Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 95 of 167
Found at i:31430205 original size:29 final size:29
Alignment explanation
Indices: 31430136--31430281 Score: 161
Period size: 29 Copynumber: 5.1 Consensus size: 29
31430126 ACCCCTACAT
*
31430136 ACATGCATATGGCCCA-CACGGCCCAA-TC
1 ACATTCATATGGCCCATCA-GGCCCAATTC
* * **
31430164 TCATTTATATGGCCTGTCAGGCCCAATTC
1 ACATTCATATGGCCCATCAGGCCCAATTC
31430193 ACATTCATATGGCCCATCAGGCCCAATTC
1 ACATTCATATGGCCCATCAGGCCCAATTC
* * *
31430222 ATATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATCAGGCCCAATTC
* * * *
31430251 ACCTTTATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATCAGGCCCAATTC
31430280 AC
1 AC
31430282 CTTATATTCA
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
28 18 0.18
29 83 0.82
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCATCAGGCCCAATTC
Found at i:31438959 original size:29 final size:28
Alignment explanation
Indices: 31438889--31439034 Score: 150
Period size: 29 Copynumber: 5.1 Consensus size: 28
31438879 ACCCCTACAT
*
31438889 ACATGCATATGGCCCACTTA-GCCCAATC
1 ACATTCATATGGCCCA-TTAGGCCCAATC
* * *
31438917 TCATTTATATGGCCCGTTAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAA-TC
*
31438946 ACATTCATATGGCCCATCAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAA-TC
*
31438975 ATATTCATATGGCCCATTAGGCCCTAATC
1 ACATTCATATGGCCCATTAGGCCC-AATC
* * **
31439004 ACCTTTATATGGCCTGTTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCC-AATC
31439033 AC
1 AC
31439035 CTTATATTCA
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
27 3 0.03
28 18 0.18
29 76 0.77
30 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (28 bp):
ACATTCATATGGCCCATTAGGCCCAATC
Found at i:31440866 original size:21 final size:19
Alignment explanation
Indices: 31440823--31440866 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
31440813 TTAATTGCAC
31440823 TTTAATTATTTTATAAAAA
1 TTTAATTATTTTATAAAAA
*
31440842 -TTAATTATTTTTTGACAAAA
1 TTTAATTATTTTAT-A-AAAA
31440862 TTTAA
1 TTTAA
31440867 CCGAATTCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.57
19 1 0.05
20 4 0.19
21 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTATTTTATAAAAA
Found at i:31448278 original size:15 final size:15
Alignment explanation
Indices: 31448239--31448318 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
31448229 GTATCTTGGG
*
31448239 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
31448254 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
31448269 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
31448284 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
31448299 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
31448313 TTTCTT
1 TTTCTT
31448319 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:31448308 original size:30 final size:30
Alignment explanation
Indices: 31448230--31448317 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
31448220 CATAGTATCG
* * *
31448230 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
31448260 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
31448290 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
31448318 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:31450758 original size:46 final size:45
Alignment explanation
Indices: 31450705--31450880 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
31450695 TATTTGGGCA
31450705 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
31450751 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
31450798 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
31450844 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31450881 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:31450860 original size:93 final size:93
Alignment explanation
Indices: 31450701--31450872 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
31450691 GGGATATTTG
* *
31450701 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31450766 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
31450794 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31450859 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
31450873 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:31453840 original size:15 final size:15
Alignment explanation
Indices: 31453820--31453888 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
31453810 GTATCTTGGG
31453820 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
31453835 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
31453850 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
31453865 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
31453880 TTTCTTTAT
1 TTTCTTTAT
31453889 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:31453889 original size:30 final size:30
Alignment explanation
Indices: 31453811--31453898 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
31453801 CATAGTATCG
* * * *
31453811 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
31453841 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
31453871 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
31453899 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:31456338 original size:46 final size:45
Alignment explanation
Indices: 31456285--31456460 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
31456275 TATTTGGGCA
31456285 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
31456331 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
31456378 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
31456424 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31456461 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:31456440 original size:93 final size:93
Alignment explanation
Indices: 31456281--31456452 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
31456271 AGGATATTTG
* *
31456281 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31456346 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
31456374 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31456439 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
31456453 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:31458197 original size:29 final size:30
Alignment explanation
Indices: 31458143--31458200 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
31458133 CTTTTGAAAA
* *
31458143 TATTTACAAAAAGAGGCATCTAATTTTTAT
1 TATTTACAAAAAGAGGCAACCAATTTTTAT
31458173 TATTTACAAAAAGA-GCAACCAATTTTTA
1 TATTTACAAAAAGAGGCAACCAATTTTTA
31458201 AAAATACTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (30 bp):
TATTTACAAAAAGAGGCAACCAATTTTTAT
Found at i:31472654 original size:22 final size:22
Alignment explanation
Indices: 31472624--31472665 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31472614 TAGTGCAAAG
31472624 CAGTCTGGGCCTAAGCCCATAT
1 CAGTCTGGGCCTAAGCCCATAT
* *
31472646 CAGTGTGGGCCTTAGCCCAT
1 CAGTCTGGGCCTAAGCCCAT
31472666 TACAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.31, G:0.26, T:0.24
Consensus pattern (22 bp):
CAGTCTGGGCCTAAGCCCATAT
Found at i:31473546 original size:19 final size:18
Alignment explanation
Indices: 31473514--31473549 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
31473504 CTGAGATCAA
31473514 CACAAGCGTGAACACGCT
1 CACAAGCGTGAACACGCT
*
31473532 CACATAGCGTTAACACGC
1 CACA-AGCGTGAACACGC
31473550 ACAGTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.14
Consensus pattern (18 bp):
CACAAGCGTGAACACGCT
Found at i:31490087 original size:15 final size:16
Alignment explanation
Indices: 31490055--31490088 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
31490045 ATTTCATCTC
31490055 ATTTGCATTTAGGTTA
1 ATTTGCATTTAGGTTA
31490071 ATTTGCATTTA-GTTA
1 ATTTGCATTTAGGTTA
31490086 ATT
1 ATT
31490089 AATTTAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (16 bp):
ATTTGCATTTAGGTTA
Found at i:31493441 original size:18 final size:19
Alignment explanation
Indices: 31493406--31493442 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
31493396 TGAATTGGCC
31493406 AAACAGGCCAGAATGGGCT
1 AAACAGGCCAGAATGGGCT
*
31493425 AAACAGGCCCG-ATGGGCT
1 AAACAGGCCAGAATGGGCT
31493443 GTTGGGCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.32, C:0.24, G:0.32, T:0.11
Consensus pattern (19 bp):
AAACAGGCCAGAATGGGCT
Found at i:31493555 original size:28 final size:29
Alignment explanation
Indices: 31493515--31493595 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 29
31493505 CATGACTGTA
31493515 AATGTGATTTGGGCCTAGT-GGCCAAATG
1 AATGTGATTTGGGCCTAGTAGGCCAAATG
* * * *
31493543 AATGTGATTTGGGCCTAATGGGTCATATG
1 AATGTGATTTGGGCCTAGTAGGCCAAATG
* *
31493572 AAAGAGA-TTGGGCCTAGTAGGCCA
1 AATGTGATTTGGGCCTAGTAGGCCA
31493596 TATATATATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 32 0.73
29 12 0.27
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAGTAGGCCAAATG
Found at i:31501061 original size:16 final size:16
Alignment explanation
Indices: 31501051--31501096 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
31501041 CGAAAAGCTG
31501051 AAATGCAGAAAAGCCA
1 AAATGCAGAAAAGCCA
31501067 AAATGCAGAAAAGCCA
1 AAATGCAGAAAAGCCA
*
31501083 AAATGCGGAAAAGC
1 AAATGCAGAAAAGC
31501097 TGAAAGTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.54, C:0.17, G:0.22, T:0.07
Consensus pattern (16 bp):
AAATGCAGAAAAGCCA
Found at i:31507829 original size:40 final size:40
Alignment explanation
Indices: 31507677--31507822 Score: 172
Period size: 40 Copynumber: 3.6 Consensus size: 40
31507667 TTGAATGATG
* * * *
31507677 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
31507717 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
31507757 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTCCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
31507798 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31507823 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 81 0.88
41 10 0.11
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31507829 original size:80 final size:80
Alignment explanation
Indices: 31507677--31507855 Score: 188
Period size: 80 Copynumber: 2.2 Consensus size: 80
31507667 TTGAATGATG
* *
31507677 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
31507742 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * *
31507757 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGT-TCCTATAACCGGGCTATG-TCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACC-ATAACCGGACTAAGAT-CCGAAGGCA
*
31507819 TTTGAACGAGTAGCTATA
63 TTTGAACGAGTAGCTAAA
* *
31507837 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
31507856 TACGTGATTT
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
79 19 0.23
80 58 0.69
81 7 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:31507836 original size:40 final size:39
Alignment explanation
Indices: 31507678--31507841 Score: 154
Period size: 40 Copynumber: 4.1 Consensus size: 39
31507668 TGAATGATGT
* * *
31507678 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAA
*
31507718 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
31507757 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTCCTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
* ** *
31507798 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATAA
31507838 CCGG
1 CCGG
31507842 TTAAATTCCG
Statistics
Matches: 104, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
39 3 0.03
40 90 0.87
41 11 0.11
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAA
Found at i:31509354 original size:28 final size:28
Alignment explanation
Indices: 31509314--31509416 Score: 118
Period size: 28 Copynumber: 3.6 Consensus size: 28
31509304 CATGACTGTA
31509314 AATGTGATTTGGGCCTAAT-GGCCAAATG
1 AATGTGA-TTGGGCCTAATAGGCCAAATG
* *
31509342 AATGTGATTTGGGCCTAATAGGCCACATA
1 AATGTGA-TTGGGCCTAATAGGCCAAATG
* * *
31509371 AATGTGAATGGGCCTAATGGGCCATATG
1 AATGTGATTGGGCCTAATAGGCCAAATG
* *
31509399 AAAGGGATTGGGCCTAAT
1 AATGTGATTGGGCCTAAT
31509417 GGGTCATATA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
28 51 0.78
29 14 0.22
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (28 bp):
AATGTGATTGGGCCTAATAGGCCAAATG
Found at i:31520250 original size:55 final size:55
Alignment explanation
Indices: 31520168--31520278 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
31520158 AAACGAATTA
* * *
31520168 TATTGTCATCACCAATGCTTAACCTTAAACCTGCAAATGATATATAATAATACAT
1 TATTGTCATCACCAATGCTTAACCTTAAACCTACAAATGAGATACAATAATACAT
31520223 TATTGTCATCACCAATGCTTAACCTTAAACCTACAAATGAGATACAATAATACAT
1 TATTGTCATCACCAATGCTTAACCTTAAACCTACAAATGAGATACAATAATACAT
31520278 T
1 T
31520279 TCCATGTATC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.32
Consensus pattern (55 bp):
TATTGTCATCACCAATGCTTAACCTTAAACCTACAAATGAGATACAATAATACAT
Found at i:31527180 original size:30 final size:31
Alignment explanation
Indices: 31527104--31527181 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
31527094 CTCGACATAT
*
31527104 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
* *
31527135 ACTGGGTCAAAGCCTTTTCATAAATCAAATC
1 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
31527166 ACT-GGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
31527182 ACTGTAAGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 11 0.26
31 31 0.74
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCAAATC
Found at i:31527429 original size:25 final size:25
Alignment explanation
Indices: 31527401--31527470 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
31527391 CTCTTTTAAT
31527401 AACTGGGGCAAAG-CCTTTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
*
31527426 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
31527451 AACTGGGGTAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
31527471 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 34 0.83
26 7 0.17
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:31528310 original size:27 final size:27
Alignment explanation
Indices: 31528280--31528344 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
31528270 GGGCATATTC
31528280 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * * *
31528307 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
31528334 GTCTTTTTACC
1 GTCATTTTACC
31528345 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:31528346 original size:26 final size:28
Alignment explanation
Indices: 31528302--31528353 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
31528292 TACAAGGGTA
31528302 TTACGGTCACTTTACCCTA-TAGGGGCT
1 TTACGGTCACTTTACCCTATTAGGGGCT
**
31528329 TTACGGTCTTTTTA-CCTATTAGGGG
1 TTACGGTCACTTTACCCTATTAGGGG
31528354 TATTTTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (28 bp):
TTACGGTCACTTTACCCTATTAGGGGCT
Found at i:31528428 original size:27 final size:27
Alignment explanation
Indices: 31528398--31528494 Score: 119
Period size: 27 Copynumber: 3.6 Consensus size: 27
31528388 GTAAATCTAC
31528398 AAACCAAGGGTATTTC-AGTAATTTTGT
1 AAACCAAGGGTATTTCTA-TAATTTTGT
*
31528425 AAACCAATGGTATTTCTATAATTTT-T
1 AAACCAAGGGTATTTCTATAATTTTGT
31528451 AGAAAGCCAAGGGTATTTCTATAATTTTGT
1 --AAA-CCAAGGGTATTTCTATAATTTTGT
*
31528481 AAATC-AGGGTATTT
1 AAACCAAGGGTATTT
31528495 TGGTAATTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
26 10 0.16
27 23 0.37
28 7 0.11
29 21 0.34
30 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (27 bp):
AAACCAAGGGTATTTCTATAATTTTGT
Found at i:31528550 original size:54 final size:54
Alignment explanation
Indices: 31528486--31528643 Score: 176
Period size: 54 Copynumber: 2.9 Consensus size: 54
31528476 TTTGTAAATC
*
31528486 AGGGTATTTTGGTAATTTTACAAA-TTGAAGGTATTTCGGTAATTTCACAAACCA
1 AGGGTATTTTGGTAATTTTACAAACTAG-AGGTATTTCGGTAATTTCACAAACCA
* * * * *
31528540 ATGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTA
1 AGGGTATTTTGGTAATTTTACAAACTAGAGGTATTTCGGTAATTTCACAAACCA
* * ** * *
31528594 GGGGTATTTTGGTAATTCTATCCTAC-AGGGGTATTTCAGTAATTTCACAA
1 AGGGTATTTTGGTAATTTTA-CAAACTAGAGGTATTTCGGTAATTTCACAA
31528644 TCGAGGGTAA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 83 0.94
55 5 0.06
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAACTAGAGGTATTTCGGTAATTTCACAAACCA
Found at i:31528629 original size:27 final size:27
Alignment explanation
Indices: 31528487--31528610 Score: 169
Period size: 27 Copynumber: 4.6 Consensus size: 27
31528477 TTGTAAATCA
*
31528487 GGGTATTTTGGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* * * * *
31528513 AAGGTATTTCGGTAATTTCACAAACCAA
1 -GGGTATTTTGGTAATTTTACAAACTAG
*
31528541 TGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
31528568 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
31528595 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
31528611 CTATCCTACA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 84 1.00
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:31528661 original size:26 final size:25
Alignment explanation
Indices: 31528632--31528747 Score: 81
Period size: 27 Copynumber: 4.4 Consensus size: 25
31528622 GGGTATTTCA
*
31528632 GTAATTTCACAATCGAGGGTAAAATG
1 GTAATTTTA-AATCGAGGGTAAAATG
*
31528658 GTAATTTTGTAAA-CTGAAGGTAAAATG
1 GTAA-TTT-TAAATC-GAGGGTAAAATG
**
31528685 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAA-TTT-TAAATCGAGGGTAAAATG
* ***
31528712 ATAATTCTATAAATCGAGGGTACTTTG
1 GTAATT-T-TAAATCGAGGGTAAAATG
31528739 GTAATTTTA
1 GTAATTTTA
31528748 CAAGTTGAGG
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
25 2 0.03
26 8 0.11
27 60 0.83
28 2 0.03
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (25 bp):
GTAATTTTAAATCGAGGGTAAAATG
Found at i:31528706 original size:27 final size:27
Alignment explanation
Indices: 31528642--31528733 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
31528632 GTAATTTCAC
31528642 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
*
31528669 AA-CTGAAGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTGTA
*** * *
31528696 AATCGAGGGTAAAACAATAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
31528723 AATCGAGGGTA
1 AATCGAGGGTA
31528734 CTTTGGTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.02
27 54 0.96
28 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTGTA
Found at i:31529232 original size:31 final size:31
Alignment explanation
Indices: 31529197--31529399 Score: 325
Period size: 31 Copynumber: 6.5 Consensus size: 31
31529187 CGTTTACAGT
31529197 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* * * *
31529228 AAAGGCTTCGGTCCAGTGATATAATTTAAGT
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
31529259 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
31529290 AAAGGCTTCAGCCCAGTGATGTGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
31529321 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
31529352 AAACGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
31529383 AAACGCTTCAGCCCAGT
1 AAAGGCTTCGGCCCAGT
31529400 AACCGTTAAA
Statistics
Matches: 158, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 158 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:31534511 original size:46 final size:46
Alignment explanation
Indices: 31534460--31534551 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
31534450 TCCGAACTCG
* *
31534460 TGGATGCGAATGTCCGAACACGTTGAGTTGAGTCCGAGTTCACTTA
1 TGGATGCCAATGCCCGAACACGTTGAGTTGAGTCCGAGTTCACTTA
* * *
31534506 TGGATGCCAATGCCCGAGCTCGTTGAGTTGATTCCGAGTTCACTTA
1 TGGATGCCAATGCCCGAACACGTTGAGTTGAGTCCGAGTTCACTTA
31534552 GGGGCGGGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
TGGATGCCAATGCCCGAACACGTTGAGTTGAGTCCGAGTTCACTTA
Found at i:31539554 original size:27 final size:27
Alignment explanation
Indices: 31539522--31539711 Score: 222
Period size: 27 Copynumber: 7.1 Consensus size: 27
31539512 TGAAATGCCT
**
31539522 TCGATTTGTAGAATTACCATTTTACCC
1 TCGATTTACAGAATTACCATTTTACCC
* * * *
31539549 TTGATTTATAGAATTACCGTTTCACCC
1 TCGATTTACAGAATTACCATTTTACCC
* * *
31539576 GCAATTTACA-AATTACCGTTTTACCC
1 TCGATTTACAGAATTACCATTTTACCC
*
31539602 TCGATTTATAGAATTACCATTTTACCC
1 TCGATTTACAGAATTACCATTTTACCC
*
31539629 TCGATTTACAGAATTACTATTTTACCC
1 TCGATTTACAGAATTACCATTTTACCC
* * * *
31539656 TTGATTTAAAAAATTACCGA-CTTACCC
1 TCGATTTACAGAATTACC-ATTTTACCC
31539683 TCGATTTACAGAATTACCATTTTACCC
1 TCGATTTACAGAATTACCATTTTACCC
31539710 TC
1 TC
31539712 AATGTAAAAA
Statistics
Matches: 136, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
26 23 0.17
27 112 0.82
28 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.38
Consensus pattern (27 bp):
TCGATTTACAGAATTACCATTTTACCC
Found at i:31539598 original size:53 final size:53
Alignment explanation
Indices: 31539522--31539710 Score: 245
Period size: 54 Copynumber: 3.5 Consensus size: 53
31539512 TGAAATGCCT
**
31539522 TCGATTTGTAGAATTACCATTTTACCCTTGATTTATAGAATTACCGTTTCACCC
1 TCGATTTACAGAATTACCATTTTACCCTTGATTTATAGAATTACCGTTT-ACCC
* * * * *
31539576 GCAATTTACA-AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCC
1 TCGATTTACAGAATTACCATTTTACCCTTGATTTATAGAATTACC-GTTTACCC
* * * *
31539629 TCGATTTACAGAATTACTATTTTACCCTTGATTTAAAAAATTACCGACTTACCC
1 TCGATTTACAGAATTACCATTTTACCCTTGATTTATAGAATTACCG-TTTACCC
31539683 TCGATTTACAGAATTACCATTTTACCCT
1 TCGATTTACAGAATTACCATTTTACCCT
31539711 CAATGTAAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
53 44 0.38
54 71 0.62
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (53 bp):
TCGATTTACAGAATTACCATTTTACCCTTGATTTATAGAATTACCGTTTACCC
Found at i:31539642 original size:80 final size:81
Alignment explanation
Indices: 31539522--31539711 Score: 256
Period size: 80 Copynumber: 2.4 Consensus size: 81
31539512 TGAAATGCCT
* * * * *
31539522 TCGATTTGTAGAATTACCATTTTACCCTTGATTTATAGAATTACCGTTTCACCCGCAATTT-ACA
1 TCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTCACCCGCAATTTAAAA
**
31539586 AATTACCGTTTTACCC
66 AATTACCGACTTACCC
* * ***
31539602 TCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACTATTTTACCCTTGATTTAAAA
1 TCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTCACCCGCAATTTAAAA
31539667 AATTACCGACTTACCC
66 AATTACCGACTTACCC
*
31539683 TCGATTTACAGAATTACCATTTTACCCTC
1 TCGATTTATAGAATTACCATTTTACCCTC
31539712 AATGTAAAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 52 0.54
81 44 0.46
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.38
Consensus pattern (81 bp):
TCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTCACCCGCAATTTAAAA
AATTACCGACTTACCC
Found at i:31539725 original size:81 final size:81
Alignment explanation
Indices: 31539585--31539754 Score: 225
Period size: 81 Copynumber: 2.1 Consensus size: 81
31539575 CGCAATTTAC
** * * * * *
31539585 AAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACT-AT
1 AAATTACCGACTTACCCTCGATTTACAGAATTACCATTTTACCCTCAATGTAAAAAATTACTGA-
**
31539649 TTTACCCTTGATTTAAA
65 AATACCCTTGATTTAAA
31539666 AAATTACCGACTTACCCTCGATTTACAGAATTACCATTTTACCCTCAATGTAAAAAATTACTGAA
1 AAATTACCGACTTACCCTCGATTTACAGAATTACCATTTTACCCTCAATGTAAAAAATTACTGAA
* *
31539731 ATACCCTTGGTTTACA
66 ATACCCTTGATTTAAA
31539747 AAATTACC
1 AAATTACC
31539755 AAAATACCCC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 76 0.99
82 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (81 bp):
AAATTACCGACTTACCCTCGATTTACAGAATTACCATTTTACCCTCAATGTAAAAAATTACTGAA
ATACCCTTGATTTAAA
Found at i:31539736 original size:54 final size:54
Alignment explanation
Indices: 31539522--31539755 Score: 231
Period size: 54 Copynumber: 4.4 Consensus size: 54
31539512 TGAAATGCCT
** * * * *
31539522 TCGATTTGTAGAATTACCATTTTACCCTTGATTTATAGAATTACCG-TTTCACCC
1 TCGATTTACAGAATTACCATTTTACCCTCGATTTAAAAAATTACCGAATT-ACCC
* * * * * *
31539576 GCAATTTACA-AATTACCGTTTTACCCTCGATTTATAGAATTACC-ATTTTACCC
1 TCGATTTACAGAATTACCATTTTACCCTCGATTTAAAAAATTACCGA-ATTACCC
* * *
31539629 TCGATTTACAGAATTACTATTTTACCCTTGATTTAAAAAATTACCGACTTACCC
1 TCGATTTACAGAATTACCATTTTACCCTCGATTTAAAAAATTACCGAATTACCC
* * * *
31539683 TCGATTTACAGAATTACCATTTTACCCTCAATGTAAAAAATTACTGAAATACCC
1 TCGATTTACAGAATTACCATTTTACCCTCGATTTAAAAAATTACCGAATTACCC
* * *
31539737 TTGGTTTACAAAATTACCA
1 TCGATTTACAGAATTACCA
31539756 AAATACCCCT
Statistics
Matches: 152, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
53 44 0.29
54 107 0.70
55 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (54 bp):
TCGATTTACAGAATTACCATTTTACCCTCGATTTAAAAAATTACCGAATTACCC
Found at i:31539894 original size:27 final size:28
Alignment explanation
Indices: 31539820--31539905 Score: 99
Period size: 27 Copynumber: 3.1 Consensus size: 28
31539810 NNNNNNNTGA
*
31539820 TTTACAAAATTAC-AGAAATACCCTTGAC
1 TTTACAAAATTACTAGAAATACCCTTG-G
*
31539848 TTT-CTAAAAATTA-TAGAAATACCATTGG
1 TTTAC--AAAATTACTAGAAATACCCTTGG
31539876 TTTACAAAATTACTA-AAATACCCTTGG
1 TTTACAAAATTACTAGAAATACCCTTGG
31539903 TTT
1 TTT
31539906 GTAGATTTAC
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
27 22 0.44
28 8 0.16
29 20 0.40
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (28 bp):
TTTACAAAATTACTAGAAATACCCTTGG
Found at i:31540279 original size:24 final size:24
Alignment explanation
Indices: 31540222--31540279 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
31540212 NNNNNNNCCG
31540222 AAAAGGGCTTTGCCCCAGTTTATC
1 AAAAGGGCTTTGCCCCAGTTTATC
*
31540246 AGAAAGGGCTTTGCCCCAG-TTATT
1 A-AAAGGGCTTTGCCCCAGTTTATC
31540270 AAAAGAGGCT
1 AAAAG-GGCT
31540280 AGGCCTCCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 4 0.13
24 10 0.32
25 17 0.55
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:31540569 original size:42 final size:42
Alignment explanation
Indices: 31540510--31540589 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
31540500 GCCCATTATA
31540510 CATACATTCATTGACATTACATGTGATATTGAAATGGGATTG
1 CATACATTCATTGACATTACATGTGATATTGAAATGGGATTG
31540552 CATACATTCATTGACATTACATGTGATATTGAAATGGG
1 CATACATTCATTGACATTACATGTGATATTGAAATGGG
31540590 CCTAAGGGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (42 bp):
CATACATTCATTGACATTACATGTGATATTGAAATGGGATTG
Found at i:31540753 original size:31 final size:31
Alignment explanation
Indices: 31540711--31540775 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
31540701 AATATGAAAA
* * **
31540711 AGTGATCTGATTTATGAAAAGGCTTTGGCCC
1 AGTGATATGATTTATGAAAACGCTTCAGCCC
31540742 AGTGATATGATTTATGAAAACGCTTCAGCCC
1 AGTGATATGATTTATGAAAACGCTTCAGCCC
31540773 AGT
1 AGT
31540776 AACCGTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (31 bp):
AGTGATATGATTTATGAAAACGCTTCAGCCC
Found at i:31556911 original size:46 final size:46
Alignment explanation
Indices: 31556840--31556946 Score: 169
Period size: 46 Copynumber: 2.3 Consensus size: 46
31556830 NNNNNNNAAG
*
31556840 GCCGAATGGCTAATGCGAAATGTGTATGAGATAGATATGAGATAAA
1 GCCGAATGGCTAATGCGAAACGTGTATGAGATAGATATGAGATAAA
* * *
31556886 GCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGTGGTAAA
1 GCCGAATGGCTAATGCGAAACGTGTATGAGATAGATATGAGATAAA
*
31556932 GCCAAATGGCTAATG
1 GCCGAATGGCTAATG
31556947 AGATATGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 56 1.00
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (46 bp):
GCCGAATGGCTAATGCGAAACGTGTATGAGATAGATATGAGATAAA
Found at i:31560287 original size:40 final size:40
Alignment explanation
Indices: 31560238--31560317 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
31560228 TCACATTTTT
* *
31560238 CATTTTAGGATTTAAAACTCACCCCCGGGCAAAATGACCA
1 CATTGTAGGATTTAAAAATCACCCCCGGGCAAAATGACCA
*
31560278 CATTGTAGGATTTAAAAATCACCCTCGGGCAAAATGACCA
1 CATTGTAGGATTTAAAAATCACCCCCGGGCAAAATGACCA
31560318 ATTTTCCCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (40 bp):
CATTGTAGGATTTAAAAATCACCCCCGGGCAAAATGACCA
Found at i:31565680 original size:16 final size:16
Alignment explanation
Indices: 31565643--31565680 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
31565633 AAATGCTTGA
31565643 AAAAAGTACAAAAAAT
1 AAAAAGTACAAAAAAT
31565659 AGAAAA-TACAAAAACAT
1 A-AAAAGTACAAAAA-AT
31565676 AAAAA
1 AAAAA
31565681 AAATATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.76, C:0.08, G:0.05, T:0.11
Consensus pattern (16 bp):
AAAAAGTACAAAAAAT
Found at i:31566629 original size:24 final size:24
Alignment explanation
Indices: 31566601--31566649 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
31566591 GACAACAAAG
31566601 TAAGCATTTCTATGCTTAGTAAGT
1 TAAGCATTTCTATGCTTAGTAAGT
31566625 TAAGCATTTCTATGCTTAGTAAGT
1 TAAGCATTTCTATGCTTAGTAAGT
31566649 T
1 T
31566650 GTAAGCAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (24 bp):
TAAGCATTTCTATGCTTAGTAAGT
Found at i:31569708 original size:39 final size:39
Alignment explanation
Indices: 31569652--31569796 Score: 181
Period size: 39 Copynumber: 3.7 Consensus size: 39
31569642 TTCCAACACA
* *
31569652 AATGCCTTTGAGG-CTTAGCCCAGATATAACACCAGCACG
1 AATGCCTTCG-GGACTTAGCCCGGATATAACACCAGCACG
31569691 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
31569730 AATGCCTTCGGGACTTAGCCCGGATATAA-ATCTCA-CAC-
1 AATGCCTTCGGGACTTAGCCCGGATATAACA-C-CAGCACG
* * * *
31569768 AAGGCCTGCGGGTCTTAGCCCGGTTATAA
1 AATGCCTTCGGGACTTAGCCCGGATATAA
31569797 TCCTCAATTA
Statistics
Matches: 97, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
38 28 0.29
39 67 0.69
40 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG
Found at i:31570267 original size:19 final size:19
Alignment explanation
Indices: 31570229--31570267 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31570219 TTATTCATAC
*
31570229 CTCTCATTCAATAATTACA
1 CTCTCATTCAATAATGACA
31570248 CTCTCATTCCAAT-ATGACA
1 CTCTCATT-CAATAATGACA
31570267 C
1 C
31570268 ACACACACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (19 bp):
CTCTCATTCAATAATGACA
Found at i:31576190 original size:197 final size:197
Alignment explanation
Indices: 31575855--31576223 Score: 702
Period size: 197 Copynumber: 1.9 Consensus size: 197
31575845 TTTGCTTCAC
31575855 CTAAATAGATACATGGTGTAAGGTTGGTACGGGGGTGTATACGACAGGACATGGGTTGGGTTTTC
1 CTAAATAGATACATGGTGTAAGGTTGGTACGGGGGTGTATACGACAGGACATGGGTTGGGTTTTC
*
31575920 TGCATACATGAAATATCTGTTCAGTATCTGTTATGGACCTATGGGCTTCATTCTAAATTTGATTC
66 TGCATACATGAAATATATGTTCAGTATCTGTTATGGACCTATGGGCTTCATTCTAAATTTGATTC
31575985 TGCGGTTTGATTCTGATTCTCATTTTGATTCTAGTTCTGATACTGCTACAAGATAGTTCATCGAA
131 TGCGGTTTGATTCTGATTCTCATTTTGATTCTAGTTCTGATACTGCTACAAGATAGTTCATCGAA
31576050 TA
196 TA
*
31576052 CTAAATAGATACATGGTGTAAGGTTGGTACGGGGGTGTATACGACTGGACATGGGTTGGGTTTTC
1 CTAAATAGATACATGGTGTAAGGTTGGTACGGGGGTGTATACGACAGGACATGGGTTGGGTTTTC
* *
31576117 TGCATACATGAAATATATGTTCGGTATCTGTTATGGGCCTATGGGCTTCATTCTAAATTTGATTC
66 TGCATACATGAAATATATGTTCAGTATCTGTTATGGACCTATGGGCTTCATTCTAAATTTGATTC
31576182 TGCGGTTTGATTCTGATTCTCATTTTGATTCTAGTTCTGATA
131 TGCGGTTTGATTCTGATTCTCATTTTGATTCTAGTTCTGATA
31576224 ATGTTTCTTA
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
197 168 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (197 bp):
CTAAATAGATACATGGTGTAAGGTTGGTACGGGGGTGTATACGACAGGACATGGGTTGGGTTTTC
TGCATACATGAAATATATGTTCAGTATCTGTTATGGACCTATGGGCTTCATTCTAAATTTGATTC
TGCGGTTTGATTCTGATTCTCATTTTGATTCTAGTTCTGATACTGCTACAAGATAGTTCATCGAA
TA
Found at i:31584198 original size:20 final size:20
Alignment explanation
Indices: 31584169--31584213 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
31584159 AGCACATGTA
* *
31584169 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
31584189 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
31584209 TTCAT
1 TTCAT
31584214 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:31585984 original size:17 final size:17
Alignment explanation
Indices: 31585938--31585983 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
31585928 TAAATAAAAT
31585938 AATAATTTAAATATTTA
1 AATAATTTAAATATTTA
**
31585955 AATAAAAT-AATAATTTA
1 AATAATTTAAAT-ATTTA
31585972 AAT-ATTTAAATA
1 AATAATTTAAATA
31585984 AAATAATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATTTAAATATTTA
Found at i:31586002 original size:25 final size:25
Alignment explanation
Indices: 31585922--31585995 Score: 139
Period size: 25 Copynumber: 3.0 Consensus size: 25
31585912 ATTTTATATT
*
31585922 AATATATAAATAAAATAATAATTTA
1 AATATTTAAATAAAATAATAATTTA
31585947 AATATTTAAATAAAATAATAATTTA
1 AATATTTAAATAAAATAATAATTTA
31585972 AATATTTAAATAAAATAATAATTT
1 AATATTTAAATAAAATAATAATTT
31585996 TATTATTGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATTTAAATAAAATAATAATTTA
Found at i:31586405 original size:18 final size:18
Alignment explanation
Indices: 31586374--31586408 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31586364 CAAATTTTAA
*
31586374 ATTTGAACATTAAAAAGG
1 ATTTGAACAATAAAAAGG
*
31586392 ATTTGCACAATAAAAAG
1 ATTTGAACAATAAAAAG
31586409 AGTTACGGTA
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:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (18 bp):
ATTTGAACAATAAAAAGG
Found at i:31588775 original size:17 final size:16
Alignment explanation
Indices: 31588733--31588779 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
31588723 AATTGATTCA
*
31588733 AATTTAG-ATTATTTC
1 AATTTAGAATTATTTT
* *
31588748 AATTCAAAATTGATTTT
1 AATTTAGAATT-ATTTT
31588765 AATTTAGAATTATTT
1 AATTTAGAATTATTT
31588780 AAATAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 5 0.20
16 7 0.28
17 13 0.52
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (16 bp):
AATTTAGAATTATTTT
Found at i:31589607 original size:22 final size:21
Alignment explanation
Indices: 31589569--31589625 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
31589559 ATTTTAAGTA
*
31589569 TTAAAATATAACCATTACAAAT
1 TTAAAATATAA-TATTACAAAT
* *
31589591 TTAAATATATAATATTATATAT
1 TTAAA-ATATAATATTACAAAT
31589613 TTAAAATA-AATAT
1 TTAAAATATAATAT
31589626 CAGTAGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 5 0.16
21 3 0.10
22 17 0.55
23 6 0.19
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TTAAAATATAATATTACAAAT
Found at i:31589826 original size:13 final size:13
Alignment explanation
Indices: 31589810--31589839 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31589800 AATTGATTCT
31589810 ATTAACTGATTTG
1 ATTAACTGATTTG
*
31589823 ATTAACTGATTTT
1 ATTAACTGATTTG
31589836 ATTA
1 ATTA
31589840 TCTGTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (13 bp):
ATTAACTGATTTG
Found at i:31603837 original size:40 final size:40
Alignment explanation
Indices: 31603625--31603837 Score: 243
Period size: 40 Copynumber: 5.3 Consensus size: 40
31603615 GCTACTCGTT
* * *
31603625 CAAATGCCTTTGGGACATAGCCCG-GTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGAATT-TAGTAACTCGCA
* * *
31603665 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGAATTTAGTAACTCGCA
* * *
31603705 CAAGTGCTTTCGGGACTTAACCCGAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGAATTTAGTAACTCGCA
* * *
31603745 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGAATTTAGTAACTCGCA
* * *
31603785 CAAGTGCTTTCGGGACTTAACCCGAATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGAATTTAGTAACTCGCA
31603825 CAAATGCCTTCGG
1 CAAATGCCTTCGG
31603838 ATCTTAGTTC
Statistics
Matches: 143, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
39 6 0.04
40 130 0.91
41 7 0.05
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGAATTTAGTAACTCGCA
Found at i:31603883 original size:80 final size:80
Alignment explanation
Indices: 31603653--31603845 Score: 386
Period size: 80 Copynumber: 2.4 Consensus size: 80
31603643 AGCCCGGTTA
31603653 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGTAACTCGCACAAGTGCTTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGTAACTCGCACAAGTGCTTTCGG
31603718 GACTTAACCCGAATT
66 GACTTAACCCGAATT
31603733 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGTAACTCGCACAAGTGCTTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGTAACTCGCACAAGTGCTTTCGG
31603798 GACTTAACCCGAATT
66 GACTTAACCCGAATT
31603813 TAGTAACTCGCACAAATGCCTTCGGATCTTAGT
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGT
31603846 TCATGACACA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 113 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGTAACTCGCACAAGTGCTTTCGG
GACTTAACCCGAATT
Found at i:31608097 original size:41 final size:41
Alignment explanation
Indices: 31608014--31608136 Score: 147
Period size: 41 Copynumber: 3.0 Consensus size: 41
31608004 TAAAAGCCAC
* * * * * * * *
31608014 CGGTAGATTCACGGTCATCAAGCCACTATGCAATTCTTAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
* *
31608055 CGGTGGATCCATGGTTGTCAAGCAACCATGCGATCCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
*
31608096 CGGTGGATCCACGGTCGTCAGGCAACCATGCGATCCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
31608137 TTCTTCCTCC
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (41 bp):
CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
Found at i:31608426 original size:27 final size:27
Alignment explanation
Indices: 31608396--31608717 Score: 159
Period size: 27 Copynumber: 12.0 Consensus size: 27
31608386 GGTAAATCTA
* *
31608396 CAAACTAAGGGTATTTCTTTAATTTTG
1 CAAACTAAGGGTATTTCTGTAATTTTC
* *
31608423 CAAACCAATGGTATTTCTGTAATTTTC
1 CAAACTAAGGGTATTTCTGTAATTTTC
* *
31608450 CAAA-TCAAGGGTATTTCGGTAACTTTC
1 CAAACT-AAGGGTATTTCTGTAATTTTC
* *
31608477 CAAA-TCAGGGGTATTT-TGGTAATTTTA
1 CAAACT-AAGGGTATTTCT-GTAATTTTC
* *
31608504 CAAA-TCAAGGGTATTTCAGTAATTTTA
1 CAAACT-AAGGGTATTTCTGTAATTTTC
* * * * * *
31608531 C-AAGTCGAGAGTATTTCGGTAAATTTA
1 CAAACT-AAGGGTATTTCTGTAATTTTC
* * *
31608558 C-AAGTCGAGGGTATTT-TGGTAATTTTA
1 CAAACT-AAGGGTATTTCT-GTAATTTTC
* * *
31608585 CAAA-TAGGGGTATTTCAGTAATTTTG
1 CAAACTAAGGGTATTTCTGTAATTTTC
* * *
31608611 C-AAGTCGAGGGTATTT-TAGTAATTTTA
1 CAAACT-AAGGGTATTTCT-GTAATTTTC
* *
31608638 CAAA-TCAGGGGTATTTCTGTAATTTTA
1 CAAACT-AAGGGTATTTCTGTAATTTTC
*
31608665 CAAAGC-AAGGGTATTTCAGTAA-TTTC
1 CAAA-CTAAGGGTATTTCTGTAATTTTC
* *
31608691 ACAAACCAGGGGTATTT-TGGTAATTTT
1 -CAAACTAAGGGTATTTCT-GTAATTTT
31608718 GCTAATCGAG
Statistics
Matches: 241, Mismatches: 36, Indels: 35
0.77 0.12 0.11
Matches are distributed among these distances:
25 2 0.01
26 24 0.10
27 207 0.86
28 8 0.03
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (27 bp):
CAAACTAAGGGTATTTCTGTAATTTTC
Found at i:31608463 original size:54 final size:54
Alignment explanation
Indices: 31608394--31608769 Score: 320
Period size: 54 Copynumber: 7.0 Consensus size: 54
31608384 TTGGTAAATC
* * **
31608394 TACAAA-CTAAGGGTATTTCTTTAATTTTGCAAACCAATGGTATTTCTGTAATTT
1 TACAAATC-AAGGGTATTTCTGTAATTTTACAAACCAGGGGTATTTCTGTAATTT
* * * * *
31608448 TCCAAATCAAGGGTATTTCGGTAACTTTCCAAATCAGGGGTATTT-TGGTAATTT
1 TACAAATCAAGGGTATTTCTGTAATTTTACAAACCAGGGGTATTTCT-GTAATTT
* ** * * *
31608502 TACAAATCAAGGGTATTTCAGTAATTTTACAAGTC-GAGAGTATTTCGGTAAATT
1 TACAAATCAAGGGTATTTCTGTAATTTTACAAACCAG-GGGTATTTCTGTAATTT
* * * *
31608556 TACAAGTCGAGGGTATTT-TGGTAATTTTACAAA-TAGGGGTATTTCAGTAATTT
1 TACAAATCAAGGGTATTTCT-GTAATTTTACAAACCAGGGGTATTTCTGTAATTT
* * * *
31608609 TGCAAGTCGAGGGTATTT-TAGTAATTTTACAAATCAGGGGTATTTCTGTAATTT
1 TACAAATCAAGGGTATTTCT-GTAATTTTACAAACCAGGGGTATTTCTGTAATTT
* * *
31608663 TACAAAGCAAGGGTATTTCAGTAATTTCACAAACCAGGGGTATTT-TGGTAATTT
1 TACAAATCAAGGGTATTTCTGTAATTTTACAAACCAGGGGTATTTCT-GTAATTT
* * * * ** *
31608717 TGCTAATCGAGGGTATTT-TGGTAACTTTGTAAACCAAGGGTATTT-TAGTAATT
1 TACAAATCAAGGGTATTTCT-GTAATTTTACAAACCAGGGGTATTTCT-GTAATT
31608770 CTACCTTACA
Statistics
Matches: 266, Mismatches: 46, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
53 48 0.18
54 217 0.82
55 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (54 bp):
TACAAATCAAGGGTATTTCTGTAATTTTACAAACCAGGGGTATTTCTGTAATTT
Found at i:31608489 original size:81 final size:81
Alignment explanation
Indices: 31608415--31608769 Score: 378
Period size: 81 Copynumber: 4.4 Consensus size: 81
31608405 GGTATTTCTT
* * * * *
31608415 TAATTTTGCAAACCAATGGTATTTCTGTAATTTTCCAAATCAAGGGTATTTCGGTAACTTTCCAA
1 TAATTTTACAAACCAAGGGTATTTCAGTAATTTTCCAAATCAAGGGTATTTCGGTAATTTTACAA
31608480 ATC-AGGGGTATTTTGG
66 ATCGA-GGGTATTTTGG
* * * * * *
31608496 TAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAGTCGAGAGTATTTCGGTAAATTTACAA
1 TAATTTTACAAACCAAGGGTATTTCAGTAATTTTCCAAATCAAGGGTATTTCGGTAATTTTACAA
*
31608561 GTCGAGGGTATTTTGG
66 ATCGAGGGTATTTTGG
* * * * * **
31608577 TAATTTTACAAA-TAGGGGTATTTCAGTAATTTTGCAAGTCGAGGGTATTTTAGTAATTTTACAA
1 TAATTTTACAAACCAAGGGTATTTCAGTAATTTTCCAAATCAAGGGTATTTCGGTAATTTTACAA
31608641 ATC-AGGGGTATTTCT-G
66 ATCGA-GGGTATTT-TGG
* * * * * *
31608657 TAATTTTACAAAGCAAGGGTATTTCAGTAA-TTTCACAAACCAGGGGTATTTTGGTAATTTTGCT
1 TAATTTTACAAACCAAGGGTATTTCAGTAATTTTC-CAAATCAAGGGTATTTCGGTAATTTTACA
31608721 AATCGAGGGTATTTTGG
65 AATCGAGGGTATTTTGG
* ** *
31608738 TAACTTTGTAAACCAAGGGTATTTTAGTAATT
1 TAATTTTACAAACCAAGGGTATTTCAGTAATT
31608770 CTACCTTACA
Statistics
Matches: 232, Mismatches: 34, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
79 1 0.00
80 72 0.31
81 156 0.67
82 3 0.01
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.38
Consensus pattern (81 bp):
TAATTTTACAAACCAAGGGTATTTCAGTAATTTTCCAAATCAAGGGTATTTCGGTAATTTTACAA
ATCGAGGGTATTTTGG
Found at i:31608730 original size:27 final size:27
Alignment explanation
Indices: 31608432--31608769 Score: 292
Period size: 27 Copynumber: 12.6 Consensus size: 27
31608422 GCAAACCAAT
* *
31608432 GGTATTTCT-GTAATTTTCCAAATCAAG
1 GGTATTT-TGGTAATTTTACAAATCGAG
* * *
31608459 GGTATTTCGGTAACTTTCCAAATC-AGG
1 GGTATTTTGGTAATTTTACAAATCGA-G
*
31608486 GGTATTTTGGTAATTTTACAAATCAAG
1 GGTATTTTGGTAATTTTACAAATCGAG
** *
31608513 GGTATTTCAGTAATTTTACAAGTCGAG
1 GGTATTTTGGTAATTTTACAAATCGAG
* * * *
31608540 AGTATTTCGGTAAATTTACAAGTCGAG
1 GGTATTTTGGTAATTTTACAAATCGAG
*
31608567 GGTATTTTGGTAATTTTACAAATAG-G
1 GGTATTTTGGTAATTTTACAAATCGAG
** * *
31608593 GGTATTTCAGTAATTTTGCAAGTCGAG
1 GGTATTTTGGTAATTTTACAAATCGAG
*
31608620 GGTATTTTAGTAATTTTACAAATC-AGG
1 GGTATTTTGGTAATTTTACAAATCGA-G
* *
31608647 GGTATTTCT-GTAATTTTACAAAGCAAG
1 GGTATTT-TGGTAATTTTACAAATCGAG
** * *
31608674 GGTATTTCAGTAATTTCACAAA-CCAGG
1 GGTATTTTGGTAATTTTACAAATCGA-G
* *
31608701 GGTATTTTGGTAATTTTGCTAATCGAG
1 GGTATTTTGGTAATTTTACAAATCGAG
* ** * *
31608728 GGTATTTTGGTAACTTTGTAAACCAAG
1 GGTATTTTGGTAATTTTACAAATCGAG
*
31608755 GGTATTTTAGTAATT
1 GGTATTTTGGTAATT
31608770 CTACCTTACA
Statistics
Matches: 259, Mismatches: 42, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
26 25 0.10
27 229 0.88
28 5 0.02
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (27 bp):
GGTATTTTGGTAATTTTACAAATCGAG
Found at i:31608788 original size:27 final size:27
Alignment explanation
Indices: 31608758--31608834 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
31608748 AACCAAGGGT
*
31608758 ATTTTAGTAATTCTACCTTACAGGGGC
1 ATTTTAGTAATTCTACCCTACAGGGGC
* *
31608785 ATTTTAGTAATTCTACCCTATAGGGGT
1 ATTTTAGTAATTCTACCCTACAGGGGC
* * *
31608812 ATTTCAGTAATACTAGCCTACAG
1 ATTTTAGTAATTCTACCCTACAG
31608835 ATATGAGATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (27 bp):
ATTTTAGTAATTCTACCCTACAGGGGC
Found at i:31608918 original size:17 final size:19
Alignment explanation
Indices: 31608896--31608938 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
31608886 TATCCACTTG
31608896 GGCCCAT-AGGCCTA-CAT
1 GGCCCATCAGGCCTATCAT
*
31608913 GGCCCATCCCGGCCTATCAT
1 GGCCCAT-CAGGCCTATCAT
31608933 GGCCCA
1 GGCCCA
31608939 AAGTAACCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
19 6 0.27
20 9 0.41
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.16
Consensus pattern (19 bp):
GGCCCATCAGGCCTATCAT
Found at i:31611167 original size:24 final size:24
Alignment explanation
Indices: 31611139--31611196 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
31611129 CATCCTTCTC
*
31611139 TATCTCTAAATTCAATTGGATCTT
1 TATCTCTAAATTCAATTAGATCTT
*
31611163 TATCTCTAATTTCAATTAGATCTT
1 TATCTCTAAATTCAATTAGATCTT
* *
31611187 TGTATCTAAA
1 TATCTCTAAA
31611197 AGCTCTGCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.47
Consensus pattern (24 bp):
TATCTCTAAATTCAATTAGATCTT
Found at i:31618875 original size:45 final size:45
Alignment explanation
Indices: 31618825--31619055 Score: 160
Period size: 47 Copynumber: 5.0 Consensus size: 45
31618815 ATTGACAGTT
31618825 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTC
* **** * *
31618870 AAGGATCCCATGTAAGACCATGTCAAGACATGGCATCAACATTGATT
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTA-AG-TC
** * ** *
31618917 AAGGACT-CCATGTAAGACCACATTAAGATGTGGCATTGGCACTAAGAC
1 AAGGA-TACCATGTAAGACCATGTCAAGACATGGCATTGG---TAAGTC
***
31618965 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGAT-
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGTAAG-TC
* * * ** * *
31619012 AATGATATCATGTAAGACTATACCAAGGCATGGCATTGATAAGT
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGT
31619056 TCTATAAGGC
Statistics
Matches: 140, Mismatches: 36, Indels: 21
0.71 0.18 0.11
Matches are distributed among these distances:
44 1 0.01
45 43 0.31
46 8 0.06
47 54 0.39
48 22 0.16
49 7 0.05
50 5 0.04
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (45 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTC
Found at i:31619219 original size:53 final size:54
Alignment explanation
Indices: 31619015--31619218 Score: 207
Period size: 53 Copynumber: 3.8 Consensus size: 54
31619005 GTAAGATAAT
* * ** *
31619015 GATATCATGTAAGACTATACCAAGGCATGGCATTGATAAGTTCTATAAGGCAAA
1 GATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGCAAA
* * * *
31619069 GAAATCATGTAAGACC-TGTTAAGACATGGCATTGATGAGTTACTATAAGGCAAA
1 GATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-CTATAAGGCAAA
* * * * * *
31619123 GATCCCATGTAAGACGATG-CTAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAG
1 GATACCATGTAAGACCATGTC-AAGACATGGCATTGATAAGTTCTATAAGGCAAA
* * *
31619176 GATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 GATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTC
31619219 AAAAAGGAAA
Statistics
Matches: 125, Mismatches: 21, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
53 64 0.51
54 40 0.32
55 21 0.17
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (54 bp):
GATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTATAAGGCAAA
Found at i:31622305 original size:23 final size:25
Alignment explanation
Indices: 31622274--31622319 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
31622264 TTATATGAAA
31622274 ATATACTCATTAAG-CTCTAATTTG
1 ATATACTCATTAAGTCTCTAATTTG
*
31622298 ATAT-CTCATTCAGTCTCTAATT
1 ATATACTCATTAAGTCTCTAATT
31622320 CAATTTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (25 bp):
ATATACTCATTAAGTCTCTAATTTG
Found at i:31627291 original size:30 final size:31
Alignment explanation
Indices: 31627243--31627300 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
31627233 TTTTCGAGCC
31627243 TAGGGGAAAAATCATAATTCTG-CAAAGGTT
1 TAGGGGAAAAATCATAATTCTGCCAAAGGTT
* ** *
31627273 TAGGGGCAAAATTGTAATTTTGCCAAAG
1 TAGGGGAAAAATCATAATTCTGCCAAAG
31627301 TTTGAGTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (31 bp):
TAGGGGAAAAATCATAATTCTGCCAAAGGTT
Found at i:31627978 original size:45 final size:45
Alignment explanation
Indices: 31627928--31628157 Score: 192
Period size: 47 Copynumber: 5.0 Consensus size: 45
31627918 ATTGACGGTT
*
31627928 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGAC
* * * * * *
31627973 AAGGATCCCGTGTAAGACCATGTCAAGACATGGCATCGGCATTGATT
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTA-AGA-C
** **
31628020 AAGGACT-CCATGTAAGACCACATCAAGATGTGGCATTGGCACTAAGAC
1 AAGGA-TACCATGTAAGACCATGTCAAGACATGGCATTGG---TAAGAC
*** *
31628068 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGAT
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGTAAGAC
* * * * * *
31628115 AATGATATCATGTAAGACCATGCCAAGGCATGACATTGATAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAG
31628158 TTCTATAAGG
Statistics
Matches: 143, Mismatches: 33, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
45 44 0.31
46 7 0.05
47 58 0.41
48 21 0.15
49 8 0.06
50 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (45 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGAC
Found at i:31628239 original size:55 final size:53
Alignment explanation
Indices: 31628118--31628308 Score: 213
Period size: 55 Copynumber: 3.5 Consensus size: 53
31628108 GTAAGATAAT
* * *
31628118 GATATCATGTAAGACCATGCCAAGGCATGACATTGATAAGTTCTATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGACATTGATGAGTTC-ATAAGGCAAG
* * * *
31628172 GAAATCATGTAAGGCCATGTCAAGACATGACATTGATGAGTTACGATAAGGCAAAG
1 GATACCATGTAAGACCATGCCAAGACATGACATTGATGAGTT-C-ATAAGGC-AAG
* * * * *
31628228 G-TCCCATGTAAGACAATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGACATTGATGAGTTCATAAGGCAAG
* *
31628280 GATACCACGTAAGACCATGTCAAGACATG
1 GATACCATGTAAGACCATGCCAAGACATG
31628309 GCAATGGTAA
Statistics
Matches: 114, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
52 4 0.04
53 29 0.25
54 38 0.33
55 39 0.34
56 4 0.04
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (53 bp):
GATACCATGTAAGACCATGCCAAGACATGACATTGATGAGTTCATAAGGCAAG
Found at i:31628323 original size:53 final size:54
Alignment explanation
Indices: 31628118--31628322 Score: 207
Period size: 53 Copynumber: 3.8 Consensus size: 54
31628108 GTAAGATAAT
* * *
31628118 GATATCATGTAAGACCATGCCAAGGCATGACATTGATAAGTTCTATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTCGATAAGGCAAG
* * * * *
31628172 GAAATCATGTAAGGCCATGTCAAGACATGACATTGATGAGTTACGATAAGGCAAAG
1 GATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTT-CGATAAGGC-AAG
* * * * * *
31628228 G-TCCCATGTAAGACAATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTCGATAAGGCAAG
* * * * *
31628280 GATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 GATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTC
31628323 AAAAAGGAAA
Statistics
Matches: 126, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
52 4 0.03
53 41 0.33
54 38 0.30
55 39 0.31
56 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (54 bp):
GATACCATGTAAGACCATGCCAAGACATGACATTGATAAGTTCGATAAGGCAAG
Found at i:31633020 original size:76 final size:74
Alignment explanation
Indices: 31632900--31633062 Score: 202
Period size: 76 Copynumber: 2.2 Consensus size: 74
31632890 TGATCTACTT
* * * *
31632900 CATTATGTTTTTTTTTGTTAAATGCATCTTTATTTAATGTTTTGCATTAATACATCTA-CATCTT
1 CATTATGTTTTTGTTTATTAAATGCATCTTTAGTTAATGCTTTGCATTAATACAT-TAGCATCTT
31632964 TTAAAAATGTG
65 TT-AAAATGTG
* **
31632975 CATTATGTTTCTTGTTTATTGAATGTGTCTTTAGTTAATGCTTTGCATTAATACATTAGCATCTT
1 CATTATGTTT-TTGTTTATTAAATGCATCTTTAGTTAATGCTTTGCATTAATACATTAGCATCTT
* *
31633040 TTAAGATTTG
65 TTAAAATGTG
31633050 CATTATGTGTTTT
1 CATTATGT-TTTT
31633063 TTTCATATTT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
75 28 0.37
76 48 0.63
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.52
Consensus pattern (74 bp):
CATTATGTTTTTGTTTATTAAATGCATCTTTAGTTAATGCTTTGCATTAATACATTAGCATCTTT
TAAAATGTG
Found at i:31634207 original size:21 final size:21
Alignment explanation
Indices: 31634181--31634247 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
31634171 AGAGGGGAGA
*
31634181 CCACAACGAGGTCGTTCACCT
1 CCACAACGAGGCCGTTCACCT
* * **
31634202 CCACAACGA-GCCTATTTACAA
1 CCACAACGAGGCC-GTTCACCT
31634223 CCACAACGAGGCCGTTCACCT
1 CCACAACGAGGCCGTTCACCT
31634244 CCAC
1 CCAC
31634248 CTCGAGATCA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
20 2 0.06
21 30 0.86
22 3 0.09
ACGTcount: A:0.28, C:0.40, G:0.15, T:0.16
Consensus pattern (21 bp):
CCACAACGAGGCCGTTCACCT
Found at i:31638295 original size:49 final size:50
Alignment explanation
Indices: 31638219--31638357 Score: 183
Period size: 49 Copynumber: 2.8 Consensus size: 50
31638209 AGCCGAAGCT
* * *
31638219 ATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGAGA-C-CAAC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGAGACCTCAAC
* * *
31638267 AGTCTGGTACACGTAGTAGCCTGAACTTAGTACTACACACGTGACCTCACC
1 A-TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGAGACCTCAAC
**
31638318 ATCTAATACACGTAGTAGCCTGCACTTAGTACTACACACG
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACG
31638358 TGATCATAGT
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
48 1 0.01
49 37 0.47
50 37 0.47
51 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (50 bp):
ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGAGACCTCAAC
Found at i:31638338 original size:50 final size:49
Alignment explanation
Indices: 31638231--31638360 Score: 181
Period size: 50 Copynumber: 2.6 Consensus size: 49
31638221 CTGGTACGCA
* * **
31638231 TAGTAGCCTGCACTTAGTACTACACATGAGACCAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
* *
31638280 TAGTAGCCTGAACTTAGTACTACACACGTGACCTCACCA-TCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACG
31638330 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
31638361 TCATAGTTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
49 28 0.39
50 40 0.56
51 4 0.06
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
Found at i:31644152 original size:76 final size:75
Alignment explanation
Indices: 31644046--31644209 Score: 190
Period size: 76 Copynumber: 2.2 Consensus size: 75
31644036 TGATCTACTT
* * *
31644046 CATTATGTATTTTGTTTGTTAAATGCATCTTTA-TTAAATGTTTTGCATTAATACATCTA-CATC
1 CATTATGTATTTTGTTTATTAAATGCATCTTTAGTT-AATGCTTTGAATTAATACAT-TAGCATC
*
31644109 TTTTAAAAATGTG
64 ATTTAAAAAT-TG
* *
31644122 CATTATGT-TTCTTGTTTATTGAATGTATCTTTAGTTAATGCTTTGAATTAATACATTAGCATCA
1 CATTATGTATT-TTGTTTATTAAATGCATCTTTAGTTAATGCTTTGAATTAATACATTAGCATCA
* *
31644186 TTTAAGACTTG
65 TTTAAAAATTG
*
31644197 CATTATGTGTTTT
1 CATTATGTATTTT
31644210 TCCATATTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
75 16 0.21
76 58 0.76
77 2 0.03
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.49
Consensus pattern (75 bp):
CATTATGTATTTTGTTTATTAAATGCATCTTTAGTTAATGCTTTGAATTAATACATTAGCATCAT
TTAAAAATTG
Found at i:31645386 original size:34 final size:35
Alignment explanation
Indices: 31645343--31645459 Score: 164
Period size: 35 Copynumber: 3.3 Consensus size: 35
31645333 ACTCTCTATT
* * *
31645343 TTGGTGTGTTTTGGATGGA-TAGCTCTTATGTGTA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
*
31645377 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
* *
31645412 TTGATGTGTTCCGGATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
31645447 TCTGGTGTGTTTC
1 T-TGGTGTGTTTC
31645460 AATTGGATTA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 17 0.24
35 46 0.64
36 9 0.12
ACGTcount: A:0.16, C:0.11, G:0.30, T:0.43
Consensus pattern (35 bp):
TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
Found at i:31648860 original size:41 final size:41
Alignment explanation
Indices: 31648772--31648868 Score: 140
Period size: 41 Copynumber: 2.4 Consensus size: 41
31648762 GATACTTGTT
*
31648772 AGCTTGTGTGAGTAGCACCATGTAGCTTCGTCATGACCATC
1 AGCTTGTGTGAGCAGCACCATGTAGCTTCGTCATGACCATC
* * **
31648813 AACTTGTGTGAGCAGCACCATGTGGCTTCGTCATGACTGTC
1 AGCTTGTGTGAGCAGCACCATGTAGCTTCGTCATGACCATC
*
31648854 GGCTTGTGTGAGCAG
1 AGCTTGTGTGAGCAG
31648869 ACCTCTTGAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (41 bp):
AGCTTGTGTGAGCAGCACCATGTAGCTTCGTCATGACCATC
Found at i:31651274 original size:40 final size:40
Alignment explanation
Indices: 31651176--31651438 Score: 300
Period size: 40 Copynumber: 6.6 Consensus size: 40
31651166 TCCTCGTTCA
* * * ** *
31651176 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
31651215 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
31651255 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
31651295 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
31651335 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
31651375 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
31651415 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31651439 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:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:31659124 original size:27 final size:27
Alignment explanation
Indices: 31659094--31659271 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31659084 ATATTGAGTC
* * * *
31659094 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
31659121 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31659148 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
31659176 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31659203 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31659230 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31659257 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31659272 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:31659233 original size:82 final size:81
Alignment explanation
Indices: 31659115--31659270 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31659105 TGCTATATAA
* *
31659115 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31659180 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31659197 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31659261 CACTTAGTGC
65 CACTTAGTGC
31659271 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:31666430 original size:53 final size:53
Alignment explanation
Indices: 31666366--31666622 Score: 241
Period size: 53 Copynumber: 4.8 Consensus size: 53
31666356 CCATAGATCA
* * ** * *
31666366 CCACAAAGGCTTCAATTTCATAGATTGACAAAAATTCTTCCATTTTAGATATG
1 CCACAAAGGCTTCCATTTCATAGATTGCCAAAAAGGCTTCCATTTCAGATACG
* * *
31666419 CCACAAAGGCTTCTATTTCACAGATTGCCACAAAGGCTTCCATTTCAGATACG
1 CCACAAAGGCTTCCATTTCATAGATTGCCAAAAAGGCTTCCATTTCAGATACG
** *** * *
31666472 CCACAAATACTTCCATTTC--AGATATGCTGTAAAGGTTTCCATTTCATAGAT-TG
1 CCACAAAGGCTTCCATTTCATAGAT-TGCCAAAAAGGCTTCCATTTC--AGATACG
* * *
31666525 CCACAAAGGCTTCCATTTCATATATTTCCATAAAGGCTTCCATTTCAGATACG
1 CCACAAAGGCTTCCATTTCATAGATTGCCAAAAAGGCTTCCATTTCAGATACG
* * * * * *
31666578 CCACAAAGACTTTCATTTCATAGATTTCTACAAAGGCTTACATTT
1 CCACAAAGGCTTCCATTTCATAGATTGCCAAAAAGGCTTCCATTT
31666623 TCTAGCATGT
Statistics
Matches: 168, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
51 4 0.02
52 21 0.12
53 119 0.71
54 21 0.12
55 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (53 bp):
CCACAAAGGCTTCCATTTCATAGATTGCCAAAAAGGCTTCCATTTCAGATACG
Found at i:31666452 original size:27 final size:27
Alignment explanation
Indices: 31666357--31666622 Score: 215
Period size: 27 Copynumber: 10.0 Consensus size: 27
31666347 CAATCCTTTC
** *
31666357 CATAGATCACCACAAAGGCTTCAATTT
1 CATAGATTGCCACAAAGGCTTCCATTT
* * **
31666384 CATAGATTGACAAAAATTCTTCCATTT
1 CATAGATTGCCACAAAGGCTTCCATTT
*
31666411 --TAGATATGCCACAAAGGCTTCTATTT
1 CATAGAT-TGCCACAAAGGCTTCCATTT
*
31666437 CACAGATTGCCACAAAGGCTTCCATTT
1 CATAGATTGCCACAAAGGCTTCCATTT
* **
31666464 C--AGATACGCCACAAATACTTCCATTT
1 CATAGAT-TGCCACAAAGGCTTCCATTT
*** *
31666490 C--AGATATGCTGTAAAGGTTTCCATTT
1 CATAGAT-TGCCACAAAGGCTTCCATTT
31666516 CATAGATTGCCACAAAGGCTTCCATTT
1 CATAGATTGCCACAAAGGCTTCCATTT
* * *
31666543 CATATATTTCCATAAAGGCTTCCATTT
1 CATAGATTGCCACAAAGGCTTCCATTT
* * *
31666570 C--AGATACGCCACAAAGACTTTCATTT
1 CATAGAT-TGCCACAAAGGCTTCCATTT
* * *
31666596 CATAGATTTCTACAAAGGCTTACATTT
1 CATAGATTGCCACAAAGGCTTCCATTT
31666623 TCTAGCATGT
Statistics
Matches: 188, Mismatches: 42, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
25 12 0.06
26 68 0.36
27 96 0.51
28 12 0.06
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (27 bp):
CATAGATTGCCACAAAGGCTTCCATTT
Found at i:31666506 original size:79 final size:78
Alignment explanation
Indices: 31666366--31666622 Score: 235
Period size: 80 Copynumber: 3.2 Consensus size: 78
31666356 CCATAGATCA
* * * *
31666366 CCACAAAGGCTTCAATTTCATAGATTGACAAAAATTCTTCCATTTTAGATATGCCACAAAGGCTT
1 CCACAAAGGCTTCCATTTC--AGATCGACAAAAATACTTCCATTTCAGATATGCCACAAAGGCTT
*
31666431 CTATTTCACAGATTG
64 CCATTTCACAGATTG
* * *** *
31666446 CCACAAAGGCTTCCATTTCAGATACGCCACAAATACTTCCATTTCAGATATGCTGTAAAGGTTTC
1 CCACAAAGGCTTCCATTTCAGAT-CGACAAAAATACTTCCATTTCAGATATGCCACAAAGGCTTC
*
31666511 CATTTCATAGATTG
65 CATTTCACAGATTG
* *** * ** * *
31666525 CCACAAAGGCTTCCATTTCATATATTTCCATAAAGGCTTCCATTTCAGATACGCCACAAAGACTT
1 CCACAAAGGCTTCCATTTC--AGATCGACAAAAATACTTCCATTTCAGATATGCCACAAAGGCTT
* * *
31666590 TCATTTCATAGATTT
64 CCATTTCACAGATTG
* *
31666605 CTACAAAGGCTTACATTT
1 CCACAAAGGCTTCCATTT
31666623 TCTAGCATGT
Statistics
Matches: 146, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
78 4 0.03
79 63 0.43
80 76 0.52
81 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (78 bp):
CCACAAAGGCTTCCATTTCAGATCGACAAAAATACTTCCATTTCAGATATGCCACAAAGGCTTCC
ATTTCACAGATTG
Found at i:31666560 original size:106 final size:105
Alignment explanation
Indices: 31666403--31666597 Score: 302
Period size: 106 Copynumber: 1.8 Consensus size: 105
31666393 ACAAAAATTC
*
31666403 TTCCATTTTAGATATGCCACAAAGGCTTCTATTTCACAGATTGCCACAAAGGCTTCCATTTCAGA
1 TTCCATTTTAGATATGCCACAAAGGCTTCCATTTCACAGATTGCCACAAAGGCTTCCATTTCAGA
*
31666468 TACGCCACAAATACTTCCATTTCAGATATGCTGTAAAGGT
66 TACGCCACAAAGACTTCCATTTCAGATATGCTGTAAAGGT
* * * *
31666508 TTCCATTTCATAGAT-TGCCACAAAGGCTTCCATTTCATATATTTCCATAAAGGCTTCCATTTCA
1 TTCCATTT--TAGATATGCCACAAAGGCTTCCATTTCACAGATTGCCACAAAGGCTTCCATTTCA
*
31666572 GATACGCCACAAAGACTTTCATTTCA
64 GATACGCCACAAAGACTTCCATTTCA
31666598 TAGATTTCTA
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
105 8 0.10
106 68 0.84
107 5 0.06
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (105 bp):
TTCCATTTTAGATATGCCACAAAGGCTTCCATTTCACAGATTGCCACAAAGGCTTCCATTTCAGA
TACGCCACAAAGACTTCCATTTCAGATATGCTGTAAAGGT
Found at i:31672592 original size:46 final size:46
Alignment explanation
Indices: 31672536--31672711 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
31672526 TGGTTGAGCA
*
31672536 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
31672582 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
31672629 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
31672675 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31672712 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 61 0.56
47 28 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:31672692 original size:93 final size:93
Alignment explanation
Indices: 31672533--31672704 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
31672523 GGATGGTTGA
* *
31672533 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
31672598 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
31672626 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC-GAACTCGTTGAG
31672690 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
31672705 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:31680166 original size:46 final size:46
Alignment explanation
Indices: 31680116--31680288 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
31680106 TGGTTGAGCA
31680116 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
31680162 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
31680207 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
31680255 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
31680289 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:31680272 original size:93 final size:93
Alignment explanation
Indices: 31680113--31680283 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
31680103 GGATGGTTGA
* *
31680113 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31680178 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
31680206 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31680271 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
31680284 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:31690700 original size:37 final size:37
Alignment explanation
Indices: 31690650--31690728 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
31690640 TTATTACGAA
* * *
31690650 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
31690687 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
31690724 GTCTT
1 GTCTT
31690729 TAGAGCTCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:31690974 original size:49 final size:49
Alignment explanation
Indices: 31690847--31691211 Score: 616
Period size: 49 Copynumber: 7.6 Consensus size: 49
31690837 CCCTTCGGGA
* * * * *
31690847 CTTATCACAT-T-TATGCACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
31690894 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31690941 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31690990 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31691039 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31691088 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31691137 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31691186 CTTATCAC--ATATATACACTTTCACAT
1 CTTATCACATATATATACACTTTCACAT
31691212 ATGGGTTTAA
Statistics
Matches: 304, Mismatches: 10, Indels: 8
0.94 0.03 0.02
Matches are distributed among these distances:
46 1 0.00
47 61 0.20
49 242 0.80
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31708093 original size:27 final size:27
Alignment explanation
Indices: 31708031--31708121 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 27
31708021 ATTACATGAC
* **
31708031 TATGAATGTGATTGGGCTTGACGGGCCA
1 TATGAATGTGATTGGGC-CGATAGGCCA
*
31708059 TATCAATGTGATTGGGCCGATAGGCCA
1 TATGAATGTGATTGGGCCGATAGGCCA
* *
31708086 TATGAATGAGATTGGGCCTAAATAGGCCA
1 TATGAATGTGATTGGGCC--GATAGGCCA
*
31708115 AATGAAT
1 TATGAAT
31708122 AAGTGTGGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 23 0.43
28 16 0.30
29 14 0.26
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (27 bp):
TATGAATGTGATTGGGCCGATAGGCCA
Found at i:31710434 original size:71 final size:70
Alignment explanation
Indices: 31710297--31710435 Score: 163
Period size: 71 Copynumber: 2.0 Consensus size: 70
31710287 CATAGGTGAG
* * * * * *
31710297 TACATGTCAGCTTATATTGAACTAGTATATTTGGTTGCATGTGAGATTATATTGAATTTTAGTAT
1 TACATGTCAGCTTATATTGAACTAGTACACTTGGTTACATGTGAGATTATATTGAATATGAATAT
31710362 TCGAT
66 TCGAT
* * * *
31710367 TACATGTGAGCTTATATTTGAACTTGTACACTTGGTTATATGTGA-AGTTATTTTGAATATGAAT
1 TACATGTCAGCTTATA-TTGAACTAGTACACTTGGTTACATGTGAGA-TTATATTGAATATGAAT
31710431 ATTCG
64 ATTCG
31710436 GCTATATGTG
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
70 16 0.28
71 41 0.72
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.44
Consensus pattern (70 bp):
TACATGTCAGCTTATATTGAACTAGTACACTTGGTTACATGTGAGATTATATTGAATATGAATAT
TCGAT
Found at i:31713181 original size:39 final size:39
Alignment explanation
Indices: 31713122--31713202 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
31713112 TCCGCAACTT
31713122 AATTTTTAAATGACAAGTTTTCATAGATCATCTGTTTTA
1 AATTTTTAAATGACAAGTTTTCATAGATCATCTGTTTTA
* **
31713161 AATTTTTAAGTGACGTGTTTTCATAGATCATCTGTTTTA
1 AATTTTTAAATGACAAGTTTTCATAGATCATCTGTTTTA
31713200 AAT
1 AAT
31713203 AAAGCTTCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (39 bp):
AATTTTTAAATGACAAGTTTTCATAGATCATCTGTTTTA
Found at i:31713366 original size:19 final size:18
Alignment explanation
Indices: 31713319--31713375 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 18
31713309 GGGATTTTAC
* *
31713319 ACAAGGTTTTTATTGTAA
1 ACAAGGTTTTTAATGAAA
* *
31713337 AGAAGGGTTTTCAATGAAA
1 ACAA-GGTTTTTAATGAAA
*
31713356 ACAAGGTTTTTGAT-AAA
1 ACAAGGTTTTTAATGAAA
31713373 ACA
1 ACA
31713376 CTTCAATGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
17 6 0.19
18 11 0.35
19 14 0.45
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (18 bp):
ACAAGGTTTTTAATGAAA
Found at i:31725489 original size:46 final size:46
Alignment explanation
Indices: 31725338--31725469 Score: 255
Period size: 46 Copynumber: 2.9 Consensus size: 46
31725328 ACCATGTTTT
31725338 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC
1 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC
31725384 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC
1 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC
*
31725430 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
31725470 ATGCTCAACC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (46 bp):
GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC
Found at i:31727256 original size:17 final size:18
Alignment explanation
Indices: 31727223--31727256 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31727213 TTTAAAGAGG
31727223 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
31727241 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
31727257 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:31729929 original size:18 final size:17
Alignment explanation
Indices: 31729908--31729959 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
31729898 ACAATTCTTT
31729908 TCTCTTCTTCTTTTCTCC
1 TCTCTTCTTCTTTT-TCC
* *
31729926 TCTCTTCATCTATTTCC
1 TCTCTTCTTCTTTTTCC
31729943 TCTTCTTCTTCTTTTTC
1 TC-TCTTCTTCTTTTTC
31729960 TCTATAGCCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.62
Consensus pattern (17 bp):
TCTCTTCTTCTTTTTCC
Found at i:31732689 original size:29 final size:29
Alignment explanation
Indices: 31732650--31732728 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
31732640 CTTAATAATC
*
31732650 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
31732680 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
31732709 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
31732729 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:31732771 original size:43 final size:43
Alignment explanation
Indices: 31732710--31732812 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
31732700 TGCATTTCAA
31732710 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
31732753 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
31732796 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
31732813 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:31749056 original size:119 final size:120
Alignment explanation
Indices: 31748807--31749064 Score: 337
Period size: 119 Copynumber: 2.2 Consensus size: 120
31748797 GCTACTCGTT
* * * *
31748807 CAAATGCCTTTGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAACTCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* * *
31748871 GTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
65 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
*
31748927 CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
* * * *
31748991 A-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
66 ATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TAGCA
31749047 CAAA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGACTTA
31749065 GCCCGGACAT
Statistics
Matches: 122, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
118 4 0.03
119 62 0.51
120 54 0.44
121 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
Found at i:31749071 original size:40 final size:40
Alignment explanation
Indices: 31748788--31749071 Score: 353
Period size: 40 Copynumber: 7.1 Consensus size: 40
31748778 CGGAATTTAA
** * *
31748788 CCGGATATAGCT-ACTCGTTCAAATGCCTTTGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
31748828 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
31748868 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31748908 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
31748948 TCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31748987 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
31749027 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
31749067 CCGGA
1 CCGGA
31749072 CATCATTCGA
Statistics
Matches: 216, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 31 0.14
40 171 0.79
41 12 0.06
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:31756088 original size:30 final size:30
Alignment explanation
Indices: 31756054--31756114 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
31756044 TCCTTAACTC
31756054 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
31756084 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
31756114 A
1 A
31756115 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:31757268 original size:19 final size:18
Alignment explanation
Indices: 31757240--31757279 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
31757230 ATAAAATTTT
31757240 AATTAGTATTATGAGATAA
1 AATTAGTATTATGAGA-AA
* *
31757259 AATTATTATTATTAGAAA
1 AATTAGTATTATGAGAAA
31757277 AAT
1 AAT
31757280 AATACTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (18 bp):
AATTAGTATTATGAGAAA
Found at i:31757373 original size:15 final size:16
Alignment explanation
Indices: 31757353--31757390 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
31757343 TTTGAAATTT
31757353 TTATTATTTATAA-AA
1 TTATTATTTATAATAA
*
31757368 TTATTA-TTATAATTA
1 TTATTATTTATAATAA
31757383 TTATTATT
1 TTATTATT
31757391 AGATAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 13 0.65
16 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTATTTATAATAA
Found at i:31758381 original size:18 final size:18
Alignment explanation
Indices: 31758360--31758410 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
31758350 ACAATTCTTT
31758360 TCTCTTCTTCTTTTCTCC
1 TCTCTTCTTCTTTTCTCC
* *
31758378 TCTCTTCATCTATT-TCC
1 TCTCTTCTTCTTTTCTCC
31758395 TCTTCTTCTTCTTTTC
1 TC-TCTTCTTCTTTTC
31758411 CTCTATAGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.04, C:0.35, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTCTTCTTCTTTTCTCC
Found at i:31766061 original size:18 final size:18
Alignment explanation
Indices: 31766038--31766074 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31766028 GTGCTACATG
31766038 AATAAGTGCTGAATTGCT
1 AATAAGTGCTGAATTGCT
*
31766056 AATAAGTGTTGAATTGCT
1 AATAAGTGCTGAATTGCT
31766074 A
1 A
31766075 TGTCTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (18 bp):
AATAAGTGCTGAATTGCT
Found at i:31767095 original size:42 final size:42
Alignment explanation
Indices: 31767040--31767157 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
31767030 TAGGATTTTG
*
31767040 ATATGTGATTTCATGTAAGACCATGTCTGGGACA-TCAGCATC-
1 ATATTTGA-TTCATGTAAGACCATGTCTGGGACAGT-AGCATCT
* * * *
31767082 GTATTTGACTTCATGTAAGACCCTGTCTGGGATAGTGGCATCT
1 ATATTTGA-TTCATGTAAGACCATGTCTGGGACAGTAGCATCT
*
31767125 ATATTTGATTACATGTAAGACCACGTCTGGGAC
1 ATATTTGATT-CATGTAAGACCATGTCTGGGAC
31767158 GTTGGTATTG
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 36 0.57
43 27 0.43
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (42 bp):
ATATTTGATTCATGTAAGACCATGTCTGGGACAGTAGCATCT
Found at i:31773616 original size:40 final size:40
Alignment explanation
Indices: 31773539--31773760 Score: 297
Period size: 40 Copynumber: 5.6 Consensus size: 40
31773529 AAACCAAGTA
* * *
31773539 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
31773578 CCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
31773618 CCTTCGGGACTTAGCCTGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
31773658 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * * * * *
31773698 CCTTCGGGGCTTAGCCCGG-AATTAGTCATTAGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATG
*
31773738 CCTTCGGGACTTAGCCCAGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
31773761 CATCCGAATA
Statistics
Matches: 163, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
39 15 0.09
40 147 0.90
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:31777093 original size:13 final size:13
Alignment explanation
Indices: 31777075--31777102 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31777065 AATTACGATG
31777075 CATGGGAGAGATA
1 CATGGGAGAGATA
31777088 CATGGGAGAGATA
1 CATGGGAGAGATA
31777101 CA
1 CA
31777103 AAGACTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.11, G:0.36, T:0.14
Consensus pattern (13 bp):
CATGGGAGAGATA
Found at i:31784024 original size:28 final size:28
Alignment explanation
Indices: 31783987--31784047 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
31783977 TAGTATCAGC
* *
31783987 ACAGTCTGGGCCTTAGCCCTATACAGTA
1 ACAGTCTGGGCCTAAGCCCAATACAGTA
* *
31784015 ACAGTGTGGGCCTAAGCTCAATACAGTA
1 ACAGTCTGGGCCTAAGCCCAATACAGTA
*
31784043 TCAGT
1 ACAGT
31784048 ACAATGTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (28 bp):
ACAGTCTGGGCCTAAGCCCAATACAGTA
Found at i:31784253 original size:27 final size:27
Alignment explanation
Indices: 31784198--31784254 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
31784188 AACATAGCTG
*
31784198 CCAGAAACAGTAAATGTGGCAAAGCCA
1 CCAGAAACAGTAAATGTGACAAAGCCA
* * * *
31784225 CCAGTAACAGTGAATGTGACATAGTCA
1 CCAGAAACAGTAAATGTGACAAAGCCA
31784252 CCA
1 CCA
31784255 TTACCGTACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (27 bp):
CCAGAAACAGTAAATGTGACAAAGCCA
Found at i:31807910 original size:25 final size:25
Alignment explanation
Indices: 31807881--31807954 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
31807871 TACAAACTAT
*
31807881 GAATCGGTATGCTCTCATGAGTTGCA
1 GAATCGGTAAGCTCTCATGAGTTG-A
* *
31807907 -AATCAGTAAGCTCAT-ATGAGCTGA
1 GAATCGGTAAGCTC-TCATGAGTTGA
*
31807931 GAATCGGTAAGCTCTCACGAGTTG
1 GAATCGGTAAGCTCTCATGAGTTG
31807955 TAATCAGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
24 2 0.05
25 36 0.92
26 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (25 bp):
GAATCGGTAAGCTCTCATGAGTTGA
Found at i:31814186 original size:27 final size:26
Alignment explanation
Indices: 31814132--31814186 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
31814122 ACCTTAACTG
* * *
31814132 TAGGGGTATATCAGTAATTTTGCTCC
1 TAGGGGTAAATCAGTAATTTTCCACC
*
31814158 TAGGGGTAAATCTGTAAATTTTCCACC
1 TAGGGGTAAATCAGT-AATTTTCCACC
31814185 TA
1 TA
31814187 TAAAGGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (26 bp):
TAGGGGTAAATCAGTAATTTTCCACC
Found at i:31831343 original size:21 final size:21
Alignment explanation
Indices: 31831312--31831362 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
31831302 CCCTTATTTG
*
31831312 TCAACTTTTGCAGATGTGCTT
1 TCAACTCTTGCAGATGTGCTT
* *
31831333 TCAATTCTTGCAGATGTGGTT
1 TCAACTCTTGCAGATGTGCTT
31831354 TCAACTCTT
1 TCAACTCTT
31831363 TTAACTTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.43
Consensus pattern (21 bp):
TCAACTCTTGCAGATGTGCTT
Found at i:31833249 original size:37 final size:37
Alignment explanation
Indices: 31833190--31833298 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
31833180 AGCTCAGATG
* * *
31833190 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
31833227 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* * *
31833264 TAATCTCCACACGTAGTCATCGTGTCTCACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
31833299 ATATATTTCC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:31833641 original size:47 final size:47
Alignment explanation
Indices: 31833506--31833651 Score: 202
Period size: 47 Copynumber: 3.1 Consensus size: 47
31833496 ATATATATTC
* * * * *
31833506 CACATTGACCATTCGGCTTTACCACATATATGCATGTTCATATTCAC
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
* *
31833553 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
* **
31833600 CACATTGGCCATTCGGCCTTATCACATATATACACATTCACATTCAT
1 CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
31833647 CACAT
1 CACAT
31833652 AAAATCCTAA
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 87 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
CACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCAT
Done.