Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 156 of 770
Found at i:45842822 original size:27 final size:26
Alignment explanation
Indices: 45842791--45842904 Score: 122
Period size: 27 Copynumber: 4.2 Consensus size: 26
45842781 TAGTTTACCA
45842791 AATTACTGAAATACCTCTGTAGGGTAG
1 AATTACTGAAATACC-CTGTAGGGTAG
45842818 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCC-TGTAGGGTAG
* *
45842845 AAATA-TCGAAATACCCCTATAGGGTAG
1 AATTACT-GAAATA-CCCTGTAGGGTAG
* * * *
45842872 AATTACCGAGATACCCTCGTGGGGTAA
1 AATTACTGAAATACCCT-GTAGGGTAG
45842899 AATTAC
1 AATTAC
45842905 CATTTTGCCC
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
26 6 0.08
27 65 0.88
28 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (26 bp):
AATTACTGAAATACCCTGTAGGGTAG
Found at i:45842868 original size:54 final size:53
Alignment explanation
Indices: 45842798--45842901 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 53
45842788 CCAAATTACT
* * * *
45842798 GAAATACCTCTGTAGGGTAGAATTACTGAAATACCCTTGTAGGGTAGAAATATC
1 GAAATACCCCTATAGGGTAGAATTACCGAAATACCCTCGTAGGGTA-AAATATC
* *
45842852 GAAATACCCCTATAGGGTAGAATTACCGAGATACCCTCGTGGGGTAAAAT
1 GAAATACCCCTATAGGGTAGAATTACCGAAATACCCTCGTAGGGTAAAAT
45842902 TACCATTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 4 0.09
54 40 0.91
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (53 bp):
GAAATACCCCTATAGGGTAGAATTACCGAAATACCCTCGTAGGGTAAAATATC
Found at i:45847360 original size:2 final size:2
Alignment explanation
Indices: 45847353--45847385 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
45847343 GAGACTAGTC
45847353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45847386 CATGTCATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45851510 original size:27 final size:27
Alignment explanation
Indices: 45851479--45851593 Score: 142
Period size: 27 Copynumber: 4.3 Consensus size: 27
45851469 TAGTTTACCA
* *
45851479 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
45851506 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
45851533 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
45851560 AATTACCGAGATA-CCCTCGTGGGGTAA
1 AATTACCGAAATACCCCT-GTAGGGTAG
45851587 AATTACC
1 AATTACC
45851594 ATTTTGCCCC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
26 4 0.05
27 72 0.95
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:45851719 original size:15 final size:15
Alignment explanation
Indices: 45851699--45851729 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
45851689 GTTAGTGATT
45851699 GATTGTAGGATTATC
1 GATTGTAGGATTATC
45851714 GATTGTAGGATTATC
1 GATTGTAGGATTATC
45851729 G
1 G
45851730 CGTGGGAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.39
Consensus pattern (15 bp):
GATTGTAGGATTATC
Found at i:45852528 original size:6 final size:6
Alignment explanation
Indices: 45852490--45852618 Score: 61
Period size: 6 Copynumber: 21.2 Consensus size: 6
45852480 TGCATTCACG
* * *
45852490 TTCTGA TTTTGA TTCTG- TTACCTGA TACTGA TTCTGA TTCTAA TT-TG-
1 TTCTGA TTCTGA TTCTGA TT--CTGA TTCTGA TTCTGA TTCTGA TTCTGA
* * * * *
45852537 TCACCTAA TTCTGA TTCTTA TTCTGA TTCTGA TTCTG- TCACCTGA TTTTGA
1 T--TCTGA TTCTGA TTCTGA TTCTGA TTCTGA TTCTGA T--TCTGA TTCTGA
* * *
45852588 TTTTGA TTCTCA TTTTGA TTCT-A GTTCTGA T
1 TTCTGA TTCTGA TTCTGA TTCTGA -TTCTGA T
45852619 AATGTTTCTT
Statistics
Matches: 91, Mismatches: 20, Indels: 24
0.67 0.15 0.18
Matches are distributed among these distances:
4 1 0.01
5 5 0.05
6 74 0.81
7 8 0.09
8 3 0.03
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (6 bp):
TTCTGA
Found at i:45852553 original size:30 final size:31
Alignment explanation
Indices: 45852490--45852567 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
45852480 TGCATTCACG
* * * *
45852490 TTCTGATTTTGATTCTGTTACCTGATACTGA
1 TTCTGATTCTAATTCTGTCACCTAATACTGA
*
45852521 TTCTGATTCTAATT-TGTCACCTAATTCTGA
1 TTCTGATTCTAATTCTGTCACCTAATACTGA
* *
45852551 TTCTTATTCTGATTCTG
1 TTCTGATTCTAATTCTG
45852568 ATTCTGTCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 25 0.64
31 14 0.36
ACGTcount: A:0.19, C:0.18, G:0.13, T:0.50
Consensus pattern (31 bp):
TTCTGATTCTAATTCTGTCACCTAATACTGA
Found at i:45852589 original size:37 final size:37
Alignment explanation
Indices: 45852518--45852609 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
45852508 TACCTGATAC
*
45852518 TGATTCTGATTCTAATT-TGTCACCTAATTCTGATTCT
1 TGATTCTGATTCTGATTCTGTCACCTAATTCTGATT-T
* *
45852555 T-ATTCTGATTCTGATTCTGTCACCTGATTTTGATTT
1 TGATTCTGATTCTGATTCTGTCACCTAATTCTGATTT
* *
45852591 TGATTCTCATTTTGATTCT
1 TGATTCTGATTCTGATTCT
45852610 AGTTCTGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 16 0.33
37 32 0.67
ACGTcount: A:0.18, C:0.17, G:0.12, T:0.52
Consensus pattern (37 bp):
TGATTCTGATTCTGATTCTGTCACCTAATTCTGATTT
Found at i:45853651 original size:30 final size:30
Alignment explanation
Indices: 45853610--45853671 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
45853600 AAGTTCTAGT
45853610 TGAACTGTGATAGTGATAGTAGGATCAGAG
1 TGAACTGTGATAGTGATAGTAGGATCAGAG
*
45853640 TGAAGTGTGATAGTGATAGTAGGATCAGAG
1 TGAACTGTGATAGTGATAGTAGGATCAGAG
45853670 TG
1 TG
45853672 CGCAGCGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.05, G:0.35, T:0.27
Consensus pattern (30 bp):
TGAACTGTGATAGTGATAGTAGGATCAGAG
Found at i:45854785 original size:27 final size:26
Alignment explanation
Indices: 45854754--45854867 Score: 131
Period size: 27 Copynumber: 4.2 Consensus size: 26
45854744 TAGTTTACCA
45854754 AATTACTGAAATACCTCTGTAGGGTAG
1 AATTACTGAAATACC-CTGTAGGGTAG
45854781 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCC-TGTAGGGTAG
*
45854808 AAATA-TCGAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATA-CCCTGTAGGGTAG
* * * *
45854835 AATTACCGAGATACCCTCGTGGGGTAA
1 AATTACTGAAATACCCT-GTAGGGTAG
45854862 AATTAC
1 AATTAC
45854868 CATTTTGCCC
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
26 6 0.08
27 67 0.88
28 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (26 bp):
AATTACTGAAATACCCTGTAGGGTAG
Found at i:45854828 original size:54 final size:53
Alignment explanation
Indices: 45854761--45854864 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 53
45854751 CCAAATTACT
* * *
45854761 GAAATACCTCTGTAGGGTAGAATTACTGAAATACCCTTGTAGGGTAGAAATATC
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTCGTAGGGTA-AAATATC
* *
45854815 GAAATACCCCTGTAGGGTAGAATTACCGAGATACCCTCGTGGGGTAAAAT
1 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTCGTAGGGTAAAAT
45854865 TACCATTTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 4 0.09
54 41 0.91
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (53 bp):
GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTCGTAGGGTAAAATATC
Found at i:45855585 original size:2 final size:2
Alignment explanation
Indices: 45855578--45855607 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45855568 GCTTCGCCAC
45855578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45855608 TTGTTCTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45855853 original size:6 final size:6
Alignment explanation
Indices: 45855838--45855878 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
45855828 ATGTCACCTA
* * *
45855838 ATTCTG ATTCTT ATTCTG ATTCTG ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
45855879 AGTTATGATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.56
Consensus pattern (6 bp):
ATTCTG
Found at i:45855861 original size:18 final size:18
Alignment explanation
Indices: 45855838--45855878 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
45855828 ATGTCACCTA
*
45855838 ATTCTGATTCTTATTCTG
1 ATTCTGATTCTCATTCTG
*
45855856 ATTCTGATTCTCATTTTG
1 ATTCTGATTCTCATTCTG
45855874 ATTCT
1 ATTCT
45855879 AGTTATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.56
Consensus pattern (18 bp):
ATTCTGATTCTCATTCTG
Found at i:45858261 original size:18 final size:18
Alignment explanation
Indices: 45858230--45858279 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
45858220 TTTTTCAATT
45858230 TTCTTTTTC-TTCTC-ACA
1 TTCTTTTTCATTCTCGA-A
*
45858247 TTCTTTTTCACTCTCGAA
1 TTCTTTTTCATTCTCGAA
*
45858265 CTCTTTTTCATTCTC
1 TTCTTTTTCATTCTC
45858280 TTTTTCAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.32
18 18 0.64
19 1 0.04
ACGTcount: A:0.12, C:0.30, G:0.02, T:0.56
Consensus pattern (18 bp):
TTCTTTTTCATTCTCGAA
Found at i:45858282 original size:30 final size:30
Alignment explanation
Indices: 45858248--45858314 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
45858238 CTTCTCACAT
*
45858248 TCTTTTTCACTCTCGA-ACTCTTTTTCATTC
1 TCTTTTTCAATCTC-ATACTCTTTTTCATTC
** *
45858278 TCTTTTTCAATCTCATTTTCTTTTTCATTT
1 TCTTTTTCAATCTCATACTCTTTTTCATTC
45858308 TCTTTTT
1 TCTTTTT
45858315 ATTTTTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.12, C:0.24, G:0.01, T:0.63
Consensus pattern (30 bp):
TCTTTTTCAATCTCATACTCTTTTTCATTC
Found at i:45858314 original size:18 final size:18
Alignment explanation
Indices: 45858272--45858323 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
45858262 GAACTCTTTT
*
45858272 TCATTCTCTTTTTCAATC
1 TCATTTTCTTTTTCAATC
* *
45858290 TCATTTTCTTTTTCATTT
1 TCATTTTCTTTTTCAATC
* *
45858308 TCTTTTTATTTTTCAA
1 TCATTTTCTTTTTCAA
45858324 AGGCTTTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.65
Consensus pattern (18 bp):
TCATTTTCTTTTTCAATC
Found at i:45858321 original size:12 final size:12
Alignment explanation
Indices: 45858290--45858319 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
45858280 TTTTTCAATC
45858290 TCATTTTCTTTT
1 TCATTTTCTTTT
45858302 TCATTTTCTTTT
1 TCATTTTCTTTT
45858314 T-ATTTT
1 TCATTTT
45858320 TCAAAGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:45858412 original size:6 final size:5
Alignment explanation
Indices: 45858383--45858444 Score: 65
Period size: 5 Copynumber: 12.0 Consensus size: 5
45858373 CTTTTGCCTC
*
45858383 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTTT TCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TC-TTT TC-TTT TCTTT
45858430 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
45858445 GTTTTCTCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
4 4 0.08
5 31 0.62
6 14 0.28
7 1 0.02
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:45858441 original size:15 final size:15
Alignment explanation
Indices: 45858385--45858451 Score: 66
Period size: 16 Copynumber: 4.4 Consensus size: 15
45858375 TTTGCCTCTC
45858385 TTTTCTTTTTATTTCG
1 TTTTCTTTTT-TTTCG
* *
45858401 TTTTCTTTTTCTTCT
1 TTTTCTTTTTTTTCG
45858416 TTTTCTTTTTCTTTTC-
1 TTTTC-TTTT-TTTTCG
*
45858432 TTTTCTTTTCTTT-G
1 TTTTCTTTTTTTTCG
45858446 TTTTCT
1 TTTTCT
45858452 CATTACAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.20
15 12 0.27
16 19 0.43
17 4 0.09
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTTTTCG
Found at i:45860512 original size:46 final size:46
Alignment explanation
Indices: 45860457--45860581 Score: 196
Period size: 46 Copynumber: 2.7 Consensus size: 46
45860447 GGTTGAGCAT
* * *
45860457 CCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
45860503 CTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
45860549 CCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
45860582 GGGGTGGGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:45863090 original size:10 final size:10
Alignment explanation
Indices: 45863071--45863105 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
45863061 AATTTCGGTT
45863071 GAGCTCAAAC
1 GAGCTCAAAC
*
45863081 GAGCTGAAAC
1 GAGCTCAAAC
*
45863091 GAGCTCAAAT
1 GAGCTCAAAC
45863101 GAGCT
1 GAGCT
45863106 GAGTTAAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:45866645 original size:46 final size:46
Alignment explanation
Indices: 45866578--45866752 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
45866568 TGTAACCCGC
45866578 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
45866624 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
45866674 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
45866717 CCATAAGTGAACTCGGACTCAACTCGACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
45866753 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 62 0.57
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:45866698 original size:93 final size:93
Alignment explanation
Indices: 45866586--45866756 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
45866576 GCCCATAAGT
** *
45866586 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
45866651 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* *
45866679 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCGA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
45866744 CGAGTTCGGATGC
66 CGAGCTCGGATGC
45866757 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:45870200 original size:46 final size:44
Alignment explanation
Indices: 45870126--45870383 Score: 195
Period size: 46 Copynumber: 5.6 Consensus size: 44
45870116 GTTGATGCCG
* * *
45870126 TGTCCCAGACAGGTCTTACACT-GACACATGTAACCGT-GCTGATGCA
1 TGTCCCAGACATGTCTTACACTAG-CACATCT---CGTAGCCGATGCA
*
45870172 TGTCCCAGACATGTCTTACACTAGCACATCTCGTAGCCGACGCA
1 TGTCCCAGACATGTCTTACACTAGCACATCTCGTAGCCGATGCA
* *
45870216 TGTCCCAGACATGTCTGACACTGGCTAACATCTCG-AGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTAGC--ACATCTCGTA-GCCGATGCA
* * * * *
45870262 TGTCCCAGACATGTCTTACAGTGGCTC-TCATACTGTGGCTGATGCA
1 TGTCCCAGACATGTCTTACACTAGCACATC-T-C-GTAGCCGATGCA
* *
45870308 TGTCCCAGACATGACTTACACTAGC-CCTCGTC-TCAATGCCGATGCCA
1 TGTCCCAGACATGTCTTACACTAGCACATC-TCGT--A-GCCGATG-CA
* *
45870355 TGTCCCATACATGGTCTTACACTGGCACA
1 TGTCCCAGACAT-GTCTTACACTAGCACA
45870384 CAAATCTCAT
Statistics
Matches: 174, Mismatches: 22, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
43 6 0.03
44 32 0.18
45 4 0.02
46 106 0.61
47 14 0.08
48 11 0.06
49 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.25
Consensus pattern (44 bp):
TGTCCCAGACATGTCTTACACTAGCACATCTCGTAGCCGATGCA
Found at i:45870349 original size:92 final size:91
Alignment explanation
Indices: 45870166--45870385 Score: 237
Period size: 92 Copynumber: 2.4 Consensus size: 91
45870156 TAACCGTGCT
* *
45870166 GATGCATGTCCCAGACATGTCTTACACTAG-CACATCTCGTAGCCGACGCATGTCCCAGACATGT
1 GATGCATGTCCCAGACATGTCTTACACTGGCCACATCTCGTAGCCGACGCATGTCCCAGACATGA
* * *
45870230 CTGACACTGGCTAACATCTCGAGGCC
66 CTGACACTAGCCAACATCTCAAGGCC
* * * * *
45870256 GATGCATGTCCCAGACATGTCTTACAGTGGCTCTCATACT-GTGGCTGATGCATGTCCCAGACAT
1 GATGCATGTCCCAGACATGTCTTACACTGGC-CACAT-CTCGTAGCCGACGCATGTCCCAGACAT
* ** * *
45870320 GACTTACACTAGCCCTCGTCTCAATGCC
64 GACTGACACTAGCCAACATCTCAAGGCC
*
45870348 GATGCCATGTCCCATACATGGTCTTACACTGGCACACA
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGC-CACA
45870386 AATCTCATGT
Statistics
Matches: 106, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
90 28 0.26
92 48 0.45
93 15 0.14
94 15 0.14
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (91 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCCACATCTCGTAGCCGACGCATGTCCCAGACATGA
CTGACACTAGCCAACATCTCAAGGCC
Found at i:45872967 original size:46 final size:46
Alignment explanation
Indices: 45872900--45873074 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
45872890 TGTAACCCGC
45872900 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
45872946 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
45872996 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
45873039 CCATAAGTGAACTCGGACTCAACTCGACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
45873075 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 62 0.57
47 26 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:45873020 original size:93 final size:93
Alignment explanation
Indices: 45872908--45873078 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
45872898 GCCCATAAGT
** *
45872908 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
45872973 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* *
45873001 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCGA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
45873066 CGAGTTCGGATGC
66 CGAGCTCGGATGC
45873079 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:45875386 original size:40 final size:40
Alignment explanation
Indices: 45875326--45875509 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 40
45875316 TATTCGAATG
*
45875326 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
45875366 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * * * *
45875406 ATATCCAGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
45875446 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
*
45875486 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
45875510 CTTGTGCGAG
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 118 0.97
41 3 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:45875459 original size:80 final size:80
Alignment explanation
Indices: 45875326--45875545 Score: 270
Period size: 80 Copynumber: 2.8 Consensus size: 80
45875316 TATTCGAATG
* * * *
45875326 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAGGC
* *
45875390 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* *
45875406 ATATCCAGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAG-TCCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAGGC
*
45875470 ATTTATGCTAGTGACC
65 ATTTATGCGAGTGACC
* * *
45875486 ATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAG
45875546 ATACTTGGGT
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
78 14 0.11
79 20 0.16
80 88 0.72
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGATCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:45882235 original size:59 final size:60
Alignment explanation
Indices: 45882139--45882271 Score: 205
Period size: 59 Copynumber: 2.2 Consensus size: 60
45882129 GACAAGATTG
* * *
45882139 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
* * *
45882199 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
45882258 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
45882272 GATTCACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 52 0.78
60 15 0.22
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (60 bp):
GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
Found at i:45882284 original size:29 final size:29
Alignment explanation
Indices: 45882169--45882271 Score: 188
Period size: 29 Copynumber: 3.5 Consensus size: 29
45882159 AAAATTGTAC
*
45882169 AGCACTAAGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
45882198 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
45882228 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
45882257 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
45882272 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 43 0.60
30 29 0.40
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:45889770 original size:59 final size:60
Alignment explanation
Indices: 45889674--45889806 Score: 205
Period size: 59 Copynumber: 2.2 Consensus size: 60
45889664 GACAAGATTG
* * *
45889674 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
* * *
45889734 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
45889793 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
45889807 GATTCACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 52 0.78
60 15 0.22
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (60 bp):
GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
Found at i:45889819 original size:29 final size:29
Alignment explanation
Indices: 45889704--45889806 Score: 188
Period size: 29 Copynumber: 3.5 Consensus size: 29
45889694 AAAATTGTAC
*
45889704 AGCACTAAGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
45889733 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
45889763 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
45889792 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
45889807 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 43 0.60
30 29 0.40
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:45895725 original size:49 final size:49
Alignment explanation
Indices: 45895665--45895971 Score: 483
Period size: 49 Copynumber: 6.3 Consensus size: 49
45895655 GTATGAGATA
45895665 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
45895714 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
45895763 TATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
45895812 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * *
45895861 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGAGAAGGTGTA
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
* * * * * * *
45895910 TATATATGTGATAGGGCCGAGTGGCCAAAGTGATGGATGTGGAA--GTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
*
45895957 TATAAATGTGATAAG
1 TATATATGTGATAAG
45895972 TCCCGAAGGG
Statistics
Matches: 241, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
47 15 0.06
49 226 0.94
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (49 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
Found at i:45902176 original size:40 final size:39
Alignment explanation
Indices: 45902127--45902333 Score: 236
Period size: 40 Copynumber: 5.2 Consensus size: 39
45902117 TCTTCGGAAT
* *
45902127 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAA-TGCCTTCGGGTC
* * *** *
45902166 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCAC-AATGCCTTCGGGTC
*
45902206 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCAC-AATGCCTTCGGGTC
*
45902246 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCAC-AATGCCTTCGGGTC
* * * *
45902286 TTAGCCCGGATGTAATAACTAGCATAAATGCCTTCGGGGC
1 TTAGCCCGGATATAACAACTAGCA-CAATGCCTTCGGGTC
45902326 TTAGCCCG
1 TTAGCCCG
45902334 TGTATCATTC
Statistics
Matches: 145, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 3 0.02
40 140 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (39 bp):
TTAGCCCGGATATAACAACTAGCACAATGCCTTCGGGTC
Found at i:45907356 original size:19 final size:20
Alignment explanation
Indices: 45907332--45907379 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
45907322 GATCAGTTGG
45907332 ACCTTT-GATTAATTAACAT
1 ACCTTTGGATTAATTAACAT
45907351 ACCTTTTTTGGATTAATTAACAT
1 ACC---TTTGGATTAATTAACAT
45907374 ACCTTT
1 ACCTTT
45907380 TTTTGACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
22 3 0.12
23 16 0.64
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (20 bp):
ACCTTTGGATTAATTAACAT
Found at i:45907364 original size:23 final size:23
Alignment explanation
Indices: 45907338--45907382 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
45907328 TTGGACCTTT
45907338 GATTAATTAACATACCTTTTTTG
1 GATTAATTAACATACCTTTTTTG
45907361 GATTAATTAACATACCTTTTTT
1 GATTAATTAACATACCTTTTTT
45907383 TGACTGACCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (23 bp):
GATTAATTAACATACCTTTTTTG
Found at i:45909727 original size:21 final size:21
Alignment explanation
Indices: 45909701--45909741 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
45909691 AGATTGATTA
* *
45909701 TATAGATATATCCAACTTTTC
1 TATAGAAATATACAACTTTTC
*
45909722 TATAGAAATATAGAACTTTT
1 TATAGAAATATACAACTTTT
45909742 ATCAGTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (21 bp):
TATAGAAATATACAACTTTTC
Found at i:45909773 original size:21 final size:21
Alignment explanation
Indices: 45909749--45909789 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
45909739 TTTATCAGTA
*
45909749 ATTCCATTTCATTTATATTAT
1 ATTCCATATCATTTATATTAT
*
45909770 ATTCTATATCATTTATATTA
1 ATTCCATATCATTTATATTA
45909790 CTAATCCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTCCATATCATTTATATTAT
Found at i:45909858 original size:19 final size:18
Alignment explanation
Indices: 45909829--45909880 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
45909819 TCTTCTGACC
45909829 AAAATAGAAAATAT-ATCAA
1 AAAATA-AAAATATAAT-AA
45909848 AAAACTAAAAAGTATAATAA
1 AAAA-TAAAAA-TATAATAA
45909868 AAAATAATAAATA
1 AAAATAA-AAATA
45909881 AAAAATTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 13 0.45
20 14 0.48
21 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (18 bp):
AAAATAAAAATATAATAA
Found at i:45910036 original size:21 final size:21
Alignment explanation
Indices: 45910011--45910051 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
45910001 TAGATGATTA
* *
45910011 TATAGATATATCCAACTTTTC
1 TATAGAGATATACAACTTTTC
*
45910032 TATAGAGATATAGAACTTTT
1 TATAGAGATATACAACTTTT
45910052 ATCAGTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (21 bp):
TATAGAGATATACAACTTTTC
Found at i:45910083 original size:21 final size:21
Alignment explanation
Indices: 45910059--45910098 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45910049 TTTATCAGTA
* *
45910059 ATTCCATTTCATTTATATTAT
1 ATTCCATATCAGTTATATTAT
*
45910080 ATTCTATATCAGTTATATT
1 ATTCCATATCAGTTATATT
45910099 TTGAAATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTCCATATCAGTTATATTAT
Found at i:45911210 original size:21 final size:21
Alignment explanation
Indices: 45911171--45911210 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45911161 TTTATTTCAA
*
45911171 AATATAAATGATATAGAATAT
1 AATATAAATGAAATAGAATAT
*
45911192 AATATAAATGAAATGGAAT
1 AATATAAATGAAATAGAAT
45911211 TACTGATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
AATATAAATGAAATAGAATAT
Found at i:45913209 original size:16 final size:16
Alignment explanation
Indices: 45913188--45913238 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
45913178 TTTCTAGTAT
* *
45913188 TTTATTTCCTAGCGTG
1 TTTATTTACTAGCGTA
45913204 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
45913220 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
45913236 TTT
1 TTT
45913239 GCTCTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.53
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:45914177 original size:16 final size:16
Alignment explanation
Indices: 45914156--45914188 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45914146 TCTTATTCCT
*
45914156 TTGCTACTATAGAATA
1 TTGCTACTATAAAATA
45914172 TTGCTACTATAAAATA
1 TTGCTACTATAAAATA
45914188 T
1 T
45914189 AGAATACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTGCTACTATAAAATA
Found at i:45919144 original size:16 final size:15
Alignment explanation
Indices: 45919123--45919153 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
45919113 CCTTTTTTTT
45919123 ATATAAAATATAAAAA
1 ATATAAAATA-AAAAA
45919139 ATATAAAATAAAAAA
1 ATATAAAATAAAAAA
45919154 TAAGTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATATAAAATAAAAAA
Found at i:45928999 original size:52 final size:51
Alignment explanation
Indices: 45928936--45929066 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 51
45928926 TGAGCAAATA
* *
45928936 AGTTACTTAATGCATGACTTAATTTAATGATACAAACTTTAACTAACATGGG
1 AGTTACATAATGCATGACTTAATTTAATGATACAAAC-TTAACTAACATGAG
* * * *
45928988 AGTTATATAATGCATGTA-ATAATTT-ATGATGCAAACTTAACTTACATGAG
1 AGTTACATAATGCATG-ACTTAATTTAATGATACAAACTTAACTAACATGAG
* *
45929038 AGTTACATAATGCATGACTTTATTAAATG
1 AGTTACATAATGCATGACTTAATTTAATG
45929067 CAAAACACAT
Statistics
Matches: 66, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
49 1 0.02
50 31 0.47
51 13 0.20
52 20 0.30
53 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (51 bp):
AGTTACATAATGCATGACTTAATTTAATGATACAAACTTAACTAACATGAG
Found at i:45929133 original size:39 final size:39
Alignment explanation
Indices: 45929071--45929159 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
45929061 TAAATGCAAA
* * * *
45929071 ACACATATTAATGATGTTCAAACTATGACATGATTAAAG
1 ACACATACTAATGATGTTCAAACTATAACATAACTAAAG
*
45929110 ACTCATACTAATGATGTTCAAACTATAACATAACTAAAG
1 ACACATACTAATGATGTTCAAACTATAACATAACTAAAG
*
45929149 ACACAAACTAA
1 ACACATACTAA
45929160 AATAACTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.27
Consensus pattern (39 bp):
ACACATACTAATGATGTTCAAACTATAACATAACTAAAG
Found at i:45929184 original size:22 final size:21
Alignment explanation
Indices: 45929134--45929184 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
45929124 TGTTCAAACT
45929134 ATAACATAACTAAAGACACAAA
1 ATAA-ATAACTAAAGACACAAA
*
45929156 CTAAAATAACTAAAGTA-ACTAAA
1 AT-AAATAACTAAAG-ACAC-AAA
45929179 ATAAAT
1 ATAAAT
45929185 GAATCAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.63, C:0.14, G:0.04, T:0.20
Consensus pattern (21 bp):
ATAAATAACTAAAGACACAAA
Found at i:45929803 original size:16 final size:15
Alignment explanation
Indices: 45929776--45929815 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
45929766 AAAGAGAGTG
*
45929776 AAAAGAAAATGA-G-
1 AAAAGAAAAAGATGA
45929789 AAAAGAAAAAGATGA
1 AAAAGAAAAAGATGA
45929804 AAAAGAAAAAGA
1 AAAAGAAAAAGA
45929816 GAGTGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.46
14 1 0.04
15 12 0.50
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (15 bp):
AAAAGAAAAAGATGA
Found at i:45929809 original size:15 final size:13
Alignment explanation
Indices: 45929775--45929817 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
45929765 AAAAGAGAGT
*
45929775 GAAAAGAAAATGA
1 GAAAAGAAAAAGA
45929788 GAAAAGAAAAAGA
1 GAAAAGAAAAAGA
45929801 TGAAAAAGAAAAAGA
1 -G-AAAAGAAAAAGA
45929816 GA
1 GA
45929818 GTGAGAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 13 0.48
14 2 0.07
15 12 0.44
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (13 bp):
GAAAAGAAAAAGA
Found at i:45930309 original size:39 final size:39
Alignment explanation
Indices: 45930266--45930351 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
45930256 TTTAGTTATT
* *
45930266 TTAGTTTGTGTATTTAATTATGTCATAGTTTGAACATCA
1 TTAGTATGAGTATTTAATTATGTCATAGTTTGAACATCA
* * *
45930305 TTAGTATGAGTCTTTAATTATTTCATAGTTTGAATATCA
1 TTAGTATGAGTATTTAATTATGTCATAGTTTGAACATCA
*
45930344 TTAATATG
1 TTAGTATG
45930352 TGTTCTGCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (39 bp):
TTAGTATGAGTATTTAATTATGTCATAGTTTGAACATCA
Found at i:45934757 original size:40 final size:40
Alignment explanation
Indices: 45934712--45934879 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
45934702 CGGAATATAA
45934712 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
45934752 CCGGATAAAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
45934792 CCGGATGTAGCCACTAGCGCAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
45934832 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
45934872 CCGGATAT
1 CCGGATAT
45934880 CATTCAATTT
Statistics
Matches: 101, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
39 1 0.01
40 99 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:45942210 original size:40 final size:40
Alignment explanation
Indices: 45942165--45942332 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
45942155 CGGAATATAA
45942165 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
45942205 CCGGATAAAATGTCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
45942245 CCGGATGTAGCCACTAGCGCAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
45942285 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
45942325 CCGGATAT
1 CCGGATAT
45942333 CATTCAATTT
Statistics
Matches: 101, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
39 1 0.01
40 99 0.98
41 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:45944585 original size:39 final size:39
Alignment explanation
Indices: 45944542--45944616 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
45944532 TAGTTTGTGT
* *
45944542 CTTTAATTATGTCATAGTTTGAACATTATTAGTATGAGC
1 CTTTAATTATGTCATAGTTTGAACATCATTAATATGAGC
*
45944581 CTTTAATTATTTCATAGTTTGAACATCATTAATATG
1 CTTTAATTATGTCATAGTTTGAACATCATTAATATG
45944617 TGTTCTACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (39 bp):
CTTTAATTATGTCATAGTTTGAACATCATTAATATGAGC
Found at i:45948365 original size:20 final size:20
Alignment explanation
Indices: 45948305--45948365 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
45948295 ATAAATATGG
*
45948305 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
45948325 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
45948345 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
45948365 T
1 T
45948366 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:45948442 original size:24 final size:24
Alignment explanation
Indices: 45948415--45948557 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
45948405 GAGGAAGTGA
45948415 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
45948439 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
45948463 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
45948486 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
45948510 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
45948534 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
45948558 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:45948508 original size:47 final size:47
Alignment explanation
Indices: 45948415--45948557 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
45948405 GAGGAAGTGA
45948415 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
45948463 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
45948510 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
45948558 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:45948531 original size:71 final size:72
Alignment explanation
Indices: 45948415--45948558 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
45948405 GAGGAAGTGA
*
45948415 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
45948478 CCAGTTAT
65 CCAGTTAT
** * *
45948486 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
45948551 CAGTTAT
66 CAGTTAT
45948558 A
1 A
45948559 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:45948784 original size:31 final size:31
Alignment explanation
Indices: 45948749--45948812 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
45948739 CGTTTACAGT
45948749 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
45948780 AAAGGCTTCGGCCCAGTGTTATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
45948811 AA
1 AA
45948813 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:45953864 original size:19 final size:19
Alignment explanation
Indices: 45953827--45953918 Score: 75
Period size: 19 Copynumber: 5.0 Consensus size: 19
45953817 ATAAATTACA
**
45953827 CATCTTAGTTAATCGAGTT
1 CATCTTAGTTAATTAAGTT
*
45953846 CATCTAAGTTAATTAAGTT
1 CATCTTAGTTAATTAAGTT
* * * *
45953865 --TCTGGAATAAATT-A-CT
1 CATCT-TAGTTAATTAAGTT
45953881 CATCTTAGTTAATTAAGTT
1 CATCTTAGTTAATTAAGTT
*
45953900 CATCTTAGTTAATTTAGTT
1 CATCTTAGTTAATTAAGTT
45953919 GCAAGAATAA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
16 1 0.02
17 10 0.18
18 10 0.18
19 35 0.62
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (19 bp):
CATCTTAGTTAATTAAGTT
Found at i:45953928 original size:54 final size:54
Alignment explanation
Indices: 45953801--45953920 Score: 186
Period size: 54 Copynumber: 2.2 Consensus size: 54
45953791 TTAGTTTAAC
*
45953801 TAATTAAGTTGCTGGAATAAATTACACATCTTAGTTAATCGAGTTCATCTAAGT
1 TAATTAAGTTGCTGGAATAAATTACACATCTTAGTTAATCAAGTTCATCTAAGT
* * * *
45953855 TAATTAAGTTTCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGT
1 TAATTAAGTTGCTGGAATAAATTACACATCTTAGTTAATCAAGTTCATCTAAGT
*
45953909 TAATTTAGTTGC
1 TAATTAAGTTGC
45953921 AAGAATAATT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (54 bp):
TAATTAAGTTGCTGGAATAAATTACACATCTTAGTTAATCAAGTTCATCTAAGT
Found at i:45953987 original size:33 final size:33
Alignment explanation
Indices: 45953945--45954008 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
45953935 GTTGTATGTG
45953945 TTTTTAAGTTTACTAATTAAGCTTATTAAGTGT
1 TTTTTAAGTTTACTAATTAAGCTTATTAAGTGT
45953978 TTTTTAAGTTTACTAATTAAGCTTATTAAGT
1 TTTTTAAGTTTACTAATTAAGCTTATTAAGT
45954009 CTAATATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (33 bp):
TTTTTAAGTTTACTAATTAAGCTTATTAAGTGT
Found at i:45954022 original size:33 final size:33
Alignment explanation
Indices: 45953949--45954015 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
45953939 TATGTGTTTT
* ** *
45953949 TAAGTTTACTAATTAAGCTTATTAAGTGTTTTT
1 TAAGTTTACTAATTAAGCTTATTAAGTCTAATA
45953982 TAAGTTTACTAATTAAGCTTATTAAGTCTAATA
1 TAAGTTTACTAATTAAGCTTATTAAGTCTAATA
45954015 T
1 T
45954016 GTGTTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (33 bp):
TAAGTTTACTAATTAAGCTTATTAAGTCTAATA
Found at i:45954037 original size:9 final size:9
Alignment explanation
Indices: 45954014--45954059 Score: 65
Period size: 9 Copynumber: 4.9 Consensus size: 9
45954004 TAAGTCTAAT
45954014 ATGTGTTTAA
1 ATGTGTTT-A
45954024 ATGTGTTTA
1 ATGTGTTTA
45954033 ATGTGTTTA
1 ATGTGTTTA
*
45954042 ATGAGTTTTA
1 ATGTG-TTTA
45954052 ATGTGTTT
1 ATGTGTTT
45954060 GTTTGTAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 17 0.52
10 16 0.48
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (9 bp):
ATGTGTTTA
Found at i:45954038 original size:19 final size:19
Alignment explanation
Indices: 45954014--45954059 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
45954004 TAAGTCTAAT
*
45954014 ATGTGTTTAAATGTG-TTTA
1 ATGTGTTT-AATGAGTTTTA
45954033 ATGTGTTTAATGAGTTTTA
1 ATGTGTTTAATGAGTTTTA
45954052 ATGTGTTT
1 ATGTGTTT
45954060 GTTTGTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (19 bp):
ATGTGTTTAATGAGTTTTA
Found at i:45965922 original size:33 final size:33
Alignment explanation
Indices: 45965885--45965980 Score: 106
Period size: 34 Copynumber: 2.9 Consensus size: 33
45965875 CTATGGGCCA
* *
45965885 TACTGTTATCTGAAAAGGGGCTAAGGCCCAGT-T
1 TACTGTTATCTGAAAA-GGGCTTAGGCCCAGTAC
*
45965918 TACTG-TATTCTGAAAAGGGCTTTGGCCCAGTACC
1 TACTGTTA-TCTGAAAAGGGCTTAGGCCCAGTA-C
* *
45965952 TGCTGTTATCTGAATAGGGCTTAGGCCCA
1 TACTGTTATCTGAAAAGGGCTTAGGCCCA
45965981 ATGGGCTTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
32 15 0.28
33 13 0.25
34 23 0.43
35 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (33 bp):
TACTGTTATCTGAAAAGGGCTTAGGCCCAGTAC
Found at i:45969772 original size:26 final size:28
Alignment explanation
Indices: 45969701--45969773 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
45969691 TAAAACTGAT
* * * *
45969701 AAAATTACTGAAATACCTTTATAGGTGG
1 AAAATTACTGATATACCCTTATAGGAGC
* *
45969729 AAAATTTACAGATTTACCCTTA-A-GAGC
1 AAAA-TTACTGATATACCCTTATAGGAGC
45969756 AAAATTACTGATATACCC
1 AAAATTACTGATATACCC
45969774 CTAGGGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 12 0.33
27 6 0.17
28 5 0.14
29 13 0.36
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (28 bp):
AAAATTACTGATATACCCTTATAGGAGC
Found at i:45972750 original size:40 final size:40
Alignment explanation
Indices: 45972698--45972879 Score: 215
Period size: 40 Copynumber: 4.5 Consensus size: 40
45972688 CGCACAAGGT
* * *
45972698 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* **
45972738 CTTCGGGACTTAGCCCGAATATAGTTGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
** * * *
45972778 CTTCGGGTTTTGGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
45972818 CTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCAC-TAGCACAAATGC
45972859 CTT-GGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
45972880 CATTCGAATA
Statistics
Matches: 118, Mismatches: 21, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
39 2 0.02
40 100 0.85
41 16 0.14
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:45983939 original size:39 final size:40
Alignment explanation
Indices: 45983849--45983997 Score: 153
Period size: 39 Copynumber: 3.8 Consensus size: 40
45983839 ATAATCTCGT
* * *
45983849 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATAACTA
* ***
45983889 GCACGAA-TGCCTTC-GGCCTTAGCCCGGATATAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATAACTA
** *
45983928 GCACAATTGCCTTCGGGTCTTA-CCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATAACTA
* *
45983967 GCATAATTGTCTTCGGG-CTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
45983998 CATTCAATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
38 6 0.07
39 66 0.73
40 17 0.19
41 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATAACTA
Found at i:45990527 original size:41 final size:41
Alignment explanation
Indices: 45990482--45990599 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
45990472 TGAAAGATAA
45990482 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
45990523 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
45990553 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
45990594 ATGTAG
1 ATGTAG
45990600 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:45990538 original size:71 final size:71
Alignment explanation
Indices: 45990450--45990613 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
45990440 GAGATGTATC
45990450 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
45990515 AGGACA
66 AGGACA
45990521 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
45990586 AGGACA
66 AGGACA
45990592 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
45990614 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:45998062 original size:68 final size:69
Alignment explanation
Indices: 45997990--45998186 Score: 281
Period size: 70 Copynumber: 2.8 Consensus size: 69
45997980 ACACCCTGTA
* * * * *
45997990 GTAGCTAGGTCACATGTGTGATACGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAGA
1 GTAGCTAGGTCGCATGCGTGATACAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
45998053 TAAAT
65 TAAAT
*
45998058 GTAGCTAGGTCGCATGCGTGATTCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAGA
1 GTAGCTAGGTCGCATGCGTGATACAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAGA
45998123 TAAAT
65 TAAAT
*
45998128 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGA-TACAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
45998187 AGACAAATCG
Statistics
Matches: 118, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
67 3 0.03
68 23 0.19
69 1 0.01
70 55 0.47
71 36 0.31
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (69 bp):
GTAGCTAGGTCGCATGCGTGATACAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGAT
AAAT
Found at i:45998100 original size:40 final size:40
Alignment explanation
Indices: 45998056--45998172 Score: 94
Period size: 40 Copynumber: 3.1 Consensus size: 40
45998046 TGAAAGATAA
45998056 ATGTAGCTAGGTCGCATGCGTGATTCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCAAGTGAAGGACACC
* * * * *
45998096 ATGTAGAC-AAG-AG-A-GC-T-A--C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCAAGTGAAGGACACC
45998126 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATT-CAAGTGAAGGACACC
45998167 ATGTAG
1 ATGTAG
45998173 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 25
0.61 0.11 0.28
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 2 0.04
36 1 0.02
37 2 0.04
38 2 0.04
39 1 0.02
40 16 0.30
41 7 0.13
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (40 bp):
ATGTAGCTAGGTCGCATGCGTGATTCAAGTGAAGGACACC
Found at i:45998113 original size:70 final size:71
Alignment explanation
Indices: 45998024--45998186 Score: 319
Period size: 70 Copynumber: 2.3 Consensus size: 71
45998014 GAGATGTATC
45998024 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATT-CAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
45998088 AGGACA
66 AGGACA
45998094 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
45998159 AGGACA
66 AGGACA
45998165 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
45998187 AGACAAATCG
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 57 0.62
71 35 0.38
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:46006268 original size:12 final size:12
Alignment explanation
Indices: 46006246--46006290 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
46006236 TTCGAATTTG
46006246 TTGATGGAGAGAT
1 TTGA-GGAGAGAT
*
46006259 TAGAGGAGAGAT
1 TTGAGGAGAGAT
*
46006271 TTGGGGAGAGAT
1 TTGAGGAGAGAT
46006283 TTGAGGAG
1 TTGAGGAG
46006291 TGGATCAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 25 0.89
13 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.24
Consensus pattern (12 bp):
TTGAGGAGAGAT
Found at i:46011338 original size:47 final size:47
Alignment explanation
Indices: 46011287--46011480 Score: 334
Period size: 47 Copynumber: 4.1 Consensus size: 47
46011277 TTAGGATTTT
46011287 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
46011334 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
46011381 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
46011428 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
46011475 ATGTGA
1 ATGTGA
46011481 AATATGTATG
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 141 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:46011340 original size:22 final size:22
Alignment explanation
Indices: 46011312--46011434 Score: 60
Period size: 22 Copynumber: 5.3 Consensus size: 22
46011302 ACATGCATAT
46011312 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* *
46011334 ATGTGATGAATGTG-AGCAT-G-CA
1 ATGTGAT-AA-G-GCCGAATGGCCA
46011356 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
* *
46011381 ATGTGATGAATGTG-AGCAT-G-CA
1 ATGTGAT-AA-G-GCCGAATGGCCA
46011403 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
46011428 ATGTGAT
1 ATGTGAT
46011435 GAATATGAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 36
0.63 0.07 0.30
Matches are distributed among these distances:
22 25 0.33
23 16 0.21
24 16 0.21
25 18 0.24
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:46011408 original size:23 final size:23
Alignment explanation
Indices: 46011334--46011408 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 23
46011324 CGAATGGCCA
46011334 ATGTGATGAATGTGAGCATGCAT
1 ATGTGATGAATGTGAGCATGCAT
* * *
46011357 ATGTG-TGATAAG-GCCGAATGGCCA-
1 ATGTGATGA-ATGTG-AGCAT-G-CAT
46011381 ATGTGATGAATGTGAGCATGCAT
1 ATGTGATGAATGTGAGCATGCAT
46011404 ATGTG
1 ATGTG
46011409 TGATAAGGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 6 0.15
23 16 0.41
24 11 0.28
25 6 0.15
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28
Consensus pattern (23 bp):
ATGTGATGAATGTGAGCATGCAT
Found at i:46011519 original size:48 final size:48
Alignment explanation
Indices: 46011450--46011584 Score: 225
Period size: 48 Copynumber: 2.8 Consensus size: 48
46011440 TGAACATGCA
* * *
46011450 TATATGTGATAAGGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
* *
46011498 TATATGTGGTAAAGCCGAATGGCTAGTGCGAAATATGTATGAGGTATG
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
46011546 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
46011585 GGCGATGTGC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 81 1.00
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.30
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATG
Found at i:46011781 original size:37 final size:37
Alignment explanation
Indices: 46011731--46011876 Score: 265
Period size: 37 Copynumber: 3.9 Consensus size: 37
46011721 GGAAATATAT
46011731 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
46011768 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
46011805 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
46011842 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
46011877 CGTCTGAGCT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:46021095 original size:38 final size:39
Alignment explanation
Indices: 46021053--46021129 Score: 138
Period size: 40 Copynumber: 2.0 Consensus size: 39
46021043 CAGATAGACT
46021053 ATCAAAACTACCC-ATCCCCCAAAACACTCCCACTACCC
1 ATCAAAACTACCCAATCCCCCAAAACACTCCCACTACCC
46021091 ATCAAAACTACCCAAATCCCCCAAAACACTCCCACTACC
1 ATCAAAACTACCC-AATCCCCCAAAACACTCCCACTACC
46021130 TCTCAAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 13 0.35
40 24 0.65
ACGTcount: A:0.39, C:0.48, G:0.00, T:0.13
Consensus pattern (39 bp):
ATCAAAACTACCCAATCCCCCAAAACACTCCCACTACCC
Found at i:46021098 original size:21 final size:20
Alignment explanation
Indices: 46021068--46021129 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
46021058 AACTACCCAT
46021068 CCCCCAAAACACTCCCACTA
1 CCCCCAAAACACTCCCACTA
* * *
46021088 CCCATCAAAACTAC-CCAAAT-
1 CCC-CCAAAAC-ACTCCCACTA
46021108 CCCCCAAAACACTCCCACTA
1 CCCCCAAAACACTCCCACTA
46021128 CC
1 CC
46021130 TCTCAAATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 2 0.06
19 10 0.31
20 8 0.25
21 10 0.31
22 2 0.06
ACGTcount: A:0.37, C:0.52, G:0.00, T:0.11
Consensus pattern (20 bp):
CCCCCAAAACACTCCCACTA
Found at i:46022769 original size:26 final size:26
Alignment explanation
Indices: 46022733--46022785 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
46022723 CCATTCTTGA
46022733 AAGAAAATTTTCTAGTAGGACCTCCT
1 AAGAAAATTTTCTAGTAGGACCTCCT
46022759 AAGAAAATTTTCTAGTAGGACCTCCT
1 AAGAAAATTTTCTAGTAGGACCTCCT
46022785 A
1 A
46022786 CTTTATTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (26 bp):
AAGAAAATTTTCTAGTAGGACCTCCT
Found at i:46025680 original size:40 final size:40
Alignment explanation
Indices: 46025609--46025866 Score: 362
Period size: 40 Copynumber: 6.5 Consensus size: 40
46025599 AAACCAAGTA
* * *
46025609 CCTTCAGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
46025648 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
46025688 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
46025728 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAAGG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
46025768 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCACACAAAGG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
46025808 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
46025848 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
46025867 TTATCATCCG
Statistics
Matches: 201, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
39 14 0.07
40 187 0.93
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:46035872 original size:27 final size:28
Alignment explanation
Indices: 46035815--46035884 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
46035805 AAACTTGTAC
*
46035815 AGCACTAAGTGTGCGAGTTTGATCATGT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
46035843 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
46035870 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
46035885 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:46035895 original size:27 final size:27
Alignment explanation
Indices: 46035815--46035896 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
46035805 AAACTTGTAC
* * *
46035815 AGCACTAAGTGTGCGAGTTTGA-TCATGT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
46035843 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
46035870 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
46035897 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:46041039 original size:40 final size:40
Alignment explanation
Indices: 46040940--46041094 Score: 188
Period size: 40 Copynumber: 3.9 Consensus size: 40
46040930 TTCGAATGAT
* * * *
46040940 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
*
46040981 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
*
46041021 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* * *
46041062 A-CCGGGCCATGTCCCGAAGGCATTTGAGCGAGT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
46041095 AGCTATATCC
Statistics
Matches: 100, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.01
40 70 0.70
41 28 0.28
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:46041105 original size:80 final size:81
Alignment explanation
Indices: 46040938--46041110 Score: 210
Period size: 80 Copynumber: 2.2 Consensus size: 81
46040928 TATTCGAATG
* * * *
46040938 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGC
1 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTAAGTGACTATAACCGGACCAAGATCCGAAGGC
*
46041003 ATTTGTGCGAGTTACT
66 ATTTGAGCGAGTTACT
* * * * *
46041019 AAATCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCCATG-TCCCGAAGG
1 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTAAGTGACTATAACCGGACCAAGAT-CCGAAGG
46041082 CATTTGAGCGAG-TAGCT
65 CATTTGAGCGAGTTA-CT
46041099 ATATCC-GGTTAA
1 ATATCCGGGTTAA
46041111 ATTCTGAAGG
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
79 9 0.11
80 41 0.52
81 29 0.37
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (81 bp):
ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTAAGTGACTATAACCGGACCAAGATCCGAAGGC
ATTTGAGCGAGTTACT
Found at i:46048467 original size:41 final size:41
Alignment explanation
Indices: 46048422--46048539 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
46048412 TGAAAGATAA
46048422 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
46048463 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
46048493 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
46048534 ATGTAG
1 ATGTAG
46048540 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:46048478 original size:71 final size:71
Alignment explanation
Indices: 46048390--46048553 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
46048380 GAGATGTATC
46048390 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
46048455 AGGACA
66 AGGACA
46048461 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
46048526 AGGACA
66 AGGACA
46048532 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
46048554 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:46053813 original size:41 final size:41
Alignment explanation
Indices: 46053768--46053885 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
46053758 TGAAAGATAA
46053768 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
46053809 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
46053839 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
46053880 ATGTAG
1 ATGTAG
46053886 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:46053824 original size:71 final size:71
Alignment explanation
Indices: 46053736--46053899 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
46053726 GAGATGTATC
46053736 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
46053801 AGGACA
66 AGGACA
46053807 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
46053872 AGGACA
66 AGGACA
46053878 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
46053900 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:46055774 original size:14 final size:15
Alignment explanation
Indices: 46055720--46055771 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 15
46055710 GAAGTTTTTT
46055720 ATTTCAAAAATTTAA
1 ATTTCAAAAATTTAA
46055735 A-TTCAAAACA---AA
1 ATTTCAAAA-ATTTAA
46055747 ATTTTCAAAAATTTAA
1 A-TTTCAAAAATTTAA
46055763 ATTTCAAAA
1 ATTTCAAAA
46055772 TTTTCCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
12 3 0.10
13 1 0.03
14 14 0.45
15 10 0.32
16 3 0.10
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTTCAAAAATTTAA
Found at i:46060661 original size:20 final size:18
Alignment explanation
Indices: 46060610--46060662 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
46060600 ATAAAAGATA
* *
46060610 AAAAATAAAAAATTTTAG
1 AAAAATTAAAAATTTTAT
*
46060628 AAAAATTATTAAATTTTAAT
1 AAAAATTA-AAAATTTT-AT
46060648 AAAAATTTAAAAATT
1 AAAAA-TTAAAAATT
46060663 AGAAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.25
19 7 0.25
20 11 0.39
21 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAAATTAAAAATTTTAT
Found at i:46060696 original size:36 final size:36
Alignment explanation
Indices: 46060607--46060725 Score: 96
Period size: 36 Copynumber: 3.2 Consensus size: 36
46060597 ATGATAAAAG
* * ** *
46060607 ATAAAAAATAAAAAATTTTAGAAAAATTATTAAATTTTA
1 ATAAAAAATAAAAAATTGTA-AAAATTTA-TAAA-AATC
* * ** *
46060646 ATAAAAATTTAAAAATTAG-AAATTTTTATAAAATTC
1 ATAAAAAATAAAAAATT-GTAAAAATTTATAAAAATC
*
46060682 GTAAAAAATAAAAAATTGTAAAAATTTATAAAAATC
1 ATAAAAAATAAAAAATTGTAAAAATTTATAAAAATC
46060718 ATAAAAAA
1 ATAAAAAA
46060726 ATTAATGACC
Statistics
Matches: 63, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
35 1 0.02
36 37 0.59
37 4 0.06
38 5 0.08
39 16 0.25
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (36 bp):
ATAAAAAATAAAAAATTGTAAAAATTTATAAAAATC
Found at i:46060937 original size:10 final size:10
Alignment explanation
Indices: 46060922--46060947 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
46060912 TTCTTACGAC
46060922 TTTATAAAAT
1 TTTATAAAAT
46060932 TTTATAAAAT
1 TTTATAAAAT
46060942 TTTATA
1 TTTATA
46060948 TTTCTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTATAAAAT
Found at i:46060977 original size:27 final size:26
Alignment explanation
Indices: 46060930--46060998 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
46060920 ACTTTATAAA
* *
46060930 ATTTTATAAAATTTTATATTTCTATAT
1 ATTTTAT-AATTTTTAAATTTCTATAT
*
46060957 ATTTTATAATTTTTACAATTTTTATAT
1 ATTTTATAATTTTTA-AATTTCTATAT
* *
46060984 GTTTTACTATTTTTT
1 ATTTTA-TAATTTTT
46060999 TAATGAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 7 0.20
27 21 0.60
28 7 0.20
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (26 bp):
ATTTTATAATTTTTAAATTTCTATAT
Found at i:46060979 original size:18 final size:19
Alignment explanation
Indices: 46060958--46061003 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
46060948 TTTCTATATA
46060958 TTTTATAAT-TTTTACAAT
1 TTTTATAATGTTTTACAAT
*
46060976 TTTTAT-ATGTTTTACTAT
1 TTTTATAATGTTTTACAAT
*
46060994 TTTTTTAATG
1 TTTTATAATG
46061004 AATTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 19 0.79
19 3 0.12
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTATAATGTTTTACAAT
Found at i:46060988 original size:9 final size:8
Alignment explanation
Indices: 46060941--46060997 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 8
46060931 TTTTATAAAA
46060941 TTTTATAT
1 TTTTATAT
*
46060949 TTCTATAT
1 TTTTATAT
46060957 ATTTTATAAT
1 -TTTTAT-AT
*
46060967 TTTTACAAT
1 TTTTA-TAT
46060976 TTTTATAT
1 TTTTATAT
46060984 GTTTTACTAT
1 -TTTTA-TAT
46060994 TTTT
1 TTTT
46060998 TTAATGAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 9 0.22
9 26 0.65
10 5 0.12
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (8 bp):
TTTTATAT
Found at i:46061090 original size:8 final size:9
Alignment explanation
Indices: 46061068--46061111 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
46061058 TGATTTGAAT
*
46061068 TTTTTATAGT
1 TTTTTATA-A
46061078 TTTTTATAA
1 TTTTTATAA
46061087 TTTTTATAA
1 TTTTTATAA
*
46061096 TTTTTTTTAA
1 -TTTTTATAA
46061106 TTTTTA
1 TTTTTA
46061112 ATAAAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
9 14 0.47
10 16 0.53
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTTATAA
Found at i:46061092 original size:19 final size:19
Alignment explanation
Indices: 46061068--46061111 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
46061058 TGATTTGAAT
*
46061068 TTTTTATAGTTTTTTATAA
1 TTTTTATAATTTTTTATAA
*
46061087 TTTTTATAATTTTTTTTAA
1 TTTTTATAATTTTTTATAA
46061106 TTTTTA
1 TTTTTA
46061112 ATAAAATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTATAATTTTTTATAA
Found at i:46062319 original size:28 final size:28
Alignment explanation
Indices: 46062285--46062339 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
46062275 CAAATTACAT
46062285 GGACTAATAATAGAATTTAACCTTTTTG
1 GGACTAATAATAGAATTTAACCTTTTTG
46062313 GGACTAATAATAGAATTTAACCTTTTT
1 GGACTAATAATAGAATTTAACCTTTTT
46062340 TAACTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (28 bp):
GGACTAATAATAGAATTTAACCTTTTTG
Found at i:46062346 original size:27 final size:28
Alignment explanation
Indices: 46062287--46062347 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
46062277 AATTACATGG
*
46062287 ACTAATAATAGAATTTAACCTTTTTGGG
1 ACTAATAATAGAATTTAACCTTTTTGGA
*
46062315 ACTAATAATAGAATTTAACCTTTTT-TA
1 ACTAATAATAGAATTTAACCTTTTTGGA
46062342 ACTAAT
1 ACTAAT
46062348 CACGTTATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (28 bp):
ACTAATAATAGAATTTAACCTTTTTGGA
Found at i:46066856 original size:39 final size:37
Alignment explanation
Indices: 46066775--46066933 Score: 117
Period size: 38 Copynumber: 4.1 Consensus size: 37
46066765 TGGTCTGAAC
* * *
46066775 TAAAGACATGTATTAAAGACGTCTAAACTAGGACATATT
1 TAAA-ACAT-TATTAAAGATGTCTAAACTATGACATAAT
*
46066814 TAAAACATATATTTAAGATGTCCTAAACTATGACATAAT
1 TAAAACAT-TATTAAAGATGT-CTAAACTATGACATAAT
* * *
46066853 TAAAAACCCTTATTAAAGATGT-TCAGATTATGACATAAT
1 T-AAAA-CATTATTAAAGATGTCT-AAACTATGACATAAT
* * *
46066892 TAAAAC-TAATATAAATAATGT-TCAAATTATGACATAAT
1 TAAAACATTAT-TAAA-GATGTCT-AAACTATGACATAAT
46066930 TAAA
1 TAAA
46066934 TACTTAAACT
Statistics
Matches: 102, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
36 3 0.03
37 5 0.05
38 43 0.42
39 34 0.33
40 15 0.15
41 2 0.02
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.32
Consensus pattern (37 bp):
TAAAACATTATTAAAGATGTCTAAACTATGACATAAT
Found at i:46067641 original size:24 final size:23
Alignment explanation
Indices: 46067583--46067648 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
46067573 GCTTTTTTAT
*
46067583 TTTTCTTTCTTCTTTTCATACCATC
1 TTTTCTTT-TTCTTTT-TTACCATC
*
46067608 TTTT-TCTTTTCTTTTTTACTCTTC
1 TTTTCT-TTTTCTTTTTTAC-CATC
*
46067632 TTTTCTTTTTCCTTTTT
1 TTTTCTTTTTCTTTTTT
46067649 GCTTGCCTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
23 3 0.09
24 25 0.71
25 7 0.20
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTCTTTTTCTTTTTTACCATC
Found at i:46072625 original size:35 final size:35
Alignment explanation
Indices: 46072582--46072676 Score: 136
Period size: 35 Copynumber: 2.7 Consensus size: 35
46072572 TGCTCACAAA
*
46072582 AGCTAGTCCAACCGAAACACGCCAATACTCATAAG
1 AGCTAGTCCAACTGAAACACGCCAATACTCATAAG
* * * * *
46072617 AGTTAGTCCAACTAAAACACACCAGTGCTCATAAG
1 AGCTAGTCCAACTGAAACACGCCAATACTCATAAG
46072652 AGCTAGTCCAACTGAAACACGCCAA
1 AGCTAGTCCAACTGAAACACGCCAA
46072677 ACAAAGTGTA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.16
Consensus pattern (35 bp):
AGCTAGTCCAACTGAAACACGCCAATACTCATAAG
Found at i:46075974 original size:20 final size:20
Alignment explanation
Indices: 46075951--46076030 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
46075941 GAGTTCATAA
*
46075951 TTTAAGGTTCAAGGTTTGAG
1 TTTAAGGTTCAAGGTTTGGG
***
46075971 TTT-AGGTTTTGGGTTTTGGG
1 TTTAAGGTTCAAGG-TTTGGG
*
46075991 TTTAGGGTTCAAGGTTTGGG
1 TTTAAGGTTCAAGGTTTGGG
*
46076011 TTTAAGGTTAAAGGGTTTGG
1 TTTAAGGTTCAA-GGTTTGG
46076031 AGTCATGGGT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
19 7 0.15
20 27 0.57
21 13 0.28
ACGTcount: A:0.17, C:0.03, G:0.36, T:0.44
Consensus pattern (20 bp):
TTTAAGGTTCAAGGTTTGGG
Found at i:46076082 original size:20 final size:20
Alignment explanation
Indices: 46076044--46076082 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46076034 CATGGGTAAT
*
46076044 GAGTTTGAGGTTTGGGGTTC
1 GAGTTTGAGGTTTGAGGTTC
* *
46076064 GAGTTTTAGGTTTTAGGTT
1 GAGTTTGAGGTTTGAGGTT
46076083 TAGGGTTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.03, G:0.38, T:0.46
Consensus pattern (20 bp):
GAGTTTGAGGTTTGAGGTTC
Found at i:46076174 original size:79 final size:78
Alignment explanation
Indices: 46076079--46076234 Score: 276
Period size: 79 Copynumber: 2.0 Consensus size: 78
46076069 TTAGGTTTTA
*
46076079 GGTTTAGGGTTCAAGGTAAAAATTTACCAAAATTATGCGTCAATGACAAAGAAAAAATTGTTGAA
1 GGTTTAGGGTTCAAGGTAAAAATTTACCAAAATTATGCGTAAATGACAAA-AAAAAATTGTTGAA
46076144 ATGTCATTAAATAG
65 ATGTCATTAAATAG
* *
46076158 GGTTTAGGGTTCAAGGTAAAAATTTACCAAAATTATGTGTAAATGACATAAAAAAATTGTTGAAA
1 GGTTTAGGGTTCAAGGTAAAAATTTACCAAAATTATGCGTAAATGACAAAAAAAAATTGTTGAAA
46076223 TGTCATTAAATA
66 TGTCATTAAATA
46076235 ATGTGAAAAG
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 27 0.36
79 47 0.64
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (78 bp):
GGTTTAGGGTTCAAGGTAAAAATTTACCAAAATTATGCGTAAATGACAAAAAAAAATTGTTGAAA
TGTCATTAAATAG
Found at i:46077953 original size:28 final size:26
Alignment explanation
Indices: 46077898--46078010 Score: 145
Period size: 27 Copynumber: 4.2 Consensus size: 26
46077888 AGCATGGCTG
* *
46077898 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
46077924 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
46077952 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
46077979 CCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATAA--TGTGGCAGAGCCA
46078007 CCAG
1 CCAG
46078011 GACGCTTCCT
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
26 6 0.08
27 39 0.50
28 33 0.42
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:46077981 original size:55 final size:54
Alignment explanation
Indices: 46077898--46078010 Score: 165
Period size: 55 Copynumber: 2.1 Consensus size: 54
46077888 AGCATGGCTG
*
46077898 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAA-TCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAT-CAGATAATTCGTGGCAGAGCCA
* * *
46077952 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAGCCA
46078007 CCAG
1 CCAG
46078011 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 19 0.36
55 34 0.64
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATTCGTGGCAGAGCCA
Found at i:46085404 original size:27 final size:26
Alignment explanation
Indices: 46085369--46085463 Score: 127
Period size: 27 Copynumber: 3.5 Consensus size: 26
46085359 AGCATGGCTG
*
46085369 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAGCCA
* *
46085395 CCAGATACAGATAGTCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGACAGAGCCA
46085423 CCAGAACAGATATATGTGACAGAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
*
46085450 CCAGATCAGATAAT
1 CCAGAACAGATAAT
46085464 TTGTGGCATA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
26 7 0.12
27 37 0.62
28 16 0.27
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGCCA
Found at i:46085424 original size:28 final size:26
Alignment explanation
Indices: 46085369--46085480 Score: 116
Period size: 27 Copynumber: 4.1 Consensus size: 26
46085359 AGCATGGCTG
* *
46085369 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
* *
46085395 CCAGATACAGATAGTCGTGGCAGAGCCA
1 CCAGA-ACAGATA-TTGTGACAGAGCCA
46085423 CCAGAACAGATATATGTGACAGAGCCA
1 CCAGAACAGATAT-TGTGACAGAGCCA
* * *
46085450 CCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGAT-A-TTGTGACAGAGCCA
46085478 CCA
1 CCA
46085481 AGATGCTTCC
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
26 6 0.08
27 35 0.49
28 30 0.42
29 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:46085452 original size:55 final size:54
Alignment explanation
Indices: 46085369--46085480 Score: 163
Period size: 55 Copynumber: 2.1 Consensus size: 54
46085359 AGCATGGCTG
*
46085369 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGAT-AGTCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAT-CAGATAAGTCGTGGCAGAGCCA
* * *
46085423 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATCAGATAAGTCGTGGCAGAGCCA
46085478 CCA
1 CCA
46085481 AGATGCTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 17 0.33
55 35 0.67
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAAGTCGTGGCAGAGCCA
Found at i:46088307 original size:30 final size:30
Alignment explanation
Indices: 46088245--46088307 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
46088235 ATCGATTTTT
**
46088245 AAGTATAGGGGCAAAATGGTCATTTTGTCA
1 AAGTATAGGGGCAAAATGGTCATTTTACCA
* *
46088275 AAGTCTAGGGGCAAAATGGTTATTTTACCA
1 AAGTATAGGGGCAAAATGGTCATTTTACCA
46088305 AAG
1 AAG
46088308 ATGTAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (30 bp):
AAGTATAGGGGCAAAATGGTCATTTTACCA
Found at i:46088756 original size:47 final size:46
Alignment explanation
Indices: 46088647--46089009 Score: 156
Period size: 47 Copynumber: 7.7 Consensus size: 46
46088637 GATTTGTGCT
* * **
46088647 CCAGTGTAAGACATGTCTGGGACATGCTTCGGCAACATTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCAACATGACAAGAG
* * *
46088693 CCAGTATAAGACCATGTCTGGGACATGGCATCGGCATCCA-GACAAGGG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-ACATGACAAGAG
* * *
46088741 CTAGTGTAAGACATGTCTGGGACATGCATCAGTCATACTATG---ATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATC-GGCA-AC-ATGACAAGAG
* * * * * *
46088787 CCAATGTAAGACCATGTCTAGGACATGGCAACAGC-ACA-GAGATGAGTG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCAACATGACA--AGAG
* * *
46088835 CCATTGTAAGACATGGCTGGGACATGCATTGGC--C-TCGACAGAGGTAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCAACAT-GACA-A-G-AG
* * * * * * * *** *
46088882 CCATTATAAGACGTGTCTAGGACACGCATCAGCTA-A-GAGTTGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCAACATGACAAGAG
* * * *
46088926 CTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCGTAT-ATAAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCA-AC--ATGACAAGAG
*
46088974 CCAGTGTAAGACCATGTTTGGGACATGGCATCGGCA
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
46089010 CTATATCCCA
Statistics
Matches: 235, Mismatches: 55, Indels: 50
0.69 0.16 0.15
Matches are distributed among these distances:
43 1 0.00
44 29 0.12
45 6 0.03
46 35 0.15
47 88 0.37
48 52 0.22
49 16 0.07
50 8 0.03
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (46 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCAACATGACAAGAG
Found at i:46088843 original size:94 final size:92
Alignment explanation
Indices: 46088647--46089003 Score: 251
Period size: 94 Copynumber: 3.8 Consensus size: 92
46088637 GATTTGTGCT
* *
46088647 CCAGTGTAAGACATGTCTGGGACATGCTTCGGCAACATTATGAGAGCCAGTATAAGACCATGTCT
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCAACA-TATGAGAGCCAATATAAGACCATGTCT
* * *
46088712 GGGACATGGCATCGGCATCCAGACAAGGG
65 AGGACATGGCAACAGCA-CCAGACAAGGG
* * * *
46088741 CTAGTGTAAGACATGTCTGGGACATGCATCAGTCATAC-TATGATAGCCAATGTAAGACCATGTC
1 CCAGTGTAAGACATGTCTGGGACATGCATC-GGCA-ACATATGAGAGCCAATATAAGACCATGTC
* *
46088805 TAGGACATGGCAACAGCA-CAGAGATGAGTG
64 TAGGACATGGCAACAGCACCAGACA--AGGG
* * * ** * * *
46088835 CCATTGTAAGACATGGCTGGGACATGCATTGGCCTCGACA-GAGGTAGCCATTATAAGA-CGTGT
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCAAC-ATATGA-G-AGCCAATATAAGACCATGT
* * *** *
46088898 CTAGGACA-CGCATCAGCTA--AGAGTTGTG
63 CTAGGACATGGCAACAGC-ACCAGACAAGGG
* * * * * *
46088926 CTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCGTATATAAGAGCCAGTGTAAGACCATGT
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCA-AC--ATATGAGAGCCAATATAAGACCATGT
* *
46088991 TTGGGACATGGCA
63 CTAGGACATGGCA
46089004 TCGGCACTAT
Statistics
Matches: 206, Mismatches: 43, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
91 31 0.15
92 18 0.09
93 28 0.14
94 113 0.55
95 14 0.07
96 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (92 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCAACATATGAGAGCCAATATAAGACCATGTCTA
GGACATGGCAACAGCACCAGACAAGGG
Found at i:46090124 original size:193 final size:192
Alignment explanation
Indices: 46089795--46090192 Score: 679
Period size: 193 Copynumber: 2.1 Consensus size: 192
46089785 ACGGGTAAGC
*
46089795 CACACGGGCGTGTGTCCATGCCGTGTCATAAAGTCAGTATGCATGCTAGTAGTACACGGGCAAGA
1 CACACGGTCGTGTGTCCATGCCGTGTCATAAAGTCAGTATGCATGCTAGTAGTACACGGGCAAGA
* * *
46089860 GACACGGCCATGTGTCTCGGCCGTGTGAATGACACGGTTATAGGGCACGGGCGTGTGCTTGGGCC
66 GACACGGCCATGTGTCTCGGCCATGTGAATGACACGGTTATAGGGCACAGGCGTGTGCTTGGGCA
46089925 GTGTGGTTTTGGCAGAATGCCCAGGTTTTCAGACACGGGTTCGAGACACGAACGTGTCCATAG
131 GTGTGGTTTTGGCAGAATGCCCA-GTTTTCAGACACGGGTTCGAGACACGAACGTGTCCATAG
*
46089988 CACACGGTTGTGTGTCCATGCCGTGTCATAAAGTCAGTATGCATGCTAGTAGTACACGGGCAAGA
1 CACACGGTCGTGTGTCCATGCCGTGTCATAAAGTCAGTATGCATGCTAGTAGTACACGGGCAAGA
* * *
46090053 GGCACGGCCATGTGTCTCGGCCATGTGAATGGCACGGTTATAGGGCACAGGTGTGTGCTTGGGCA
66 GACACGGCCATGTGTCTCGGCCATGTGAATGACACGGTTATAGGGCACAGGCGTGTGCTTGGGCA
* * * *
46090118 GTGTGGTTTTGGTAGAATGCCCAGTTTTTAGACACGGGTTCGGGACACGAGCGTGTCCATAG
131 GTGTGGTTTTGGCAGAATGCCCAGTTTTCAGACACGGGTTCGAGACACGAACGTGTCCATAG
46090180 CACACGGTCGTGT
1 CACACGGTCGTGT
46090193 CCATAGCACA
Statistics
Matches: 192, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
192 48 0.25
193 144 0.75
ACGTcount: A:0.21, C:0.22, G:0.33, T:0.24
Consensus pattern (192 bp):
CACACGGTCGTGTGTCCATGCCGTGTCATAAAGTCAGTATGCATGCTAGTAGTACACGGGCAAGA
GACACGGCCATGTGTCTCGGCCATGTGAATGACACGGTTATAGGGCACAGGCGTGTGCTTGGGCA
GTGTGGTTTTGGCAGAATGCCCAGTTTTCAGACACGGGTTCGAGACACGAACGTGTCCATAG
Done.