397475 TTAGCGTGTTTCAGTTGGGTTAGCTCTTATAAGCA
1 TTGGCGTGTTACGGTTGGATTAACTCTTATGAGCA
* *
41397510 TCGGTGTGTTA
1 TTGGCGTGTTA
41397521 TAGTTAGACT
Statistics
Matches: 184, Mismatches: 37, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 184 1.00
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.40
Consensus pattern (35 bp):
TTGGCGTGTTACGGTTGGATTAACTCTTATGAGCA
Found at i:41403090 original size:30 final size:30
Alignment explanation
Indices: 41403056--41403225 Score: 125
Period size: 30 Copynumber: 5.7 Consensus size: 30
41403046 TCTTTATTTC
41403056 ATAGCC-AAGGCTATCCCTTTTCATAATTCG
1 ATAGCCGAA-GCTATCCCTTTTCATAATTCG
*
41403086 ATAGCCGAAGCTATCCCTTTTCATAATTTG
1 ATAGCCGAAGCTATCCCTTTTCATAATTCG
* * * * **
41403116 ATTGTCGTTA-CCAT-CCTTTTACATTGTTCG
1 ATAGCCG-AAGCTATCCCTTTT-CATAATTCG
* * * * *
41403146 ATGGTCGTCA-CAATCCCTTTTCATAATTTG
1 ATAGCCG-AAGCTATCCCTTTTCATAATTCG
* * *
41403176 ATAGCCGAAGCCAGCCCTTTTCATGA-TCG
1 ATAGCCGAAGCTATCCCTTTTCATAATTCG
*
41403205 ATAGCCGAAGCCATCCCTTTT
1 ATAGCCGAAGCTATCCCTTTT
41403226 TTATAATTTT
Statistics
Matches: 113, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
29 29 0.26
30 75 0.66
31 9 0.08
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (30 bp):
ATAGCCGAAGCTATCCCTTTTCATAATTCG
Found at i:41403146 original size:60 final size:58
Alignment explanation
Indices: 41403071--41403249 Score: 146
Period size: 60 Copynumber: 3.0 Consensus size: 58
41403061 CAAGGCTATC
* * * *
41403071 CCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTTCATAATTTGATTGTCGTTACCAT
1 CCTTTTCAT-GTTCGATAGCCGAAGCAATCCCTTTTCATAATTTGATAGTCGTAACCAT
* * * * *
41403130 CCTTTTACATTGTTCGATGGTCGTCA-CAATCCCTTTTCATAATTTGATAGCCG-AAGCCAGC
1 CCTTTT-CA-TGTTCGATAGCCG-AAGCAATCCCTTTTCATAATTTGATAGTCGTAA-CCA-T
* * * * * *
41403191 CCTTTTCATGATCGATAGCCGAAGCCATCCCTTTTTTATAATTTTATGGTCGTCACCAT
1 CCTTTTCATGTTCGATAGCCGAAGCAATCCC-TTTTCATAATTTGATAGTCGTAACCAT
41403250 TGCTTTCCAT
Statistics
Matches: 92, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
58 1 0.01
59 23 0.25
60 59 0.64
61 9 0.10
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (58 bp):
CCTTTTCATGTTCGATAGCCGAAGCAATCCCTTTTCATAATTTGATAGTCGTAACCAT
Found at i:41403309 original size:29 final size:29
Alignment explanation
Indices: 41403277--41403342 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
41403267 TGTCGTCTCC
41403277 ATCCCTTTTCATAATCAATAGCCGAAGCT
1 ATCCCTTTTCATAATCAATAGCCGAAGCT
** * * *
41403306 AT-CCTTTTTGTAGTCGATAGTCGAAGCT
1 ATCCCTTTTCATAATCAATAGCCGAAGCT
*
41403334 ATCCTTTTT
1 ATCCCTTTT
41403343 GTAGTTGATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATAATCAATAGCCGAAGCT
Found at i:41403325 original size:28 final size:28
Alignment explanation
Indices: 41403294--41403366 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
41403284 TTCATAATCA
41403294 ATAGCCGAAGCTATCCTTTTTGTAGTCG
1 ATAGCCGAAGCTATCCTTTTTGTAGTCG
* *
41403322 ATAGTCGAAGCTATCCTTTTTGTAGTTG
1 ATAGCCGAAGCTATCCTTTTTGTAGTCG
*
41403350 ATAGCTGAAGCTATCCT
1 ATAGCCGAAGCTATCCT
41403367 ATTTCACCCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (28 bp):
ATAGCCGAAGCTATCCTTTTTGTAGTCG
Found at i:41406309 original size:25 final size:25
Alignment explanation
Indices: 41406281--41406342 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
41406271 CAGCTCGTAT
* *
41406281 GAGCTTACCATTATTTAGTTCAGAG
1 GAGCTTACCATTATTCAGCTCAGAG
** *
41406306 GAGCTTACTGTTATTCAGCTCGGAG
1 GAGCTTACCATTATTCAGCTCAGAG
41406331 GAGCTTACCATT
1 GAGCTTACCATT
41406343 TATAGCTCGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (25 bp):
GAGCTTACCATTATTCAGCTCAGAG
Found at i:41407729 original size:10 final size:10
Alignment explanation
Indices: 41407716--41407740 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41407706 AGCTCAAATC
41407716 AGCTCGTTTG
1 AGCTCGTTTG
41407726 AGCTCGTTTG
1 AGCTCGTTTG
41407736 AGCTC
1 AGCTC
41407741 ATTTCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.24, G:0.28, T:0.36
Consensus pattern (10 bp):
AGCTCGTTTG
Found at i:41407791 original size:16 final size:16
Alignment explanation
Indices: 41407770--41407803 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41407760 TCATCTACTT
41407770 TATTGCTAGAATAAAC
1 TATTGCTAGAATAAAC
41407786 TATTGCTAGAATAAAC
1 TATTGCTAGAATAAAC
41407802 TA
1 TA
41407804 AGTGTTTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (16 bp):
TATTGCTAGAATAAAC
Found at i:41411577 original size:3 final size:3
Alignment explanation
Indices: 41411569--41411763 Score: 64
Period size: 3 Copynumber: 66.0 Consensus size: 3
41411559 ACTTTATTCC
** * *
41411569 TAT TAT TAT TAT TAT TAT TAT TAT T-T CGT TAC TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * *
41411616 TAC TAT TAC TAT T-T TTT TGT TTT TAT T-T TAC TAC CAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
41411662 TAT TAC TAC TCT TATT TATT TATT TAC TAC TAT TAT TCGT T-T AAT AAT
1 TAT TAT TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT T-AT TAT TAT TAT
* * *
41411710 GTAT TAT TAT T-T T-T TAT TAT TAT CAT T-G TAT TAT TAT TAC TAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
41411753 CAT T-T TAT TAT
1 TAT TAT TAT TAT
41411764 CTTTCAACTA
Statistics
Matches: 145, Mismatches: 37, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
2 13 0.09
3 117 0.81
4 15 0.10
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:41411684 original size:43 final size:42
Alignment explanation
Indices: 41411610--41411698 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 42
41411600 CTATTATTAC
* * *
41411610 TATTATTACTATTACTATTTTTTTGTTTTTATTTTACTACCAT
1 TATTATTACTATTACTATCTTATTGTATTTA-TTTACTACCAT
*
41411653 TATTATTACTATTACTACTCTTATT-TATTTATTTACTACTAT
1 TATTATTACTATTACTA-TCTTATTGTATTTATTTACTACCAT
41411695 TATT
1 TATT
41411699 CGTTTAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
42 14 0.34
43 22 0.54
44 5 0.12
ACGTcount: A:0.26, C:0.12, G:0.01, T:0.61
Consensus pattern (42 bp):
TATTATTACTATTACTATCTTATTGTATTTATTTACTACCAT
Found at i:41411748 original size:20 final size:20
Alignment explanation
Indices: 41411723--41411763 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41411713 TTATTATTTT
*
41411723 TTATTATTATCATTGTATTA
1 TTATTACTATCATTGTATTA
*
41411743 TTATTACTATCATTTTATTA
1 TTATTACTATCATTGTATTA
41411763 T
1 T
41411764 CTTTCAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (20 bp):
TTATTACTATCATTGTATTA
Found at i:41416258 original size:24 final size:23
Alignment explanation
Indices: 41416231--41416287 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 23
41416221 TACTTCACTT
41416231 GAAAAAGAAACGAAAA-GAAAAAA
1 GAAAAAGAAA-GAAAACGAAAAAA
41416254 GGAAAAA-AAAGAAAACCGAAAAAA
1 -GAAAAAGAAAGAAAA-CGAAAAAA
41416278 GAAAAAGAAA
1 GAAAAAGAAA
41416288 AAGGAGAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.17
23 9 0.30
24 16 0.53
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (23 bp):
GAAAAAGAAAGAAAACGAAAAAA
Found at i:41417475 original size:134 final size:134
Alignment explanation
Indices: 41417235--41417669 Score: 658
Period size: 134 Copynumber: 3.2 Consensus size: 134
41417225 TTTACAGTGG
* * *
41417235 AGTAGACTGAAGATAGCAGATCTTGTCTCCCTGAGCAATAGTGGAGTAGGTCGAAGATTTTAGAT
1 AGTAGACTGAAGATAGCAGATATTGTCTCCCTGAGCAACAGTGGAGTAGGTCGAAGATTGTAGAT
* * *
41417300 CTTGTCTTCCTGTATTGGCAGCAAAGTAGATTGAAGATAGCAAGTCTTGTCTTCCTGTATTGGCA
66 CTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTATTGGCA
*
41417365 GCAA
131 GCGA
* * * *
41417369 AGTAGACTGAAGATAGCAGATCTTGTCTTCTTGAGCAACAATGGAGTAGGTCGAAGATTGTAGAT
1 AGTAGACTGAAGATAGCAGATATTGTCTCCCTGAGCAACAGTGGAGTAGGTCGAAGATTGTAGAT
*
41417434 CTTGTCTTCCTATATTGGCAGCGAAGTAGATC-AACAGTAGCAAGTCTTGTCTTCCTGTATTGGC
66 CTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGA-TAGCAAGTCTTGTCTTCCTGTATTGGC
41417498 AGCGA
130 AGCGA
41417503 AGTAGACTGAAGATAGCAGATATTGTCTCCCTGAGCAACAGTGGAGTAGGTCGAAGATTGTAGAT
1 AGTAGACTGAAGATAGCAGATATTGTCTCCCTGAGCAACAGTGGAGTAGGTCGAAGATTGTAGAT
* * * *
41417568 CCTGTCTTCCTATATTGGCAGCGAAGTAGGTCGAAGATAGCAAATCTTGTCTTCCTGTATTGGTA
66 CTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTATTGGCA
41417633 GCGA
131 GCGA
* * * *
41417637 AGTGGA-TCAAAGATAGTAGATATTGTCTTCCTG
1 AGTAGACT-GAAGATAGCAGATATTGTCTCCCTG
41417670 TATTGGCAGC
Statistics
Matches: 275, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
133 4 0.01
134 268 0.97
135 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (134 bp):
AGTAGACTGAAGATAGCAGATATTGTCTCCCTGAGCAACAGTGGAGTAGGTCGAAGATTGTAGAT
CTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTTCCTGTATTGGCA
GCGA
Found at i:41417821 original size:134 final size:134
Alignment explanation
Indices: 41417646--41417995 Score: 445
Period size: 134 Copynumber: 2.6 Consensus size: 134
41417636 AAGTGGATCA
* *
41417646 AAGATAGTAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGAT-TAAAATTAGCAAGTCTTATCT
1 AAGATTGTAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAAA-TAGCAAGTCTTATCT
* * * * **
41417710 TTCTATATTGGCAGTGAAGTAGACTGAAGATAACGGATCTTGTCTCACTGAGCAGTAGTGGAGTA
65 TCCTATATTGGCAGCGAAGTAGAATGAAGATAACAGATCTTGTCTCACTGAGCAACAGTGGAGTA
41417775 GGTCG
130 GGTCG
* * *
41417780 AAGATTGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTGTCTT
1 AAGATTGTAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAAATAGCAAGTCTTATCTT
* * * ** * *
41417845 CCTTTATTGGTAGCGAAGTAGAATGAAGGTAGTAGATCTTGTCTCCCTGAGGAACAGTGGAGTAG
66 CCTATATTGGCAGCGAAGTAGAATGAAGATAACAGATCTTGTCTCACTGAGCAACAGTGGAGTAG
41417910 GTCG
131 GTCG
* * *
41417914 AAGATTGTAGATATTGTCTTCCTATATCGGCAGCGAAGTAGATC-AAAGATAGC-AGATCTTGTC
1 AAGATTGTAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAA-ATAGCAAG-TCTTATC
* *
41417977 TTCCTGTACTGGCAGCGAA
64 TTCCTATATTGGCAGCGAA
41417996 CCAGATCAAA
Statistics
Matches: 188, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
133 4 0.02
134 181 0.96
135 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (134 bp):
AAGATTGTAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAAATAGCAAGTCTTATCTT
CCTATATTGGCAGCGAAGTAGAATGAAGATAACAGATCTTGTCTCACTGAGCAACAGTGGAGTAG
GTCG
Found at i:41417880 original size:224 final size:224
Alignment explanation
Indices: 41417422--41417893 Score: 703
Period size: 224 Copynumber: 2.1 Consensus size: 224
41417412 GAGTAGGTCG
* * * *
41417422 AAGATTGTAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAACAGTAGCAAGTCTTGTCTT
1 AAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAAGTAGCAAGTCTTATCTT
* * *
41417487 CCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAGATATTGTCTCCCTGAGCAACAGTGGAGTAG
66 CCTATATTGGCAGCGAAGTAGACTGAAGATAACAGATATTGTCTCACTGAGCAACAGTGGAGTAG
*
41417552 GTCGAAGATTGTAGATCCTGTCTTCCTATATTGGCAGCGAAGTAGGTCGAAGATAGCAAATCTTG
131 GTCGAAGATTGTAGATCCTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTG
*
41417617 TCTTCCTGTATTGGTAGCGAAGTGGATCA
196 TCTTCCTGTATTGGTAGCGAAGTGAATCA
* * *
41417646 AAGATAGTAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGATTAAAATTAGCAAGTCTTATCTT
1 AAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAAGTAGCAAGTCTTATCTT
* * * * **
41417711 TCTATATTGGCAGTGAAGTAGACTGAAGATAACGGATCTTGTCTCACTGAGCAGTAGTGGAGTAG
66 CCTATATTGGCAGCGAAGTAGACTGAAGATAACAGATATTGTCTCACTGAGCAACAGTGGAGTAG
* * *
41417776 GTCGAAGATTGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCTTG
131 GTCGAAGATTGTAGATCCTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTG
* *
41417841 TCTTCCTTTATTGGTAGCGAAGTAGAAT-G
196 TCTTCCTGTATTGGTAGCGAAGT-GAATCA
* *
41417870 AAGGTAGTAGATCTTGTCTCCCTG
1 AAGATAGTAGATCTTGTCTTCCTG
41417894 AGGAACAGTG
Statistics
Matches: 221, Mismatches: 26, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
224 218 0.99
225 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (224 bp):
AAGATAGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAAGTAGCAAGTCTTATCTT
CCTATATTGGCAGCGAAGTAGACTGAAGATAACAGATATTGTCTCACTGAGCAACAGTGGAGTAG
GTCGAAGATTGTAGATCCTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTG
TCTTCCTGTATTGGTAGCGAAGTGAATCA
Found at i:41417909 original size:89 final size:89
Alignment explanation
Indices: 41417816--41417982 Score: 203
Period size: 89 Copynumber: 1.9 Consensus size: 89
41417806 TTGGCAGCGA
* * * * * * *
41417816 AGTAGATCGAAGATAGCAAG-TCTTGTCTTCCTTTATTGGTAGCGAAGTAGAAT-GAAGGTAGTA
1 AGTAGATCGAAGATAG-AAGATATTGTCTTCCTATATCGGCAGCGAAGTAG-ATCAAAGATAGCA
41417879 GATCTTGTCTCCCTGAGGAACAGTGG
64 GATCTTGTCTCCCTGAGGAACAGTGG
* * *
41417905 AGTAGGTCGAAGATTGTAGATATTGTCTTCCTATATCGGCAGCGAAGTAGATCAAAGATAGCAGA
1 AGTAGATCGAAGATAGAAGATATTGTCTTCCTATATCGGCAGCGAAGTAGATCAAAGATAGCAGA
*
41417970 TCTTGTCTTCCTG
66 TCTTGTCTCCCTG
41417983 TACTGGCAGC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
88 4 0.06
89 61 0.94
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (89 bp):
AGTAGATCGAAGATAGAAGATATTGTCTTCCTATATCGGCAGCGAAGTAGATCAAAGATAGCAGA
TCTTGTCTCCCTGAGGAACAGTGG
Found at i:41417965 original size:358 final size:358
Alignment explanation
Indices: 41417295--41417995 Score: 1075
Period size: 358 Copynumber: 2.0 Consensus size: 358
41417285 TCGAAGATTT
* * * *
41417295 TAGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATTGAAGATAGCAAGTCTTGTCTTCCTGTAT
1 TAGATATTGTCTTCCTGTATTGGCAGCAAAGTAGATTGAAAATAGCAAGTCTTATCTTCCTATAT
* *
41417360 TGGCAGCAAAGTAGACTGAAGATAGCAGATCTTGTCTTCTTGAGCAACAATGGAGTAGGTCGAAG
66 TGGCAGCAAAGTAGACTGAAGATAACAGATCTTGTCTTCCTGAGCAACAATGGAGTAGGTCGAAG
41417425 ATTGTAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAACAGTAGCAAGTCTTGTCTTCCT
131 ATTGTAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAACAGTAGCAAGTCTTGTCTTCCT
*
41417490 GTATTGGCAGCGAAGTAGACTGAAGATAGCAGATATTGTCTCCCTGAGCAACAGTGGAGTAGGTC
196 GTATTGGCAGCGAAGTAGAATGAAGATAGCAGATATTGTCTCCCTGAGCAACAGTGGAGTAGGTC
* * * *
41417555 GAAGATTGTAGATCCTGTCTTCCTATATTGGCAGCGAAGTAGGTCGAAGATAGCAAATCTTGTCT
261 GAAGATTGTAGATACTGTCTTCCTATATCGGCAGCGAAGTAGATCAAAGATAGCAAATCTTGTCT
* *
41417620 TCCTGTATTGGTAGCGAAGTGGATCAAAGATAG
326 TCCTGTACTGGCAGCGAAGTGGATCAAAGATAG
* *
41417653 TAGATATTGTCTTCCTGTATTGGCAGCGAAGTAGATT-AAAATTAGCAAGTCTTATCTTTCTATA
1 TAGATATTGTCTTCCTGTATTGGCAGCAAAGTAGATTGAAAA-TAGCAAGTCTTATCTTCCTATA
** * ** *
41417717 TTGGCAGTGAAGTAGACTGAAGATAACGGATCTTGTC-TCACTGAGCAGTAGTGGAGTAGGTCGA
65 TTGGCAGCAAAGTAGACTGAAGATAACAGATCTTGTCTTC-CTGAGCAACAATGGAGTAGGTCGA
* *
41417781 AGATTGTAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGA-AGATAGCAAGTCTTGTCTT
129 AGATTGTAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAACAG-TAGCAAGTCTTGTCTT
* * * * * *
41417845 CCTTTATTGGTAGCGAAGTAGAATGAAGGTAGTAGATCTTGTCTCCCTGAGGAACAGTGGAGTAG
193 CCTGTATTGGCAGCGAAGTAGAATGAAGATAGCAGATATTGTCTCCCTGAGCAACAGTGGAGTAG
* *
41417910 GTCGAAGATTGTAGATATTGTCTTCCTATATCGGCAGCGAAGTAGATCAAAGATAGCAGATCTTG
258 GTCGAAGATTGTAGATACTGTCTTCCTATATCGGCAGCGAAGTAGATCAAAGATAGCAAATCTTG
41417975 TCTTCCTGTACTGGCAGCGAA
323 TCTTCCTGTACTGGCAGCGAA
41417996 CCAGATCAAA
Statistics
Matches: 309, Mismatches: 31, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
357 7 0.02
358 302 0.98
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (358 bp):
TAGATATTGTCTTCCTGTATTGGCAGCAAAGTAGATTGAAAATAGCAAGTCTTATCTTCCTATAT
TGGCAGCAAAGTAGACTGAAGATAACAGATCTTGTCTTCCTGAGCAACAATGGAGTAGGTCGAAG
ATTGTAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCAACAGTAGCAAGTCTTGTCTTCCT
GTATTGGCAGCGAAGTAGAATGAAGATAGCAGATATTGTCTCCCTGAGCAACAGTGGAGTAGGTC
GAAGATTGTAGATACTGTCTTCCTATATCGGCAGCGAAGTAGATCAAAGATAGCAAATCTTGTCT
TCCTGTACTGGCAGCGAAGTGGATCAAAGATAG
Found at i:41418005 original size:45 final size:45
Alignment explanation
Indices: 41417296--41417995 Score: 552
Period size: 45 Copynumber: 15.6 Consensus size: 45
41417286 CGAAGATTTT
* *
41417296 AGATCTTGTCTTCCTGTATTGGCAGCAAAGTAGATTGAAGATAGC
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
*
41417341 A-AGTCTTGTCTTCCTGTATTGGCAGCAAAGTAGA-CTGAAGATAGC
1 AGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGC
* **** ** * * * *
41417386 AGATCTTGTCTTCTTG-AGCAACAATGGAGTAGGTCGAAGATTGT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
* *
41417430 AGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC-AACAGTAGC
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA-TAGC
41417475 A-AGTCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-CTGAAGATAGC
1 AGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGC
* * **** * * * * *
41417520 AGATATTGTCTCCCTG-AGCAACAGTGGAGTAGGTCGAAGATTGT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
* * *
41417564 AGATCCTGTCTTCCTATATTGGCAGCGAAGTAGGTCGAAGATAGC
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
* * * * *
41417609 AAATCTTGTCTTCCTGTATTGGTAGCGAAGTGGATCAAAGATAGT
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
* * *
41417654 AGATATTGTCTTCCTGTATTGGCAGCGAAGTAGAT-TAAAATTAGC
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA-TAGC
* * * * *
41417699 A-AGTCTTATCTTTCTATATTGGCAGTGAAGTAGA-CTGAAGATAAC
1 AGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-GAAGATAGC
* *** * * * * * *
41417744 GGATCTTGTC-TCACTG-AGCAGTAGTGGAGTAGGTCGAAGATTGT
1 AGATCTTGTCTTC-CTGTATTGGCAGCGAAGTAGATCGAAGATAGC
41417788 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
* * * *
41417833 A-AGTCTTGTCTTCCTTTATTGGTAGCGAAGTAGAAT-GAAGGTAGT
1 AGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAG-ATCGAAGATAGC
* * * * * *
41417878 AGATCTTGTCTCCCTG-A--GGAACAGTGGAGTAGGTCGAAGATTGT
1 AGATCTTGTCTTCCTGTATTGG--CAGCGAAGTAGATCGAAGATAGC
* * * *
41417922 AGATATTGTCTTCCTATATCGGCAGCGAAGTAGATCAAAGATAGC
1 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
*
41417967 AGATCTTGTCTTCCTGTACTGGCAGCGAA
1 AGATCTTGTCTTCCTGTATTGGCAGCGAA
41417996 CCAGATCAAA
Statistics
Matches: 503, Mismatches: 122, Indels: 60
0.73 0.18 0.09
Matches are distributed among these distances:
42 2 0.00
43 1 0.00
44 128 0.25
45 358 0.71
46 12 0.02
47 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (45 bp):
AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATAGC
Found at i:41418130 original size:44 final size:44
Alignment explanation
Indices: 41418081--41418220 Score: 165
Period size: 44 Copynumber: 3.2 Consensus size: 44
41418071 GTAGTAGGGA
* * * *
41418081 AGCAGATTTAAGCCACTAGTCTTATCCCCCTAAAGTTGCAGTGG
1 AGCAGATTGAAGCTACTAGTCTTATCTCCCTGAAGTTGCAGTGG
* * *
41418125 GGCAGATTGAAGATAC-ATGTCTTATCTCCCTGAAGTTGTAGTGG
1 AGCAGATTGAAGCTACTA-GTCTTATCTCCCTGAAGTTGCAGTGG
* * *
41418169 AGCAGATTGAAGCTACTAATCCTATCTCCCTGAAGTTGCACTGG
1 AGCAGATTGAAGCTACTAGTCTTATCTCCCTGAAGTTGCAGTGG
*
41418213 AGCGGATT
1 AGCAGATT
41418221 AAAATGATGA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
43 1 0.01
44 78 0.98
45 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (44 bp):
AGCAGATTGAAGCTACTAGTCTTATCTCCCTGAAGTTGCAGTGG
Found at i:41418580 original size:129 final size:129
Alignment explanation
Indices: 41418347--41418763 Score: 503
Period size: 129 Copynumber: 3.2 Consensus size: 129
41418337 CATGTCAAAC
* *** * * * *
41418347 CTTATCTCCCTGAAGCTGCAGTGGAGCAGGTTGCAGCAA-CAAGTCTTATCTCCTTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAA-TCCTATCTCCCTGAAGTTGCA
* * *
41418411 GTAGAGCGGATTAAAAACACAGATCTTGTCTCTCTTAAGTTAAAGTAGAACAGATCGCATCCAAT
65 GTAGAGCGGATTAAAAACACAAATCTTATCTCTCTGAAGTTAAAGTAGAACAGATCGCATCCAAT
* *
41418476 TTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTACAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAG
* ** * *
41418541 TGGAGCGGATTAAAAACACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGT
66 TAGAGCGGATTAAAAACACAAATCTTATCTCTCTGAAGTTAAAGTAGAACAGATCGCATCCAAT
* * *
41418605 CTTATCTTCCTGAAGTTGCAGTGGAGTAGACAAAAGAAACCAATCCTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAG
* * * * * * ***
41418670 TAGAGCGGATTAAAACCACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGATTTAATAAGCCA
66 TAGAGCGGATTAAAAACACAAATCTTATCTCTCTGAAGTTAAAGTAGAACAGATCGCAT---CCA
41418735 AT
128 AT
* *
41418737 CCTATCTCCCTGAAGTTGCAGTAGAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGC
41418764 GGATTAAAAT
Statistics
Matches: 247, Mismatches: 37, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
129 217 0.88
130 3 0.01
132 27 0.11
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (129 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCCTATCTCCCTGAAGTTGCAG
TAGAGCGGATTAAAAACACAAATCTTATCTCTCTGAAGTTAAAGTAGAACAGATCGCATCCAAT
Found at i:41418787 original size:44 final size:42
Alignment explanation
Indices: 41418347--41418811 Score: 274
Period size: 44 Copynumber: 10.7 Consensus size: 42
41418337 CATGTCAAAC
* * * **
41418347 CTTATCTCCCTGAAGCTGCAGTGGAGCAGGTT-GCAGCAACAAGT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAG--ACAA-T
* * *
41418391 CTTATCTCCTTGAAGTTGCAGTAGAGCGGATTAAAAACACAGAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATT-AAAAGACA-AT
* * * ** * *** **
41418435 CTTGTCTCTCTTAAGTTAAAGTAGAACAGA-TCGCATCCAAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAGACAAT
* * * *
41418476 TTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAGAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTA-AA-AGA-CAAT
* * * * *
41418520 CCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAACACAAAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATT-AAAAGAC-AAT
* *** ** *
41418564 CTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCATCCAGT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAGACAAT
* * * *
41418605 CTTATCTTCCTGAAGTTGCAGTGGAGTAGA-CAAAAGAAACCAAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAG--A-CAAT
* * *
41418649 CCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACCACAAGT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAA-GACAA-T
* * *
41418693 CTTATCTCCCTGAAGTTACAGTGGAGCAGATTTAATAAGCCAAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TTAA-AAGACAAT
* * *
41418737 CCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATGATAGAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAA-GACA-AT
* *
41418781 CTTATCTCTCTGAAGTTACAGTAGAGCAGAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
41418812 GACATCAGAC
Statistics
Matches: 316, Mismatches: 86, Indels: 38
0.72 0.20 0.09
Matches are distributed among these distances:
41 53 0.17
42 7 0.02
43 13 0.04
44 225 0.71
45 14 0.04
46 4 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAAGACAAT
Found at i:41418811 original size:88 final size:88
Alignment explanation
Indices: 41418393--41418811 Score: 358
Period size: 88 Copynumber: 4.8 Consensus size: 88
41418383 CAACAAGTCT
* * * * * *
41418393 TATCTCCTTGAAGTTGCAGTAGAGCGGATTAAAAACACAGATCTTGTCTCTCTTAAGTTAAAGTA
1 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGTG
* *** **
41418458 GAACAGATCGCAT---CCAATTT
66 GAGCAGATTTAATAAACCAATCC
* * ** * * *
41418478 TATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAAC-CA-ATCCTATCTCCCTGAAGTTACAG
1 TATCTCCCTGAAGTTGCAGTAGAGCGGA-TTAA-AATCACAGATCTTATCTCTCTGAAGTTACAG
* *
41418541 TGGAGCGGA-TTAA-AAACACAAATCT
64 TGGAGCAGATTTAATAAAC-C-AATCC
* * *** *
41418566 TATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCATC-CAG-TCTTATCT-TCCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCTTATCTCT-CTGAAGTTACAGT
* *** *
41418627 GGAGTAGACAAAAGAAACCAATCC
65 GGAGCAGATTTAATAAACCAATCC
* *
41418651 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACCACA-AGTCTTATCTCCCTGAAGTTACAGT
1 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGA-TCTTATCTCTCTGAAGTTACAGT
*
41418715 GGAGCAGATTTAATAAGCCAATCC
65 GGAGCAGATTTAATAAACCAATCC
* * *
41418739 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATGATAGATCTTATCTCTCTGAAGTTACAGTA
1 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGTG
41418804 GAGCAGAT
66 GAGCAGAT
41418812 GACATCAGAC
Statistics
Matches: 266, Mismatches: 51, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
84 1 0.00
85 108 0.41
86 11 0.04
87 11 0.04
88 134 0.50
89 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (88 bp):
TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGTG
GAGCAGATTTAATAAACCAATCC
Found at i:41420802 original size:20 final size:21
Alignment explanation
Indices: 41420771--41420817 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
41420761 AATGTATTAT
*
41420771 TATTATTTATTATTATCATTG
1 TATTATTTATTACTATCATTG
41420792 TATTA-TTATTACTATCATCT-
1 TATTATTTATTACTATCAT-TG
41420812 TATTAT
1 TATTAT
41420818 CTTTAAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTATTTATTACTATCATTG
Found at i:41420817 original size:3 final size:3
Alignment explanation
Indices: 41420597--41420802 Score: 78
Period size: 3 Copynumber: 67.7 Consensus size: 3
41420587 ACTTTATTCC
* * * *
41420597 TAT TAT TAT CAT CAT CAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * * * * * * *
41420645 TAT T-T CGT TAC TAT TAT TAA TGT TAT TAC TAT TACT TTT TTT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * * * * *
41420690 TTT TAT T-T TAC TAC CAT TAT TAT TAC TAT TAT TAC TCT TATT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T
* * * * *
41420736 TATT TAC TAC TAT TAT TCGT T-T AAT AAT GTAT TAT TAT TATT TAT TAT
1 TA-T TAT TAT TAT TAT T-AT TAT TAT TAT -TAT TAT TAT TA-T TAT TAT
* *
41420784 TAT CAT T-G TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
41420803 CTATCATCTT
Statistics
Matches: 158, Mismatches: 36, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
2 5 0.03
3 133 0.84
4 20 0.13
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:41423053 original size:20 final size:18
Alignment explanation
Indices: 41423028--41423066 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
41423018 AACAAATAAT
41423028 TAAATAAATATCAAATAAAA
1 TAAATAAATA--AAATAAAA
41423048 TAAATAAATAAAATAAAA
1 TAAATAAATAAAATAAAA
41423066 T
1 T
41423067 TAGTAACCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATAAATAAAATAAAA
Found at i:41423058 original size:13 final size:13
Alignment explanation
Indices: 41423040--41423064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41423030 AATAAATATC
41423040 AAATAAAATAAAT
1 AAATAAAATAAAT
41423053 AAATAAAATAAA
1 AAATAAAATAAA
41423065 ATTAGTAACC
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:41423878 original size:15 final size:16
Alignment explanation
Indices: 41423858--41423891 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
41423848 TTAGTTTATG
41423858 AAAAATAA-AAAATGA
1 AAAAATAATAAAATGA
41423873 AAAAATAATAAAATGA
1 AAAAATAATAAAATGA
41423889 AAA
1 AAA
41423892 TGGACAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAAATAATAAAATGA
Found at i:41433386 original size:24 final size:24
Alignment explanation
Indices: 41433354--41433411 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
41433344 CGGATTGCCC
41433354 CCACTGTAATCTTCAAAGTTCAAT
1 CCACTGTAATCTTCAAAGTTCAAT
* * *
41433378 CCACTGTAATCTTCAAGGTTTAGT
1 CCACTGTAATCTTCAAAGTTCAAT
41433402 CCACTGTAAT
1 CCACTGTAAT
41433412 TTTGGGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (24 bp):
CCACTGTAATCTTCAAAGTTCAAT
Found at i:41434380 original size:11 final size:11
Alignment explanation
Indices: 41434351--41434387 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
41434341 TCTCCTTCAT
41434351 TTCTTTTCTTC
1 TTCTTTTCTTC
41434362 TT-TTTTCTT-
1 TTCTTTTCTTC
41434371 TATCTTTTCTTC
1 T-TCTTTTCTTC
41434383 TTCTT
1 TTCTT
41434388 CTTTTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.04
10 8 0.35
11 13 0.57
12 1 0.04
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (11 bp):
TTCTTTTCTTC
Found at i:41434390 original size:14 final size:14
Alignment explanation
Indices: 41434345--41434392 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
41434335 TTGGCCTCTC
*
41434345 CTTCATTTCTT-TT
1 CTTCTTTTCTTCTT
41434358 CTTCTTTT-TTCTT
1 CTTCTTTTCTTCTT
41434371 -TATCTTTTCTTCTT
1 CT-TCTTTTCTTCTT
41434385 CTTCTTTT
1 CTTCTTTT
41434393 TTGAAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 3 0.10
13 15 0.50
14 11 0.37
15 1 0.03
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (14 bp):
CTTCTTTTCTTCTT
Found at i:41442207 original size:2 final size:2
Alignment explanation
Indices: 41442200--41442226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41442190 AATTACTTCT
41442200 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
41442227 TTCTTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:41442888 original size:22 final size:20
Alignment explanation
Indices: 41442845--41442883 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41442835 CAATTTAAAA
41442845 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
41442865 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
41442884 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:41443008 original size:20 final size:20
Alignment explanation
Indices: 41442983--41443020 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41442973 ATATTTTCAA
41442983 TAAATCATTTTCCAGAAAAG
1 TAAATCATTTTCCAGAAAAG
41443003 TAAATCATTTTCCAGAAA
1 TAAATCATTTTCCAGAAA
41443021 TCATTTTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (20 bp):
TAAATCATTTTCCAGAAAAG
Found at i:41445344 original size:15 final size:16
Alignment explanation
Indices: 41445324--41445353 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41445314 GAGAGAAGAA
41445324 AAAAAGAAA-TGAAAG
1 AAAAAGAAATTGAAAG
41445339 AAAAAGAAATTGAAA
1 AAAAAGAAATTGAAA
41445354 AATAAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (16 bp):
AAAAAGAAATTGAAAG
Found at i:41449162 original size:74 final size:74
Alignment explanation
Indices: 41449038--41449188 Score: 248
Period size: 74 Copynumber: 2.0 Consensus size: 74
41449028 GTTGCTTGGC
*
41449038 TGTGTGTCACAAGTTAGTATACCCACAAGGGCATGGACACGGGCTAGAACATGACCGTGTGTCCC
1 TGTGTGTCACAAGTTAGTATACCCACAAGGGCATGGACACGGGCTAGAACACGACCGTGTGTCCC
*
41449103 TATTTTGAA
66 TATTTCGAA
* * * *
41449112 TGTGTGTCACAAGTTAGTATACCTACACGGGTATGGACACGGGCTGGAACACGACCGTGTGTCCC
1 TGTGTGTCACAAGTTAGTATACCCACAAGGGCATGGACACGGGCTAGAACACGACCGTGTGTCCC
41449177 TATTTCGAA
66 TATTTCGAA
41449186 TGT
1 TGT
41449189 CCACACGACC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (74 bp):
TGTGTGTCACAAGTTAGTATACCCACAAGGGCATGGACACGGGCTAGAACACGACCGTGTGTCCC
TATTTCGAA
Found at i:41458073 original size:56 final size:50
Alignment explanation
Indices: 41458009--41458249 Score: 198
Period size: 50 Copynumber: 4.7 Consensus size: 50
41457999 GGAATGAGAC
**
41458009 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA---A-G--ATGAGAGGT
* * *
41458065 CCCATGTAATACCATGTCTGGGACATGGCGTTGACACCAAGATGAGAGGT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGT
** * * * * **
41458115 CCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCAATATCAGAACT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGT
* * * * ** * **
41458165 CTCATGTAAGACCATATCTGGGATATGGCATTGGTAGTACAG--GAAACAT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-AGATGAGAGGT
*
41458214 CCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41458250 TGTTATTATC
Statistics
Matches: 148, Mismatches: 36, Indels: 9
0.77 0.19 0.05
Matches are distributed among these distances:
49 34 0.23
50 77 0.52
51 1 0.01
52 1 0.01
53 1 0.01
56 34 0.23
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATGAGAGGT
Found at i:41458482 original size:16 final size:16
Alignment explanation
Indices: 41458460--41458497 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41458450 TTAAGTAAGC
41458460 AAGTAAGTAAACAAGA
1 AAGTAAGTAAACAAGA
* *
41458476 GAGTAAGTAAAGAAGA
1 AAGTAAGTAAACAAGA
41458492 AAGTAA
1 AAGTAA
41458498 ATATCATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.24, T:0.13
Consensus pattern (16 bp):
AAGTAAGTAAACAAGA
Found at i:41459953 original size:47 final size:47
Alignment explanation
Indices: 41459902--41460100 Score: 158
Period size: 47 Copynumber: 4.2 Consensus size: 47
41459892 TGGTTGGACC
* *
41459902 ATGGCAAC-ATGTGATATGTGATTTTCGTATAAGACCATATCTGGGAT
1 ATGGCATCGATGTGATATGTGA-TTTCGTGTAAGACCATATCTGGGAT
* * * * *
41459949 ATGGCATCGGTGTAATATGTG-CTACTGTGTAAGACCATATTTGGGAT
1 ATGGCATCGATGTGATATGTGATTTC-GTGTAAGACCATATCTGGGAT
* * * * *
41459996 ATGGCATCTATGTGATATGCGA-TCCGTGTAAGACCATAGCTGGGCT
1 ATGGCATCGATGTGATATGTGATTTCGTGTAAGACCATATCTGGGAT
* * *
41460042 ATGGCATCAGTATGT-ATTATGTAATTACGTGTAATACCATAGT-T-GGACT
1 ATGGCATC-G-ATGTGA-TATGTGATTTCGTGTAAGACCATA-TCTGGGA-T
41460091 ATGGCATCGA
1 ATGGCATCGA
41460101 GAAAACGAAG
Statistics
Matches: 121, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
46 28 0.23
47 47 0.39
48 22 0.18
49 24 0.20
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (47 bp):
ATGGCATCGATGTGATATGTGATTTCGTGTAAGACCATATCTGGGAT
Found at i:41463044 original size:15 final size:16
Alignment explanation
Indices: 41463015--41463044 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41463005 CAAACATGCT
41463015 TTAACACATTATCAAA
1 TTAACACATTATCAAA
41463031 TTAACACA-TATCAA
1 TTAACACATTATCAA
41463045 CAGGGCACCA
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:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:41465363 original size:32 final size:31
Alignment explanation
Indices: 41465300--41465366 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
41465290 ATTTTCACCC
*
41465300 TTTATGTAAATCTATTGAAAATAAATCAAAA
1 TTTATGAAAATCTATTGAAAATAAATCAAAA
* * * *
41465331 TTTATGAAAATTTATTATAAAATTAATTAAAA
1 TTTATGAAAATCTATT-GAAAATAAATCAAAA
41465363 TTTA
1 TTTA
41465367 ATATGTTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (31 bp):
TTTATGAAAATCTATTGAAAATAAATCAAAA
Found at i:41482697 original size:42 final size:42
Alignment explanation
Indices: 41482638--41482725 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
41482628 CTATCTTTAC
41482638 TTCTATTGTCTTCTATCTTTGATATACAATTTGCCAACATAT
1 TTCTATTGTCTTCTATCTTTGATATACAATTTGCCAACATAT
41482680 TTCTATTGTCTTCTATCTTTGATATACAATTTGCCAACATAT
1 TTCTATTGTCTTCTATCTTTGATATACAATTTGCCAACATAT
41482722 TTCT
1 TTCT
41482726 TTGCTACGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (42 bp):
TTCTATTGTCTTCTATCTTTGATATACAATTTGCCAACATAT
Found at i:41492267 original size:12 final size:11
Alignment explanation
Indices: 41492224--41492271 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
41492214 TTTGCTTTCT
41492224 TTATTTTATT-
1 TTATTTTATTA
41492234 TTA-TTTATTTA
1 TTATTTTA-TTA
*
41492245 GTATTTTATTAA
1 TTATTTTATT-A
41492257 TTATTTTATTA
1 TTATTTTATTA
41492268 TTAT
1 TTAT
41492272 GCTTCATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 4 0.12
10 5 0.16
11 9 0.28
12 14 0.44
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:41493402 original size:17 final size:18
Alignment explanation
Indices: 41493375--41493409 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41493365 ATGTAACTCA
*
41493375 CCTCACTCGACACTTCGG
1 CCTCACTCGACACATCGG
41493393 CCTC-CTCGACACATCGG
1 CCTCACTCGACACATCGG
41493410 AGTAGTCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.17, C:0.46, G:0.17, T:0.20
Consensus pattern (18 bp):
CCTCACTCGACACATCGG
Found at i:41493824 original size:6 final size:6
Alignment explanation
Indices: 41493815--41493879 Score: 67
Period size: 6 Copynumber: 10.5 Consensus size: 6
41493805 TGTTTATTTG
* * * *
41493815 TTTTCT TTTTAT TTTTTT ATTTTAT GTTTAT GTTTAT TTTTAT TTTTAGT
1 TTTTAT TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T
*
41493865 TTTTAT TGTTAT TTT
1 TTTTAT TTTTAT TTT
41493880 CGTGGACTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
6 39 0.78
7 11 0.22
ACGTcount: A:0.14, C:0.02, G:0.06, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:41493827 original size:15 final size:14
Alignment explanation
Indices: 41493802--41493861 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 14
41493792 ATGAGGACCA
*
41493802 TTATGTTTATTTGTT
1 TTATTTTTATTT-TT
*
41493817 TTCTTTTTATTTTT
1 TTATTTTTATTTTT
*
41493831 TTATTTTATGTTTATGT
1 TTATTTT-TATTT-T-T
41493848 TTATTTTTATTTTT
1 TTATTTTTATTTTT
41493862 AGTTTTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 9 0.24
15 15 0.41
16 5 0.14
17 8 0.22
ACGTcount: A:0.13, C:0.02, G:0.07, T:0.78
Consensus pattern (14 bp):
TTATTTTTATTTTT
Found at i:41493869 original size:25 final size:24
Alignment explanation
Indices: 41493821--41493879 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
41493811 TTTGTTTTCT
*
41493821 TTTTATTTTTTTATTTTATGTTTA
1 TTTTATTTTTATATTTTATGTTTA
*
41493845 TGTTTATTTTTAT-TTTTAGTTTTTA
1 T-TTTATTTTTATATTTTA-TGTTTA
41493870 TTGTTATTTT
1 TT-TTATTTT
41493880 CGTGGACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 7 0.23
25 23 0.77
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (24 bp):
TTTTATTTTTATATTTTATGTTTA
Found at i:41493869 original size:31 final size:33
Alignment explanation
Indices: 41493802--41493870 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 33
41493792 ATGAGGACCA
* *
41493802 TTATGTTTATTTGTTTTCTTTTTATTTTTTTATT
1 TTATGTTTA-TTGTTTTATTTTTATTTTTGTATT
41493836 TTATGTTTA-TG-TTTATTTTTATTTTTAGT-TT
1 TTATGTTTATTGTTTTATTTTTATTTTT-GTATT
41493867 TTAT
1 TTAT
41493871 TGTTATTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 20 0.62
32 3 0.09
34 9 0.28
ACGTcount: A:0.14, C:0.01, G:0.07, T:0.77
Consensus pattern (33 bp):
TTATGTTTATTGTTTTATTTTTATTTTTGTATT
Found at i:41497931 original size:2 final size:2
Alignment explanation
Indices: 41497919--41497951 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
41497909 ATGTTAGTGA
41497919 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41497952 GGTTTTAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41518484 original size:6 final size:6
Alignment explanation
Indices: 41518473--41518515 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
41518463 GAAGGGATGA
* * *
41518473 TGGGGT TGGGGT TGGGGT TGGGAT TGGGAT TGGGAT TGGGAT T
1 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT T
41518516 AAGGATGGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.09, C:0.00, G:0.56, T:0.35
Consensus pattern (6 bp):
TGGGAT
Found at i:41522071 original size:33 final size:33
Alignment explanation
Indices: 41522026--41522091 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
41522016 AAAAATTTTC
41522026 AACGCATCGTGTTGTGCTTGAATCCAAAGGAAG
1 AACGCATCGTGTTGTGCTTGAATCCAAAGGAAG
* * *
41522059 AACGCATTGTGTTGTGTTTGAATCCAAATGAAG
1 AACGCATCGTGTTGTGCTTGAATCCAAAGGAAG
41522092 CCTAAGTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (33 bp):
AACGCATCGTGTTGTGCTTGAATCCAAAGGAAG
Found at i:41528966 original size:24 final size:25
Alignment explanation
Indices: 41528920--41528966 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
41528910 CAAGAACTTT
* **
41528920 TAAATTATTTTTATTATTTTAAATA
1 TAAAATATTTTTATTATCATAAATA
41528945 TAAAATATTTTTA-TATCATAAA
1 TAAAATATTTTTATTATCATAAA
41528967 AACTAAAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TAAAATATTTTTATTATCATAAATA
Found at i:41529055 original size:23 final size:23
Alignment explanation
Indices: 41529028--41529098 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
41529018 ATTTGATTTG
*
41529028 ATTTAATGATAATATTTAGAATT
1 ATTTAGTGATAATATTTAGAATT
* *
41529051 CTTTAGTGATAATATTTAGGATT
1 ATTTAGTGATAATATTTAGAATT
*
41529074 ATTTAGTGATAATATTTAGGATT
1 ATTTAGTGATAATATTTAGAATT
41529097 AT
1 AT
41529099 CTTTCGCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (23 bp):
ATTTAGTGATAATATTTAGAATT
Found at i:41529092 original size:13 final size:13
Alignment explanation
Indices: 41529052--41529092 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
41529042 TTTAGAATTC
41529052 TTTAGTGATAATA
1 TTTAGTGATAATA
41529065 TTTAG-GAT--TA
1 TTTAGTGATAATA
41529075 TTTAGTGATAATA
1 TTTAGTGATAATA
41529088 TTTAG
1 TTTAG
41529093 GATTATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.28
11 3 0.12
12 3 0.12
13 12 0.48
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (13 bp):
TTTAGTGATAATA
Found at i:41532789 original size:18 final size:20
Alignment explanation
Indices: 41532754--41532790 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
41532744 GGATGCATAG
41532754 GAGTAAGGTTGCAACTTAGT
1 GAGTAAGGTTGCAACTTAGT
41532774 GAGT-AGGTTG-AACTTAG
1 GAGTAAGGTTGCAACTTAG
41532791 ATTACAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 6 0.35
20 4 0.24
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (20 bp):
GAGTAAGGTTGCAACTTAGT
Found at i:41533019 original size:31 final size:31
Alignment explanation
Indices: 41532957--41533020 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
41532947 GACATGTCAG
* **
41532957 TTGTAATATTTGTAAGTGTACAATGGGACAC
1 TTGTAATATTTGTAAATGTACAATGAAACAC
41532988 TTGTAATATTTGTAAATGTACAATGAAACAC
1 TTGTAATATTTGTAAATGTACAATGAAACAC
41533019 TT
1 TT
41533021 AGAGCAGTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (31 bp):
TTGTAATATTTGTAAATGTACAATGAAACAC
Found at i:41538244 original size:91 final size:92
Alignment explanation
Indices: 41538071--41538286 Score: 310
Period size: 91 Copynumber: 2.4 Consensus size: 92
41538061 TAATGTGGAG
* * * *
41538071 CATGCACCCGATTGTGCATGAAT-TTCAGGAGCTATTTTTCAGTTGGACATTCATGTATCTTTCA
1 CATGCACCCGATTGTGCATGAATGTT-GGGAGCTATTTTTCAGCTGGACATACATGTATCTTCCA
* *
41538135 GATTCAATGAAGCTACTTTAATGAAGAA
65 GATTCAACGAAGCTACTTTAAAGAAGAA
* * *
41538163 CATGCATCTGATTGTGCATGAATGTTGGGAGCTGTTTTT-AGCTGGACATACATGTATCTTCCAG
1 CATGCACCCGATTGTGCATGAATGTTGGGAGCTATTTTTCAGCTGGACATACATGTATCTTCCAG
41538227 ATTCAACGAAGCTACTTTAAAGAAGAA
66 ATTCAACGAAGCTACTTTAAAGAAGAA
* *
41538254 CATGCACCCGATTGTGCATGTATGTTGAGAGCT
1 CATGCACCCGATTGTGCATGAATGTTGGGAGCT
41538287 TGTTGGTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
91 76 0.69
92 32 0.29
93 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (92 bp):
CATGCACCCGATTGTGCATGAATGTTGGGAGCTATTTTTCAGCTGGACATACATGTATCTTCCAG
ATTCAACGAAGCTACTTTAAAGAAGAA
Found at i:41541562 original size:19 final size:20
Alignment explanation
Indices: 41541528--41541572 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
41541518 TGAAAGATTG
* *
41541528 AATATCTAAGAATAAAGGAA
1 AATATTTAAGAATAAAAGAA
*
41541548 AATATTTAA-AATAAAATAA
1 AATATTTAAGAATAAAAGAA
41541567 AATATT
1 AATATT
41541573 ACAACAGGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (20 bp):
AATATTTAAGAATAAAAGAA
Found at i:41542517 original size:194 final size:194
Alignment explanation
Indices: 41542188--41542579 Score: 766
Period size: 194 Copynumber: 2.0 Consensus size: 194
41542178 AATTTAGATG
*
41542188 AATTCGACAATAACTTTATCACAAGACCCCAAATACAAAGGATAACAATAACTCAGATTTAATTC
1 AATTCGACAATAACTTTATCACAAGACCCCAAATACAAAGGATAACAATAACTCAGATTTAATTA
41542253 AATTTCAGAAAAAGGGCATAATACAACTCAGATATGGCAGATTCCAGATAACTTAGATTTAATTA
66 AATTTCAGAAAAAGGGCATAATACAACTCAGATATGGCAGATTCCAGATAACTTAGATTTAATTA
*
41542318 TTACATAACATAGATGAACTCACATTAACAATTTCTTATGTTTCTTATAACTATGAATATGCCT
131 TTACATAACATAGATGAACTCACATTAACAATTTCTTATGTTTCTTATAACTATGAATACGCCT
41542382 AATTCGACAATAACTTTATCACAAGACCCCAAATACAAAGGATAACAATAACTCAGATTTAATTA
1 AATTCGACAATAACTTTATCACAAGACCCCAAATACAAAGGATAACAATAACTCAGATTTAATTA
41542447 AATTTCAGAAAAAGGGCATAATACAACTCAGATATGGCAGATTCCAGATAACTTAGATTTAATTA
66 AATTTCAGAAAAAGGGCATAATACAACTCAGATATGGCAGATTCCAGATAACTTAGATTTAATTA
41542512 TTACATAACATAGATGAACTCACATTAACAATTTCTTATGTTTCTTATAACTATGAATACGCCT
131 TTACATAACATAGATGAACTCACATTAACAATTTCTTATGTTTCTTATAACTATGAATACGCCT
41542576 AATT
1 AATT
41542580 TTAACACTAA
Statistics
Matches: 196, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 196 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30
Consensus pattern (194 bp):
AATTCGACAATAACTTTATCACAAGACCCCAAATACAAAGGATAACAATAACTCAGATTTAATTA
AATTTCAGAAAAAGGGCATAATACAACTCAGATATGGCAGATTCCAGATAACTTAGATTTAATTA
TTACATAACATAGATGAACTCACATTAACAATTTCTTATGTTTCTTATAACTATGAATACGCCT
Found at i:41545221 original size:20 final size:20
Alignment explanation
Indices: 41545187--41545243 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
41545177 CGTCCTTGGT
41545187 TCAGCTCACTT-GAGCTCAAG
1 TCAGCTCA-TTCGAGCTCAAG
*
41545207 TCAGTTCATTCGAGCTCAAG
1 TCAGCTCATTCGAGCTCAAG
41545227 TCAGCTCATTCGAGCTC
1 TCAGCTCATTCGAGCTC
41545244 GTTATTAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 32 0.94
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (20 bp):
TCAGCTCATTCGAGCTCAAG
Found at i:41554854 original size:13 final size:14
Alignment explanation
Indices: 41554836--41554867 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41554826 TTCATTAACT
41554836 CCCGATTC-ACTAA
1 CCCGATTCTACTAA
41554849 CCCGATTCTACTAA
1 CCCGATTCTACTAA
41554863 CCCGA
1 CCCGA
41554868 ATTTTAGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.28, C:0.41, G:0.09, T:0.22
Consensus pattern (14 bp):
CCCGATTCTACTAA
Found at i:41560765 original size:50 final size:50
Alignment explanation
Indices: 41560649--41560890 Score: 218
Period size: 50 Copynumber: 4.7 Consensus size: 50
41560639 GATAATAACA
* * ** * * *
41560649 TGCCAAGGCCATGTCCCAGACATGATCTTACATGGGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
41560698 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
41560748 TGCCCATGCCATGTCCCAGATATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * **
41560798 TGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
41560854 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
41560891 TCTCATTCCC
Statistics
Matches: 158, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.23
50 83 0.53
53 2 0.01
56 35 0.22
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:41561558 original size:38 final size:38
Alignment explanation
Indices: 41561514--41561597 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 38
41561504 ATCAATATTC
41561514 TAACACATGCATCCAATCAATCGGTAAATCATAAAAAT
1 TAACACATGCATCCAATCAATCGGTAAATCATAAAAAT
*
41561552 TAACACATGCATCCAATTAATCGGTAAATCATAAAAAT
1 TAACACATGCATCCAATCAATCGGTAAATCATAAAAAT
41561590 TAATCACA
1 TAA-CACA
41561598 ATAAACTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 40 0.91
39 4 0.09
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.25
Consensus pattern (38 bp):
TAACACATGCATCCAATCAATCGGTAAATCATAAAAAT
Found at i:41567654 original size:6 final size:6
Alignment explanation
Indices: 41567645--41567706 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
41567635 AAGAAAAAGA
* * *
41567645 AAAATC AAAATC AAAGTC AAAATG AAAAT- GAAA-- AAAATC AAAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC -AAAATC
41567691 AAAAATC AAAAT- AAAA
1 -AAAATC AAAATC AAAA
41567707 AAAACAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
4 3 0.06
5 7 0.15
6 25 0.52
7 13 0.27
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:41567706 original size:28 final size:28
Alignment explanation
Indices: 41567651--41567757 Score: 86
Period size: 28 Copynumber: 4.0 Consensus size: 28
41567641 AAGAAAAATC
* *
41567651 AAAATC-AAAGTCAAAATGAAAATGAAA
1 AAAATCAAAAATCAAAATCAAAATGAAA
41567678 AAAATCAAAAATCAAAAATCAAAAT-AAA
1 AAAATCAAAAATC-AAAATCAAAATGAAA
* * *
41567706 AAAAACAAAAA-GAAGAA--AGAA-G-AA
1 AAAATCAAAAATCAA-AATCAAAATGAAA
*
41567730 AAAATC-AAAATCAAGATCAAAATGAAA
1 AAAATCAAAAATCAAAATCAAAATGAAA
41567757 A
1 A
41567758 TGAGAAAAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
23 5 0.08
24 9 0.15
25 6 0.10
26 3 0.05
27 11 0.18
28 18 0.29
29 10 0.16
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.11
Consensus pattern (28 bp):
AAAATCAAAAATCAAAATCAAAATGAAA
Found at i:41567707 original size:6 final size:7
Alignment explanation
Indices: 41567677--41567701 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41567667 TGAAAATGAA
41567677 AAAAATC
1 AAAAATC
41567684 AAAAATC
1 AAAAATC
41567691 AAAAATC
1 AAAAATC
41567698 AAAA
1 AAAA
41567702 TAAAAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATC
Found at i:41567766 original size:50 final size:53
Alignment explanation
Indices: 41567671--41567784 Score: 137
Period size: 50 Copynumber: 2.2 Consensus size: 53
41567661 TCAAAATGAA
41567671 AATGAAAAAAATCAAAAATCAAAAATCAAAATAAAAAAAACAAAAAG-AAGAAAG
1 AATG-AAAAAATCAAAAATCAAAAATCAAAATAAAAAAAACAAAAAGAAAG-AAG
* * ** *
41567725 AA-GAAAAAATC-AAAATC-AAGATCAAAATGAAAATGAGAAAAAGAAAGAAG
1 AATGAAAAAATCAAAAATCAAAAATCAAAATAAAAAAAACAAAAAGAAAGAAG
41567775 AATGAAAAAA
1 AATGAAAAAA
41567785 GAGAAATCTA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
50 26 0.49
51 16 0.30
52 8 0.15
53 1 0.02
54 2 0.04
ACGTcount: A:0.73, C:0.06, G:0.11, T:0.10
Consensus pattern (53 bp):
AATGAAAAAATCAAAAATCAAAAATCAAAATAAAAAAAACAAAAAGAAAGAAG
Found at i:41568708 original size:7 final size:7
Alignment explanation
Indices: 41568688--41568756 Score: 97
Period size: 7 Copynumber: 10.0 Consensus size: 7
41568678 ACTCTGAGTA
*
41568688 AAAAATA
1 AAAAATG
41568695 AATAAATG
1 AA-AAATG
41568703 AAAAATG
1 AAAAATG
*
41568710 -AGAATG
1 AAAAATG
41568716 AAAAATG
1 AAAAATG
41568723 AAAAATG
1 AAAAATG
41568730 -AAAATG
1 AAAAATG
41568736 AAAAATG
1 AAAAATG
41568743 AAAAATG
1 AAAAATG
41568750 AAAAATG
1 AAAAATG
41568757 GAGAGGCTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
6 11 0.20
7 39 0.70
8 6 0.11
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (7 bp):
AAAAATG
Found at i:41568723 original size:20 final size:20
Alignment explanation
Indices: 41568698--41568753 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
41568688 AAAAATAAAT
*
41568698 AAATGAAAAATGAGAATGAA
1 AAATGAAAAATGAAAATGAA
41568718 AAATGAAAAATGAAAATGAA
1 AAATGAAAAATGAAAATGAA
41568738 AAATGAAAAATGAAAA
1 AAATGAAAAATGAAAA
41568754 ATGGAGAGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (20 bp):
AAATGAAAAATGAAAATGAA
Found at i:41568740 original size:14 final size:14
Alignment explanation
Indices: 41568688--41568756 Score: 97
Period size: 13 Copynumber: 5.0 Consensus size: 14
41568678 ACTCTGAGTA
*
41568688 AAAAATAAATAAATG
1 AAAAATGAA-AAATG
*
41568703 AAAAATG-AGAATG
1 AAAAATGAAAAATG
41568716 AAAAATGAAAAATG
1 AAAAATGAAAAATG
41568730 -AAAATGAAAAATG
1 AAAAATGAAAAATG
41568743 AAAAATGAAAAATG
1 AAAAATGAAAAATG
41568757 GAGAGGCTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
13 24 0.49
14 19 0.39
15 6 0.12
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (14 bp):
AAAAATGAAAAATG
Found at i:41570236 original size:44 final size:44
Alignment explanation
Indices: 41570126--41570832 Score: 355
Period size: 44 Copynumber: 15.9 Consensus size: 44
41570116 TCGCATCAGG
* *
41570126 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAG--AATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCAA----AGA
* * *
41570172 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCAAAGA
* *
41570216 TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAG--ATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCAAAG--A
* ** ***
41570260 TCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCAAA-GA
* * ** * * * *
41570304 TCTTGTCTCTCTGA-AGTTACAGCAGAGTAGATCGCA-TC--AGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGTAGATTGAAGCCAAAGA
* **
41570345 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG--AATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCAA----AGA
* * *
41570391 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCAAAGA
* * * * * **
41570435 TCTTATCTCCCTGAGATTACAGCGAAGCAGATCGAAGAC-ACTA
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCAAAGA
* * ** ***
41570478 TCCTATCTCCTTGA-AGTTACAGTGGAGCGGATT-AAAATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGTAGATTGAAGCCAAA-GA
* * * * * *
41570522 TCTTATCTCTCTAACG-TTACAGTAGAGTAGATCGCA-TC-AAG-
1 TCTTATCTCCCTGA-GATTACAGTGGAGTAGATTGAAGCCAAAGA
* * ***
41570563 TCTTATCTCCCTGAGGTTACAGTAGAGTAGACCAAAG--AATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCAA----AGA
* *
41570609 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCAAAGA
* * *
41570653 TCTTATATCCCTGAGATTACAGTGGAGTAGATTGAAGCTAGTA-A
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCA-AAGA
* * * * ***
41570697 TCCTATCTCTCTGA-AGTTACAGTTGAGTGGATT-AAAATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGTAGATTGAAGCCAAA-GA
*
41570741 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCACATCAGATTGAAGCCAAAGA
1 TCTTATCTCCCTGAGA-TTACAGT-G-G-AG------T-AGATTGAAGCCAAAGA
*
41570795 TCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGC
1 TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGC
41570833 TAGTAATCCT
Statistics
Matches: 513, Mismatches: 97, Indels: 104
0.72 0.14 0.15
Matches are distributed among these distances:
40 1 0.00
41 59 0.12
42 10 0.02
43 37 0.07
44 251 0.49
45 8 0.02
46 105 0.20
47 2 0.00
48 4 0.01
51 2 0.00
52 1 0.00
53 2 0.00
54 25 0.05
55 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCCAAAGA
Found at i:41570324 original size:88 final size:90
Alignment explanation
Indices: 41570126--41570772 Score: 297
Period size: 87 Copynumber: 7.4 Consensus size: 90
41570116 TCGCATCAGG
* * * * * *
41570126 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGCGGAGTAGATTGAAGAATGTCAGATCCTATCTCCCTGAGATTA
* **
41570191 CAGTGGAGCAGATTGAAGCCAGAGA
66 CAGTGGAGCAGATTAAAGAAAGAGA
41570216 TCTTATCTCCCTG-AGATTACAGCGGAGTAGATTGAAG-ATAGT-A-ATCCTATCTCCCTGAGAT
1 TCTTATCTCCCTGAAG-TTACAGCGGAGTAGATTGAAGAAT-GTCAGATCCTATCTCCCTGAGAT
* *
41570277 TACAGTGGAGCGGATTAAAATAAAG-GA
64 TACAGTGGAGCAGATT-AAAGAAAGAGA
* * * * * * * *
41570304 TCTTGTCTCTCTGAAGTTACAGCAGAGTAGA-T--CGCA--TCAGGTCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGCGGAGTAGATTGAAGAATGTCAGATCCTATCTCCCTGAGATTA
* *** **
41570364 CAGTGGAGTAGACCGAAGAATTTCAGA
66 CAGTGGAGCAGATTAAAGAA--AGAGA
* * * * *
41570391 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-G--AGATCTTATCTCCCTGAGATT
1 TCTTATCTCCCTGAAGTTACAGCGGAGTAGATTGAAG-AATGTCAGATCCTATCTCCCTGAGATT
* * ** * **
41570453 ACAGCGAAGCAGATCGAAGACA-CTA
65 ACAGTGGAGCAGATTAAAGAAAGAGA
* * * ** ** * * *
41570478 TCCTATCTCCTTGAAGTTACAGTGGAGCGGATT-AA-AAT-AAAGGATCTTATCTCTCTAACG-T
1 TCTTATCTCCCTGAAGTTACAGCGGAGTAGATTGAAGAATGTCA-GATCCTATCTCCCTGA-GAT
* * *** **
41570539 TACAGTAGAGTAGATCGCA-TCA-AG-
64 TACAGTGGAGCAGATTAAAGAAAGAGA
* ** *** * * *
41570563 TCTTATCTCCCTGAGGTTACAGTAGAGTAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAAGTTACAGCGGAGTAGATTGAAGAATGTCAGATCCTATCTCCCTGAGATTA
* *
41570628 CAGTGGAGCAGATTGAAGCCAA-AGA
66 CAGTGGAGCAGATTAAAG-AAAGAGA
* * * *
41570653 TCTTATATCCCTG-AGATTACAGTGGAGTAGATTGAAG-CTAGT-A-ATCCTATCTCTCTGA-AG
1 TCTTATCTCCCTGAAG-TTACAGCGGAGTAGATTGAAGAAT-GTCAGATCCTATCTCCCTGAGA-
* ** *
41570713 TTACAGTTGAGTGGATTAAAATAAAG-GA
63 TTACAGTGGAGCAGATT-AAAGAAAGAGA
* **
41570741 TCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
1 TCTTATCTCCCTGAAGTTACAGCGGAGTAGAT
41570773 CACATCAGAT
Statistics
Matches: 428, Mismatches: 96, Indels: 68
0.72 0.16 0.11
Matches are distributed among these distances:
83 1 0.00
84 6 0.01
85 53 0.12
86 9 0.02
87 120 0.28
88 118 0.28
89 20 0.05
90 99 0.23
91 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (90 bp):
TCTTATCTCCCTGAAGTTACAGCGGAGTAGATTGAAGAATGTCAGATCCTATCTCCCTGAGATTA
CAGTGGAGCAGATTAAAGAAAGAGA
Found at i:41570419 original size:219 final size:219
Alignment explanation
Indices: 41570040--41570780 Score: 1236
Period size: 219 Copynumber: 3.4 Consensus size: 219
41570030 AGAATTTCAG
* *
41570040 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAATGATCTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
*
41570105 AGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAGAATTTCA
66 AGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCA
41570170 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTA
131 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTA
41570235 CAGCGGAGTAGATTGAAGATAGTA
196 CAGCGGAGTAGATTGAAGATAGTA
*
41570259 ATCCTATCTCCCTG-AGATTACAGTGGAGCGGATTAAAATAAAGGATCTTGTCTCTCTGAAGTTA
1 ATCCTATCTCCCTGAAG-TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTA
41570323 CAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
65 CAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
41570388 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATT
130 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATT
* * * * *
41570453 ACAGCGAAGCAGATCGAAGACACT-
195 ACAGCGGAGTAGATTGAAGATAGTA
*
41570477 ATCCTATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCT-AACGTTA
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAA-GTTA
* * * *
41570541 CAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGTAGAGTAGACCAAAGAATTTC
65 CAGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
* *
41570606 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAAGATCTTATATCCCTGAGATT
130 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATT
* *
41570671 ACAGTGGAGTAGATTGAAGCTAGTA
195 ACAGCGGAGTAGATTGAAGATAGTA
* * *
41570696 ATCCTATCTCTCTGAAGTTACAGTTGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
* *
41570761 AGTAGAGTAGATCACATCAG
66 AGCAGAGTAGATCGCATCAG
41570781 ATTGAAGCCA
Statistics
Matches: 487, Mismatches: 30, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
217 2 0.00
218 199 0.41
219 284 0.58
220 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (219 bp):
ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTAC
AGCAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCA
GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTA
CAGCGGAGTAGATTGAAGATAGTA
Found at i:41570524 original size:131 final size:130
Alignment explanation
Indices: 41570126--41570690 Score: 303
Period size: 131 Copynumber: 4.3 Consensus size: 130
41570116 TCGCATCAGG
* * *
41570126 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACTGAAG-AATTTCAGATCTTATCTCCCTGAGGTT
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCA----AG-TCTTATCTCCCTGAGATT
*** * * * * *
41570190 ACAGTG-GAGCAGATTGAAGCCA-GAGATCTTATCTCCCTG-AGATTACAGCGGAGTAGATTGAA
61 ACAG-GAGAGCAGACCAAAG-AATCAGATCCTATCTCCCTGAAG-TTACAGTGGAGCAGATTGAA
* * *
41570252 GATAGTA-A
123 AACA-AAGA
* * ** * *** * *
41570260 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTGTCTCTCTGA-AGTTAC
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCAA-G-TCTTATCTCCCTGAGA-TTAC
* * * * * * * * ** *
41570324 AGCAGAGTAGATC---GCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATT
63 AGGAGAGCAGACCAAAGAATCAGATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAA-AA-C
**
41570386 TCAGA
126 AAAGA
*
41570391 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCA-AG-TCTTATCTCCCTGAGATTACA
* * * * * *
41570456 GCGA-AGCAGATCGAAG-A-CACTATCCTATCTCCTTGAAGTTACAGTGGAGCGGATT-AAAATA
64 G-GAGAGCAGACCAAAGAATCA-GATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAAACA
41570517 AAGGA
127 AA-GA
* * * * * * * * *
41570522 TCTTATCTCTCTAACGTTACAGTAGAGTAGATCGCA-TCAAGTCTTATCTCCCTGAGGTTACAGT
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCAAGTCTTATCTCCCTGAGATTACAGG
* * * **
41570586 AGAGTAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAA
66 AGAGCAGACCAAAGAA--TCAGATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAAACAAA
41570651 GA
129 GA
* *
41570653 TCTTATATCCCTGAGATTACAGTGGAGTAGATTGAAGC
1 TCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGC
41570691 TAGTAATCCT
Statistics
Matches: 333, Mismatches: 74, Indels: 50
0.73 0.16 0.11
Matches are distributed among these distances:
127 1 0.00
128 32 0.10
129 36 0.11
130 7 0.02
131 156 0.47
132 41 0.12
133 27 0.08
134 31 0.09
135 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (130 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGTAGATTGAAGCCAAGTCTTATCTCCCTGAGATTACAGG
AGAGCAGACCAAAGAATCAGATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAAACAAAGA
Found at i:41570892 original size:142 final size:142
Alignment explanation
Indices: 41570636--41571062 Score: 605
Period size: 142 Copynumber: 3.0 Consensus size: 142
41570626 TACAGTGGAG
*
41570636 CAGATTGAAGCCAAAGATCTTATATCCCTGAGATTACAGTGGAGTAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAAAGATCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCTAGTAATCCT
41570701 ATCTCTCTGAAGTTACAGTTGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCTCTGAAGTTACAGTTGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
41570766 AGTAGATCACAT
131 AGTAGATCACAT
*
41570778 CAGATTGAAGCCAAAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAAAGATCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCTAGTAATCCT
*
41570843 ATCTCTCTGAAGTTACAGTTGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGCTACAGTAG
66 ATCTCTCTGAAGTTACAGTTGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
41570908 AGTAGATCACAT
131 AGTAGATCACAT
* * * * * * *
41570920 CAGATTGAAGCCGATA-AT-TCTATCTCCCTGA-AGTTGCATTGGAGCAGA-CGAAAG-AAATCA
1 CAGATTGAAGCC-AAAGATCT-TATCTCCCTGAGA-TTACAGTGGAGTAGATTG-AAGCTAGT-A
* * * * *
41570980 ATCCTATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAACCACA-GATCTTATCTCTCTGAAGTTA
61 ATCCTATCTCTCTGAAGTTACAGTTGAGTGGATTAAAA-TAAAGGATCTTATCTCTCTGAAGTTA
* *
41571044 CAGTAGAGCAGATCGCAT
125 CAGTAGAGTAGATCACAT
41571062 C
1 C
41571063 CAGCCTTATC
Statistics
Matches: 260, Mismatches: 19, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
141 5 0.02
142 251 0.97
143 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (142 bp):
CAGATTGAAGCCAAAGATCTTATCTCCCTGAGATTACAGTGGAGTAGATTGAAGCTAGTAATCCT
ATCTCTCTGAAGTTACAGTTGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATCACAT
Found at i:41570892 original size:186 final size:176
Alignment explanation
Indices: 41570418--41570914 Score: 492
Period size: 186 Copynumber: 2.8 Consensus size: 176
41570408 TACAGTGGAG
* *
41570418 CAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGAAGCAGATCGAAGACACT-ATCCT
1 CAGATTGAAGCCA-AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CA-TAATCCT
*
41570482 ATCTCCTTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCT-AACGTTACAGTA
63 ATCTCC-TGAAGTTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAA-GTTACAGTA
*** * *
41570546 GAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGTAGAGTAGACCA
126 GAGTAGATAAAATAAAGTCTTATCTCCCTGAAGTTACAGTAGAGTAGACCA
** * * * *
41570597 -A-A--GAATTTC-AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAAAGATCTT
1 CAGATTGAA-GCCAAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CATA-ATCCT
* * ** * *
41570657 ATATCCCTG-AGATTACAGTGGAGTAGATTGAAGCT--AGTAATCCTATCTCTCTGAAGTTACAG
63 ATCT-CCTGAAG-TTACAGTGGAGTGGATT-AAAATAAAG-GATCTTATCTCTCTGAAGTTACAG
* * *
41570719 TTGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACA
124 TAGAGTAGA-TAAAATAAA-G-TCTTATCTCCCTGAAGTTACAGTAGAGTAGA-C-CA
*
41570777 TCAGATTGAAGCCAAAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCC
1 -CAGATTGAAGCC-AAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGC-A-TAATCC
* *
41570842 TATCTCTCTGAAGTTACAGTTGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGCTACAGTA
62 TATCTC-CTGAAGTTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
41570907 GAGTAGAT
126 GAGTAGAT
41570915 CACATCAGAT
Statistics
Matches: 251, Mismatches: 41, Indels: 46
0.74 0.12 0.14
Matches are distributed among these distances:
174 42 0.17
175 53 0.21
176 13 0.05
177 2 0.01
178 30 0.12
179 1 0.00
180 2 0.01
182 1 0.00
183 1 0.00
184 1 0.00
185 9 0.04
186 91 0.36
187 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (176 bp):
CAGATTGAAGCCAAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCATAATCCTATC
TCCTGAAGTTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
GATAAAATAAAGTCTTATCTCCCTGAAGTTACAGTAGAGTAGACCA
Found at i:41571032 original size:44 final size:44
Alignment explanation
Indices: 41570940--41571313 Score: 228
Period size: 44 Copynumber: 8.6 Consensus size: 44
41570930 CCGATAATTC
* * ** * *
41570940 TATCTCCCTGAAGTTGCATTGGAGCAGACGAAAGA-AATCA-ATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAA-ACCA-CAGATCT
* *
41570984 TATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* * *** * *
41571028 TATCTCTCTGAAGTTACAGTAGAGCAGA-TCGCATC-CAG-CCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* * * ** * *
41571069 TATCTCCCTAAAGTTGCAGTGGAGTAGACGAAAGA-AATCA-ATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAA-ACCA-CAGATCT
* * *
41571113 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* * ** ** * * *
41571157 TATCTATCTAAAGTTGCAGTGGAGCAGACGAAAAAAATAAATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* * *
41571201 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* ** *** *
41571245 TATTTCTCTGAAGTTGCAGCAGAGCAGA-TCGCATC-CA-ATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
* *
41571286 TATCTCCCTGAAGTTGCAGTGGAACAGA
1 TATCTCTCTGAAGTTGCAGTGGAGCAGA
41571314 CAAAAGAAAC
Statistics
Matches: 247, Mismatches: 74, Indels: 21
0.72 0.22 0.06
Matches are distributed among these distances:
41 52 0.21
42 5 0.02
43 13 0.05
44 177 0.72
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (44 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCT
Found at i:41571117 original size:85 final size:88
Alignment explanation
Indices: 41571028--41571247 Score: 284
Period size: 88 Copynumber: 2.5 Consensus size: 88
41571018 CCACAGATCT
* * *** * *
41571028 TATCTCTCTGAAGTTACAGTAGAGCAGA-TCGCATC-CAG-CCTTATCTCCCTAAAGTTGCAGTG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGACCTTATCTACCTAAAGTTGCAGTG
* * *
41571090 GAGTAGACGAAAGAAATCAATCC
66 GAGCAGACGAAAAAAATAAATCC
* * *
41571113 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTATCTAAAGTTGCAGTG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGACCTTATCTACCTAAAGTTGCAGTG
41571178 GAGCAGACGAAAAAAATAAATCC
66 GAGCAGACGAAAAAAATAAATCC
* *
41571201 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAGATCTTAT
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGACCTTAT
41571248 TTCTCTGAAG
Statistics
Matches: 119, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
85 25 0.21
86 3 0.03
87 3 0.03
88 88 0.74
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (88 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACCACAGACCTTATCTACCTAAAGTTGCAGTG
GAGCAGACGAAAAAAATAAATCC
Found at i:41571171 original size:129 final size:129
Alignment explanation
Indices: 41570940--41571184 Score: 400
Period size: 129 Copynumber: 1.9 Consensus size: 129
41570930 CCGATAATTC
* * * *
41570940 TATCTCCCTGAAGTTGCATTGGAGCAGACGAAAGAAATCAATCCTATCTCTCTGAAGTTGCAGTA
1 TATCTCCCTAAAGTTGCAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTA
* *
41571005 GAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCATCCAGCCT
66 GAGCGGATTAAAACCACAGATCTTATCTATCTAAAGTTACAGTAGAGCAGATCGCATCCAGCCT
* *
41571069 TATCTCCCTAAAGTTGCAGTGGAGTAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTG
1 TATCTCCCTAAAGTTGCAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTA
* *
41571134 GAGCGGATTAAAACCACAGATCTTATCTATCTAAAGTTGCAGTGGAGCAGA
66 GAGCGGATTAAAACCACAGATCTTATCTATCTAAAGTTACAGTAGAGCAGA
41571185 CGAAAAAAAT
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 106 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (129 bp):
TATCTCCCTAAAGTTGCAGTGGAGCAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAGTA
GAGCGGATTAAAACCACAGATCTTATCTATCTAAAGTTACAGTAGAGCAGATCGCATCCAGCCT
Found at i:41571175 original size:88 final size:88
Alignment explanation
Indices: 41571067--41571272 Score: 331
Period size: 88 Copynumber: 2.3 Consensus size: 88
41571057 CGCATCCAGC
* * * *
41571067 CTTATCTCCCTAAAGTTGCAGTGGAGTAGACGAAAGAAATCAATCCTATCTCCCTGAAGTTACAG
1 CTTATCTCTCTAAAGTTGCAGTGGAGCAGACGAAAAAAATAAATCCTATCTCCCTGAAGTTACAG
41571132 TGGAGCGGATTAAAACCACAGAT
66 TGGAGCGGATTAAAACCACAGAT
*
41571155 CTTATCTATCTAAAGTTGCAGTGGAGCAGACGAAAAAAATAAATCCTATCTCCCTGAAGTTACAG
1 CTTATCTCTCTAAAGTTGCAGTGGAGCAGACGAAAAAAATAAATCCTATCTCCCTGAAGTTACAG
41571220 TGGAGCGGATTAAAACCACAGAT
66 TGGAGCGGATTAAAACCACAGAT
* * **
41571243 CTTATTTCTCTGAAGTTGCAGCAGAGCAGA
1 CTTATCTCTCTAAAGTTGCAGTGGAGCAGA
41571273 TCGCATCCAA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 108 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (88 bp):
CTTATCTCTCTAAAGTTGCAGTGGAGCAGACGAAAAAAATAAATCCTATCTCCCTGAAGTTACAG
TGGAGCGGATTAAAACCACAGAT
Found at i:41573635 original size:108 final size:110
Alignment explanation
Indices: 41573437--41573744 Score: 475
Period size: 108 Copynumber: 2.8 Consensus size: 110
41573427 CAAAAAACAA
*
41573437 AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAATCATGCCCTAAGGTGCTG
1 AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
41573502 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCC-TTTT
66 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
* * *
41573546 AAAAATTT-TAAATAAGGTAATGTTTTGAGTTTGGAAATTTGAGAAAACATGCCCTAAGGTGCTG
1 AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
*
41573610 GGTGTCGATTTTTCTCGTTCAACCAAATTGCTTAATATCCTTTTT
66 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
** *
41573655 AAAAATTTCA-AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GGACGTGCCCTAAGGTGCT
1 AAAAATTT-ATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* *
41573718 GGGTTTCGA--TTTCTCGTTTAACCAAAT
65 GGGTGTCGATTTTTCTCGTTCAACCAAAT
41573745 TGCCAAATAT
Statistics
Matches: 183, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
107 17 0.09
108 91 0.50
109 44 0.24
110 31 0.17
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (110 bp):
AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTT
Found at i:41574818 original size:33 final size:33
Alignment explanation
Indices: 41574756--41574837 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
41574746 AGTGCCGTAA
* *
41574756 CCCAGCTATGGTCTTATCATTAGAATGCCATAG
1 CCCAACTATGGTCTTATCATTAAAATGCCATAG
*
41574789 CCCAACTATGGTCTTAT-A-TAAACACTGCCATGG
1 CCCAACTATGGTCTTATCATTAAA-A-TGCCATAG
* *
41574822 TCCAACCATGGTCTTA
1 CCCAACTATGGTCTTA
41574838 CGTCTATAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 3 0.07
32 2 0.05
33 37 0.88
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (33 bp):
CCCAACTATGGTCTTATCATTAAAATGCCATAG
Done.