Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 124 of 284
Found at i:41308332 original size:80 final size:79
Alignment explanation
Indices: 41308199--41308418 Score: 268
Period size: 80 Copynumber: 2.8 Consensus size: 79
41308189 TATTCGAATG
* * * *
41308199 ATATCCGGGCTAAGTCCCAAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGG-CTAAGATCCCGAAGGC
* *
41308263 ATTTGTGCGAGTTG-CT
64 ATTTATGCGAG-TGACC
*
41308279 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGAGCTAAG-TCCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCG-GCTAAGATCCCGAAGGC
*
41308343 ATTTATGCTAGTGACC
64 ATTTATGCGAGTGACC
* * *
41308359 ATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCCGGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGCTAAGATCCCGAAG
41308419 ATACTTGGGT
Statistics
Matches: 123, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
78 13 0.11
79 21 0.17
80 88 0.72
81 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGCTAAGATCCCGAAGGCAT
TTATGCGAGTGACC
Found at i:41312543 original size:46 final size:44
Alignment explanation
Indices: 41312437--41312653 Score: 193
Period size: 46 Copynumber: 4.7 Consensus size: 44
41312427 ACATAATCGT
* *
41312437 GCCGATGTCATGTCCCAGACATGGTCTTACACTGACACATCTCGCA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCATATCTCG-AG
* * * *
41312483 GCTGATACATGTCCCAAACATGTCTTACACTGGCTTATGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC--ATATCTCGAG
* * *
41312529 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCA-T-ATCTCGAG
* * * * * *
41312575 TCCGATGCCATGTCCCAGACATGGTCTTACACTGTCTCTCATATTGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGC-AT-ATCTCGAG
41312623 GCCGATGCATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
41312654 AGCTCACACA
Statistics
Matches: 142, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
44 13 0.09
45 15 0.11
46 64 0.45
47 28 0.20
48 22 0.15
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.28
Consensus pattern (44 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCATATCTCGAG
Found at i:41312602 original size:94 final size:92
Alignment explanation
Indices: 41312437--41312661 Score: 262
Period size: 94 Copynumber: 2.4 Consensus size: 92
41312427 ACATAATCGT
*
41312437 GCCGATGTCATGTCCCAGACATGGTCTTACACT-G-ACACATCTCGCAGCTGATACATGTCCCAA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACACATCTCGCAGCCGATACATGTCCCAA
*
41312500 ACATGTCTTACACTGGCT-T-ATGTCTCGAG
64 ACATGTCTTACACTGGCTCTCATAT-T-GAG
* * * * *
41312529 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCG-ATTCCGATGCCATGTCCCAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACACATCTCGCA-GCCGAT-ACATGTCCCAA
* *
41312593 ACATGGTCTTACACTGTCTCTCATATTGTG
64 ACAT-GTCTTACACTGGCTCTCATATTGAG
*
41312623 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCACA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACACA
41312662 CAAGTGACCC
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
90 10 0.09
91 16 0.14
92 19 0.17
93 13 0.11
94 51 0.45
95 2 0.02
96 3 0.03
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.28
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCACACATCTCGCAGCCGATACATGTCCCAAAC
ATGTCTTACACTGGCTCTCATATTGAG
Found at i:41313014 original size:30 final size:30
Alignment explanation
Indices: 41312978--41313035 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
41312968 AAATTTACAC
*
41312978 CTTTGGTAAAATGACCATTTTGCCCCTAGA
1 CTTTGGTAAAATGACAATTTTGCCCCTAGA
41313008 CTTTGGTAAAATGACAATTTTGCCCCTA
1 CTTTGGTAAAATGACAATTTTGCCCCTA
41313036 TGCTCGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (30 bp):
CTTTGGTAAAATGACAATTTTGCCCCTAGA
Found at i:41314705 original size:107 final size:109
Alignment explanation
Indices: 41314492--41314748 Score: 331
Period size: 107 Copynumber: 2.4 Consensus size: 109
41314482 TCAGTATGCT
* * * **
41314492 CACACAGCCT-AGCACACGAGCGTGTGGTTTGGCCGTGTGACCCAAGTTAGGGAGTTACACGGGC
1 CACACGGCCTAAG-ACACGAGCATGTGGCTTGGCCGTGTGACCCAAGTTAGGGAGTTACAAAGGC
41314556 ACAGACACAGTCTAGGACACGACCGTGTGTCTCAATTTTGAATGTC
65 ACAGA-ACAGTCTAGGACACGACCGTGTGTCTCAATTTTGAATGTC
* **
41314602 CATATTGCCTAAGACACGAGCATGTGGCTTGGCCGT-TGACCCAAGTTAGGGAGTTACAAAGGCA
1 CACACGGCCTAAGACACGAGCATGTGGCTTGGCCGTGTGACCCAAGTTAGGGAGTTACAAAGGCA
* * * *
41314666 CAG-ACAGTCTGGGACATGGCCGTGTGTCTCTATTTTGAATGTC
66 CAGAACAGTCTAGGACACGACCGTGTGTCTCAATTTTGAATGTC
* ** *
41314709 CACACGGCCTAAGACACGAGCGTGTCTCTTGGTCGTGTGA
1 CACACGGCCTAAGACACGAGCATGTGGCTTGGCCGTGTGA
41314749 GTCACACGGC
Statistics
Matches: 127, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
107 65 0.51
108 3 0.02
109 29 0.23
110 28 0.22
111 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (109 bp):
CACACGGCCTAAGACACGAGCATGTGGCTTGGCCGTGTGACCCAAGTTAGGGAGTTACAAAGGCA
CAGAACAGTCTAGGACACGACCGTGTGTCTCAATTTTGAATGTC
Found at i:41316252 original size:16 final size:16
Alignment explanation
Indices: 41316231--41316261 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41316221 CATATTAGAG
41316231 CATATAAATTTGAAAT
1 CATATAAATTTGAAAT
*
41316247 CATATATATTTGAAA
1 CATATAAATTTGAAA
41316262 AAAATTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
CATATAAATTTGAAAT
Found at i:41316371 original size:11 final size:10
Alignment explanation
Indices: 41316355--41316425 Score: 58
Period size: 9 Copynumber: 7.2 Consensus size: 10
41316345 ATTATGATAT
41316355 AATTTTTTAA
1 AATTTTTTAA
*
41316365 AAATTTTT-A
1 AATTTTTTAA
*
41316374 ACTTTTTTATA
1 AATTTTTTA-A
*
41316385 TATTTTTT-A
1 AATTTTTTAA
41316394 AATTTTTTGAA
1 AATTTTTT-AA
*
41316405 AATTTTATAA
1 AATTTTTTAA
*
41316415 TA-TTTTTAA
1 AATTTTTTAA
41316424 AA
1 AA
41316426 AATATAAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
9 22 0.47
10 10 0.21
11 15 0.32
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:41316410 original size:18 final size:18
Alignment explanation
Indices: 41316355--41316437 Score: 67
Period size: 20 Copynumber: 4.3 Consensus size: 18
41316345 ATTATGATAT
41316355 AATTTTTTAAAAATTTTTA
1 AATTTTTTAAAAA-TTTTA
* **
41316374 ACTTTTTTATATATTTTTTA
1 AATTTTTTA-A-AAATTTTA
*
41316394 AATTTTTTGAAAATTTTA
1 AATTTTTTAAAAATTTTA
* *
41316412 TAATATTTTTAAAAAATATA
1 -AAT-TTTTTAAAAATTTTA
41316432 AATTTT
1 AATTTT
41316438 GGAATTTTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
18 9 0.18
19 15 0.30
20 25 0.50
21 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (18 bp):
AATTTTTTAAAAATTTTA
Found at i:41316426 original size:20 final size:19
Alignment explanation
Indices: 41316352--41316426 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
41316342 ATTATTATGA
41316352 TATAATTTTTTAAAAATTT
1 TATAATTTTTTAAAAATTT
* *
41316371 T-TAACTTTTTTATATATTT
1 TATAA-TTTTTTAAAAATTT
* *
41316390 TTTAAATTTTTTGAAAATTT
1 TAT-AATTTTTTAAAAATTT
41316410 TATAATATTTTTAAAAA
1 TATAAT-TTTTTAAAAA
41316427 ATATAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 3 0.07
19 17 0.38
20 23 0.51
21 2 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (19 bp):
TATAATTTTTTAAAAATTT
Found at i:41316460 original size:27 final size:28
Alignment explanation
Indices: 41316430--41316484 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
41316420 TTAAAAAATA
**
41316430 TAAATTTTGGAATTT-TTATAAATATTT
1 TAAATTTTAAAATTTATTATAAATATTT
*
41316457 TAAATTTTAAAATTTATTTTAAATATTT
1 TAAATTTTAAAATTTATTATAAATATTT
41316485 GAAAATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
TAAATTTTAAAATTTATTATAAATATTT
Found at i:41316464 original size:18 final size:18
Alignment explanation
Indices: 41316404--41316480 Score: 52
Period size: 18 Copynumber: 4.2 Consensus size: 18
41316394 AATTTTTTGA
41316404 AAATTTTAT-AATATTTTT
1 AAATTTTATAAATA-TTTT
*** *
41316422 AAAAAATATAAAT-TTTGG
1 AAATTTTATAAATATTT-T
*
41316440 AATTTTTATAAATATTTT
1 AAATTTTATAAATATTTT
41316458 AAATTTTA-AAATTTATTTT
1 AAATTTTATAAA--TATTTT
41316477 AAAT
1 AAAT
41316481 ATTTGAAAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
17 6 0.14
18 22 0.50
19 16 0.36
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
AAATTTTATAAATATTTT
Found at i:41316474 original size:19 final size:20
Alignment explanation
Indices: 41316452--41316496 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
41316442 TTTTTATAAA
41316452 TATTTTAAAT-TTT-AAAATT
1 TATTTTAAATATTTGAAAA-T
41316471 TATTTTAAATATTTGAAAAT
1 TATTTTAAATATTTGAAAAT
41316491 TATTTT
1 TATTTT
41316497 GAACTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.42
20 10 0.42
21 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTTTAAATATTTGAAAAT
Found at i:41327299 original size:22 final size:22
Alignment explanation
Indices: 41327274--41327321 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
41327264 AAATTCATAA
41327274 AATTAAAAAAGAA-AAACGAATC
1 AATTAAAAAAGAATAAA-GAATC
* **
41327296 AATTCAAAATTAATAAAGAATC
1 AATTAAAAAAGAATAAAGAATC
41327318 AATT
1 AATT
41327322 CATTATCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.23
Consensus pattern (22 bp):
AATTAAAAAAGAATAAAGAATC
Found at i:41327332 original size:22 final size:22
Alignment explanation
Indices: 41327291--41327333 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41327281 AAAGAAAAAC
*
41327291 GAATCAATTCAAAATTAATAAA
1 GAATCAATTCAAAATCAATAAA
**
41327313 GAATCAATTCATTATCAATAA
1 GAATCAATTCAAAATCAATAA
41327334 TTCAACATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (22 bp):
GAATCAATTCAAAATCAATAAA
Found at i:41330594 original size:3 final size:3
Alignment explanation
Indices: 41330586--41330637 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
41330576 TTTAGGGTTT
* *
41330586 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG GAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41330634 AAG A
1 AAG A
41330638 GAAAAAATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41331170 original size:3 final size:3
Alignment explanation
Indices: 41331162--41331987 Score: 1643
Period size: 3 Copynumber: 275.3 Consensus size: 3
41331152 GAGAGCCAAT
41331162 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331210 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331258 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331306 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331354 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331402 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331450 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331498 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331546 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331594 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331642 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331690 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331738 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331786 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331834 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331882 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
41331930 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
41331978 AAG AAA AAG A
1 AAG AAG AAG A
41331988 GTGAAGACAT
Statistics
Matches: 821, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 821 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41332203 original size:20 final size:20
Alignment explanation
Indices: 41332166--41332205 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41332156 CAACGTGGTA
*
41332166 AGTTAACTGACCACATCAAC
1 AGTTAACTGACCAAATCAAC
41332186 AGTTAACTTG-CCAAATCAAC
1 AGTTAAC-TGACCAAATCAAC
41332206 GCTCTCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.23
Consensus pattern (20 bp):
AGTTAACTGACCAAATCAAC
Found at i:41333306 original size:26 final size:28
Alignment explanation
Indices: 41333251--41333310 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
41333241 TCAATTTTTT
*
41333251 ATATTATTTTTTTTTGTTTTTTAAATAAA
1 ATATTATTTTTTTTTGTTTATT-AATAAA
41333280 ATATTATTTTTTTATT-TTTATT-A-AAA
1 ATATTATTTTTTT-TTGTTTATTAATAAA
41333306 ATATT
1 ATATT
41333311 TAAATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 8 0.28
27 1 0.03
29 18 0.62
30 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (28 bp):
ATATTATTTTTTTTTGTTTATTAATAAA
Found at i:41333959 original size:41 final size:41
Alignment explanation
Indices: 41333884--41334133 Score: 226
Period size: 41 Copynumber: 6.1 Consensus size: 41
41333874 TCAAAAATTT
* *
41333884 TAAAATAC-AGAGCAATAGCGGCG-TTTTAAGAAAAACGCCGC
1 TAAAA-ACTAGAGCAACAGCGGCGCTTTT-AGTAAAACGCCGC
*
41333925 TAAAAA-TAGAGCAACAGTGGCG-TTTTAGTAAAAAACGCCGC
1 TAAAAACTAGAGCAACAGCGGCGCTTTTAGT--AAAACGCCGC
** ** *
41333966 TAAAAAC-AGAGCATTAGCGGCGCTTTCGGTAAAACCCCGC
1 TAAAAACTAGAGCAACAGCGGCGCTTTTAGTAAAACGCCGC
*
41334006 TAAAAACTAGAGC-ACTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAAACTAGAGCAAC-AGCGGCGCTTTTAGTAAAACGCCGC
** * *
41334047 TAAAAACTAGAGCATTAGCGGCGCTTTT-GATAAAACGTCAC
1 TAAAAACTAGAGCAACAGCGGCGCTTTTAG-TAAAACGCCGC
* ** * * *
41334088 TAAAAACCAGAGCATTAGCGGCACTTTTGGTAAAACACCGC
1 TAAAAACTAGAGCAACAGCGGCGCTTTTAGTAAAACGCCGC
41334129 TAAAA
1 TAAAA
41334134 GTCATATAAC
Statistics
Matches: 177, Mismatches: 22, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
39 2 0.01
40 35 0.20
41 134 0.76
42 6 0.03
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (41 bp):
TAAAAACTAGAGCAACAGCGGCGCTTTTAGTAAAACGCCGC
Found at i:41334081 original size:82 final size:81
Alignment explanation
Indices: 41333884--41334133 Score: 294
Period size: 82 Copynumber: 3.1 Consensus size: 81
41333874 TCAAAAATTT
* *
41333884 TAAAATACAGAGCAATAGCGGCG-TTTTAAGA-AAAACGCCGCTAAAAA-TAGAGCAAC-AGTGG
1 TAAAA-ACAGAGCATTAGCGGCGCTTTT--GATAAAACGCCGCTAAAAACTAGAGC-ACTAGCGG
*
41333945 CG-TTTTAGTAAAAAACGCCGC
62 CGCTTTTGGT--AAAACGCCGC
* * *
41333966 TAAAAACAGAGCATTAGCGGCGCTTTCGGTAAAACCCCGCTAAAAACTAGAGCACTAGCGGCGCT
1 TAAAAACAGAGCATTAGCGGCGCTTTTGATAAAACGCCGCTAAAAACTAGAGCACTAGCGGCGCT
41334031 TTTGGTAAAACGCCGC
66 TTTGGTAAAACGCCGC
* * * * *
41334047 TAAAAACTAGAGCATTAGCGGCGCTTTTGATAAAACGTCACTAAAAACCAGAGCATTAGCGGCAC
1 TAAAAAC-AGAGCATTAGCGGCGCTTTTGATAAAACGCCGCTAAAAACTAGAGCACTAGCGGCGC
*
41334112 TTTTGGTAAAACACCGC
65 TTTTGGTAAAACGCCGC
41334129 TAAAA
1 TAAAA
41334134 GTCATATAAC
Statistics
Matches: 147, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
80 1 0.01
81 50 0.34
82 90 0.61
83 6 0.04
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (81 bp):
TAAAAACAGAGCATTAGCGGCGCTTTTGATAAAACGCCGCTAAAAACTAGAGCACTAGCGGCGCT
TTTGGTAAAACGCCGC
Found at i:41334571 original size:25 final size:25
Alignment explanation
Indices: 41334542--41334595 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
41334532 GTGATTTTGA
*
41334542 ATGTGGAATTAGCATTTGTTGAACT
1 ATGTGGAATTAGCAGTTGTTGAACT
41334567 ATGTGGAATTAGCAGTTGTTGAACT
1 ATGTGGAATTAGCAGTTGTTGAACT
41334592 ATGT
1 ATGT
41334596 ATAATTTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.39
Consensus pattern (25 bp):
ATGTGGAATTAGCAGTTGTTGAACT
Found at i:41335152 original size:21 final size:21
Alignment explanation
Indices: 41335135--41335174 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41335125 TGTGTTTGTG
41335135 GTCTAAGGTTTAGGGTTTAGA
1 GTCTAAGGTTTAGGGTTTAGA
* *
41335156 GTCTTAGGTTTAGGTTTTA
1 GTCTAAGGTTTAGGGTTTA
41335175 AATTTAGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (21 bp):
GTCTAAGGTTTAGGGTTTAGA
Found at i:41335227 original size:15 final size:15
Alignment explanation
Indices: 41335207--41335238 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41335197 TTTAATTTAG
*
41335207 AAGATAAATGTATAT
1 AAGATAAATATATAT
41335222 AAGATAAATATATAT
1 AAGATAAATATATAT
41335237 AA
1 AA
41335239 ATTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:41335277 original size:24 final size:23
Alignment explanation
Indices: 41335210--41335277 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
41335200 AATTTAGAAG
* *
41335210 ATAAATGTATATAAGATAAATATAT
1 ATAAAT-TATATATGA-AAAAATAT
* *
41335235 ATAAATTATTATTTTAAAAAATAT
1 ATAAATTA-TATATGAAAAAATAT
41335259 ATAAATATATATATGAAAA
1 ATAAAT-TATATATGAAAA
41335278 GTGGTTTAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 23 0.66
25 12 0.34
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
ATAAATTATATATGAAAAAATAT
Found at i:41340784 original size:9 final size:9
Alignment explanation
Indices: 41340770--41340804 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
41340760 AAAGTTCAAA
41340770 TTACATAAC
1 TTACATAAC
41340779 TTACATAA-
1 TTACATAAC
41340787 TCTACATAAC
1 T-TACATAAC
41340797 TTACATAA
1 TTACATAA
41340805 AACATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 1 0.04
9 22 0.92
10 1 0.04
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (9 bp):
TTACATAAC
Found at i:41345385 original size:68 final size:68
Alignment explanation
Indices: 41345271--41345406 Score: 236
Period size: 68 Copynumber: 2.0 Consensus size: 68
41345261 GAGGTCTCTG
* *
41345271 ATGCCTATATCATGAAGGCATTGGGTAAAAAATGGAGAGACAATAAAAGCATTTTGAAAAAAAAA
1 ATGCCTATATCAAGAAGGCATTGGGTAAAAAATGGAGAGACAATAAAAGCAGTTTGAAAAAAAAA
41345336 TAT
66 TAT
* *
41345339 ATGCCTATATCAAGAAGGCATTGGGTAAAAAATGGAGAGACCATAAAAGCAGTTTGAAAAAAGAA
1 ATGCCTATATCAAGAAGGCATTGGGTAAAAAATGGAGAGACAATAAAAGCAGTTTGAAAAAAAAA
41345404 TAT
66 TAT
41345407 TTTAAAAAAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.22
Consensus pattern (68 bp):
ATGCCTATATCAAGAAGGCATTGGGTAAAAAATGGAGAGACAATAAAAGCAGTTTGAAAAAAAAA
TAT
Found at i:41346663 original size:43 final size:43
Alignment explanation
Indices: 41346616--41346793 Score: 202
Period size: 43 Copynumber: 4.2 Consensus size: 43
41346606 ACTGGGCAAA
*
41346616 TTAGCGGCATTTTTTAAAAAAGCGCCGCTAAAAATACATGTCT
1 TTAGCGGCATTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCT
* ** *
41346659 TTAGCAGTGTTTTTTAAAAAAGCGCCGCTAAAAGTACAGGTCT
1 TTAGCGGCATTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCT
* *
41346702 CTAGCGGTACTTTTTT-AAAAAGCGCCGCTAAAAGTACATGTCT
1 TTAGCGGCA-TTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCT
* * * *
41346745 TTAGCGGC-GTTTTCATAAAAA-CGCCGCTAAAGGT-CCTGGTCT
1 TTAGCGGCATTTTTTA-AAAAAGCGCCGCTAAAAGTACAT-GTCT
41346787 TTAGCGG
1 TTAGCGG
41346794 TGCTGCATAT
Statistics
Matches: 116, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
41 6 0.05
42 23 0.20
43 81 0.70
44 6 0.05
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (43 bp):
TTAGCGGCATTTTTTAAAAAAGCGCCGCTAAAAGTACATGTCT
Found at i:41346733 original size:86 final size:85
Alignment explanation
Indices: 41346617--41346794 Score: 234
Period size: 86 Copynumber: 2.1 Consensus size: 85
41346607 CTGGGCAAAT
* * *
41346617 TAGCGGCATTTTTTAAAAAAGCGCCGCTAAAAATACATGTCTTTAGCAGTGTTTT-TTAAAAAAG
1 TAGCGGTATTTTTTAAAAAAGCGCCGCTAAAAATACATGTCTTTAGCAGCGTTTTCAT-AAAAA-
41346681 CGCCGCTAAAAGTACAGGTCTC
64 CGCCGCTAAAAGTACAGGTCTC
* *
41346703 TAGCGGTACTTTTTT-AAAAAGCGCCGCTAAAAGTACATGTCTTTAGCGGCGTTTTCATAAAAAC
1 TAGCGGTA-TTTTTTAAAAAAGCGCCGCTAAAAATACATGTCTTTAGCAGCGTTTTCATAAAAAC
* * * *
41346767 GCCGCTAAAGGTCCTGGTCTT
65 GCCGCTAAAAGTACAGGTCTC
41346788 TAGCGGT
1 TAGCGGT
41346795 GCTGCATATA
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
85 25 0.31
86 49 0.60
87 7 0.09
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (85 bp):
TAGCGGTATTTTTTAAAAAAGCGCCGCTAAAAATACATGTCTTTAGCAGCGTTTTCATAAAAACG
CCGCTAAAAGTACAGGTCTC
Found at i:41347508 original size:17 final size:17
Alignment explanation
Indices: 41347486--41347527 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
41347476 AAAGAGCAAC
*
41347486 CATTGTTTCCATGTCTT
1 CATTGTCTCCATGTCTT
41347503 CATTGTCTCCATGTCTT
1 CATTGTCTCCATGTCTT
*
41347520 CATCGTCT
1 CATTGTCT
41347528 ACGAGTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.12, C:0.29, G:0.12, T:0.48
Consensus pattern (17 bp):
CATTGTCTCCATGTCTT
Found at i:41349691 original size:11 final size:11
Alignment explanation
Indices: 41349635--41349721 Score: 52
Period size: 11 Copynumber: 7.3 Consensus size: 11
41349625 ATGTAAAAAC
41349635 AATATATATAAAT
1 AATA-ATAT-AAT
41349648 AATTAATA-AAT
1 AA-TAATATAAT
*
41349659 ATATAATACAAGT
1 A-ATAATATAA-T
*
41349672 AAAAATATAAT
1 AATAATATAAT
*
41349683 AATAATATAAA
1 AATAATATAAT
41349694 AATAATGACGTAA-
1 AATAAT-A--TAAT
41349707 AATAATAATAAT
1 AATAAT-ATAAT
41349719 AAT
1 AAT
41349722 TTGTGAAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
11 28 0.46
12 14 0.23
13 14 0.23
14 5 0.08
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (11 bp):
AATAATATAAT
Found at i:41349693 original size:19 final size:19
Alignment explanation
Indices: 41349635--41349697 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 19
41349625 ATGTAAAAAC
41349635 AATATATATAAATAAT-TAATA
1 AATATA-AT-AATAATATAA-A
41349656 AATAT-ATAATACA-AGTAAA
1 AATATAATAATA-ATA-TAAA
41349675 AATATAATAATAATATAAA
1 AATATAATAATAATATAAA
41349694 AATA
1 AATA
41349698 ATGACGTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
18 4 0.11
19 18 0.49
20 10 0.27
21 5 0.14
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
AATATAATAATAATATAAA
Found at i:41351380 original size:14 final size:14
Alignment explanation
Indices: 41351361--41351447 Score: 61
Period size: 14 Copynumber: 6.1 Consensus size: 14
41351351 TGAATGACTC
41351361 AAGGTTTAAGGTCT
1 AAGGTTTAAGGTCT
**
41351375 AAGG-TTCGGGAT-T
1 AAGGTTTAAGG-TCT
*
41351388 AATGGTTTCAAGGTCC
1 AA-GGTTT-AAGGTCT
*
41351404 AAGGTTTAAGATCTT
1 AAGGTTTAAGGTC-T
* *
41351419 AAAGTCTAAGGTCT
1 AAGGTTTAAGGTCT
*
41351433 AAGGTCTAAGGTCT
1 AAGGTTTAAGGTCT
41351447 A
1 A
41351448 GTGTATAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
13 7 0.12
14 27 0.48
15 18 0.32
16 4 0.07
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32
Consensus pattern (14 bp):
AAGGTTTAAGGTCT
Found at i:41351445 original size:7 final size:7
Alignment explanation
Indices: 41351397--41351447 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 7
41351387 TAATGGTTTC
*
41351397 AAGGTCC
1 AAGGTCT
*
41351404 AAGGTTT
1 AAGGTCT
*
41351411 AAGATCTT
1 AAGGTC-T
*
41351419 AAAGTCT
1 AAGGTCT
41351426 AAGGTCT
1 AAGGTCT
41351433 AAGGTCT
1 AAGGTCT
41351440 AAGGTCT
1 AAGGTCT
41351447 A
1 A
41351448 GTGTATAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 31 0.86
8 5 0.14
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (7 bp):
AAGGTCT
Found at i:41354230 original size:43 final size:43
Alignment explanation
Indices: 41354140--41354236 Score: 113
Period size: 43 Copynumber: 2.3 Consensus size: 43
41354130 TGTGATTACG
* * * *
41354140 TGTAAGACCATGTCTGGGACATTGGCATCGTTAATCAATTACG
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATAATCAATAACA
* * * **
41354183 TGTAAGACCCTGTCTGGGGCAGTGGCATCGATATTTGATAACA
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATAATCAATAACA
41354226 TGTAAGACCAT
1 TGTAAGACCAT
41354237 ATCTAGGATA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGATAATCAATAACA
Found at i:41358243 original size:87 final size:87
Alignment explanation
Indices: 41358093--41358266 Score: 233
Period size: 87 Copynumber: 2.0 Consensus size: 87
41358083 AGAAAAATTT
* * * * *
41358093 TAAACTTCTTTTCTACCTAAAAACACTATTCATAAATTGATTTTTCCAATAATTGCTATTAGACT
1 TAAACTTCTTCTATACCTAAAAACACTACTCATAAATTAATTTTTCCAATAATTGCTATTAGACC
*
41358158 AGGTTGTATTATGTTTATAGTA
66 AGGTTGTACTATGTTTATAGTA
* * * *
41358180 TAAACTTCTTCTATACTTAGAAACACTGCTCACTAAATTAATTTTTCCAATAATTGGTA-TAGAC
1 TAAACTTCTTCTATACCTAAAAACACTACTCA-TAAATTAATTTTTCCAATAATTGCTATTAGAC
*
41358244 CAGGTTGTGCTATGTTTATAGTA
65 CAGGTTGTACTATGTTTATAGTA
41358267 CAAATTGAAC
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
87 51 0.68
88 24 0.32
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (87 bp):
TAAACTTCTTCTATACCTAAAAACACTACTCATAAATTAATTTTTCCAATAATTGCTATTAGACC
AGGTTGTACTATGTTTATAGTA
Found at i:41360537 original size:18 final size:20
Alignment explanation
Indices: 41360500--41360539 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
41360490 ACCTAGCACA
*
41360500 AATTAAAATTAAGCCATATC
1 AATTAAAATTAAGACATATC
41360520 AATT-AAATTAA-ACATATC
1 AATTAAAATTAAGACATATC
41360538 AA
1 AA
41360540 CATCACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (20 bp):
AATTAAAATTAAGACATATC
Found at i:41363478 original size:47 final size:47
Alignment explanation
Indices: 41363420--41363551 Score: 176
Period size: 47 Copynumber: 2.8 Consensus size: 47
41363410 TCACAATCGA
* *
41363420 TAAGTATCTATACCATGGCCCATAGCCAAATCAAGGTACCTTATC-C
1 TAAGTACCTATACCATGGCCCATAGCCAAATCAAGGTACCTCATCTC
* *
41363466 TGAAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAGCTCCTCTC
1 T-AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTACCTCATCTC
* * * *
41363514 TAAATACCTATTCCATGGCCCGTAGCTAAATCAAGGTA
1 TAAGTACCTATACCATGGCCCATAGCCAAATCAAGGTA
41363552 TTATTCACAC
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
46 1 0.01
47 73 0.96
48 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (47 bp):
TAAGTACCTATACCATGGCCCATAGCCAAATCAAGGTACCTCATCTC
Found at i:41367029 original size:26 final size:26
Alignment explanation
Indices: 41366974--41367057 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 26
41366964 CTGGAGGCCT
*
41366974 AGCCTCTTTT-AAT-AATTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
41366998 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
41367024 AGCCCTTTTCAATAAACTGGGGCAT-
1 AGCCCTTTTCAATAAACTGGGGCATA
41367049 AGCCCTTTT
1 AGCCCTTTT
41367058 GCACTTCCTC
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.10
24 5 0.10
25 18 0.35
26 24 0.46
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:41367132 original size:20 final size:21
Alignment explanation
Indices: 41367107--41367153 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
41367097 TTATGATTAC
* *
41367107 ATCATGTGGATTTCATA-CAT
1 ATCATGTGCATATCATATCAT
41367127 ATCATGTGCATATCATATCAT
1 ATCATGTGCATATCATATCAT
41367148 -TCATGT
1 ATCATGT
41367154 ATATCACATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
ATCATGTGCATATCATATCAT
Found at i:41376623 original size:12 final size:13
Alignment explanation
Indices: 41376595--41376627 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
41376585 TATTTATTTT
41376595 TTCTCCATCTACC
1 TTCTCCATCTACC
*
41376608 TTCTCC-TCTTCC
1 TTCTCCATCTACC
41376620 TTCTCCAT
1 TTCTCCAT
41376628 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:41377726 original size:28 final size:28
Alignment explanation
Indices: 41377694--41377758 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
41377684 ATTTACTAGA
*
41377694 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
41377722 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
41377750 ATACCCCTA
1 ATACCCCTA
41377759 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:41377905 original size:28 final size:28
Alignment explanation
Indices: 41377874--41377953 Score: 92
Period size: 27 Copynumber: 2.8 Consensus size: 28
41377864 CTGGTGGCTA
41377874 TGCCACAAATTATCTGTTCTGGTGGGC-C
1 TGCCACAAA-TATCTGTTCTGGTGGGCAC
** *
41377902 TGCCACGTATATCTATTCTGGT-GGCAC
1 TGCCACAAATATCTGTTCTGGTGGGCAC
41377929 TGCCACAAAATATCTGTATCTGGTG
1 TGCCAC-AAATATCTGT-TCTGGTG
41377954 ACTCTGTCAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 3 0.07
27 19 0.45
28 14 0.33
29 6 0.14
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.33
Consensus pattern (28 bp):
TGCCACAAATATCTGTTCTGGTGGGCAC
Found at i:41377964 original size:29 final size:28
Alignment explanation
Indices: 41377874--41377964 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 28
41377864 CTGGTGGCTA
* * *
41377874 TGCCACAAATTATCTGTTCTGGTGGGC-C
1 TGCCACAAAATATCTATTCTGGT-GACAC
** *
41377902 TGCCAC-GTATATCTATTCTGGTGGCAC
1 TGCCACAAAATATCTATTCTGGTGACAC
* *
41377929 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTAT-TCTGGTGACAC
*
41377958 TGTCACA
1 TGCCACA
41377965 TTTTCTGTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
26 3 0.06
27 19 0.38
28 13 0.26
29 15 0.30
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTATTCTGGTGACAC
Found at i:41379276 original size:24 final size:23
Alignment explanation
Indices: 41379244--41379289 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
41379234 GACCCCACTT
41379244 ATTTAGCAT-AATCATATATCTAA
1 ATTTAGCATGAATCATA-ATCTAA
*
41379267 ATTTAAGCATGCATCATAATCTA
1 ATTT-AGCATGAATCATAATCTA
41379290 CTAATATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (23 bp):
ATTTAGCATGAATCATAATCTAA
Found at i:41382165 original size:44 final size:44
Alignment explanation
Indices: 41382081--41382165 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
41382071 ACATGTATCA
* * *
41382081 CATCCATAATGAACTCGGACGAACTCAACGAGCTCGGATGCTTG
1 CATCCATAATGAACTCGGACCAACTCAAAGAGCTCAGATGCTTG
*
41382125 CATCCATAATGAACTCGGACCAACTCAAAGAGCTTAGATGC
1 CATCCATAATGAACTCGGACCAACTCAAAGAGCTCAGATGC
41382166 CTCATACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (44 bp):
CATCCATAATGAACTCGGACCAACTCAAAGAGCTCAGATGCTTG
Found at i:41386076 original size:43 final size:42
Alignment explanation
Indices: 41386029--41386126 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
41386019 CCCAGACGTA
*
41386029 GTCTTACATGTAATCAAATATCGATGCC-ACTGTCCCAAACAGG
1 GTCTTACACGTAATCAAATA-CGATGCCGA-TGTCCCAAACAGG
* * *
41386072 GTCTTACACGAAATCAAATACGATGCCGATGTCCTAAACATG
1 GTCTTACACGTAATCAAATACGATGCCGATGTCCCAAACAGG
41386114 GTCTTACACGTAA
1 GTCTTACACGTAA
41386127 ATATCAAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 30 0.61
43 19 0.39
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (42 bp):
GTCTTACACGTAATCAAATACGATGCCGATGTCCCAAACAGG
Found at i:41386163 original size:44 final size:42
Alignment explanation
Indices: 41386005--41386173 Score: 144
Period size: 43 Copynumber: 4.0 Consensus size: 42
41385995 GAAAAACTCG
* * * * *
41386005 TACAATGCCAATGTCCCAGACGTAGTCTTACATGTAATCAAA
1 TACAATGACAATGTCCCAAACGTGGTCTTACACGAAATCAAA
* * *
41386047 TATCGATGCCACTGTCCCAAACAG-GGTCTTACACGAAATCAAA
1 TA-CAATGACAATGTCCCAAAC-GTGGTCTTACACGAAATCAAA
* * * * *
41386090 TACGATGCCGATGTCCTAAACATGGTCTTACACGTAAATATCAAA
1 TACAATGACAATGTCCCAAACGTGGTCTTACACG--AA-ATCAAA
* *
41386135 T-CAATGACAATGTCCCAAACGTGATCTTACACAAAATCA
1 TACAATGACAATGTCCCAAACGTGGTCTTACACGAAATCA
41386174 CATATCGAAA
Statistics
Matches: 104, Mismatches: 17, Indels: 13
0.78 0.13 0.10
Matches are distributed among these distances:
41 4 0.04
42 31 0.30
43 34 0.33
44 28 0.27
45 7 0.07
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (42 bp):
TACAATGACAATGTCCCAAACGTGGTCTTACACGAAATCAAA
Found at i:41392038 original size:54 final size:54
Alignment explanation
Indices: 41391954--41392062 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 54
41391944 ACGTGAGAAA
* * **
41391954 TTATGAGATTAAAAGAGTTATGTTTCGAATACTTC-GAAAATACCTGAAAGAGTG
1 TTATGAGATTAAAAGAGCTATGTTCCGAATACTTCTG-AAATACCAAAAAGAGTG
41392008 TTATGAGATTAAAAGAGCTATG-TCCAGAATACTTCTGAAATACCAAAAAGAGTG
1 TTATGAGATTAAAAGAGCTATGTTCC-GAATACTTCTGAAATACCAAAAAGAGTG
41392062 T
1 T
41392063 AGTATGATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
53 2 0.04
54 46 0.94
55 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (54 bp):
TTATGAGATTAAAAGAGCTATGTTCCGAATACTTCTGAAATACCAAAAAGAGTG
Found at i:41395588 original size:67 final size:66
Alignment explanation
Indices: 41395478--41395610 Score: 239
Period size: 67 Copynumber: 2.0 Consensus size: 66
41395468 ACCGTTCTGG
*
41395478 CCCTGTCTCACGAGAACCTGAATATCTCTTAACATACTGTCCATATGATCGTTTCGTTACTTTCC
1 CCCTGTCTCACGAGAACCTGAATATCTCTTAACATACTATCCATATGATCGTTTCGTTACTTTCC
41395543 T
66 T
*
41395544 NCCCTGTCTTACGAGAACCTGAATATCTCTTAACATACTATCCATATGATCGTTTCGTTACTTTC
1 -CCCTGTCTCACGAGAACCTGAATATCTCTTAACATACTATCCATATGATCGTTTCGTTACTTTC
41395609 CT
65 CT
41395611 ATGAAAATAG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.23, C:0.28, G:0.11, T:0.37
Consensus pattern (66 bp):
CCCTGTCTCACGAGAACCTGAATATCTCTTAACATACTATCCATATGATCGTTTCGTTACTTTCC
T
Found at i:41397889 original size:29 final size:29
Alignment explanation
Indices: 41397854--41397930 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
41397844 CATGAGATTG
* *
41397854 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGGGTTTAAAGTATACA
* **
41397883 GCACTAAGTGTGCGAGTTTAAAGTATATG
1 GCACTAAGTGTGCGGGTTTAAAGTATACA
41397912 GCACTAAGTGTGCGCGGTT
1 GCACTAAGTGTGCG-GGTT
41397931 GATTATTAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 38 0.93
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTTAAAGTATACA
Found at i:41398151 original size:174 final size:174
Alignment explanation
Indices: 41397883--41398210 Score: 532
Period size: 174 Copynumber: 1.9 Consensus size: 174
41397873 AAATTGTACA
* * *
41397883 GCACTAAGTGTGCGAGTTTAAAGTATATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* * *
41397948 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGTGACTTTACCGAGTCGA
66 CGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
41398013 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * * *
41398057 GCACTAAGTTTTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTAT
1 GCACTAAG-TGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTAT
*
41398122 GCGTGC-AACCCTATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCA
65 GCGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCA
41398186 ATTTTGGACAGCGGAAAAGGTAAGT
130 ATTTTGGACAGCGGAAAAGGTAAGT
41398211 ACCTTGAGTT
Statistics
Matches: 141, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
174 88 0.62
175 53 0.38
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
CGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:41404834 original size:12 final size:12
Alignment explanation
Indices: 41404817--41404847 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
41404807 GCATCGACTA
41404817 TTGTTTTTGTTG
1 TTGTTTTTGTTG
41404829 TTGTTTTTGTTG
1 TTGTTTTTGTTG
41404841 TTGTTTT
1 TTGTTTT
41404848 GCTATTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (12 bp):
TTGTTTTTGTTG
Found at i:41411915 original size:43 final size:42
Alignment explanation
Indices: 41411849--41411936 Score: 131
Period size: 43 Copynumber: 2.1 Consensus size: 42
41411839 TTCGTGATAT
* *
41411849 ATGTGGCATCCGAGCTCATTGAGTGGTCCGAGTTCATTATGG
1 ATGTGGCATCAGAGCTCATTGAGTGGTCCGAGTTCATAATGG
* *
41411891 ATGTGAGCATCAGGGCTCGTTGAGTGGTCCGAGTTCATAATGG
1 ATGTG-GCATCAGAGCTCATTGAGTGGTCCGAGTTCATAATGG
41411934 ATG
1 ATG
41411937 CGATACATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 5 0.12
43 36 0.88
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (42 bp):
ATGTGGCATCAGAGCTCATTGAGTGGTCCGAGTTCATAATGG
Found at i:41418130 original size:16 final size:16
Alignment explanation
Indices: 41418109--41418141 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41418099 AAGTTTAGGG
41418109 GCAAAAATATAATTTT
1 GCAAAAATATAATTTT
*
41418125 GCAAAAATATGATTTT
1 GCAAAAATATAATTTT
41418141 G
1 G
41418142 GGTTAATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (16 bp):
GCAAAAATATAATTTT
Found at i:41419099 original size:60 final size:60
Alignment explanation
Indices: 41419003--41419122 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
41418993 CTCCTGAAGA
*
41419003 ATATGGGTACATTAAGGATTTAGCCTGGACGAGTAATCCAATTAAAGACTGAATTTAGCC
1 ATATGGGTACATTAAGGATTTAGCCTAGACGAGTAATCCAATTAAAGACTGAATTTAGCC
* * ** *
41419063 ATATGGGTGCATTAAGGATTTAGGCC-AGACGGGTAATCTGATTAAGGACTGAATTTAGCC
1 ATATGGGTACATTAAGGATTTA-GCCTAGACGAGTAATCCAATTAAAGACTGAATTTAGCC
41419123 TGGACTGGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 50 0.94
61 3 0.06
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (60 bp):
ATATGGGTACATTAAGGATTTAGCCTAGACGAGTAATCCAATTAAAGACTGAATTTAGCC
Found at i:41419632 original size:175 final size:175
Alignment explanation
Indices: 41419341--41419685 Score: 591
Period size: 175 Copynumber: 2.0 Consensus size: 175
41419331 GATTCCGAGG
* *
41419341 AGTTCAACGGGAATTAATATGAGAAATGGAATGGAAATATTTGAAATGATAAACTCATCTATGTT
1 AGTTCAACGGGAATTAATATGAGAAATGGAATGGAAATACTTGAAATGATAAACTCATCTATGCT
*
41419406 TAGATAATACTAGTATGATGTATATGATTGTCATGTTTAGATGAGTGGTTGTGCTAAGAGATAGC
66 TAGATAATACTAGTATGATGTATATGATTGCCATGTTTAGATGAGTGGTTGTGCTAAGAGATAGC
* * * *
41419471 ATAGGTATGTACTCGAAACCTATGAGCATGTGTTTTCCATCTAAA
131 ACAGGTACGTACTCGAAACCCATGAGCATGTGTTTGCCATCTAAA
41419516 AGTTCAACGGGAATTAATATGAGAAATGGAATGGAAATACTTGAAATGATAAACTCATCTATGCT
1 AGTTCAACGGGAATTAATATGAGAAATGGAATGGAAATACTTGAAATGATAAACTCATCTATGCT
* * *
41419581 TAGATGATACTAGTATGATTTATATGATTGCCATGTTTAGTTGAGTGGTTGTGCTAAGAGATAGC
66 TAGATAATACTAGTATGATGTATATGATTGCCATGTTTAGATGAGTGGTTGTGCTAAGAGATAGC
*
41419646 ACATGTACGTACTCGAAACCCATGAGCATGTGTTTGCCAT
131 ACAGGTACGTACTCGAAACCCATGAGCATGTGTTTGCCAT
41419686 GTGAAATGAA
Statistics
Matches: 159, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
175 159 1.00
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (175 bp):
AGTTCAACGGGAATTAATATGAGAAATGGAATGGAAATACTTGAAATGATAAACTCATCTATGCT
TAGATAATACTAGTATGATGTATATGATTGCCATGTTTAGATGAGTGGTTGTGCTAAGAGATAGC
ACAGGTACGTACTCGAAACCCATGAGCATGTGTTTGCCATCTAAA
Found at i:41424090 original size:43 final size:43
Alignment explanation
Indices: 41424037--41424122 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
41424027 GATATATGTG
* *
41424037 GCATTCGAGCTCGTTGAATGGTCCGAGTTCATTATGAATGCGA
1 GCATCCGAGCTCGTTGAATGGTCCGAGTTCATAATGAATGCGA
* * * *
41424080 GCATCCGAGCTTGTTGAGTGGTCTGAGTTCATAATGGATGCGA
1 GCATCCGAGCTCGTTGAATGGTCCGAGTTCATAATGAATGCGA
41424123 TACATGTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
GCATCCGAGCTCGTTGAATGGTCCGAGTTCATAATGAATGCGA
Found at i:41444637 original size:7 final size:7
Alignment explanation
Indices: 41444622--41444652 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
41444612 ATGTATATGT
*
41444622 ATATGTA
1 ATATATA
41444629 ATATATA
1 ATATATA
41444636 ATATATA
1 ATATATA
41444643 ATATATA
1 ATATATA
41444650 ATA
1 ATA
41444653 AATGAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (7 bp):
ATATATA
Found at i:41452889 original size:24 final size:24
Alignment explanation
Indices: 41452857--41452912 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
41452847 CTGTCAGGAG
41452857 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
41452881 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
41452905 AGGATTTA
1 AGGATTTA
41452913 AGAGCAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.30
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:41452923 original size:24 final size:24
Alignment explanation
Indices: 41452872--41452927 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
41452862 TTAGGAGTTG
* ***
41452872 ATAAGGGATAGGATTTAGGAGTTG
1 ATAAGGGATAGGATTTAAGAGCAA
41452896 ATAAGGGATAGGATTTAAGAGCAA
1 ATAAGGGATAGGATTTAAGAGCAA
41452920 ATAAGGGA
1 ATAAGGGA
41452928 GGAAATCTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.02, G:0.34, T:0.23
Consensus pattern (24 bp):
ATAAGGGATAGGATTTAAGAGCAA
Found at i:41454386 original size:27 final size:27
Alignment explanation
Indices: 41454346--41454457 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
41454336 AGGAAGCGTC
*
41454346 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* *
41454373 CTGGTGGCTCTGCCACATATT-TTTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
41454400 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
41454428 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
41454454 CTGG
1 CTGG
41454458 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.11
27 47 0.64
28 18 0.25
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:41454454 original size:54 final size:54
Alignment explanation
Indices: 41454346--41454457 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
41454336 AGGAAGCGTC
* * *
41454346 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTTTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
41454400 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
41454454 CTGG
1 CTGG
41454458 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:41456390 original size:40 final size:40
Alignment explanation
Indices: 41456337--41456412 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
41456327 CTAAAAAAAA
41456337 TGGCACTTAGTGTGC-AGTTCGAAATAGCTTCGGCTAAATG
1 TGGCACTTAGTGTGCGA-TTCGAAATAGCTTCGGCTAAATG
* * *
41456377 TGGCACTTGGTGTGCGATTGGAGATAGCTTCGGCTA
1 TGGCACTTAGTGTGCGATTCGAAATAGCTTCGGCTA
41456413 TATATGTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 31 0.97
41 1 0.03
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTCGAAATAGCTTCGGCTAAATG
Found at i:41456453 original size:28 final size:28
Alignment explanation
Indices: 41456422--41456491 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
41456412 ATATATGTAT
41456422 ATGGCACTTAGTGTGAAAAATATTAAGA
1 ATGGCACTTAGTGTGAAAAATATTAAGA
* ** * * *
41456450 ATGGCACTTGGTGTGTGAGATATTGAGT
1 ATGGCACTTAGTGTGAAAAATATTAAGA
41456478 ATGGCACTTAGTGT
1 ATGGCACTTAGTGT
41456492 ATGAGACATC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.30, C:0.09, G:0.29, T:0.33
Consensus pattern (28 bp):
ATGGCACTTAGTGTGAAAAATATTAAGA
Found at i:41466088 original size:40 final size:40
Alignment explanation
Indices: 41466006--41466224 Score: 248
Period size: 40 Copynumber: 5.5 Consensus size: 40
41465996 ACCCAAGTAT
* ** * *
41466006 CTTCGGG-ATTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
41466043 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
41466083 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
41466123 CTTCAGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
41466163 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
41466203 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
41466225 CATTCGAATA
Statistics
Matches: 151, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
37 7 0.05
38 4 0.03
39 16 0.11
40 123 0.81
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:41470141 original size:23 final size:23
Alignment explanation
Indices: 41470008--41470153 Score: 122
Period size: 23 Copynumber: 6.4 Consensus size: 23
41469998 GCTAATGAAT
* *
41470008 AGTAAGCTCTAATGAACTGAAAT
1 AGTAAGCTCTAATGAGCTGAAAC
*
41470031 GGTAAGCTCTAATGAGCTGAAA-
1 AGTAAGCTCTAATGAGCTGAAAC
* * *
41470053 TGATAAGCTCTATTGAGCT-CAAC
1 AG-TAAGCTCTAATGAGCTGAAAC
* *
41470076 AGTAAGCTCTATTGAGCT-AAAT
1 AGTAAGCTCTAATGAGCTGAAAC
* *
41470098 AGTAAGCCCATACA--AGTTGAAAC
1 AGTAAGCTC-TA-ATGAGCTGAAAC
*
41470121 AGTAAGCTCCAATGAGCTGAAAAC
1 AGTAAGCTCTAATGAGCTG-AAAC
41470145 AGTAAGCTC
1 AGTAAGCTC
41470154 CCACAAGCTG
Statistics
Matches: 100, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
21 1 0.01
22 33 0.33
23 53 0.53
24 13 0.13
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (23 bp):
AGTAAGCTCTAATGAGCTGAAAC
Found at i:41470162 original size:24 final size:24
Alignment explanation
Indices: 41470098--41470164 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
41470088 TGAGCTAAAT
*
41470098 AGTAAGC-CCATACAAGTTG-AAAC
1 AGTAAGCTCCA-ACAAGCTGAAAAC
**
41470121 AGTAAGCTCCAATGAGCTGAAAAC
1 AGTAAGCTCCAACAAGCTGAAAAC
*
41470145 AGTAAGCTCCCACAAGCTGA
1 AGTAAGCTCCAACAAGCTGA
41470165 CGAGTTGTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 12 0.33
24 24 0.67
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.16
Consensus pattern (24 bp):
AGTAAGCTCCAACAAGCTGAAAAC
Found at i:41478223 original size:27 final size:26
Alignment explanation
Indices: 41478193--41478246 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
41478183 AGGACTACCG
* *
41478193 ATTTACCCCTGGAGGGTAAAATGACTA
1 ATTTACCCCTCGAGCGT-AAATGACTA
* *
41478220 ATTTGCCCCTCGTGCGTAAATGACTA
1 ATTTACCCCTCGAGCGTAAATGACTA
41478246 A
1 A
41478247 CTTGTGTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (26 bp):
ATTTACCCCTCGAGCGTAAATGACTA
Found at i:41479021 original size:104 final size:104
Alignment explanation
Indices: 41478841--41479326 Score: 922
Period size: 104 Copynumber: 4.7 Consensus size: 104
41478831 CTCGCTGCAA
*
41478841 TCTGGTGGCCTCGCCACATATATCTGT-T-TAGATGACTTCGTCACAATATCTGGCAGCCTCGTT
1 TCTGGTGGCCTAGCCACA-ATATCTGTATCTAG-TGACTTCGTCACAATATCTGGCAGCCTCGTT
41478904 GCAATCTGGTGGCTTCACCACATGTATATATATATATCTTT
64 GCAATCTGGTGGCTTCACCACATGTATATATATATATCTTT
41478945 TCTGGTGGCCTAGCCACAATATCTGTATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGTTGC
1 TCTGGTGGCCTAGCCACAATATCTGTATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGTTGC
41479010 AATCTGGTGGCTTCACCACATGTATATATATATATCTTT
66 AATCTGGTGGCTTCACCACATGTATATATATATATCTTT
41479049 TCTGGTGGCCTAGCCACAATATCTGTATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGTTGC
1 TCTGGTGGCCTAGCCACAATATCTGTATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGTTGC
41479114 AATCTGGTGGCTTCACCACATGTATATATATATATCTTT
66 AATCTGGTGGCTTCACCACATGTATATATATATATCTTT
41479153 TCTGGTGGCCTAGCCACAATATCTGTATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGTTGC
1 TCTGGTGGCCTAGCCACAATATCTGTATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGTTGC
41479218 AATCTGGTGGCTTCACCACATGTATATATATATATCTTT
66 AATCTGGTGGCTTCACCACATGTATATATATATATCTTT
*
41479257 TCTGGTGGCCTAGCCACAATATCTGTATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGCTGC
1 TCTGGTGGCCTAGCCACAATATCTGTATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGTTGC
41479322 AATCT
66 AATCT
41479327 TTGTGGTGTG
Statistics
Matches: 378, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
103 8 0.02
104 367 0.97
105 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (104 bp):
TCTGGTGGCCTAGCCACAATATCTGTATCTAGTGACTTCGTCACAATATCTGGCAGCCTCGTTGC
AATCTGGTGGCTTCACCACATGTATATATATATATCTTT
Found at i:41481104 original size:40 final size:40
Alignment explanation
Indices: 41481006--41481268 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
41480996 TCCTCGTTCA
* * * * *
41481006 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41481045 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
41481085 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGAACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41481125 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41481165 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
41481205 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
41481245 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41481269 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41489179 original size:40 final size:40
Alignment explanation
Indices: 41489081--41489343 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
41489071 TCCTCGTTCA
* * * * *
41489081 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41489120 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
41489160 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGTACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41489200 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41489240 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
41489280 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
41489320 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41489344 CAGCATTCAC
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41508812 original size:15 final size:16
Alignment explanation
Indices: 41508777--41508815 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
41508767 AACTAAAATA
*
41508777 AAAATAAACATTAAGT
1 AAAATAAACAATAAGT
*
41508793 AAAATAAATAATAA-T
1 AAAATAAACAATAAGT
41508808 AAAATAAA
1 AAAATAAA
41508816 ATCACTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAATAAACAATAAGT
Found at i:41511340 original size:15 final size:17
Alignment explanation
Indices: 41511320--41511351 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
41511310 ACATAAGATC
41511320 ACAAACA-AGTA-AAAA
1 ACAAACACAGTACAAAA
41511335 ACAAACACAGTACAAAA
1 ACAAACACAGTACAAAA
41511352 GTTGGTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.69, C:0.19, G:0.06, T:0.06
Consensus pattern (17 bp):
ACAAACACAGTACAAAA
Found at i:41516168 original size:25 final size:25
Alignment explanation
Indices: 41516132--41516179 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
41516122 CCCATTATCC
41516132 ATTAGTCCTAATTTACCTTTTTACT
1 ATTAGTCCTAATTTACCTTTTTACT
*
41516157 ATTAGTCTTAATTTACCTTTTTA
1 ATTAGTCCTAATTTACCTTTTTA
41516180 AGTTCTCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.25, C:0.17, G:0.04, T:0.54
Consensus pattern (25 bp):
ATTAGTCCTAATTTACCTTTTTACT
Found at i:41516928 original size:13 final size:13
Alignment explanation
Indices: 41516910--41516943 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
41516900 GGGGGTACAC
41516910 GGTCGTGTGACTA
1 GGTCGTGTGACTA
41516923 GGTCGTGTGACTA
1 GGTCGTGTGACTA
*
41516936 GGTTGTGT
1 GGTCGTGT
41516944 AACAGACTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.41, T:0.35
Consensus pattern (13 bp):
GGTCGTGTGACTA
Found at i:41523036 original size:2 final size:2
Alignment explanation
Indices: 41523023--41523072 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
41523013 GCTAAAATAG
* *
41523023 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
41523065 TC TT TC TC
1 TC TC TC TC
41523073 GCTCACTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:41529392 original size:6 final size:7
Alignment explanation
Indices: 41529353--41529419 Score: 68
Period size: 7 Copynumber: 9.6 Consensus size: 7
41529343 ATTTAATCCC
*
41529353 CAATTTC
1 CAATTTT
41529360 CAATTTT
1 CAATTTT
41529367 ACAA-TTT
1 -CAATTTT
41529374 CAATCTTT
1 CAAT-TTT
*
41529382 AAATTTT
1 CAATTTT
41529389 -AATTTT
1 CAATTTT
41529395 CAATTTT
1 CAATTTT
41529402 CAA-TTT
1 CAATTTT
41529408 CGAATTTT
1 C-AATTTT
41529416 CAAT
1 CAAT
41529420 CCTCAATCCT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
6 13 0.25
7 26 0.50
8 13 0.25
ACGTcount: A:0.33, C:0.15, G:0.01, T:0.51
Consensus pattern (7 bp):
CAATTTT
Found at i:41529473 original size:15 final size:15
Alignment explanation
Indices: 41529455--41529488 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41529445 ATTCTTTTTT
*
41529455 TTTTGAAATTTATTC
1 TTTTCAAATTTATTC
*
41529470 TTTTCAATTTTATTC
1 TTTTCAAATTTATTC
41529485 TTTT
1 TTTT
41529489 TTTTTAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTCAAATTTATTC
Found at i:41543730 original size:27 final size:27
Alignment explanation
Indices: 41543708--41544207 Score: 241
Period size: 27 Copynumber: 18.5 Consensus size: 27
41543698 TTAGTTTACC
41543708 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
41543735 ACATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
41543762 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
41543789 AAATTACCAAAATACCCCT-GATTTGTG
1 AAATTACCAAAATACCCCTAG-TTTGTA
** * **
41543816 AAATTACTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCTAG-TTTGTA
*** **
41543843 AAATTATTGAAATA-CCCTCAACTTGTA
1 AAATTACCAAAATACCCCT-AGTTTGTA
* * *
41543870 AAATTACCAAAGTACCCCTAATTTATA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * *
41543897 AAATTACCTAAATA-TCCTCGATTTGTA
1 AAATTACCAAAATACCCCTAG-TTTGTA
*
41543924 AAATTACCAAAATA-CCCTCAGTTTGCA
1 AAATTACCAAAATACCCCT-AGTTTGTA
** * *
41543951 AAATTACTGAAATA-CCCTCGATTTATA
1 AAATTACCAAAATACCCCTAG-TTTGTA
* * **
41543978 AAATTACTAAAATACTCCT-GTAAGATA
1 AAATTACCAAAATACCCCTAGTTTG-TA
* *** * *
41544005 GAATTACCATTTTA-CCCTCGATTTATA
1 AAATTACCAAAATACCCCTAG-TTTGTA
**** * *
41544032 AAATTACCGTTTTA-CCCTCAATTTATA
1 AAATTACCAAAATACCCCT-AGTTTGTA
* *** * **
41544059 GAATTACCATTTTA-CCCTCGATTTACA
1 AAATTACCAAAATACCCCTAG-TTTGTA
** * * **
41544086 AAATTACTGAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * ***
41544113 AAATTACCAAAATA-CCTTCGATCAATA
1 AAATTACCAAAATACCCCTAG-TTTGTA
*
41544140 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
41544167 AAATTACCAAAATACCCCT-GATTTGTG
1 AAATTACCAAAATACCCCTAG-TTTGTA
* *
41544194 GAATTACCGAAATA
1 AAATTACCAAAATA
41544208 TAGGGTAGAA
Statistics
Matches: 374, Mismatches: 82, Indels: 34
0.76 0.17 0.07
Matches are distributed among these distances:
26 19 0.05
27 338 0.90
28 17 0.05
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTTTGTA
Found at i:41543773 original size:54 final size:54
Alignment explanation
Indices: 41543708--41544207 Score: 318
Period size: 54 Copynumber: 9.3 Consensus size: 54
41543698 TTAGTTTACC
* *
41543708 AAATTACCAAAATACCCCTAGTTTGTAACATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTA
* *
41543762 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTA
** * ** *** * *
41543816 AAATTACTGAAATA-CCCTCGACCTGTAAAATTATTGAAATA-CCCTCAACTTGTA
1 AAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCCT-GATTTGTA
* * * * *
41543870 AAATTACCAAAGTACCCCTAATTTATAAAATTACCTAAATA-TCCTCGATTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCT-GATTTGTA
* ** *
41543924 AAATTACCAAAATA-CCCTCAGTTTGCAAAATTACTGAAATA-CCCTCGATTTATA
1 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCCT-GATTTGTA
* * ** * *** *
41543978 AAATTACTAAAATACTCCT-GTAAGATAGAATTACCATTTTA-CCCTCGATTTATA
1 AAATTACCAAAATACCCCTAGTTTG-TAAAATTACCAAAATACCCCT-GATTTGTA
**** * * * *** **
41544032 AAATTACCGTTTTA-CCCTCAATTTATAGAATTACCATTTTA-CCCTCGATTTACA
1 AAATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCCT-GATTTGTA
** * * ** * ***
41544086 AAATTACTGAAATACCCTTGGTTTACAAAATTACCAAAATA-CCTTCGATCAATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCT-GATTTGTA
* *
41544140 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTA
* *
41544194 GAATTACCGAAATA
1 AAATTACCAAAATA
41544208 TAGGGTAGAA
Statistics
Matches: 348, Mismatches: 88, Indels: 20
0.76 0.19 0.04
Matches are distributed among these distances:
53 19 0.05
54 315 0.91
55 14 0.04
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTA
Found at i:41543843 original size:81 final size:81
Alignment explanation
Indices: 41543708--41543992 Score: 310
Period size: 81 Copynumber: 3.5 Consensus size: 81
41543698 TTAGTTTACC
* * * *
41543708 AAATTACCAAAATACCCCT-AGTTTGTAACATTACCAAAATACCC-CTGGTTTGTAAAATTATCA
1 AAATTACCAAAATACCCCTGA-TTTATAAAATTACTAAAATACCCTC-GATTTGTAAAATTATCA
41543771 AAATACCC-CTAGTTTGTA
64 AAATACCCTC-AGTTTGTA
* * * ** **
41543789 AAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATACCCTCGACCTGTAAAATTATTGAA
1 AAATTACCAAAATACCCCTGATTTATAAAATTACTAAAATACCCTCGATTTGTAAAATTATCAAA
**
41543854 ATACCCTCAACTTGTA
66 ATACCCTCAGTTTGTA
* * * *
41543870 AAATTACCAAAGTACCCCTAATTTATAAAATTACCT-AAATATCCTCGATTTGTAAAATTACCAA
1 AAATTACCAAAATACCCCTGATTTATAAAATTA-CTAAAATACCCTCGATTTGTAAAATTATCAA
*
41543934 AATACCCTCAGTTTGCA
65 AATACCCTCAGTTTGTA
**
41543951 AAATTACTGAAATA-CCCTCGATTTATAAAATTACTAAAATAC
1 AAATTACCAAAATACCCCT-GATTTATAAAATTACTAAAATAC
41543993 TCCTGTAAGA
Statistics
Matches: 169, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
80 6 0.04
81 158 0.93
82 5 0.03
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (81 bp):
AAATTACCAAAATACCCCTGATTTATAAAATTACTAAAATACCCTCGATTTGTAAAATTATCAAA
ATACCCTCAGTTTGTA
Found at i:41544238 original size:27 final size:27
Alignment explanation
Indices: 41544208--41544356 Score: 210
Period size: 27 Copynumber: 5.6 Consensus size: 27
41544198 TACCGAAATA
*
41544208 TAGGGTAGAATTACCGAAATACCCATG
1 TAGGGTAGAATTACCGAAATACCCCTG
*
41544235 TAGGGTAGAATTACCGAAATACCCCTA
1 TAGGGTAGAATTACCGAAATACCCCTG
41544262 TAGGGTAGAATTACCGAAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
* * *
41544289 TAGCGTAGAATTACCAAAATACCCCTA
1 TAGGGTAGAATTACCGAAATACCCCTG
* *
41544316 TAGGGTAGAATTACCGAGATA-CCTTG
1 TAGGGTAGAATTACCGAAATACCCCTG
* *
41544342 TGGGGTAAAATTACC
1 TAGGGTAGAATTACC
41544357 ATTTTGCCCT
Statistics
Matches: 109, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
26 16 0.15
27 93 0.85
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (27 bp):
TAGGGTAGAATTACCGAAATACCCCTG
Found at i:41544291 original size:54 final size:54
Alignment explanation
Indices: 41544206--41544357 Score: 234
Period size: 54 Copynumber: 2.8 Consensus size: 54
41544196 ATTACCGAAA
*
41544206 TATAGGGTAGAATTACCGAAATACCCATGTAGGGTAGAATTACCGAAATACCCC
1 TATAGGGTAGAATTACCGAAATACCCATGTAGGGTAGAATTACCAAAATACCCC
* *
41544260 TATAGGGTAGAATTACCGAAATACCCCTGTAGCGTAGAATTACCAAAATACCCC
1 TATAGGGTAGAATTACCGAAATACCCATGTAGGGTAGAATTACCAAAATACCCC
* * * *
41544314 TATAGGGTAGAATTACCGAGATA-CCTTGTGGGGTAAAATTACCA
1 TATAGGGTAGAATTACCGAAATACCCATGTAGGGTAGAATTACCA
41544358 TTTTGCCCTT
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
53 17 0.19
54 73 0.81
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (54 bp):
TATAGGGTAGAATTACCGAAATACCCATGTAGGGTAGAATTACCAAAATACCCC
Found at i:41544835 original size:22 final size:22
Alignment explanation
Indices: 41544783--41544847 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
41544773 TTAAAGCCTT
* *
41544783 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
41544805 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
41544827 TTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
41544848 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:41545036 original size:27 final size:27
Alignment explanation
Indices: 41545006--41545107 Score: 125
Period size: 27 Copynumber: 3.8 Consensus size: 27
41544996 ATTCTGTTAA
*
41545006 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTTTGCCACAATATCTGTTTCTG
* *
41545033 GTGGCTATGCCGCAAATATCTG-TTCTG
1 GTGGCTTTGCCAC-AATATCTGTTTCTG
* *
41545060 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTTTGCCACAATATCTGTTTCTG
* *
41545087 GTGACTTTGTCACAATATCTG
1 GTGGCTTTGCCACAATATCTG
41545108 ATAACTGAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 8 0.12
27 49 0.77
28 7 0.11
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (27 bp):
GTGGCTTTGCCACAATATCTGTTTCTG
Found at i:41545282 original size:6 final size:6
Alignment explanation
Indices: 41545267--41545388 Score: 74
Period size: 6 Copynumber: 19.8 Consensus size: 6
41545257 AGTCTGTTAC
* * *
41545267 CTGATA CTGATT CTGATT CTG-TT ACCTGATAT -TGATT CTAATT TTGATT
1 CTGATT CTGATT CTGATT CTGATT --CTGAT-T CTGATT CTGATT CTGATT
* * *
41545316 CTG-TT ACCTGATA CTGATT CTAATT CTGATT CTG-TCAC CTGATT CTGATT
1 CTGATT --CTGATT CTGATT CTGATT CTGATT CTGAT--T CTGATT CTGATT
*
41545366 CTGATT CTAATT CT-AGTT CTGAT
1 CTGATT CTGATT CTGA-TT CTGAT
41545389 AATGTTTCTT
Statistics
Matches: 91, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
5 7 0.08
6 70 0.77
7 10 0.11
8 3 0.03
9 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (6 bp):
CTGATT
Found at i:41545289 original size:25 final size:25
Alignment explanation
Indices: 41545259--41545368 Score: 100
Period size: 25 Copynumber: 4.2 Consensus size: 25
41545249 GATTTTTGAG
41545259 TCTGTTACCTGATACTGATTCTGAT
1 TCTGTTACCTGATACTGATTCTGAT
*
41545284 TCTGTTACCTGATATTGATTCTAATTTTGAT
1 TCTGTTACCTGATACTGATTC------TGAT
*
41545315 TCTGTTACCTGATACTGATTCTAAT
1 TCTGTTACCTGATACTGATTCTGAT
41545340 TCTGATT--CTG-TCACCTGATTCTGAT
1 TCTG-TTACCTGAT-A-CTGATTCTGAT
41545365 TCTG
1 TCTG
41545369 ATTCTAATTC
Statistics
Matches: 72, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
23 1 0.01
24 4 0.06
25 41 0.57
26 2 0.03
31 24 0.33
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (25 bp):
TCTGTTACCTGATACTGATTCTGAT
Found at i:41545318 original size:31 final size:31
Alignment explanation
Indices: 41545276--41545404 Score: 147
Period size: 31 Copynumber: 4.2 Consensus size: 31
41545266 CCTGATACTG
41545276 ATTCTGATTCTGTTACCTGATATTGATTCTA
1 ATTCTGATTCTGTTACCTGATATTGATTCTA
* *
41545307 ATTTTGATTCTGTTACCTGATACTGATTCTA
1 ATTCTGATTCTGTTACCTGATATTGATTCTA
* *
41545338 ATTCTGATTCTGTCACCTGAT-TCTGATTCTG
1 ATTCTGATTCTGTTACCTGATAT-TGATTCTA
* * * *
41545369 ATTCTAATTCTAGTT--CTGATAATGTTTCTT
1 ATTCTGATTCT-GTTACCTGATATTGATTCTA
41545399 ATTCTG
1 ATTCTG
41545405 TAATGGGTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
30 16 0.19
31 65 0.78
32 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGTTACCTGATATTGATTCTA
Found at i:41545359 original size:56 final size:55
Alignment explanation
Indices: 41545252--41545373 Score: 149
Period size: 56 Copynumber: 2.2 Consensus size: 55
41545242 ACATTCTGAT
* * *
41545252 TTTTGAGTCTGTTACCTGATACTGATTCTGATTCTGTTACCTGATATTGATTCTAA
1 TTTTGATTCTGTTACCTGATACTGATTCTAATTCTGTTA-CTGATACTGATTCTAA
*
41545308 TTTTGATTCTGTTACCTGATACTGATTCTAATTCTGATT-CTG-TCACCTGATTCTGA
1 TTTTGATTCTGTTACCTGATACTGATTCTAATTCTG-TTACTGAT-A-CTGATTCTAA
*
41545364 TTCTGATTCT
1 TTTTGATTCT
41545374 AATTCTAGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
54 1 0.02
55 4 0.07
56 51 0.88
57 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (55 bp):
TTTTGATTCTGTTACCTGATACTGATTCTAATTCTGTTACTGATACTGATTCTAA
Found at i:41550328 original size:23 final size:23
Alignment explanation
Indices: 41550302--41550346 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
41550292 CATTTCTACG
41550302 CCTTAATCATCGAGGCAGGTTCA
1 CCTTAATCATCGAGGCAGGTTCA
*
41550325 CCTTAATCATCGAGGTAGGTTC
1 CCTTAATCATCGAGGCAGGTTC
41550347 GTATGATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (23 bp):
CCTTAATCATCGAGGCAGGTTCA
Found at i:41577371 original size:12 final size:12
Alignment explanation
Indices: 41577354--41577380 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41577344 ATTCCGAAGT
41577354 ATATATATATAC
1 ATATATATATAC
41577366 ATATATATATAC
1 ATATATATATAC
41577378 ATA
1 ATA
41577381 AGTATGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:41577893 original size:27 final size:27
Alignment explanation
Indices: 41577862--41578039 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41577852 TAAATTGTAC
41577862 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41577889 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41577915 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
41577943 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41577971 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41577998 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41578025 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41578040 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41577976 original size:82 final size:81
Alignment explanation
Indices: 41577863--41578018 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41577853 AAATTGTACA
* *
41577863 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
41577927 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41577944 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
41578009 TGCGAGTTGA
65 TGCGAATTGA
41578019 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41578030 original size:82 final size:81
Alignment explanation
Indices: 41577859--41578039 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
41577849 GATTAAATTG
* *
41577859 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
41577924 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
41577940 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
41578004 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41578022 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41578040 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41584454 original size:14 final size:14
Alignment explanation
Indices: 41584435--41584464 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
41584425 CATTCCGAAG
41584435 TATATATATATACA
1 TATATATATATACA
41584449 TATATATATATACA
1 TATATATATATACA
41584463 TA
1 TA
41584465 AGTATGCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TATATATATATACA
Found at i:41584977 original size:27 final size:27
Alignment explanation
Indices: 41584946--41585123 Score: 207
Period size: 27 Copynumber: 6.6 Consensus size: 27
41584936 TGAATTGTAC
41584946 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41584973 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
41584999 ATGCACTAAGTGTGCGAATTGACCATG-
1 A-GCACTAAGTGTGCGATTTGACTATGT
41585026 AGGCACTAAGTGTGCGAGTTTGACTATGT
1 A-GCACTAAGTGTGCGA-TTTGACTATGT
* *
41585055 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41585082 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41585109 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41585124 GACTCAATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 107 0.82
28 23 0.18
29 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41585060 original size:82 final size:81
Alignment explanation
Indices: 41584947--41585102 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41584937 GAATTGTACA
* *
41584947 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
41585011 TGCGAATTGACCATGAG
65 TGCGAATTGACCATGAG
** *
41585028 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
41585093 TGCGAGTTGA
65 TGCGAATTGA
41585103 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGAG
Found at i:41586180 original size:150 final size:150
Alignment explanation
Indices: 41585908--41586215 Score: 589
Period size: 150 Copynumber: 2.1 Consensus size: 150
41585898 TAATTGATGA
41585908 ATAAATTATGTAATCGAAGCTCGATGAGTCTGTTTTCATGAGGAAGTAACGAAAAGATCATATGG
1 ATAAATTATGTAATCGAAGCTCGATGAGTCTGTTTTCATGAGGAAGTAACGAAAAGATCATATGG
41585973 GCAGTATATTAAGAGATAATCAGATTTTTGTGGGACAGGGCCAGAACAGTTTCTGGATTCCCTGC
66 GCAGTATATTAAGAGATAATCAGATTTTTGTGGGACAGGGCCAGAACAGTTTCTGGATTCCCTGC
41586038 TCCGAATTTGGAAATTCATT
131 TCCGAATTTGGAAATTCATT
*
41586058 GTAAATTATGTAATCGAAGCTCGATGAGTCTGTTTTCATGAGGAAGTAACGAAAAGATCATATGG
1 ATAAATTATGTAATCGAAGCTCGATGAGTCTGTTTTCATGAGGAAGTAACGAAAAGATCATATGG
*
41586123 GCAGTATATTAAGAGATAATCAGATTTTTGTGGGACAGGGCCAGAACGGTTTCTGGATTCCCTGC
66 GCAGTATATTAAGAGATAATCAGATTTTTGTGGGACAGGGCCAGAACAGTTTCTGGATTCCCTGC
*
41586188 TCCGACTTTGGAAATTCATT
131 TCCGAATTTGGAAATTCATT
41586208 ATAAATTA
1 ATAAATTA
41586216 ACCAGAGATA
Statistics
Matches: 154, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 154 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (150 bp):
ATAAATTATGTAATCGAAGCTCGATGAGTCTGTTTTCATGAGGAAGTAACGAAAAGATCATATGG
GCAGTATATTAAGAGATAATCAGATTTTTGTGGGACAGGGCCAGAACAGTTTCTGGATTCCCTGC
TCCGAATTTGGAAATTCATT
Found at i:41587686 original size:12 final size:12
Alignment explanation
Indices: 41587654--41587687 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41587644 ATCCTGGAAT
* *
41587654 ATTAAGAAAAGA
1 ATTAAGAACACA
41587666 ATTAAGAACACA
1 ATTAAGAACACA
41587678 ATTAAGAACA
1 ATTAAGAACA
41587688 AGTCAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.18
Consensus pattern (12 bp):
ATTAAGAACACA
Found at i:41599603 original size:24 final size:24
Alignment explanation
Indices: 41599576--41599622 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
41599566 TAGGGGTAGG
*
41599576 ATCTAATTCTGTATTTGAAATTGC
1 ATCTAATTCTGTATATGAAATTGC
* *
41599600 ATCTAATTTTGTATATGAGATTG
1 ATCTAATTCTGTATATGAAATTG
41599623 ACATTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (24 bp):
ATCTAATTCTGTATATGAAATTGC
Found at i:41605803 original size:25 final size:25
Alignment explanation
Indices: 41605775--41605853 Score: 113
Period size: 25 Copynumber: 3.2 Consensus size: 25
41605765 TCTTCTAAGG
*
41605775 TGAATAATGAGAAGCTCATGCGAGC
1 TGAATAACGAGAAGCTCATGCGAGC
* *
41605800 TGAATAACGGGAAGCTCAAGCGAGC
1 TGAATAACGAGAAGCTCATGCGAGC
**
41605825 TGAATAACGAGAAGCTCATAAGAGC
1 TGAATAACGAGAAGCTCATGCGAGC
41605850 TGAA
1 TGAA
41605854 ATTGGTGACC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.16
Consensus pattern (25 bp):
TGAATAACGAGAAGCTCATGCGAGC
Found at i:41613659 original size:38 final size:38
Alignment explanation
Indices: 41613627--41613755 Score: 163
Period size: 38 Copynumber: 3.4 Consensus size: 38
41613617 GCAGGCTATA
*
41613627 TGCTGGAATTATATCCGGGTTAAATCTCGCAGGCTTCG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
* *
41613665 TGTTGGTAA-TATA-CTTGGGTTAAATCCCGCAGGCTTCG
1 TGCTGG-AATTATATC-CGGGTTAAATCCCGCAGGCTTCG
* * *
41613703 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
*
41613741 TGCTGGTATTATATC
1 TGCTGGAATTATATC
41613756 TGAGCTTCAA
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
37 2 0.03
38 74 0.94
39 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (38 bp):
TGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:41613784 original size:40 final size:38
Alignment explanation
Indices: 41613598--41613787 Score: 159
Period size: 38 Copynumber: 4.9 Consensus size: 38
41613588 ATTTGATGTG
* * *
41613598 TATCCGGGCTTAAAGACTCGCAGGCTATA-TGCTGGAATTA
1 TATCC-GGCTTAAA-TCCCGCAGGCT-TAGTGCTGGTATTA
* * * * *
41613638 TATCCGGGTTAAATCTCGCAGGCTTCGTGTTGGTAATA
1 TATCCGGCTTAAATCCCGCAGGCTTAGTGCTGGTATTA
* * *
41613676 TA-CTTGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATC-CGGCTTAAATCCCGCAGGCTTAGTGCTGGTATTA
* *
41613714 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGCTTAAATCCCGCAGGCTTAGTGCTGGTATTA
* * * *
41613752 TATCTGAGCTTCAAGTCCCGCAGGTTTTGTGCTGGT
1 TATCCG-GCTT-AAATCCCGCAGGCTTAGTGCTGGT
41613788 GACTGGATTC
Statistics
Matches: 126, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
37 2 0.02
38 88 0.70
39 11 0.09
40 25 0.20
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (38 bp):
TATCCGGCTTAAATCCCGCAGGCTTAGTGCTGGTATTA
Found at i:41621786 original size:38 final size:38
Alignment explanation
Indices: 41621744--41621887 Score: 175
Period size: 38 Copynumber: 3.8 Consensus size: 38
41621734 GGCTTAAAGA
* **
41621744 CTCGCAGGCTAT-ATGCTGGAATTATATCCAGGTTAAAT
1 CTCGCAGGCT-TCGTGCTGGAATTATATCTGGGTTAAAT
41621782 CTCGCAGGCTTCGTGCTGGTAA-TATATCTGGGTTAAAT
1 CTCGCAGGCTTCGTGCTGG-AATTATATCTGGGTTAAAT
* *
41621820 CCCGCAGGCTTCGTGCTGGTATTATATCTGGGTTAAAT
1 CTCGCAGGCTTCGTGCTGGAATTATATCTGGGTTAAAT
* * * *
41621858 CTCACAGGCCTAGTGCTGGTATTATATCTG
1 CTCGCAGGCTTCGTGCTGGAATTATATCTG
41621888 AGCTTAAAGT
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
37 2 0.02
38 90 0.96
39 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (38 bp):
CTCGCAGGCTTCGTGCTGGAATTATATCTGGGTTAAAT
Found at i:41621844 original size:76 final size:78
Alignment explanation
Indices: 41621735--41621904 Score: 211
Period size: 76 Copynumber: 2.2 Consensus size: 78
41621725 GTGTATCCGG
* * * * * *
41621735 GCTTAAAGACTCGCAGGCTAT-ATGCTGGAATTATATCCAGGTTAAATCTCGCAGGCTTCGTGCT
1 GCTTAAAGTCCCGCAGGCT-TCGTGCTGGAATTATATCCAGGTTAAATCTCACAGGCCTAGTGCT
41621799 GGTAATATATCTG-
65 GGTAATATATCTGA
* * **
41621812 GGTTAAA-TCCCGCAGGCTTCGTGCTGGTATTATATCTGGGTTAAATCTCACAGGCCTAGTGCTG
1 GCTTAAAGTCCCGCAGGCTTCGTGCTGGAATTATATCCAGGTTAAATCTCACAGGCCTAGTGCTG
*
41621876 GTATTATATCTGA
66 GTAATATATCTGA
41621889 GCTTAAAGTCCCGCAG
1 GCTTAAAGTCCCGCAG
41621905 TTTTTGTGTT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
75 1 0.01
76 57 0.73
77 12 0.15
78 8 0.10
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (78 bp):
GCTTAAAGTCCCGCAGGCTTCGTGCTGGAATTATATCCAGGTTAAATCTCACAGGCCTAGTGCTG
GTAATATATCTGA
Found at i:41624972 original size:40 final size:40
Alignment explanation
Indices: 41624905--41624980 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
41624895 AGTATATTTG
* *
41624905 ACACTTAGTGTGCGCTTCAAAATAGCTTCAGCTATAAATA
1 ACACTTAGTGTGCGATTCAAAACAGCTTCAGCTATAAATA
* *
41624945 ACACTTAGTGTGCGAATT-AGAACAGCTTCGGCTATA
1 ACACTTAGTGTGCG-ATTCAAAACAGCTTCAGCTATA
41624981 TGAGGCATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (40 bp):
ACACTTAGTGTGCGATTCAAAACAGCTTCAGCTATAAATA
Found at i:41627294 original size:42 final size:42
Alignment explanation
Indices: 41627224--41627373 Score: 130
Period size: 42 Copynumber: 3.5 Consensus size: 42
41627214 CGAAAAACTC
*
41627224 ATACAATGCCAACGTCCCAGA-AGTGGTCTTACATGTAATC-A
1 ATACGATGCCAACGTCCCAGACAG-GGTCTTACATGTAATCAA
*
41627265 ATATCGATGCC-ACTGTCCCAGACAGGGTCTTACACG-AGATCAA
1 ATA-CGATGCCAAC-GTCCCAGACAGGGTCTTACATGTA-ATCAA
* * * * *
41627308 ATACGATGCCGACGTCCAAGTCATGGTCTTATATGTAAATCATA
1 ATACGATGCCAACGTCCCAGACAGGGTCTTACATGT-AATCA-A
*
41627352 AGT-CAATGCCAACGTCCCAGAC
1 A-TACGATGCCAACGTCCCAGAC
41627374 TTTGTCTTAC
Statistics
Matches: 88, Mismatches: 11, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
41 6 0.07
42 51 0.58
43 12 0.14
44 18 0.20
45 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (42 bp):
ATACGATGCCAACGTCCCAGACAGGGTCTTACATGTAATCAA
Found at i:41628968 original size:17 final size:17
Alignment explanation
Indices: 41628929--41628961 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41628919 TAGCTCAAGT
41628929 GGCAACAACAATCTGTA
1 GGCAACAACAATCTGTA
41628946 GGCAACAACAATCTGT
1 GGCAACAACAATCTGT
41628962 GTGCAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (17 bp):
GGCAACAACAATCTGTA
Found at i:41635364 original size:79 final size:79
Alignment explanation
Indices: 41635233--41635393 Score: 286
Period size: 79 Copynumber: 2.0 Consensus size: 79
41635223 ACCTTGTACG
*
41635233 GAAAGCTGTCTTTGGAATGTCGCTTCCTTTTACTTTCAACTGGTAGTAGCCTGACCTTAAGTCAA
1 GAAAGCTGTCTTTGGAATGTCGCTTCCTTTTAATTTCAACTGGTAGTAGCCTGACCTTAAGTCAA
*
41635298 TCTTCGAAAATACA
66 TCTTCAAAAATACA
*
41635312 GAAAGCTGTCTTTGGAATGTCGCTTCCTTTTAATTTTAACTGGTAGTAGCCTGACCTTAAGTCAA
1 GAAAGCTGTCTTTGGAATGTCGCTTCCTTTTAATTTCAACTGGTAGTAGCCTGACCTTAAGTCAA
*
41635377 TCTTTAAAAATACA
66 TCTTCAAAAATACA
41635391 GAA
1 GAA
41635394 GCTCCTTTTA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (79 bp):
GAAAGCTGTCTTTGGAATGTCGCTTCCTTTTAATTTCAACTGGTAGTAGCCTGACCTTAAGTCAA
TCTTCAAAAATACA
Found at i:41637995 original size:42 final size:42
Alignment explanation
Indices: 41637935--41638022 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
41637925 GGGCTCCCAT
* * *
41637935 GGCCGTAGGGCCAGCCTGTAGGCATATCTGA-CTTACTCACAC
1 GGCCGTAGGACCAACCTGTAGGCAGATCTGACCTTAC-CACAC
* * * *
41637977 GGCCGTAGGACTAACCTGTGGGCAGGTCTGACCTTTCCACAC
1 GGCCGTAGGACCAACCTGTAGGCAGATCTGACCTTACCACAC
41638019 GGCC
1 GGCC
41638023 TGGGCACACG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 34 0.89
43 4 0.11
ACGTcount: A:0.19, C:0.32, G:0.28, T:0.20
Consensus pattern (42 bp):
GGCCGTAGGACCAACCTGTAGGCAGATCTGACCTTACCACAC
Found at i:41640408 original size:40 final size:40
Alignment explanation
Indices: 41640310--41640572 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
41640300 TCCTCGTTCA
* * * ** *
41640310 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
41640349 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
41640389 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
41640429 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
41640469 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
41640509 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
41640549 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41640573 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:41648358 original size:40 final size:40
Alignment explanation
Indices: 41648260--41648522 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
41648250 TCCTCGTTCA
* * * * *
41648260 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41648299 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41648339 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41648379 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41648419 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
41648459 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
41648499 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41648523 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41648531 original size:41 final size:41
Alignment explanation
Indices: 41648454--41648531 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41648444 TTAGTATCTC
* * *
41648454 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41648495 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41648532 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41651152 original size:3 final size:3
Alignment explanation
Indices: 41651131--41651174 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
41651121 TTATCTCAAT
41651131 TAA TAGA TAA -AA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41651175 GTAAATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:41656402 original size:41 final size:40
Alignment explanation
Indices: 41656331--41656445 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 40
41656321 TAAATAAGGC
*
41656331 CACGTATGTGCAATTCAAGGGTATTAAAGTACAAACATAGG
1 CACGTATGTGCAATT-AAGGGTATTAAAGTACAAACAGAGG
* * *
41656372 CACGTATGTGTAATTAAGGGTTATTTAAGTACAAATAGAGG
1 CACGTATGTGCAATTAAGGG-TATTAAAGTACAAACAGAGG
* * *
41656413 CACGTGTGTGCAATTCAGGGGTATTGAAGTACA
1 CACGTATGTGCAATT-AAGGGTATTAAAGTACA
41656446 CTTACATTGA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 5 0.08
41 55 0.86
42 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (40 bp):
CACGTATGTGCAATTAAGGGTATTAAAGTACAAACAGAGG
Found at i:41658589 original size:21 final size:20
Alignment explanation
Indices: 41658567--41658606 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
41658557 TTTTACTTAA
41658567 TTAACTAACTAAATGTTAAAAT
1 TTAA-TAACTAAAT-TTAAAAT
*
41658589 TTTATAACTAAATTTAAA
1 TTAATAACTAAATTTAAA
41658607 TACCACACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 9 0.53
22 3 0.18
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (20 bp):
TTAATAACTAAATTTAAAAT
Found at i:41660445 original size:25 final size:24
Alignment explanation
Indices: 41660412--41660461 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
41660402 GAAACTGAAC
41660412 TAAAACATAACGAAATGCTTGTAT
1 TAAAACATAACGAAATGCTTGTAT
*
41660436 TAAATACATAACGAAATGTTTGTAT
1 TAAA-ACATAACGAAATGCTTGTAT
41660461 T
1 T
41660462 CAATCTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (24 bp):
TAAAACATAACGAAATGCTTGTAT
Found at i:41672099 original size:47 final size:47
Alignment explanation
Indices: 41672039--41672382 Score: 496
Period size: 47 Copynumber: 7.3 Consensus size: 47
41672029 GTACAAGATA
41672039 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
** *
41672086 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
41672133 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACGTG
1 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
41672180 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
1 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
* *
41672227 TGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-AGTG
1 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
* * * **
41672274 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTG
1 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
41672321 TGTATATGTGATAAGGCCTAATGGCCAATGTGATGGATGTGAA-AGTG
1 TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
* *
41672368 TTTAAATGTGATAAG
1 TGTATATGTGATAAG
41672383 TCCCGAAGGG
Statistics
Matches: 274, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
47 274 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TGTATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
Found at i:41672166 original size:22 final size:22
Alignment explanation
Indices: 41672139--41672213 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
41672129 CATGTGTATG
41672139 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
41672161 TGTGATGAATG-TGAACGTGTG-TATA
1 TGTGAT-AAGGCCGAA--TG-GCCA-A
41672186 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
41672208 TGTGAT
1 TGTGAT
41672214 GAATGTGAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 17 0.43
23 6 0.15
24 6 0.15
25 11 0.28
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.27
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:41680281 original size:47 final size:47
Alignment explanation
Indices: 41679944--41680269 Score: 620
Period size: 47 Copynumber: 7.0 Consensus size: 47
41679934 NNNNNNNNNN
41679944 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
41679991 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
*
41680038 TATGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
41680085 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
41680132 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
41680179 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
*
41680226 TGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAA-A-GTGTAT
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTAT
41680270 AAATGTGATA
Statistics
Matches: 276, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
45 6 0.02
46 1 0.00
47 269 0.97
ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28
Consensus pattern (47 bp):
TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATG
Done.