Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 90 of 279
Found at i:29676369 original size:21 final size:21
Alignment explanation
Indices: 29676331--29676379 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
29676321 CTAATTATAA
* *
29676331 AGAACTTTGAGAAATTTAATG
1 AGAAATTTGAGAAATTTAAGG
** *
29676352 AGAAATTTGAGAGCTTTAGGG
1 AGAAATTTGAGAAATTTAAGG
29676373 AGAAATT
1 AGAAATT
29676380 GTAGAGATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (21 bp):
AGAAATTTGAGAAATTTAAGG
Found at i:29678577 original size:69 final size:69
Alignment explanation
Indices: 29678421--29678563 Score: 223
Period size: 69 Copynumber: 2.1 Consensus size: 69
29678411 TTCTCGAATG
* * *
29678421 AACAAACGAGAAAGAGAGGGAGGGAGCATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTGAA
1 AACAAACAAGAAAGAGAGGAAGGGAACATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTGAA
29678486 GATA
66 GATA
* * *
29678490 AACAAACAAGAAAGAGAGGAAGGGAACATGTTTGGCGGCATGGTTTGGAGGTTGGGACAGTTGAA
1 AACAAACAAGAAAGAGAGGAAGGGAACATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTGAA
29678555 GATA
66 GATA
*
29678559 GACAA
1 AACAA
29678564 TTTGCAAAGA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.36, C:0.10, G:0.36, T:0.17
Consensus pattern (69 bp):
AACAAACAAGAAAGAGAGGAAGGGAACATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTGAA
GATA
Found at i:29683150 original size:16 final size:16
Alignment explanation
Indices: 29683129--29683180 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
29683119 TTATATTTAA
29683129 TAATATAATAAATTAT
1 TAATATAATAAATTAT
29683145 TAATATAATAAATTAT
1 TAATATAATAAATTAT
29683161 T--T-TAATAAATTACT
1 TAATATAATAAATTA-T
29683175 TAATAT
1 TAATAT
29683181 TTTAATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 10 0.31
14 3 0.09
16 18 0.56
17 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATATAATAAATTAT
Found at i:29683216 original size:16 final size:16
Alignment explanation
Indices: 29683195--29683225 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29683185 ATTTTATTTT
29683195 AATAATAATTTTAAAA
1 AATAATAATTTTAAAA
29683211 AATAATAATTTTAAA
1 AATAATAATTTTAAA
29683226 TTACATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAATTTTAAAA
Found at i:29683284 original size:15 final size:15
Alignment explanation
Indices: 29683264--29683320 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
29683254 ATTCAATATT
29683264 AATATTTTAATAATA
1 AATATTTTAATAATA
*
29683279 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
29683298 AATATATTAATAATA
1 AATATTTTAATAATA
29683313 AATATTTT
1 AATATTTT
29683321 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:29683623 original size:39 final size:39
Alignment explanation
Indices: 29683555--29683631 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
29683545 GTTATAAAAA
* * *
29683555 GTATTTAGTTACAAAGTTGAGTTTCCAATAGGAGTTTGT
1 GTATTTAGCTACAAAATTGAGTTTCCAATAGGAATTTGT
* * *
29683594 GTATTTGGCTACAAAATTGTGTTTTCAATAGGAATTTG
1 GTATTTAGCTACAAAATTGAGTTTCCAATAGGAATTTG
29683632 AGTAATAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.42
Consensus pattern (39 bp):
GTATTTAGCTACAAAATTGAGTTTCCAATAGGAATTTGT
Found at i:29688723 original size:13 final size:13
Alignment explanation
Indices: 29688705--29688729 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29688695 TGTGGGTTCA
29688705 CACGGCCGTGTTG
1 CACGGCCGTGTTG
29688718 CACGGCCGTGTT
1 CACGGCCGTGTT
29688730 TAGCTTCGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (13 bp):
CACGGCCGTGTTG
Found at i:29694772 original size:23 final size:23
Alignment explanation
Indices: 29694742--29694788 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
29694732 GAGTTTGTGA
29694742 AAACTCACCCCTTTATTTATTTT
1 AAACTCACCCCTTTATTTATTTT
29694765 AAACTCACCCCTTTATTTATTTT
1 AAACTCACCCCTTTATTTATTTT
29694788 A
1 A
29694789 TGTCAGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.47
Consensus pattern (23 bp):
AAACTCACCCCTTTATTTATTTT
Found at i:29703316 original size:43 final size:42
Alignment explanation
Indices: 29703212--29703320 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
29703202 CGAGATGTGT
* * *
29703212 TTACATGTAAGACCATGTCTGGGACATTGGAATGTATTGCGA
1 TTACGTGTAAGACCATGTCTGGGACATTAGAATGTAATGCGA
* *
29703254 TTACGTGTAATACCATGTCTGGGACATTAGCATCGTTAAT-CGA
1 TTACGTGTAAGACCATGTCTGGGACATTAGAAT-G-TAATGCGA
* *
29703297 TTTCGTGTAAGACCCTGTCTGGGA
1 TTACGTGTAAGACCATGTCTGGGA
29703321 TAGTGGCATC
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 29 0.51
43 25 0.44
44 3 0.05
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (42 bp):
TTACGTGTAAGACCATGTCTGGGACATTAGAATGTAATGCGA
Found at i:29703330 original size:43 final size:43
Alignment explanation
Indices: 29703212--29703331 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 43
29703202 CGAGATGTGT
* * *
29703212 TTACATGTAAGACCATGTCTGGGACATTGGAAT-GTATTGCGA
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTAATGCGA
* *
29703254 TTACGTGTAATACCATGTCTGGGACATTAGCATCGTTAAT-CGA
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATCG-TAATGCGA
* * * *
29703297 TTTCGTGTAAGACCCTGTCTGGGATAGTGGCATCG
1 TTACGTGTAAGACCATGTCTGGGACATTGGCATCG
29703332 ATATGTGATA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 29 0.45
43 33 0.51
44 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACATTGGCATCGTAATGCGA
Found at i:29709805 original size:18 final size:18
Alignment explanation
Indices: 29709762--29709805 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
29709752 CGTGTGGGCC
* *
29709762 ACACGGGAGTGTGGGAGT
1 ACACGGGCGTGTGGGAGA
29709780 ACACGGGCGTGTGGGAGA
1 ACACGGGCGTGTGGGAGA
29709798 ACACGGGC
1 ACACGGGC
29709806 AGGCCATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.18, G:0.48, T:0.11
Consensus pattern (18 bp):
ACACGGGCGTGTGGGAGA
Found at i:29710212 original size:23 final size:24
Alignment explanation
Indices: 29710186--29710230 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
29710176 TAATCCACAT
*
29710186 ATGGAGTGTAG-GGTTGGATGGAG
1 ATGGAGTGTAGAGGCTGGATGGAG
*
29710209 ATGGTGTGTAGAGGCTGGATGG
1 ATGGAGTGTAGAGGCTGGATGG
29710231 GTAGGACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.02, G:0.51, T:0.27
Consensus pattern (24 bp):
ATGGAGTGTAGAGGCTGGATGGAG
Found at i:29717455 original size:21 final size:18
Alignment explanation
Indices: 29717429--29717473 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
29717419 ATTATATATG
29717429 TATATATA-ATCGAGACACA
1 TATATATATATCG-GA-ACA
29717448 TATATATATATCGGAACA
1 TATATATATATCGGAACA
29717466 TAT-TATAT
1 TATATATAT
29717474 GAACTGAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.20
18 6 0.24
19 10 0.40
20 4 0.16
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
TATATATATATCGGAACA
Found at i:29719784 original size:39 final size:39
Alignment explanation
Indices: 29719730--29719811 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
29719720 AATTAACCTT
29719730 AAAAAAACAACTTAAACTTTTAACAGTCTAGTAGTATTG
1 AAAAAAACAACTTAAACTTTTAACAGTCTAGTAGTATTG
*
29719769 AAAAAAACAACTTAAACTTTTAACGGTCTAGTAGTATTG
1 AAAAAAACAACTTAAACTTTTAACAGTCTAGTAGTATTG
29719808 AAAA
1 AAAA
29719812 TCTATAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (39 bp):
AAAAAAACAACTTAAACTTTTAACAGTCTAGTAGTATTG
Found at i:29720275 original size:38 final size:38
Alignment explanation
Indices: 29720195--29720276 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 38
29720185 AAGGTCATAG
* * *
29720195 CCACAATTAACCCCAACGGTAATGGGTTGGAACAAAAG
1 CCACAATTAACCCCAACGGTAATGGATTGAAACAAAAA
** * *
29720233 CCACAATTAACCCCAGTGGTAGTGGATTGAAAGAAAAA
1 CCACAATTAACCCCAACGGTAATGGATTGAAACAAAAA
29720271 CCACAA
1 CCACAA
29720277 ATCACTCCAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (38 bp):
CCACAATTAACCCCAACGGTAATGGATTGAAACAAAAA
Found at i:29721980 original size:40 final size:38
Alignment explanation
Indices: 29721888--29721985 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 38
29721878 ACCAACTCCG
* *
29721888 TCCAACCCAACACACCATGTGGGGATAAAATCGACCCA
1 TCCAACCCTACACACCATATGGGGATAAAATCGACCCA
* * * * *
29721926 CCCATCCTTGCACACCGAATATGGGGATAAAATCGACGCA
1 TCCAACCCTACACACC--ATATGGGGATAAAATCGACCCA
29721966 TCCAACCCTACACACCATAT
1 TCCAACCCTACACACCATAT
29721986 AGTATCGTAG
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
38 15 0.32
40 32 0.68
ACGTcount: A:0.35, C:0.35, G:0.14, T:0.16
Consensus pattern (38 bp):
TCCAACCCTACACACCATATGGGGATAAAATCGACCCA
Found at i:29723965 original size:34 final size:33
Alignment explanation
Indices: 29723914--29723978 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
29723904 AGTCAAATGT
*
29723914 AGTCTGGGCCTATGCCCATCTT-AGTCTTAGTAAC
1 AGTCCGGGCCTATGCCCAT-TTCAGT-TTAGTAAC
29723948 AGTCCGGGCCT-TAGCCCATTTCAGTTTAGTA
1 AGTCCGGGCCTAT-GCCCATTTCAGTTTAGTA
29723979 TCAAATATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 9 0.32
34 19 0.68
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (33 bp):
AGTCCGGGCCTATGCCCATTTCAGTTTAGTAAC
Found at i:29727837 original size:21 final size:21
Alignment explanation
Indices: 29727805--29727851 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
29727795 GTTTTAGTTA
29727805 TTTATTGATTTTAATTTATT-T
1 TTTATTGATTTTAA-TTATTAT
*
29727826 TTTATT-ATTTTTCATTATTAT
1 TTTATTGA-TTTTAATTATTAT
29727847 TTTAT
1 TTTAT
29727852 CTTTTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTATTGATTTTAATTATTAT
Found at i:29727850 original size:28 final size:28
Alignment explanation
Indices: 29727796--29727867 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
29727786 AATTGTTTAG
*
29727796 TTTTAGTTATTTATTGATTTTAATTTAT-T
1 TTTTA-TTATTT-TTCATTTTAATTTATCT
*
29727825 TTTTATTATTTTTCATTATTATTTTATCT
1 TTTTATTATTTTTCATT-TTAATTTATCT
*
29727854 TTTGTTTTATTTTT
1 TTT-TATTATTTTT
29727868 TGTTTCCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.14
28 14 0.38
29 9 0.24
30 9 0.24
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.74
Consensus pattern (28 bp):
TTTTATTATTTTTCATTTTAATTTATCT
Found at i:29732612 original size:18 final size:18
Alignment explanation
Indices: 29732591--29732629 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29732581 TGGGCCATAT
29732591 GGGCGTGT-GAGTCCACAC
1 GGGCGTGTAG-GTCCACAC
*
29732609 GGGCTTGTAGGTCCACAC
1 GGGCGTGTAGGTCCACAC
29732627 GGG
1 GGG
29732630 TAGTCTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.41, T:0.18
Consensus pattern (18 bp):
GGGCGTGTAGGTCCACAC
Found at i:29735180 original size:34 final size:34
Alignment explanation
Indices: 29735098--29735182 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
29735088 CAGTACTATT
* * *
29735098 TAGTGTACTGGATGGTTTAGCTCATACGAGCATT
1 TAGTGTGCTGGATGGATTAGCTCATACGAGCATC
* * *
29735132 TGGTATGCTGGATGGATTAGCTCATACGAGTATC
1 TAGTGTGCTGGATGGATTAGCTCATACGAGCATC
*
29735166 TAGTGTGCTAGATGGAT
1 TAGTGTGCTGGATGGAT
29735183 AACGTGTACT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (34 bp):
TAGTGTGCTGGATGGATTAGCTCATACGAGCATC
Found at i:29736524 original size:21 final size:21
Alignment explanation
Indices: 29736495--29736535 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29736485 TCAATATCGG
29736495 ACTAAAGTATTAATAATTTAT
1 ACTAAAGTATTAATAATTTAT
* * *
29736516 ACTAGAGTATTGATACTTTA
1 ACTAAAGTATTAATAATTTA
29736536 CAAGGGTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (21 bp):
ACTAAAGTATTAATAATTTAT
Found at i:29738334 original size:31 final size:31
Alignment explanation
Indices: 29738293--29738366 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
29738283 AGGGAATCTA
* *
29738293 GTGGGTGGTTATTTGTGGGACTTAGTGGGAT
1 GTGGGTGGTTAATTATGGGACTTAGTGGGAT
*
29738324 GTGGATGGTTAATTATGGGACTTAGTGGGAT
1 GTGGGTGGTTAATTATGGGACTTAGTGGGAT
29738355 GTGGGTGGTTAA
1 GTGGGTGGTTAA
29738367 GAAATTATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.18, C:0.03, G:0.43, T:0.36
Consensus pattern (31 bp):
GTGGGTGGTTAATTATGGGACTTAGTGGGAT
Found at i:29738437 original size:19 final size:19
Alignment explanation
Indices: 29738415--29738453 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29738405 TTTCTTCCCC
29738415 TCTTTCCATTTT-TTTTCTT
1 TCTTTCC-TTTTATTTTCTT
*
29738434 TCTTTTCTTTTATTTTCTT
1 TCTTTCCTTTTATTTTCTT
29738453 T
1 T
29738454 TCTCCGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (19 bp):
TCTTTCCTTTTATTTTCTT
Found at i:29742074 original size:28 final size:28
Alignment explanation
Indices: 29742043--29742098 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
29742033 TTTCTAATTA
* * *
29742043 AATTCAATTTTAATCCTTTTTATATTTT
1 AATTCAATTTAAATACTTTATATATTTT
* *
29742071 AATTTACTTTAAATACTTTATATATTTT
1 AATTCAATTTAAATACTTTATATATTTT
29742099 TATAAATATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (28 bp):
AATTCAATTTAAATACTTTATATATTTT
Found at i:29742194 original size:14 final size:14
Alignment explanation
Indices: 29742149--29742213 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
29742139 TTATTTTATC
*
29742149 ATATATTTTATCTAT
1 ATATATTTTAT-TTT
* * *
29742164 AAATTATATTATATT
1 ATA-TATTTTATTTT
29742179 ATATATTTTATTTT
1 ATATATTTTATTTT
*
29742193 ATATA-TTT-CTTT
1 ATATATTTTATTTT
29742205 ATATATTTT
1 ATATATTTT
29742214 TATAAAATTG
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
12 8 0.20
13 6 0.15
14 14 0.35
15 5 0.12
16 7 0.17
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATATTTTATTTT
Found at i:29743295 original size:45 final size:45
Alignment explanation
Indices: 29743246--29743371 Score: 191
Period size: 45 Copynumber: 2.8 Consensus size: 45
29743236 ATCATTTCAT
29743246 CGGCATTATAGCCTGCTAGGCTCGAAA-GCCCGAATAGTATCTCAC
1 CGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAGTATCTCAC
* * * *
29743291 CGGCATTATGGCCTGCTAGTCCCAAAGGCCCGAATAGTGTCTCAC
1 CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCAC
*
29743336 CGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATA
1 CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
29743372 TAATACCAGC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 3 0.04
45 69 0.96
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (45 bp):
CGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCTCAC
Found at i:29743412 original size:38 final size:38
Alignment explanation
Indices: 29743364--29743572 Score: 292
Period size: 38 Copynumber: 5.5 Consensus size: 38
29743354 GGCTCAAAGG
* * *
29743364 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
29743402 CCAGGATATAATACCAGCACGAAGCCTGCGGGAATTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
29743440 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * *
29743478 CCCAGATATATTACCAGCACGAAGCCTGCAGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * *
29743516 CCCGGATATATTACCAGCACGAAACCTGTGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
29743554 CCCGAATATAATTCCAGCA
1 CCCGGATATAATACCAGCA
29743573 TATAGCCTGC
Statistics
Matches: 154, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 154 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:29743977 original size:43 final size:44
Alignment explanation
Indices: 29743869--29744003 Score: 184
Period size: 43 Copynumber: 3.1 Consensus size: 44
29743859 ACATAACATT
*
29743869 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAA-GCCCGAAT-A
* * *
29743915 T-ATTTCACCGGCATCATAGCCTACTAAGCTCAAAGCCCG-ATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATA
* *
29743957 TCATTTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGAATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATA
29744001 TCA
1 TCA
29744004 CATTTCGATA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
42 2 0.03
43 35 0.45
44 10 0.13
45 30 0.38
46 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (44 bp):
TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGAATA
Found at i:29747170 original size:18 final size:18
Alignment explanation
Indices: 29747144--29747184 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
29747134 TACCATATTA
* *
29747144 TATTTCATACTATATTTT
1 TATTACATACAATATTTT
29747162 TATTACATACAATATTTT
1 TATTACATACAATATTTT
29747180 TATTA
1 TATTA
29747185 TTCAATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTACATACAATATTTT
Found at i:29747192 original size:16 final size:17
Alignment explanation
Indices: 29747150--29747193 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
29747140 ATTATATTTC
*
29747150 ATACTATATTTTTATTA
1 ATACAATATTTTTATTA
29747167 CATACAATATTTTTATT-
1 -ATACAATATTTTTATTA
*
29747184 ATTCAATATT
1 ATACAATATT
29747194 CCTTATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 9 0.38
18 15 0.62
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (17 bp):
ATACAATATTTTTATTA
Found at i:29747266 original size:25 final size:25
Alignment explanation
Indices: 29747221--29747280 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
29747211 TTCTCATATA
29747221 TTTTTTAT-TATATATTATTTA-AT
1 TTTTTTATATATATATTATTTACAT
29747244 TTTTTTATATACTA-ATTATTTTACCAT
1 TTTTTTATATA-TATATTA-TTTA-CAT
*
29747271 ATTTTTATAT
1 TTTTTTATAT
29747281 GTAAAATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 8 0.26
24 6 0.19
25 6 0.19
27 11 0.35
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTTTATATATATATTATTTACAT
Found at i:29747317 original size:21 final size:22
Alignment explanation
Indices: 29747291--29747351 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
29747281 GTAAAATACT
29747291 TATTATATTT-TTATTATTTTA
1 TATTATATTTCTTATTATTTTA
29747312 TATTATATTTCCTTA-TATTTTA
1 TATTATATTT-CTTATTATTTTA
* *
29747334 T-TCATATTATATTATTAT
1 TATTATATT-TCTTATTAT
29747352 ACATAACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 19 0.56
22 12 0.35
23 3 0.09
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTATATTTCTTATTATTTTA
Found at i:29749321 original size:33 final size:32
Alignment explanation
Indices: 29749245--29749324 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
29749235 GGAAATTGTT
* * **
29749245 AAATGTAAGACCATAGCTGGGTTATGGCATTT
1 AAATGTAAGACCATAACTAGGTTATGGCATAC
* *
29749277 TAATGAAAAGACCATAACTAGGTTATGGCACTAC
1 AAATG-TAAGACCATAACTAGGTTATGGCA-TAC
29749311 AAATGTAAGACCAT
1 AAATGTAAGACCAT
29749325 GGCAGGGCCA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
32 4 0.11
33 29 0.76
34 5 0.13
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (32 bp):
AAATGTAAGACCATAACTAGGTTATGGCATAC
Found at i:29750228 original size:37 final size:37
Alignment explanation
Indices: 29750185--29750287 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 37
29750175 TACTTGAAAT
29750185 ACTTGGAAATGATATTTAATTGATATATTGAAACATG
1 ACTTGGAAATGATATTTAATTGATATATTGAAACATG
* * * *
29750222 TCTTGGAAATGATATTTGCA-TGACATATTGAAACGTG
1 ACTTGGAAATGATATTT-AATTGATATATTGAAACATG
* * * *
29750259 ACATGGAAATGGTATTTACTTAATATATT
1 ACTTGGAAATGATATTTAATTGATATATT
29750288 AAAAAGTGAC
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
37 52 0.98
38 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (37 bp):
ACTTGGAAATGATATTTAATTGATATATTGAAACATG
Found at i:29750297 original size:37 final size:37
Alignment explanation
Indices: 29750188--29750305 Score: 112
Period size: 37 Copynumber: 3.2 Consensus size: 37
29750178 TTGAAATACT
* * * *
29750188 TGGAAATGATATTTAATTGATATATTGAAACA-TGTCT
1 TGGAAATGATATTTACTTGATATATT-AAAAAGTGACA
* * * * *
29750225 TGGAAATGATATTTGCATGACATATTGAAACGTGACA
1 TGGAAATGATATTTACTTGATATATTAAAAAGTGACA
* *
29750262 TGGAAATGGTATTTACTTAATATATTAAAAAGTGACA
1 TGGAAATGATATTTACTTGATATATTAAAAAGTGACA
*
29750299 TGTAAAT
1 TGGAAAT
29750306 ATGTGATTAT
Statistics
Matches: 63, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
36 2 0.03
37 61 0.97
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.36
Consensus pattern (37 bp):
TGGAAATGATATTTACTTGATATATTAAAAAGTGACA
Found at i:29753506 original size:22 final size:21
Alignment explanation
Indices: 29753476--29753522 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
29753466 TACAAATTAA
29753476 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
29753498 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
29753519 ATCT
1 ATCT
29753523 AGGATTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:29753519 original size:21 final size:19
Alignment explanation
Indices: 29753493--29753535 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
29753483 AGATTACAAG
29753493 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
*
29753514 ATCATATCTAGGATTGCAT
1 ATCATATCTAAGATTGCAT
29753533 ATC
1 ATC
29753536 CTTAAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 1 0.05
21 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:29753904 original size:14 final size:16
Alignment explanation
Indices: 29753870--29753905 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
29753860 AAACAACTTA
*
29753870 ATATAAGCAAATATTT
1 ATATAAACAAATATTT
29753886 ATATAAACAAATATTT
1 ATATAAACAAATATTT
29753902 ATAT
1 ATAT
29753906 TTATGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATAAACAAATATTT
Found at i:29757248 original size:25 final size:25
Alignment explanation
Indices: 29757197--29757264 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
29757187 GACTCACCAC
29757197 AGCTCGTACGAGCTTACCGATTCTT
1 AGCTCGTACGAGCTTACCGATTCTT
* * *
29757222 AGCTCGTATGAGCTTACTG-TGTTTT
1 AGCTCGTACGAGCTTACCGAT-TCTT
* *
29757247 AGCTTGGACGAGCTTACC
1 AGCTCGTACGAGCTTACC
29757265 AATTATGGCT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
24 1 0.03
25 34 0.97
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.34
Consensus pattern (25 bp):
AGCTCGTACGAGCTTACCGATTCTT
Found at i:29765549 original size:27 final size:27
Alignment explanation
Indices: 29765515--29765738 Score: 270
Period size: 27 Copynumber: 8.3 Consensus size: 27
29765505 TAGTTTACAA
29765515 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
29765542 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
29765569 AAATACTGAAATACACC-TGTAGGGTAG
1 AATTACCGAAATAC-CCTTGTAGGGTAG
**
29765596 AATTACTAAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
29765623 AATTACCGAAATACCCTTGTAGGGGTAG
1 AATTACCGAAATACCCTTGTA-GGGTAG
* * * *
29765651 AAATACCAAAATACCCCTGTAGGCTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
29765678 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * * * *
29765705 AATTACTGAGATACCCTTGTGGGGAAA
1 AATTACCGAAATACCCTTGTAGGGTAG
29765732 AATTACC
1 AATTACC
29765739 ATTTTACCCC
Statistics
Matches: 173, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
26 2 0.01
27 145 0.84
28 26 0.15
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGTAGGGTAG
Found at i:29765747 original size:109 final size:108
Alignment explanation
Indices: 29765513--29765738 Score: 362
Period size: 109 Copynumber: 2.1 Consensus size: 108
29765503 TTTAGTTTAC
* *
29765513 AAAATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAAATACTGA
1 AAAATTACCGAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTGTAGGCTAGAAATACTGA
*
29765578 AATACACCTGTAGGGTAGAATTACTAAAATACCCTTGTAGGGT
66 AATACACCTGTAGGGTAGAATTACTAAAATACCCTTGTAGGGA
* *
29765621 AGAATTACCGAAATACCCTTGTAGGGGTAGAAATACCAAAATACCCCTGTAGGCTAGAATTACTG
1 AAAATTACCGAAATACCCTTGTA-GGGTAGAAATACCAAAATACCCCTGTAGGCTAGAAATACTG
* * * *
29765686 AAATACCCCTGTAGGGTAGAATTACTGAGATACCCTTGTGGGGA
65 AAATACACCTGTAGGGTAGAATTACTAAAATACCCTTGTAGGGA
29765730 AAAATTACC
1 AAAATTACC
29765739 ATTTTACCCC
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
108 22 0.21
109 85 0.79
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (108 bp):
AAAATTACCGAAATACCCTTGTAGGGTAGAAATACCAAAATACCCCTGTAGGCTAGAAATACTGA
AATACACCTGTAGGGTAGAATTACTAAAATACCCTTGTAGGGA
Found at i:29766038 original size:67 final size:67
Alignment explanation
Indices: 29765930--29766108 Score: 295
Period size: 67 Copynumber: 2.7 Consensus size: 67
29765920 TTTTGTACGG
* *
29765930 ATATTTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTATTTTGGTGACTTCGTCA
1 ATATTTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTATTATAGTGACTTCGTCA
29765995 CA
66 CA
*
29765997 ATATTTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTGTTATAGTGACTTCGTCA
1 ATATTTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTATTATAGTGACTTCGTCA
29766062 CA
66 CA
* * * *
29766064 ATATCTGGCAGCTTCACTGCAATCTGGTGGCTTCGCCACATATAT
1 ATATTTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATAT
29766109 ATATCTGTTC
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 105 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.32
Consensus pattern (67 bp):
ATATTTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATATCTATTATAGTGACTTCGTCA
CA
Found at i:29766138 original size:26 final size:27
Alignment explanation
Indices: 29766109--29766168 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
29766099 CCACATATAT
29766109 ATATCTGT-TCTAGTGACCTAGCCACA
1 ATATCTGTATCTAGTGACCTAGCCACA
* * * *
29766135 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTAGTGACCTAGCCACA
29766162 ATATCTG
1 ATATCTG
29766169 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTAGTGACCTAGCCACA
Found at i:29766318 original size:6 final size:6
Alignment explanation
Indices: 29766287--29766374 Score: 83
Period size: 6 Copynumber: 14.3 Consensus size: 6
29766277 TTGCATTCAC
* *
29766287 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
*
29766336 -TCACCTG ATTCTG ATTCTG ATTCTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
29766375 AATATTTCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
5 4 0.06
6 55 0.81
7 7 0.10
8 2 0.03
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:29766322 original size:31 final size:31
Alignment explanation
Indices: 29766287--29766365 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
29766277 TTGCATTCAC
* *
29766287 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
*
29766318 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTGTCACCTGATACTG
29766349 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
29766366 AGTTCTGATA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTGATACTG
Found at i:29769862 original size:18 final size:18
Alignment explanation
Indices: 29769835--29769869 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29769825 AATAAAATAA
* *
29769835 TACAATTAATATTAACAT
1 TACAAATAATATAAACAT
29769853 TACAAATAATATAAACA
1 TACAAATAATATAAACA
29769870 ATAAAAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (18 bp):
TACAAATAATATAAACAT
Found at i:29770620 original size:32 final size:35
Alignment explanation
Indices: 29770584--29770655 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 35
29770574 GACTACTAAG
29770584 GTAAAT-CCCTTC-T-TTTTATTTTAAAATTTCAT
1 GTAAATCCCCTTCTTCTTTTATTTTAAAATTTCAT
*
29770616 GTAAATCCCCTTCTTTCTTTTGTTTTAAAATTTCAT
1 GTAAATCCCCTTC-TTCTTTTATTTTAAAATTTCAT
29770652 GTAA
1 GTAA
29770656 TCCTAAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
32 6 0.17
33 6 0.17
35 1 0.03
36 22 0.63
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (35 bp):
GTAAATCCCCTTCTTCTTTTATTTTAAAATTTCAT
Found at i:29776994 original size:23 final size:23
Alignment explanation
Indices: 29776968--29777015 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
29776958 TCATGAGAAG
29776968 TAGATCTCTATTTCATTTATACT
1 TAGATCTCTATTTCATTTATACT
29776991 TAGATCTCTATTTCATTTATACT
1 TAGATCTCTATTTCATTTATACT
29777014 TA
1 TA
29777016 TGCCTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (23 bp):
TAGATCTCTATTTCATTTATACT
Found at i:29784151 original size:103 final size:103
Alignment explanation
Indices: 29784030--29784235 Score: 387
Period size: 103 Copynumber: 2.0 Consensus size: 103
29784020 TATACCAGAC
29784030 ACGCCCCTAAAGATCTCCGCTCCGTTAGCCTGAAGTCGTTCAGAAATAGATCCCCGAATTCCGTT
1 ACGCCCCTAAAGATCTCCGCTCCGTTAGCCTGAAGTCGTTCAGAAATAGATCCCCGAATTCCGTT
29784095 GCCCATACTTACCCC-GACAACCCTTTCCAGAACACGAA
66 GCCCATACTTACCCCAG-CAACCCTTTCCAGAACACGAA
*
29784133 ACGCCCCTAAAGATCTCCGCTCCGTTAGCCTGAAGTCGTTCAGAAATAGATCCCCGGATTCCGTT
1 ACGCCCCTAAAGATCTCCGCTCCGTTAGCCTGAAGTCGTTCAGAAATAGATCCCCGAATTCCGTT
29784198 GCCCATACTTACCCCAGCAACCCTTTCCAGAACACGAA
66 GCCCATACTTACCCCAGCAACCCTTTCCAGAACACGAA
29784236 GCATTGCCTG
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
103 100 0.99
104 1 0.01
ACGTcount: A:0.27, C:0.36, G:0.16, T:0.21
Consensus pattern (103 bp):
ACGCCCCTAAAGATCTCCGCTCCGTTAGCCTGAAGTCGTTCAGAAATAGATCCCCGAATTCCGTT
GCCCATACTTACCCCAGCAACCCTTTCCAGAACACGAA
Found at i:29787492 original size:26 final size:26
Alignment explanation
Indices: 29787461--29787568 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
29787451 TGAAATTCCC
*
29787461 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
29787487 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
29787513 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
29787539 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29787565 ATCA
1 ATCA
29787569 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29793713 original size:26 final size:26
Alignment explanation
Indices: 29793684--29793791 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
29793674 TGATACAAAT
*
29793684 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
29793710 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29793736 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29793762 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29793788 TGAT
1 TGAT
29793792 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29801470 original size:26 final size:26
Alignment explanation
Indices: 29801440--29801547 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
29801430 TGATACAAAT
*
29801440 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
29801466 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29801492 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
29801518 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
29801544 TGAT
1 TGAT
29801548 GGGAATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:29804941 original size:20 final size:20
Alignment explanation
Indices: 29804899--29804941 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
29804889 TTTATATTAA
* *
29804899 ATTATTATTATTTAATAGGT
1 ATTATTATTAGTTAATAGAT
29804919 ATTATTATTAAGTTAA-AGAT
1 ATTATTATT-AGTTAATAGAT
29804939 ATT
1 ATT
29804942 TACTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (20 bp):
ATTATTATTAGTTAATAGAT
Found at i:29805350 original size:11 final size:12
Alignment explanation
Indices: 29805320--29805353 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
29805310 GTATGTTTAC
29805320 TTATTATATAAG
1 TTATTATATAAG
29805332 TATATTAT-TAAG
1 T-TATTATATAAG
29805344 TTATTATATA
1 TTATTATATA
29805354 TATATATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.30
12 8 0.40
13 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (12 bp):
TTATTATATAAG
Found at i:29806438 original size:16 final size:16
Alignment explanation
Indices: 29806417--29806450 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
29806407 ATATATAGTT
29806417 AATTAATT-AAAATATG
1 AATTAATTGAAAAT-TG
29806433 AATTAATTGAAAATTG
1 AATTAATTGAAAATTG
29806449 AA
1 AA
29806451 AAGTGACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (16 bp):
AATTAATTGAAAATTG
Found at i:29806919 original size:18 final size:18
Alignment explanation
Indices: 29806905--29806968 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
29806895 AATTGATTGA
29806905 TACTGAATAACTGATTAT
1 TACTGAATAACTGATTAT
* * *
29806923 TATTGAATAATTGATTGT
1 TACTGAATAACTGATTAT
* *
29806941 TACCGAATAACTGACTAT
1 TACTGAATAACTGATTAT
29806959 TACTGAATAA
1 TACTGAATAA
29806969 ATAATTGTTC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (18 bp):
TACTGAATAACTGATTAT
Found at i:29806932 original size:62 final size:62
Alignment explanation
Indices: 29806838--29806954 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 62
29806828 GAATAATTTA
* * * * * *
29806838 ATTGTTACTGTATATCTGATTTTTACTTAATAATTGACTATTACTGGATAACTGATCAATTG
1 ATTGATACTGAATAACTGATTATTACTTAATAATTGACTATTACCGAATAACTGATCAATTG
* *
29806900 ATTGATACTGAATAACTGATTATTA-TTGAATAATTGATTGTTACCGAATAACTGA
1 ATTGATACTGAATAACTGATTATTACTT-AATAATTGACTATTACCGAATAACTGA
29806955 CTATTACTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
61 2 0.04
62 44 0.96
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (62 bp):
ATTGATACTGAATAACTGATTATTACTTAATAATTGACTATTACCGAATAACTGATCAATTG
Found at i:29806949 original size:36 final size:36
Alignment explanation
Indices: 29806895--29806977 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
29806885 ATAACTGATC
* * * *
29806895 AATTGATTGATACTGAATAACTGATTATTATTGAAT
1 AATTGATTGTTACCGAATAACTGACTATTACTGAAT
29806931 AATTGATTGTTACCGAATAACTGACTATTACTGAAT
1 AATTGATTGTTACCGAATAACTGACTATTACTGAAT
* *
29806967 AAATAATTGTT
1 AATTGATTGTT
29806978 CTGATTGACT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (36 bp):
AATTGATTGTTACCGAATAACTGACTATTACTGAAT
Found at i:29811685 original size:30 final size:30
Alignment explanation
Indices: 29811649--29811708 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
29811639 TATTTTAGAA
29811649 TAATAAATGATTTCACATGTCAATTTGGAC
1 TAATAAATGATTTCACATGTCAATTTGGAC
29811679 TAATAAATGATTTCACATGTCAATTTGGAC
1 TAATAAATGATTTCACATGTCAATTTGGAC
29811709 CCGTGTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (30 bp):
TAATAAATGATTTCACATGTCAATTTGGAC
Found at i:29814669 original size:38 final size:37
Alignment explanation
Indices: 29814631--29814703 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
29814621 GATTGGAACA
* *
29814631 AAAAACACAATTGACTCCAATGGCAATAGGTCAAAAC
1 AAAAACACAAATCACTCCAATGGCAATAGGTCAAAAC
* * * *
29814668 AAGACCATAAATCACTCCATTGGCAATAGGTCAAAA
1 AAAAACACAAATCACTCCAATGGCAATAGGTCAAAA
29814704 ACCACTATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.47, C:0.22, G:0.14, T:0.18
Consensus pattern (37 bp):
AAAAACACAAATCACTCCAATGGCAATAGGTCAAAAC
Found at i:29815331 original size:25 final size:26
Alignment explanation
Indices: 29815303--29815372 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 26
29815293 TAAGATATTA
29815303 ATACCAAATGAAAATTTATAATTTC-
1 ATACCAAATGAAAATTTATAATTTCG
29815328 ATACTACAAA--AAATATTTA-AATTTCG
1 ATAC--CAAATGAAA-ATTTATAATTTCG
* *
29815354 A-AACAAATGAACATTTATA
1 ATACCAAATGAAAATTTATA
29815373 GGTAGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
23 4 0.11
24 5 0.14
25 17 0.47
26 6 0.17
27 4 0.11
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.33
Consensus pattern (26 bp):
ATACCAAATGAAAATTTATAATTTCG
Found at i:29820829 original size:47 final size:46
Alignment explanation
Indices: 29820710--29820887 Score: 207
Period size: 47 Copynumber: 3.8 Consensus size: 46
29820700 ATAATCTCAC
* * * *
29820710 CCATAATGAGCTCGGAACACAACTCAACGAGCTCGGGTGTTTGCAT
1 CCATAATGAACTCGGAACACAACTCAACGAGTTCGGATGCTTGCAT
* *
29820756 CCATAATGAACTCAGAACACAACTCAACAAGTTCGGATGCTTGCAT
1 CCATAATGAACTCGGAACACAACTCAACGAGTTCGGATGCTTGCAT
* *
29820802 CCATAAGTGAACTCGGAACGCAACTCAACGAGTTCGGATGCCT-CAT
1 CCATAA-TGAACTCGGAACACAACTCAACGAGTTCGGATGCTTGCAT
* * *
29820848 -AATTCTCACGAACTCGGAACACAACTCAACGAGTTCGGAT
1 CCA---TAATGAACTCGGAACACAACTCAACGAGTTCGGAT
29820888 CTCAATTTCC
Statistics
Matches: 114, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
45 1 0.01
46 49 0.43
47 62 0.54
48 2 0.02
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAATGAACTCGGAACACAACTCAACGAGTTCGGATGCTTGCAT
Found at i:29825430 original size:67 final size:67
Alignment explanation
Indices: 29825351--29825485 Score: 234
Period size: 67 Copynumber: 2.0 Consensus size: 67
29825341 AATCCTTTTC
*
29825351 AGAGAGCACACTCCCGCAAACCTCATTGCTTACAGTGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCAAACCTCATTGCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
29825416 TA
66 TA
* * *
29825418 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTTCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCAAACCTCATTGCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
29825483 TA
66 TA
29825485 A
1 A
29825486 CATATACTCA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCAAACCTCATTGCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
TA
Found at i:29828665 original size:28 final size:28
Alignment explanation
Indices: 29828597--29828698 Score: 170
Period size: 28 Copynumber: 3.7 Consensus size: 28
29828587 TGGCCCCTTT
*
29828597 AGGCCCAATCTCATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
*
29828625 -GGCCCAATCACATTCATATGGCCTATC
1 AGGCCCAATCACATTCATATGGCCCATC
*
29828652 AGGCCCAATCACATTCATATGGCCCGTC
1 AGGCCCAATCACATTCATATGGCCCATC
29828680 AGGCCCAATCACATTCATA
1 AGGCCCAATCACATTCATA
29828699 GTCATGAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 25 0.36
28 44 0.64
ACGTcount: A:0.27, C:0.34, G:0.15, T:0.24
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:29830311 original size:14 final size:13
Alignment explanation
Indices: 29830291--29830322 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
29830281 TATATATACT
29830291 AAATAAAATAATA
1 AAATAAAATAATA
29830304 ATAATAAAATAATA
1 A-AATAAAATAATA
29830318 AAATA
1 AAATA
29830323 TCTTATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:29834636 original size:20 final size:20
Alignment explanation
Indices: 29834598--29834635 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29834588 GGACTAAACC
* *
29834598 GGAAACTTTGGAAACTTTTG
1 GGAAACTTAGAAAACTTTTG
29834618 GGAAACTTAGAAAA-TTTT
1 GGAAACTTAGAAAACTTTT
29834636 TCATGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (20 bp):
GGAAACTTAGAAAACTTTTG
Found at i:29837214 original size:22 final size:23
Alignment explanation
Indices: 29837166--29837214 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
29837156 AACTCACCAT
* *
29837166 AGCTTGTATGAGCTTACTGATTC
1 AGCTTGAAAGAGCTTACTGATTC
29837189 AGCTTGAAAGAGCTTACTG-TTC
1 AGCTTGAAAGAGCTTACTGATTC
29837211 AGCT
1 AGCT
29837215 CAATAAAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (23 bp):
AGCTTGAAAGAGCTTACTGATTC
Found at i:29837264 original size:24 final size:22
Alignment explanation
Indices: 29837175--29837277 Score: 66
Period size: 24 Copynumber: 4.4 Consensus size: 22
29837165 TAGCTTGTAT
* *
29837175 GAGCTTACTGATTCAGCTTGAA-A
1 GAGCTTACT-TTTCAGC-TCAATA
*
29837198 GAGCTTACTGTTCAGCTCAATA
1 GAGCTTACTTTTCAGCTCAATA
* * *
29837220 AAGCTTCCCGTTTTCAACTCAATA
1 GAGCTT-AC-TTTTCAGCTCAATA
29837244 GAGCTTACTATTATCAGCTC-ATGAA
1 GAGCTTACT-TT-TCAGCTCAAT--A
29837269 GAGCTTACT
1 GAGCTTACT
29837278 GGCCATATCT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
21 3 0.05
22 13 0.20
23 15 0.23
24 23 0.36
25 10 0.16
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (22 bp):
GAGCTTACTTTTCAGCTCAATA
Found at i:29839609 original size:30 final size:30
Alignment explanation
Indices: 29839565--29839621 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
29839555 ACGGCCATGA
* *
29839565 CACACAGGCGTGTGGACTACCCGTGTGTCT
1 CACACAGGCATGTGGACTACCCATGTGTCT
* *
29839595 CACACGGGCATGTGGATTACCCATGTG
1 CACACAGGCATGTGGACTACCCATGTG
29839622 GGAGTGTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.23
Consensus pattern (30 bp):
CACACAGGCATGTGGACTACCCATGTGTCT
Found at i:29843015 original size:26 final size:25
Alignment explanation
Indices: 29842947--29843042 Score: 97
Period size: 26 Copynumber: 3.8 Consensus size: 25
29842937 GAGGAAGTGC
* * *
29842947 AAAAGGGCTATGCCTCAG-TTACCG
1 AAAAGGGCTTTGCCCCAGTTTACAG
*
29842971 AAAAGAGCTTTGCCCCAGTTTACAG
1 AAAAGGGCTTTGCCCCAGTTTACAG
29842996 AAAAGGGCTTTTGCCCCAGTTTATCA-
1 AAAAGGGC-TTTGCCCCAGTTTA-CAG
* *
29843022 AAAAGGGATTTTTCCCCAGTT
1 AAAAGGG-CTTTGCCCCAGTT
29843043 ATTAAAAGAG
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
24 15 0.25
25 12 0.20
26 32 0.52
27 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACAG
Found at i:29843153 original size:81 final size:81
Alignment explanation
Indices: 29843056--29843219 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 81
29843046 AAAAGAGGCT
29843056 AGGCCTCCAGTTATATGATAAAGCAGCTATGCTGCCAGTGGAGAGTTTGGTTGGGTGGGTTGAGT
1 AGGCCTCCAGTTATATGATAAAGCAGCTATGCTGCCAGTGGAGAGTTTGGTTGGGTGGGTTGAGT
29843121 TATTCCCCACATGGAG
66 TATTCCCCACATGGAG
*
29843137 AGGCCTCCAGTTATATGATAAAGTAGCTATGCTGCCAGTGGAGAGTTTGGTTGGGTGGGTTGAGT
1 AGGCCTCCAGTTATATGATAAAGCAGCTATGCTGCCAGTGGAGAGTTTGGTTGGGTGGGTTGAGT
29843202 TATTCCCCACATGGAG
66 TATTCCCCACATGGAG
29843218 AG
1 AG
29843220 CTTGGTTGGT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (81 bp):
AGGCCTCCAGTTATATGATAAAGCAGCTATGCTGCCAGTGGAGAGTTTGGTTGGGTGGGTTGAGT
TATTCCCCACATGGAG
Found at i:29843381 original size:31 final size:31
Alignment explanation
Indices: 29843343--29843426 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
29843333 TCGTTATAGT
29843343 AAAGGCTTCGGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
29843374 AAAGGCTTCGGCCCAGTGACATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
29843405 GAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
29843427 CTGAGATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 4 0.08
31 45 0.92
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:29844875 original size:27 final size:27
Alignment explanation
Indices: 29844845--29845002 Score: 183
Period size: 27 Copynumber: 5.9 Consensus size: 27
29844835 ATTACCAAAG
* * * **
29844845 TACCTTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
29844872 TACCCTCGACTTACAAAATTA-TCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTT
29844899 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
29844926 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
29844953 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
**
29844980 TACCCTCGATTTGTAAAATTACT
1 TACCCTCGATTTACAAAATTACT
29845003 AAAATACCCT
Statistics
Matches: 112, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
27 111 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:29844941 original size:81 final size:81
Alignment explanation
Indices: 29844845--29845002 Score: 237
Period size: 81 Copynumber: 2.0 Consensus size: 81
29844835 ATTACCAAAG
*
29844845 TACCTTCGATTTATAGAATTACCATTTTACCCTCGACTTACAAAATTA-TCGTTTTACCCTCGAT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAAAATTACT-GTTTTACCCTCGAT
29844909 TTACAAAATTACTGTTT
65 TTACAAAATTACTGTTT
* * * *
29844926 TACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAGAATTACTGTTTTACCCTCGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAAAATTACTGTTTTACCCTCGATT
**
29844991 TGTAAAATTACT
66 TACAAAATTACT
29845003 AAAATACCCT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
81 68 0.99
82 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (81 bp):
TACCCTCGATTTATAGAATTACCATTTTACCCTCGACTTACAAAATTACTGTTTTACCCTCGATT
TACAAAATTACTGTTT
Found at i:29845011 original size:54 final size:54
Alignment explanation
Indices: 29844899--29845194 Score: 168
Period size: 54 Copynumber: 5.4 Consensus size: 54
29844889 ATTATCGTTT
* * ***
29844899 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACTATTT
1 TACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTATAAAATTACTAAAA
* *
29844953 TACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTGTAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTATAAAATTACTAAAA
** ***** * * *
29845007 TACCCTT-AGTTTGTAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTACAAAATTACTGTTTTACCCTCGA-TTTATAAAATTACTAAAA
* *** * *** * * *
29845061 TACCAC-TGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAA
1 TACC-CTTGATTTACAAAATTACTGTTTTACCCTCGATTTATAAAATTACTAAAA
* * * *** * *
29845115 TACCCCTGATTTACAAAGTTACAGAAATACCCTTGACTTTCTAAAAATTA-TAGAAA
1 TACCCTTGATTTACAAAATTACTGTTTTACCCTCGA-TTTAT-AAAATTACTA-AAA
* *
29845171 TACCATTGGTTTACAAAATTACTG
1 TACCCTTGATTTACAAAATTACTG
29845195 AAATACCCTT
Statistics
Matches: 197, Mismatches: 36, Indels: 16
0.79 0.14 0.06
Matches are distributed among these distances:
53 4 0.02
54 156 0.79
55 8 0.04
56 29 0.15
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (54 bp):
TACCCTTGATTTACAAAATTACTGTTTTACCCTCGATTTATAAAATTACTAAAA
Found at i:29845011 original size:81 final size:80
Alignment explanation
Indices: 29844818--29845012 Score: 230
Period size: 81 Copynumber: 2.4 Consensus size: 80
29844808 ATTACTGAAA
* * * *
29844818 TACCCTCAAATTTTAAAATTACCAAAGTACCTTCGATTTATAGAATTACCATTTTACCCTCGACT
1 TACCCTC-GATTTTAAAATTACTAAAATACCCTCGATTTATAGAATTACCATTTTACCCTCGACT
29844883 TACAAAATTATCGTTT
65 TACAAAATTATCGTTT
* **** * * *
29844899 TACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTATAGAATTACTATTTTACCCTTGATT
1 TACCCTCGATTT-TAAAATTACTAAAATACCCTCGATTTATAGAATTACCATTTTACCCTCGACT
*
29844964 TACAGAATTA-CTGTTT
65 TACAAAATTATC-GTTT
29844980 TACCCTCGATTTGTAAAATTACTAAAATACCCT
1 TACCCTCGATTT-TAAAATTACTAAAATACCCT
29845013 TAGTTTGTAA
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
80 5 0.05
81 89 0.95
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (80 bp):
TACCCTCGATTTTAAAATTACTAAAATACCCTCGATTTATAGAATTACCATTTTACCCTCGACTT
ACAAAATTATCGTTT
Found at i:29845038 original size:81 final size:80
Alignment explanation
Indices: 29844987--29845145 Score: 187
Period size: 81 Copynumber: 2.0 Consensus size: 80
29844977 TTTTACCCTC
* * * * *
29844987 GATTTGTAAAATTACTAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTA-AA
1 GATTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATA-CCCTTGATT-TACAA
29845051 ATTACCAAAATACCACT
64 ATTACCAAAATACCACT
* * * *
29845068 GGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAG
1 GATTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCTTGATTTACAAA-
29845133 TTA-CAGAAATACC
65 TTACCA-AAATACC
29845146 CTTGACTTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
79 2 0.03
80 11 0.17
81 53 0.80
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.30
Consensus pattern (80 bp):
GATTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCTTGATTTACAAAT
TACCAAAATACCACT
Found at i:29845126 original size:27 final size:27
Alignment explanation
Indices: 29844982--29845126 Score: 170
Period size: 27 Copynumber: 5.3 Consensus size: 27
29844972 TACTGTTTTA
*
29844982 CCCTCGATTTGTAAAATTACTAAAATA-
1 CCCT-GATTTGTAAAATTACCAAAATAC
*
29845009 CCCTTAGTTTGTAAAATTACCAAAATAC
1 CCCTGA-TTTGTAAAATTACCAAAATAC
29845037 CCCT-AGTTTGTAAAATTACCAAAATAC
1 CCCTGA-TTTGTAAAATTACCAAAATAC
* * * *
29845064 CACTGGTTTGTGAAATTACCGAAATA-
1 CCCTGATTTGTAAAATTACCAAAATAC
*
29845090 CCCTCAATTTGTAAAATTACCAAAATAC
1 CCCT-GATTTGTAAAATTACCAAAATAC
29845118 CCCTGATTT
1 CCCTGATTT
29845127 ACAAAGTTAC
Statistics
Matches: 101, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.04
27 89 0.88
28 8 0.08
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (27 bp):
CCCTGATTTGTAAAATTACCAAAATAC
Found at i:29845136 original size:27 final size:26
Alignment explanation
Indices: 29844993--29845146 Score: 118
Period size: 27 Copynumber: 5.7 Consensus size: 26
29844983 CCTCGATTTG
* * *
29844993 TAAAATTACTAAAATACCCTTAGTTT
1 TAAAATTACCAAAATACCCCTAGATT
*
29845019 GTAAAATTACCAAAATACCCCTAGTTT
1 -TAAAATTACCAAAATACCCCTAGATT
* * *
29845046 GTAAAATTACCAAAATACCACTGGTTT
1 -TAAAATTACCAAAATACCCCTAGATT
* *
29845073 GTGAAATTACCGAAATA-CCCTCA-ATTT
1 -TAAAATTACCAAAATACCCCT-AGA-TT
29845100 GTAAAATTACCAAAATACCCCT-GATT
1 -TAAAATTACCAAAATACCCCTAGATT
29845126 TACAAAGTTA-CAGAAATACCC
1 TA-AAA-TTACCA-AAATACCC
29845147 TTGACTTTCT
Statistics
Matches: 109, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
25 2 0.02
26 10 0.09
27 93 0.85
28 4 0.04
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (26 bp):
TAAAATTACCAAAATACCCCTAGATT
Found at i:29845197 original size:27 final size:27
Alignment explanation
Indices: 29845158--29845209 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
29845148 TGACTTTCTA
29845158 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
29845185 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
29845210 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:29845327 original size:27 final size:27
Alignment explanation
Indices: 29845250--29845327 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
29845240 AAATGACTAA
* *
29845250 AATACCCCTAT-TAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* *
29845277 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
29845304 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
29845328 GAATATGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 40 0.95
28 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:29846000 original size:26 final size:25
Alignment explanation
Indices: 29845948--29845996 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
29845938 CCCTTATAAT
29845948 GTGAAAATGACTATTTTTCCCCTAG
1 GTGAAAATGACTATTTTTCCCCTAG
*
29845973 GTGAAAATGACTGTTTTTCCCCTA
1 GTGAAAATGACTATTTTTCCCCTA
29845997 AGGTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (25 bp):
GTGAAAATGACTATTTTTCCCCTAG
Found at i:29846059 original size:20 final size:20
Alignment explanation
Indices: 29846025--29846101 Score: 97
Period size: 20 Copynumber: 4.0 Consensus size: 20
29846015 GATACGTGGG
29846025 GTATGATAT--ACATGAT-T
1 GTATGATATGCACATGATAT
29846042 GATATGATATGCACATGATAT
1 G-TATGATATGCACATGATAT
* *
29846063 GTATAATATGTACATGATAT
1 GTATGATATGCACATGATAT
*
29846083 GTATGAAATGCACATGATA
1 GTATGATATGCACATGATA
29846102 AATTCATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.02
18 8 0.16
20 40 0.78
21 2 0.04
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (20 bp):
GTATGATATGCACATGATAT
Found at i:29846061 original size:11 final size:10
Alignment explanation
Indices: 29846027--29846101 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 10
29846017 TACGTGGGGT
29846027 ATGATAT-AC
1 ATGATATGAC
*
29846036 ATGAT-TGAT
1 ATGATATGAC
29846045 ATGATATGCAC
1 ATGATATG-AC
*
29846056 ATGATATG-T
1 ATGATATGAC
*
29846065 ATAATATGTAC
1 ATGATATG-AC
*
29846076 ATGATATG-T
1 ATGATATGAC
*
29846085 ATGAAATGCAC
1 ATGATATG-AC
29846096 ATGATA
1 ATGATA
29846102 AATTCATAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
8 1 0.02
9 25 0.51
10 2 0.04
11 21 0.43
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (10 bp):
ATGATATGAC
Found at i:29846179 original size:26 final size:26
Alignment explanation
Indices: 29846150--29846324 Score: 264
Period size: 26 Copynumber: 6.8 Consensus size: 26
29846140 GAGGAAGTGC
**
29846150 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
29846176 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
29846202 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
29846228 AAAAGGACTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
29846254 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
29846280 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
29846305 AGAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
29846325 ATTAAAGAGG
Statistics
Matches: 136, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
25 32 0.24
26 104 0.76
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:29846228 original size:52 final size:52
Alignment explanation
Indices: 29846150--29846324 Score: 318
Period size: 52 Copynumber: 3.4 Consensus size: 52
29846140 GAGGAAGTGC
29846150 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
29846202 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGACTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
29846254 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
29846305 AGAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
29846325 ATTAAAGAGG
Statistics
Matches: 120, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
50 10 0.08
51 24 0.20
52 86 0.72
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:29846528 original size:42 final size:42
Alignment explanation
Indices: 29846469--29846560 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
29846459 TAGTCTCCCC
* ** *
29846469 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
29846511 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
29846553 AAATGGGC
1 AAATGGGC
29846561 CTAAGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:29846619 original size:31 final size:31
Alignment explanation
Indices: 29846584--29846698 Score: 205
Period size: 31 Copynumber: 3.7 Consensus size: 31
29846574 CGTTTACAGT
*
29846584 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29846615 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
29846646 AAAGGCTTCGGCCCAGTGATTTGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29846677 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
29846699 TCGAGACTGA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
30 4 0.05
31 77 0.95
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:29847430 original size:27 final size:27
Alignment explanation
Indices: 29847392--29847557 Score: 197
Period size: 27 Copynumber: 6.1 Consensus size: 27
29847382 GATCCGGCCT
*
29847392 GATTTATAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
* *
29847419 GATTTATAGAATTATCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
*** *
29847446 GATTTACAGAATTATAATTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTC
* * * *
29847473 TATTTATAGAATTACTGTTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTC
**
29847500 GATTTACAGAATTACTATTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
* *
29847527 GACTTACAAAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
29847554 GATT
1 GATT
29847558 GTGAAATTAC
Statistics
Matches: 120, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 120 1.00
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (27 bp):
GATTTACAGAATTACCGTTTTACCCTC
Found at i:29847548 original size:81 final size:81
Alignment explanation
Indices: 29847393--29847552 Score: 223
Period size: 81 Copynumber: 2.0 Consensus size: 81
29847383 ATCCGGCCTG
* * * *
29847393 ATTTATAGAATTACCGTTTTACCCTCGATTTATAGAATTATCGTTTTACCCTCGATTTACAGAAT
1 ATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTATCATTTTACCCTCGACTTACAAAAT
*
29847458 TATAATTTTACCCTTT
66 TACAATTTTACCCTTT
* *
29847474 ATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTA-CTATTTTACCCTCGACTTACAAAA
1 ATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTATC-ATTTTACCCTCGACTTACAAAA
**
29847538 TTACCGTTTTACCCT
65 TTACAATTTTACCCT
29847553 CGATTGTGAA
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 1 0.01
81 68 0.99
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (81 bp):
ATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTATCATTTTACCCTCGACTTACAAAAT
TACAATTTTACCCTTT
Found at i:29847579 original size:27 final size:27
Alignment explanation
Indices: 29847549--29847685 Score: 100
Period size: 27 Copynumber: 5.1 Consensus size: 27
29847539 TACCGTTTTA
*
29847549 CCCTCGATTGTGAAATTACTGAAATAC
1 CCCTCGATTGTGAAATTACCGAAATAC
* * *
29847576 CCCT--ATAGGGTAGAATTACCTAAATAC
1 CCCTCGATTGTG-A-AATTACCGAAATAC
* * * *
29847603 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCTCGATTGTGAAATTACCGAAATAC
* * *
29847630 CACTGGTTTGTGAAATTACCGAAATA-
1 CCCTCGATTGTGAAATTACCGAAATAC
* * *
29847656 CCCTCGATTTATAAAATTACCAAAATAC
1 CCCTCGA-TTGTGAAATTACCGAAATAC
29847684 CC
1 CC
29847686 TTGATTTACA
Statistics
Matches: 85, Mismatches: 19, Indels: 11
0.74 0.17 0.10
Matches are distributed among these distances:
25 4 0.05
26 5 0.06
27 71 0.84
28 3 0.04
29 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (27 bp):
CCCTCGATTGTGAAATTACCGAAATAC
Found at i:29847686 original size:27 final size:27
Alignment explanation
Indices: 29847589--29847701 Score: 113
Period size: 27 Copynumber: 4.2 Consensus size: 27
29847579 TATAGGGTAG
* * *
29847589 AATTACCTAAATACCC-CTAGTTTGTAA
1 AATTACCAAAATACCCTCGA-TTTATAA
* * *
29847616 AATTACCAAAATACCACT-GGTTTGTGA
1 AATTACCAAAATACC-CTCGATTTATAA
*
29847643 AATTACCGAAATACCCTCGATTTATAA
1 AATTACCAAAATACCCTCGATTTATAA
* *
29847670 AATTACCAAAATACCCTTGATTTACAA
1 AATTACCAAAATACCCTCGATTTATAA
29847697 AATTA
1 AATTA
29847702 TAGAAATACC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.03
27 69 0.96
28 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTCGATTTATAA
Found at i:29847700 original size:54 final size:55
Alignment explanation
Indices: 29847589--29847798 Score: 169
Period size: 54 Copynumber: 3.9 Consensus size: 55
29847579 TATAGGGTAG
* * * * ***
29847589 AATTACCTAAATACCC-CTAGTTTGTAAAATTACCAAAATACCAC-TGGTTTGTGA
1 AATTACCGAAATACCCTCGACTTTGTAAAATTACCAAAATACC-CTTGATTTACAA
*
29847643 AATTACCGAAATACCCTCGA-TTTATAAAATTACCAAAATACCCTTGATTTACAA
1 AATTACCGAAATACCCTCGACTTTGTAAAATTACCAAAATACCCTTGATTTACAA
** * * * * *
29847697 AATTATAGAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGTTTTACAA
1 AATTACCGAAATACCCTCGACTTTGT-AAAATTACCA-AAATACCCTTGATTTACAA
* * * * * *
29847753 AATTACTGAAATACCCTTG-GTTTGTAGATTTACCAAAACACCCTTG
1 AATTACCGAAATACCCTCGACTTTGTAAAATTACCAAAATACCCTTG
29847799 TAGGATGAAA
Statistics
Matches: 127, Mismatches: 23, Indels: 12
0.78 0.14 0.07
Matches are distributed among these distances:
53 1 0.01
54 73 0.57
55 12 0.09
56 41 0.32
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (55 bp):
AATTACCGAAATACCCTCGACTTTGTAAAATTACCAAAATACCCTTGATTTACAA
Found at i:29847708 original size:27 final size:28
Alignment explanation
Indices: 29847642--29847771 Score: 137
Period size: 27 Copynumber: 4.8 Consensus size: 28
29847632 CTGGTTTGTG
* * *
29847642 AAATTAC-CGAAATACCCTCGATTTATA
1 AAATTACTAGAAATACCCTTGATTTACA
*
29847669 AAATTACCA-AAATACCCTTGATTTACA
1 AAATTACTAGAAATACCCTTGATTTACA
29847696 AAATTA-TAGAAATACCCTTGACTTT-CTAA
1 AAATTACTAGAAATACCCTTGA-TTTAC--A
* *
29847725 AAATTA-TAGAAATACCATTGTTTTACA
1 AAATTACTAGAAATACCCTTGATTTACA
29847752 AAATTACT-GAAATACCCTTG
1 AAATTACTAGAAATACCCTTG
29847772 GTTTGTAGAT
Statistics
Matches: 89, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
26 1 0.01
27 60 0.67
28 7 0.08
29 21 0.24
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.32
Consensus pattern (28 bp):
AAATTACTAGAAATACCCTTGATTTACA
Found at i:29849478 original size:6 final size:6
Alignment explanation
Indices: 29849467--29849491 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29849457 AAGAAAAGAT
29849467 AGGGAA AGGGAA AGGGAA AGGGAA A
1 AGGGAA AGGGAA AGGGAA AGGGAA A
29849492 AGNNNNNNNN
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AGGGAA
Found at i:29863504 original size:27 final size:27
Alignment explanation
Indices: 29863474--29863651 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29863464 ATATTGAGTC
* * * *
29863474 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29863501 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29863528 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29863556 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29863583 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29863610 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29863637 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29863652 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29863613 original size:82 final size:81
Alignment explanation
Indices: 29863495--29863650 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29863485 TGCTATATAA
* *
29863495 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29863560 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29863577 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29863641 CACTTAGTGC
65 CACTTAGTGC
29863651 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29866396 original size:21 final size:21
Alignment explanation
Indices: 29866372--29866417 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
29866362 TTGAAGTTTA
29866372 ATGATAGATTATGGAAGCTAG
1 ATGATAGATTATGGAAGCTAG
29866393 ATGATAGATTATGGAAGCTAG
1 ATGATAGATTATGGAAGCTAG
29866414 ATGA
1 ATGA
29866418 CAGCTATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.28, T:0.28
Consensus pattern (21 bp):
ATGATAGATTATGGAAGCTAG
Found at i:29866878 original size:16 final size:17
Alignment explanation
Indices: 29866854--29866886 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29866844 GTATATAATA
*
29866854 GAATTATTTGAT-ATAT
1 GAATGATTTGATGATAT
29866870 GAATGATTTGATGATAT
1 GAATGATTTGATGATAT
29866887 ATCGAATCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (17 bp):
GAATGATTTGATGATAT
Found at i:29867094 original size:24 final size:23
Alignment explanation
Indices: 29867014--29867112 Score: 89
Period size: 24 Copynumber: 4.2 Consensus size: 23
29867004 TGTATGAGAA
*
29867014 TACTGATTCAGCTCGAA-AGAGCT
1 TACTGTTTCAGCTC-AATAGAGCT
29867037 TACTG-TTCAGCTCAATAGAGCT
1 TACTGTTTCAGCTCAATAGAGCT
* *
29867059 TCCCAT-TTTCAGCTCAATAGAGTT
1 T-AC-TGTTTCAGCTCAATAGAGCT
29867083 TACTGTTATCAGCTC-ATGAAGAGCT
1 TACTGTT-TCAGCTCAAT--AGAGCT
29867108 TACTG
1 TACTG
29867113 GCCATGTCTC
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
21 2 0.03
22 16 0.25
23 11 0.17
24 25 0.39
25 10 0.16
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (23 bp):
TACTGTTTCAGCTCAATAGAGCT
Found at i:29868478 original size:15 final size:15
Alignment explanation
Indices: 29868458--29868494 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
29868448 ATTTAGCTAT
*
29868458 TATATTTTGTATTTG
1 TATATTTTGTATTTC
29868473 TATATTTT-TATTTC
1 TATATTTTGTATTTC
29868487 TAT-TTTTG
1 TATATTTTG
29868495 GTTTGGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 8 0.40
15 8 0.40
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.70
Consensus pattern (15 bp):
TATATTTTGTATTTC
Found at i:29868550 original size:12 final size:13
Alignment explanation
Indices: 29868508--29868553 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
29868498 TGGATGTTCC
29868508 TCTTCTTTTTCTT
1 TCTTCTTTTTCTT
* *
29868521 T-TTGTTTTTCCT
1 TCTTCTTTTTCTT
29868533 TC-TCTTTTT-TT
1 TCTTCTTTTTCTT
29868544 TCTTCTTTTT
1 TCTTCTTTTT
29868554 GGGGGTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
11 3 0.11
12 23 0.85
13 1 0.04
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (13 bp):
TCTTCTTTTTCTT
Found at i:29869174 original size:59 final size:59
Alignment explanation
Indices: 29869082--29869193 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
29869072 CACACGGTCG
* *
29869082 TGTGGCTAATGGGGAATTTAGGGATTCCACACGGGCGTGTGTTTTGGGACACATGACCA
1 TGTGGCTAATGGGGAATTTAGGGATTCCACACGGGCATGTGTTTTGAGACACATGACCA
* *
29869141 TGTGGCTAATTGGGAATTTAGGGATTCCACACGGGTATGTGTTTTGAGACACA
1 TGTGGCTAATGGGGAATTTAGGGATTCCACACGGGCATGTGTTTTGAGACACA
29869194 CGGTCGTGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.29
Consensus pattern (59 bp):
TGTGGCTAATGGGGAATTTAGGGATTCCACACGGGCATGTGTTTTGAGACACATGACCA
Found at i:29878175 original size:24 final size:24
Alignment explanation
Indices: 29878122--29878175 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
29878112 TTATTAGATG
29878122 TTTTGA-ATGTATTTGAGATTCAA
1 TTTTGATATGTATTTGAGATTCAA
* * *
29878145 TTATGATATG-ATTTGTGATTATAA
1 TTTTGATATGTATTTGAGATT-CAA
29878169 TTTTGAT
1 TTTTGAT
29878176 TCGATAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (24 bp):
TTTTGATATGTATTTGAGATTCAA
Found at i:29881009 original size:69 final size:69
Alignment explanation
Indices: 29880905--29881127 Score: 261
Period size: 69 Copynumber: 3.2 Consensus size: 69
29880895 TGCACAAACG
* * *
29880905 AGAAAGAGAGGGAGGGAGCATGCTTGGCGGCATGGATTGGAGCTTGGGACAATTACAGATATACA
1 AGAAAGAGAGTGAGGGAGCATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTACAGATAAACA
29880970 AATA
66 AATA
* * * * ** *
29880974 CA-AAAGAGAGTGCGGAAGCATGTTTGGGGGCATGGATTGGAGATTGGGACAATTGTAGATAAAG
1 -AGAAAGAGAGTGAGGGAGCATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTACAGATAAAC
29881038 AAATA
65 AAATA
* * * * *
29881043 AGAAAGAGAGTGTGGGAGCATGTTTGGCGGCATGGATTGGAGCTTTGTACAA-TAGTAGATACAC
1 AGAAAGAGAGTGAGGGAGCATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTA-CAGATAAAC
*
29881107 AAATG
65 AAATA
29881112 AGAAAGAGAGGTGAGG
1 AGAAAGAGA-GTGAGG
29881128 TGTTGAAACC
Statistics
Matches: 129, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
68 2 0.02
69 121 0.94
70 6 0.05
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (69 bp):
AGAAAGAGAGTGAGGGAGCATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTACAGATAAACA
AATA
Found at i:29887729 original size:18 final size:18
Alignment explanation
Indices: 29887706--29887743 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
29887696 AATTATAGTT
29887706 TTTAGGATTTTAAATAAA
1 TTTAGGATTTTAAATAAA
29887724 TTTAGGATTTTAAATAAA
1 TTTAGGATTTTAAATAAA
29887742 TT
1 TT
29887744 AGGGCTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
TTTAGGATTTTAAATAAA
Found at i:29890533 original size:86 final size:86
Alignment explanation
Indices: 29890443--29890623 Score: 355
Period size: 86 Copynumber: 2.1 Consensus size: 86
29890433 AATATAATTG
29890443 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
29890508 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
29890529 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
29890594 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
29890615 TAATT-TTAT
1 TAATTATTAT
29890624 GTGGAGAGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 4 0.04
86 91 0.96
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (86 bp):
TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
TGTTAAGTATTAATGTTGATA
Found at i:29890765 original size:51 final size:51
Alignment explanation
Indices: 29890690--29890894 Score: 387
Period size: 51 Copynumber: 4.0 Consensus size: 51
29890680 TATACGTAAA
29890690 AATTAT-CATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
1 AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
29890740 AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
1 AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
29890791 AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
1 AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
29890842 AATTATACATACACCAACAATGTTTTTTAGGG-ACAATAACATTAAACCAAC
1 AATTATACATACACCAACAATGTTTTTTAGGGTA-AATAACATTAAACCAAC
29890893 AA
1 AA
29890895 GTAATTTTAG
Statistics
Matches: 153, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
50 7 0.05
51 146 0.95
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (51 bp):
AATTATACATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAAC
Found at i:29890903 original size:33 final size:34
Alignment explanation
Indices: 29890840--29890950 Score: 115
Period size: 33 Copynumber: 3.4 Consensus size: 34
29890830 CATTAAACCA
* *
29890840 ACAATTATACATACACCAACAATGT-TTTTTAGGG
1 ACAATTATACATAAACCAACAA-GTAATTTTAGGG
29890874 ACAA-TA-ACATTAAACCAACAAGTAATTTTA-GG
1 ACAATTATACA-TAAACCAACAAGTAATTTTAGGG
* * *
29890906 TCAATTATACATACACCAACAATTAATTTTA-GG
1 ACAATTATACATAAACCAACAAGTAATTTTAGGG
*
29890939 TCAATTATACAT
1 ACAATTATACAT
29890951 GCTTTATAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.15
33 51 0.75
34 7 0.10
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (34 bp):
ACAATTATACATAAACCAACAAGTAATTTTAGGG
Found at i:29894168 original size:120 final size:120
Alignment explanation
Indices: 29893971--29894593 Score: 1201
Period size: 120 Copynumber: 5.2 Consensus size: 120
29893961 TTTTCAAGTT
29893971 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
29894036 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
29894091 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
29894156 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
29894211 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
29894276 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
*
29894331 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
29894396 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
*
29894451 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
29894516 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
29894571 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
29894594 TAAATATGAT
Statistics
Matches: 500, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 500 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
Found at i:29894450 original size:18 final size:17
Alignment explanation
Indices: 29894422--29894456 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29894412 ATTATTAAGA
*
29894422 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29894439 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29894457 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29894570 original size:18 final size:17
Alignment explanation
Indices: 29894542--29894576 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29894532 ATTATTAAGA
*
29894542 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
29894559 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
29894577 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:29894790 original size:44 final size:45
Alignment explanation
Indices: 29894741--29894831 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
29894731 ACCTCTATTC
* * *
29894741 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
29894785 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
29894830 CA
1 CA
29894832 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:29894833 original size:16 final size:16
Alignment explanation
Indices: 29894812--29894880 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
29894802 GATTAGCTAT
29894812 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
29894828 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
29894845 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
29894861 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
29894877 TACA
1 TACA
29894881 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:29894854 original size:33 final size:32
Alignment explanation
Indices: 29894812--29894880 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
29894802 GATTAGCTAT
29894812 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
29894845 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
29894877 TACA
1 TACA
29894881 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:29894986 original size:34 final size:34
Alignment explanation
Indices: 29894947--29895015 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
29894937 TTGGGTTTAT
* * *
29894947 TAAATTAAGGTT-TGGGTTTTTTAAATAGATTAAG
1 TAAATTAAGGTTCTAGG-ATTTTAAATAAATTAAG
*
29894981 TAAATTAGGGTTCTAGGATTTTAAATAAATTAAG
1 TAAATTAAGGTTCTAGGATTTTAAATAAATTAAG
29895015 T
1 T
29895016 TAGGGTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 27 0.90
35 3 0.10
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (34 bp):
TAAATTAAGGTTCTAGGATTTTAAATAAATTAAG
Found at i:29895028 original size:22 final size:22
Alignment explanation
Indices: 29894994--29895045 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
29894984 ATTAGGGTTC
* * *
29894994 TAGGATTTTAAATAAATTAAGT
1 TAGGGTTTAAAATAAATTAAAT
29895016 TAGGGTTTAAAATAAATTAAAT
1 TAGGGTTTAAAATAAATTAAAT
29895038 TAGGGTTT
1 TAGGGTTT
29895046 TTGGTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (22 bp):
TAGGGTTTAAAATAAATTAAAT
Found at i:29895078 original size:21 final size:22
Alignment explanation
Indices: 29895031--29895080 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
29895021 TTTAAAATAA
* *
29895031 ATTAAATTAGGGTTTTTGGTTT
1 ATTAAATTAAGGTTTGTGGTTT
29895053 ATTAAATTAAGGTTTGT-GTTT
1 ATTAAATTAAGGTTTGTGGTTT
*
29895074 TTTAAAT
1 ATTAAAT
29895081 AGATTAAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (22 bp):
ATTAAATTAAGGTTTGTGGTTT
Found at i:29895093 original size:34 final size:34
Alignment explanation
Indices: 29895055--29895123 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
29895045 TTTGGTTTAT
** *
29895055 TAAATTAAGGTTTGT-GTTTTTTAAATAGATTAAG
1 TAAATTAAGGTTT-TAGGGTTTTAAATAAATTAAG
29895089 TAAATTAAGGTTTTAGGGTTTTAAATAAATTAAG
1 TAAATTAAGGTTTTAGGGTTTTAAATAAATTAAG
29895123 T
1 T
29895124 TAGGTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 1 0.03
34 30 0.97
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (34 bp):
TAAATTAAGGTTTTAGGGTTTTAAATAAATTAAG
Done.