Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_pilon, whole genome shotgun sequence
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: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 17
Found at i:2073823 original size:13 final size:13
Alignment explanation
Indices: 2073805--2073829 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2073795 AGCCATTAGT
2073805 TTCATAATCAATA
1 TTCATAATCAATA
2073818 TTCATAATCAAT
1 TTCATAATCAAT
2073830 GTGACATGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCATAATCAATA
Found at i:2075925 original size:21 final size:22
Alignment explanation
Indices: 2075841--2075924 Score: 98
Period size: 24 Copynumber: 3.8 Consensus size: 22
2075831 CCAGGACCCT
* *
2075841 AGGGGGTATCGATTCCCCTAC-
1 AGGGGGAATCGATTCCCCTTCA
*
2075862 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
2075884 ATGGGGGGAATCGGTTCCCCTTCA
1 A--GGGGGAATCGATTCCCCTTCA
*
2075908 AGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
2075925 TCTGCACTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.33
22 15 0.27
24 22 0.40
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:2080225 original size:21 final size:21
Alignment explanation
Indices: 2080201--2080240 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2080191 AAGACTCTAT
2080201 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
2080222 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
2080241 AAATAGTCTT
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:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:2084100 original size:23 final size:21
Alignment explanation
Indices: 2084054--2084113 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 21
2084044 ATAGGGCAGA
*
2084054 GGGAATCGATATCCCCTTGAAG
1 GGGAACCGAT-TCCCCTTGAAG
2084076 GGGAACCGATTCCTCCTTTGAAG
1 GGGAACCGATTCC-CC-TTGAAG
2084099 GGGAACCGATTCCCC
1 GGGAACCGATTCCCC
2084114 CTAGGGGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 3 0.09
22 13 0.37
23 19 0.54
ACGTcount: A:0.23, C:0.28, G:0.27, T:0.22
Consensus pattern (21 bp):
GGGAACCGATTCCCCTTGAAG
Found at i:2084121 original size:19 final size:19
Alignment explanation
Indices: 2084074--2084138 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
2084064 ATCCCCTTGA
*
2084074 AGGGGAACCGATTCCTCCTTT
1 AGGGGAACCGATTCC-CC-CT
2084095 GAAGGGGAACCGATTCCCCCT
1 --AGGGGAACCGATTCCCCCT
* *
2084116 AGGGGAATCGATACCCCCT
1 AGGGGAACCGATTCCCCCT
2084135 -GGGG
1 AGGGG
2084139 TTCTGGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
18 4 0.10
19 17 0.44
21 1 0.03
22 2 0.05
23 15 0.38
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.18
Consensus pattern (19 bp):
AGGGGAACCGATTCCCCCT
Found at i:2089333 original size:22 final size:21
Alignment explanation
Indices: 2089291--2089330 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2089281 GAGTTTGTTT
*
2089291 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2089312 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2089331 ACAATTGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2091680 original size:41 final size:41
Alignment explanation
Indices: 2091635--2091721 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
2091625 GAATTGTGAA
* * * *
2091635 ATGCTTCCATGACTGAATTAAGTTGAATTCTAAATTATTAC
1 ATGCTTCCATGACTAAACTAAATCGAATTCTAAATTATTAC
* * *
2091676 ATGCTTCCATGATTAAACTAAATCGAATTGTAAATTATTGC
1 ATGCTTCCATGACTAAACTAAATCGAATTCTAAATTATTAC
2091717 ATGCT
1 ATGCT
2091722 GCCAAGATTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGCTTCCATGACTAAACTAAATCGAATTCTAAATTATTAC
Found at i:2091745 original size:41 final size:41
Alignment explanation
Indices: 2091657--2091756 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
2091647 CTGAATTAAG
* * * *
2091657 TTGAATTCTAAATTATTACATGCTTCCATGATTAAACTAAA
1 TTGAATTGTAAATTATTGCATGCTGCCAAGATTAAACTAAA
* * ** *
2091698 TCGAATTGTAAATTATTGCATGCTGCCAAGATTGAGTTGAA
1 TTGAATTGTAAATTATTGCATGCTGCCAAGATTAAACTAAA
*
2091739 TTGAATTGTGAATTATTG
1 TTGAATTGTAAATTATTG
2091757 TTATTGCCAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (41 bp):
TTGAATTGTAAATTATTGCATGCTGCCAAGATTAAACTAAA
Found at i:2095743 original size:21 final size:21
Alignment explanation
Indices: 2095719--2095758 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2095709 TTTTCAAAGG
2095719 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
2095740 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
2095759 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:2095864 original size:17 final size:19
Alignment explanation
Indices: 2095836--2095884 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2095826 ATTTTTCAAA
2095836 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
2095854 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
2095873 CACCGATGCACT
1 CATCGATGCACT
2095885 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:2101610 original size:24 final size:22
Alignment explanation
Indices: 2101582--2101661 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 22
2101572 CACTTAACAA
2101582 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
2101606 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
2101626 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
2101650 TGCATCGATGCA
1 TGCATCGATGCA
2101662 CAAGATCATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 2 0.04
23 13 0.27
24 17 0.35
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:2104192 original size:21 final size:21
Alignment explanation
Indices: 2104168--2104207 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2104158 TTTTCAAAGG
2104168 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
2104189 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
2104208 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:2104257 original size:19 final size:19
Alignment explanation
Indices: 2104233--2104271 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2104223 TCGAATGCAT
2104233 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
2104252 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
2104271 T
1 T
2104272 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:2104296 original size:64 final size:63
Alignment explanation
Indices: 2104168--2104395 Score: 223
Period size: 64 Copynumber: 3.5 Consensus size: 63
2104158 TTTTCAAAGG
* * *
2104168 CATGCACCGATGCA-TCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCA
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCATC-ATGATTTAATTAAAACATCGAATGCA
2104232 TT
62 TT
2104234 CCATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATT
1 -CATGCACCGATGCACTCTCCATGCATCGATGCA-TCATGATTTAATTAAAACATCGAATGCA-T
2104298 T
63 T
* * ** * *
2104299 GATGCATCGATGCACAATCCATGCATCGATGCATCAGGCTATTT--TTCAAACATCGAATGCACT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCATG--ATTTAATTAAAACATCGAATGCA-T
2104362 T
63 T
* *
2104363 CATGCATCGATGCACTCT-TAGTGCATCGATGCA
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCA
2104396 CTAGGAGTCC
Statistics
Matches: 140, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
63 3 0.02
64 97 0.69
65 17 0.12
66 7 0.05
67 14 0.10
68 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCATGATTTAATTAAAACATCGAATGCATT
Found at i:2104377 original size:17 final size:19
Alignment explanation
Indices: 2104349--2104397 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
2104339 ATTTTTCAAA
2104349 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
2104367 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
2104386 CATCGATGCACT
1 CATCGATGCACT
2104398 AGGAGTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.25
18 7 0.25
19 14 0.50
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:2109543 original size:41 final size:40
Alignment explanation
Indices: 2109424--2109714 Score: 291
Period size: 41 Copynumber: 7.1 Consensus size: 40
2109414 AATTATTGAC
* *
2109424 TGCCATGATTGAATTGAATTGAATTGTGAATTATTGCATGC
1 TGCCATGACTGAATT-AATTGAATTGTGAATTATTGCATGT
* * * *
2109465 TACCACGAC-CAATTTAAGTTG-ATTGTGAAATATTGCATGT
1 TGCCATGACTGAA-TTAA-TTGAATTGTGAATTATTGCATGT
2109505 TGCCATGACCT-AATTAAGTTGAATTGTGAATTATTGCATGT
1 TGCCATGA-CTGAATTAA-TTGAATTGTGAATTATTGCATGT
* * * * *
2109546 TGTCATGATTGAATCGAATCGAATTGTGAATTATTGCATGG
1 TGCCATGACTGAAT-TAATTGAATTGTGAATTATTGCATGT
* * *
2109587 TGTCATGATTAAATTGAATTGAATTGTGAATTATTGCATGT
1 TGCCATGACTGAATT-AATTGAATTGTGAATTATTGCATGT
* *
2109628 TGCCATGACTGAATTGAGTTGAATGGTGAATTATTGCATGT
1 TGCCATGACTGAATT-AATTGAATTGTGAATTATTGCATGT
* * * * *
2109669 TGTCATGATTGAACTTAATCGAATTGTGAATTAGTGCATGC
1 TGCCATGACTGAA-TTAATTGAATTGTGAATTATTGCATGT
2109710 TGCCA
1 TGCCA
2109715 AGATCGAACT
Statistics
Matches: 210, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
40 36 0.17
41 170 0.81
42 4 0.02
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (40 bp):
TGCCATGACTGAATTAATTGAATTGTGAATTATTGCATGT
Found at i:2109730 original size:123 final size:122
Alignment explanation
Indices: 2109427--2109743 Score: 401
Period size: 123 Copynumber: 2.6 Consensus size: 122
2109417 TATTGACTGC
* * * * *
2109427 CATGATTGAATTGAATTGAATTGTGAATTATTGCATGCTACCACGA-CCAATTTAAGTTG-ATTG
1 CATGATTGAATT-AATCGAATTGTGAATTATTGCATGCTGCCAAGATCAAATTCAA-TTGAATTG
*
2109490 TGAAATATTGCATGTTGCCATGACCTAATTAAGTTGAATTGTGAATTATTGCATGTTGT
64 TGAAATATTGCATGTTGCCATGACCTAATTAAGTTGAATGGTGAATTATTGCATGTTGT
* * * * * *
2109549 CATGATTGAATCGAATCGAATTGTGAATTATTGCATGGTGTCATGATTAAATTGAATTGAATTGT
1 CATGATTGAAT-TAATCGAATTGTGAATTATTGCATGCTGCCAAGATCAAATTCAATTGAATTGT
* *
2109614 GAATTATTGCATGTTGCCATGA-CTGAATTGAGTTGAATGGTGAATTATTGCATGTTGT
65 GAAATATTGCATGTTGCCATGACCT-AATTAAGTTGAATGGTGAATTATTGCATGTTGT
* * *
2109672 CATGATTGAACTTAATCGAATTGTGAATTAGTGCATGCTGCCAAGATCGAACTCAATTGAA-T-T
1 CATGATTGAA-TTAATCGAATTGTGAATTATTGCATGCTGCCAAGATCAAATTCAATTGAATTGT
2109735 GAAATATTG
65 GAAATATTG
2109744 AATGAACAAA
Statistics
Matches: 168, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
121 9 0.05
122 45 0.27
123 113 0.67
124 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (122 bp):
CATGATTGAATTAATCGAATTGTGAATTATTGCATGCTGCCAAGATCAAATTCAATTGAATTGTG
AAATATTGCATGTTGCCATGACCTAATTAAGTTGAATGGTGAATTATTGCATGTTGT
Found at i:2119294 original size:41 final size:40
Alignment explanation
Indices: 2119249--2119343 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
2119239 GTTGATGGAA
* *
2119249 AATAAATAAAGATATGAGTTTAGGACAA-AGAAAACAAGGGT
1 AATAAATAAAGATA-GAATTAAGGACAATAGAAAACAA-GGT
*
2119290 AATAAAATTAA-ATAGAATTAAGGACAATAGAAAACAAGGT
1 AAT-AAATAAAGATAGAATTAAGGACAATAGAAAACAAGGT
2119330 AATAAATAAAGATA
1 AATAAATAAAGATA
2119344 AGGATTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
39 6 0.13
40 20 0.43
41 15 0.32
42 6 0.13
ACGTcount: A:0.59, C:0.04, G:0.17, T:0.20
Consensus pattern (40 bp):
AATAAATAAAGATAGAATTAAGGACAATAGAAAACAAGGT
Found at i:2136587 original size:134 final size:134
Alignment explanation
Indices: 2136378--2136670 Score: 390
Period size: 134 Copynumber: 2.2 Consensus size: 134
2136368 TCTGGTTATT
* * * **
2136378 GGATAACACGGCTCATACGTGATGAATAGTTTTGGCCATCTTTAGGAAGGGTGATAACACAATTC
1 GGATGACACGGCTCATACGTGATGAAGAGTTCTCACCATCTTTAGGAAGGGTGATAACACAATTC
* ** *
2136443 CTAAGCGATGAGGACGACTGGTTATCTAAAGGTAACATGGCTCCTATGTGATGAGGATATCTAGT
66 ATAAGCGATGAGGACGACTGGTTATCTAAAGGTAACATGGCTCCTACATGATAAGGATATCTAGT
*
2136508 CGGG
131 CGAG
**
2136512 GGATGACACGGCTCATACGTGATGAAGAGTTCTCACCATCTTTAGGAAGGGTGATAACACGGTTC
1 GGATGACACGGCTCATACGTGATGAAGAGTTCTCACCATCTTTAGGAAGGGTGATAACACAATTC
* * ** *
2136577 ATACA-TGATGAGGACGGCTGGTTATCTAGGGGTAACATGGCTCCTACATGATAAGGATATCTGG
66 ATA-AGCGATGAGGACGACTGGTTATCTAAAGGTAACATGGCTCCTACATGATAAGGATATCTAG
2136641 TCGAG
130 TCGAG
* * *
2136646 GGATGACACGGTTCCTATGTGATGA
1 GGATGACACGGCTCATACGTGATGA
2136671 GGAGGACAGA
Statistics
Matches: 138, Mismatches: 20, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
134 137 0.99
135 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (134 bp):
GGATGACACGGCTCATACGTGATGAAGAGTTCTCACCATCTTTAGGAAGGGTGATAACACAATTC
ATAAGCGATGAGGACGACTGGTTATCTAAAGGTAACATGGCTCCTACATGATAAGGATATCTAGT
CGAG
Found at i:2136767 original size:31 final size:31
Alignment explanation
Indices: 2136732--2136822 Score: 123
Period size: 31 Copynumber: 2.9 Consensus size: 31
2136722 AGAGACAAAA
*
2136732 TTTTGTTTCAA-AGGAAA-ATACTCAAAGACT
1 TTTTGTTTCAATA-GAAACAAACTCAAAGACT
* *
2136762 GTTTTGTTTTAATAGAAACAAACTCAAAAACT
1 -TTTTGTTTCAATAGAAACAAACTCAAAGACT
2136794 TTTTGTTTCAATAGAAACAAACTCAAAGA
1 TTTTGTTTCAATAGAAACAAACTCAAAGA
2136823 TATTGTCTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
31 41 0.77
32 12 0.23
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (31 bp):
TTTTGTTTCAATAGAAACAAACTCAAAGACT
Found at i:2136871 original size:28 final size:29
Alignment explanation
Indices: 2136835--2136890 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2136825 TTGTCTCAAG
*
2136835 AGAGACAAA-ATTTTGT-TTCCAAAGAAAC
1 AGAGACAAAGATTTT-TCTTCAAAAGAAAC
*
2136863 AGAGTCAAAGATTTTTCTTCAAAAGAAA
1 AGAGACAAAGATTTTTCTTCAAAAGAAA
2136891 TTGTCTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.27
Consensus pattern (29 bp):
AGAGACAAAGATTTTTCTTCAAAAGAAAC
Found at i:2136927 original size:66 final size:66
Alignment explanation
Indices: 2136818--2136941 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 66
2136808 AAACAAACTC
* * * *
2136818 AAAGATATTGTCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACA-GAGTCAAAGATTTTTCTT
1 AAAGAAATTGTCTCAAAAGAGACAAAATTATGTTTCCAAAGAAA-ATGACTCAAAGATTTTTCTT
2136882 CA
65 CA
* * *
2136884 AAAGAAATTGTCTGAAAAGAGATAAAATTATGTTT-TAAGAGAAAATGACTCAAAGATT
1 AAAGAAATTGTCTCAAAAGAGACAAAATTATGTTTCCAA-AGAAAATGACTCAAAGATT
2136942 ATGTGTTTCA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
65 3 0.06
66 46 0.94
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (66 bp):
AAAGAAATTGTCTCAAAAGAGACAAAATTATGTTTCCAAAGAAAATGACTCAAAGATTTTTCTTC
A
Found at i:2144374 original size:3 final size:3
Alignment explanation
Indices: 2144366--2144422 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
2144356 GTAAATTACC
2144366 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2144413 ATA AT- ATA AT
1 ATA ATA ATA AT
2144423 GTTTTTGTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.08
3 48 0.92
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2149669 original size:196 final size:196
Alignment explanation
Indices: 2149335--2149727 Score: 723
Period size: 196 Copynumber: 2.0 Consensus size: 196
2149325 ACCACCAATC
2149335 CAAGACCATGGAGAATTTCTTCATGCTTTGGATGTGATTCTACTCGATATCAACTCCTCCTCCTC
1 CAAGACCATGGAGAATTTCTTCATGCTTTGGATGTGATTCTACTCGATATCAACTCCTCCTCCTC
*
2149400 CCACTCCTTCTCCGGCTCCCCATTTGTCAATATCAAAAGAGTTTAAAAGTTTAGGGGTGACAAAG
66 CCACTCCTTCTCCGGCTCCCCATTTGTCAATATCAAAAGAGTTTAAAAGTTTAGGGGCGACAAAG
*
2149465 TTTAAGGGAGAAAAATACGATGGTCCTATAGTTGTAAACCTATGGTTGAATGGTATCAAAGTGAT
131 TTTAAGGGAGAAAAATACGATGGTCCTATAGTTGCAAACCTATGGTTGAATGGTATCAAAGTGAT
2149530 G
196 G
*
2149531 CAAGACCATGGGGAATTTCTTCATGCTTTGGATGTGATTCTACTCGATATCAACTCCTCCTCCTC
1 CAAGACCATGGAGAATTTCTTCATGCTTTGGATGTGATTCTACTCGATATCAACTCCTCCTCCTC
* * *
2149596 CCACTCCTTTTCCGGCTCCCCATTTGTCAATATCAAAAGAGTTTAAAAGTTTAGGGGCGCCACAG
66 CCACTCCTTCTCCGGCTCCCCATTTGTCAATATCAAAAGAGTTTAAAAGTTTAGGGGCGACAAAG
*
2149661 TTTAAGGGAGAAAAATATGATGGTCCTATAGTTGCAAACCTATGGTTGAATGGTATCAAAGTGAT
131 TTTAAGGGAGAAAAATACGATGGTCCTATAGTTGCAAACCTATGGTTGAATGGTATCAAAGTGAT
2149726 G
196 G
2149727 C
1 C
2149728 TAGATAATCT
Statistics
Matches: 190, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
196 190 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (196 bp):
CAAGACCATGGAGAATTTCTTCATGCTTTGGATGTGATTCTACTCGATATCAACTCCTCCTCCTC
CCACTCCTTCTCCGGCTCCCCATTTGTCAATATCAAAAGAGTTTAAAAGTTTAGGGGCGACAAAG
TTTAAGGGAGAAAAATACGATGGTCCTATAGTTGCAAACCTATGGTTGAATGGTATCAAAGTGAT
G
Found at i:2155520 original size:41 final size:41
Alignment explanation
Indices: 2155475--2155556 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
2155465 AGTACTACTT
2155475 TTGGTATTAATATGTGCATAAAATGTTAGTAAGAATACTAA
1 TTGGTATTAATATGTGCATAAAATGTTAGTAAGAATACTAA
* * *
2155516 TTGGTATTATTATGTGTATAAAATGTTTGTAAGAATACTAA
1 TTGGTATTAATATGTGCATAAAATGTTAGTAAGAATACTAA
2155557 CATGTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (41 bp):
TTGGTATTAATATGTGCATAAAATGTTAGTAAGAATACTAA
Found at i:2161652 original size:20 final size:20
Alignment explanation
Indices: 2161609--2161659 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
2161599 AAAATGATTT
2161609 AATTTT-AAAAACAAAAGTTG
1 AATTTTGAAAAACAAAAG-TG
2161629 -ATTTTGAAAAACAAAA-TG
1 AATTTTGAAAAACAAAAGTG
2161647 AAATTTTGGAAAA
1 -AATTTT-GAAAA
2161660 TGTTTAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.07
19 5 0.19
20 15 0.56
21 5 0.19
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (20 bp):
AATTTTGAAAAACAAAAGTG
Found at i:2168251 original size:77 final size:78
Alignment explanation
Indices: 2168122--2168275 Score: 183
Period size: 77 Copynumber: 2.0 Consensus size: 78
2168112 TTTAAATGTG
*
2168122 TTAAACTCTTATTTAGTTAATTCAAATTAAATATCCATGAAAGACTTATAATCCA-AATTACACT
1 TTAAACTCTTATTTAATTAATTCAAATTAAATATCCATGAAAGACTTATAAT-CAGAATTACACT
2168186 C-TTTAATGTTTAT
65 CTTTTAATGTTTAT
* * * *
2168199 TTAAATTCTTATTTAATT-ATTCCAAATTAAATAT-CATTAAA-TCTGTTGTAATCAGAATTACA
1 TTAAACTCTTATTTAATTAATT-CAAATTAAATATCCATGAAAGAC--TTATAATCAGAATTACA
*
2168261 TTCTTTTAATGTTTA
63 CTCTTTTAATGTTTA
2168276 CTTACTATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
75 1 0.02
76 11 0.17
77 43 0.65
78 11 0.17
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (78 bp):
TTAAACTCTTATTTAATTAATTCAAATTAAATATCCATGAAAGACTTATAATCAGAATTACACTC
TTTTAATGTTTAT
Found at i:2171120 original size:17 final size:17
Alignment explanation
Indices: 2171086--2171127 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2171076 CCCCTCCATT
* *
2171086 TCTTT-GAGAGAAATTC
1 TCTTTCGAGAAAAACTC
2171102 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
*
2171119 TCGTTCGAG
1 TCTTTCGAG
2171128 CAATAAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Found at i:2174177 original size:2 final size:2
Alignment explanation
Indices: 2174170--2174236 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
2174160 TGCAAATCAA
2174170 AT AT AT AT AT AT 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 AT AT AT AT AT AT
2174212 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 A
2174237 CGTCGTTACA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2175545 original size:18 final size:18
Alignment explanation
Indices: 2175522--2175566 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
2175512 TCCTTTATAT
2175522 CTAGAATAGGCATAAGTC
1 CTAGAATAGGCATAAGTC
2175540 CTAGAATAGGCATAAGTC
1 CTAGAATAGGCATAAGTC
2175558 CTAGAATAG
1 CTAGAATAG
2175567 TCACACTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (18 bp):
CTAGAATAGGCATAAGTC
Found at i:2179521 original size:3 final size:3
Alignment explanation
Indices: 2179507--2179548 Score: 57
Period size: 3 Copynumber: 13.0 Consensus size: 3
2179497 TTCTAACAAA
2179507 TAT TAT TAAT TAT TAT TAT TAAT TAT TAT TAT TAAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT T-AT TAT TAT TAT T-AT TAT TAT
2179549 ATTTTATAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 27 0.75
4 9 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2179522 original size:10 final size:9
Alignment explanation
Indices: 2179507--2179548 Score: 57
Period size: 10 Copynumber: 4.3 Consensus size: 9
2179497 TTCTAACAAA
2179507 TATTATTAAT
1 TATTATT-AT
2179517 TATTATTAT
1 TATTATTAT
2179526 TAATTATTAT
1 T-ATTATTAT
2179536 TATTAATTAT
1 TATT-ATTAT
2179546 TAT
1 TAT
2179549 ATTTTATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.20
10 24 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TATTATTAT
Found at i:2179525 original size:13 final size:13
Alignment explanation
Indices: 2179507--2179548 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
2179497 TTCTAACAAA
2179507 TATTATTAATTAT
1 TATTATTAATTAT
2179520 TATTATTAATTAT
1 TATTATTAATTAT
2179533 TATTATTAATTAT
1 TATTATTAATTAT
2179546 TAT
1 TAT
2179549 ATTTTATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATTAATTAT
Found at i:2185477 original size:36 final size:35
Alignment explanation
Indices: 2185432--2185524 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 35
2185422 CGTCTCACTA
* * *
2185432 GAGATAATTTTTCTTAAAAACAAATTTTATCTTGCTT
1 GAGA-AATTTTTC-TCAAAACAAATTTCATCTCGCTT
* *
2185469 GAGAAATTTCTCTCAAAACAAATTTCGTCTCGCTT
1 GAGAAATTTTTCTCAAAACAAATTTCATCTCGCTT
*
2185504 GAGACATTTTTCCTCAAAACA
1 GAGAAATTTTT-CTCAAAACA
2185525 CACAATTTGG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 28 0.58
36 16 0.33
37 4 0.08
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (35 bp):
GAGAAATTTTTCTCAAAACAAATTTCATCTCGCTT
Found at i:2185479 original size:34 final size:35
Alignment explanation
Indices: 2185403--2185512 Score: 96
Period size: 35 Copynumber: 3.1 Consensus size: 35
2185393 TCTGAGATTG
* * * *
2185403 TTTCTCTAAAAA-AAATGGTCGTCTCACTAGAGATAA
1 TTTCTCTAAAAACAAAT-TTCATCTCGCTTGAGA-AA
* * *
2185439 TTTTTCTTAAAAACAAATTTTATCTTGCTTGAGAAA
1 TTTCTC-TAAAAACAAATTTCATCTCGCTTGAGAAA
* * *
2185475 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTCATCTCGCTTGAGAAA
2185510 TTT
1 TTT
2185513 TTCCTCAAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
35 27 0.46
36 12 0.20
37 16 0.27
38 4 0.07
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (35 bp):
TTTCTCTAAAAACAAATTTCATCTCGCTTGAGAAA
Found at i:2185718 original size:36 final size:35
Alignment explanation
Indices: 2185673--2185784 Score: 89
Period size: 36 Copynumber: 3.3 Consensus size: 35
2185663 TTTGAGATCG
*
2185673 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAT
1 TTTCTCTTGAAA-GAATTTTGTCTCTCTTGAGACAT
* *
2185709 TTTCTCTTGAAA-CA-----TCATCT-TTGAGA-TT
1 TTTCTCTTGAAAGAATTTTGTC-TCTCTTGAGACAT
*
2185737 ATTTC-CTTGAAACGAATTTTGTCTCTCTTGAGACAA
1 -TTTCTCTTGAAA-GAATTTTGTCTCTCTTGAGACAT
2185773 TTTCTCTTGAAA
1 TTTCTCTTGAAA
2185785 CATCATCTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 24
0.66 0.07 0.27
Matches are distributed among these distances:
28 8 0.14
29 12 0.21
30 4 0.07
34 4 0.07
35 12 0.21
36 18 0.31
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (35 bp):
TTTCTCTTGAAAGAATTTTGTCTCTCTTGAGACAT
Found at i:2185741 original size:29 final size:29
Alignment explanation
Indices: 2185700--2185815 Score: 83
Period size: 29 Copynumber: 3.8 Consensus size: 29
2185690 TTTGTCTCTC
* *
2185700 TTGAGACATTTTCTCTTGAAACATCATCT
1 TTGAGATAATTTCTCTTGAAACATCATCT
*
2185729 TTGAGATTATTTC-CTTGAAACGAATTTTGTC-TCT
1 TTGAGATAATTTCTCTTGAAAC--A-----TCATCT
*
2185763 CTTGAGACAATTTCTCTTGAAACATCATCT
1 -TTGAGATAATTTCTCTTGAAACATCATCT
** *
2185793 TTGAGATCGTTTCCCTTGAAACA
1 TTGAGATAATTTCTCTTGAAACA
2185816 AAGTTTATCT
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
28 8 0.12
29 31 0.46
30 4 0.06
34 4 0.06
35 13 0.19
36 8 0.12
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (29 bp):
TTGAGATAATTTCTCTTGAAACATCATCT
Found at i:2185777 original size:64 final size:65
Alignment explanation
Indices: 2185606--2185852 Score: 334
Period size: 65 Copynumber: 3.8 Consensus size: 65
2185596 CTTTAAGTCT
* * *
2185606 ATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTCTCTCATGAAACATCATATTTGAGAT
1 ATTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGAT
2185671 C
65 C
* ** * *
2185672 GTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACATTTTCTCTTGAAACATCATCTTTGAGATT
1 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATC
* *
2185737 ATTT-CCTTGAAACGAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGATC
1 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATC
* * * * * *
2185801 GTTTCCCTTGAAACAAAGTTTATCTCACTTGAGATAGTTTCTCTTAAAACAT
1 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAT
2185853 TATCCCTAAA
Statistics
Matches: 160, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
64 60 0.38
65 88 0.55
66 12 0.08
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (65 bp):
ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATC
Found at i:2185787 original size:129 final size:131
Alignment explanation
Indices: 2185605--2185852 Score: 365
Period size: 129 Copynumber: 1.9 Consensus size: 131
2185595 TCTTTAAGTC
*
2185605 TATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAGTCTCTCATGAAACATCATATTTGAGA
1 TATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAATCTCTCATGAAACATCATATTTGAGA
** * * * * *
2185670 TCGTTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACATTTTCTCTTGAAACATCATCTTTGAGA
66 TCGTTTCCCTTGAAACAAAGTTTATCTCACTTGAGACAGTTTCTCTTAAAACATCATCTTTGAGA
2185735 T
131 T
* * * *
2185736 TATTT-CCTTGAAAC-GAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACATCATCTTTGAGA
1 TATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAATCTCTCATGAAACATCATATTTGAGA
*
2185799 TCGTTTCCCTTGAAACAAAGTTTATCTCACTTGAGATAGTTTCTCTTAAAACAT
66 TCGTTTCCCTTGAAACAAAGTTTATCTCACTTGAGACAGTTTCTCTTAAAACAT
2185853 TATCCCTAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
129 90 0.87
130 9 0.09
131 5 0.05
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.40
Consensus pattern (131 bp):
TATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAATCTCTCATGAAACATCATATTTGAGA
TCGTTTCCCTTGAAACAAAGTTTATCTCACTTGAGACAGTTTCTCTTAAAACATCATCTTTGAGA
T
Found at i:2185930 original size:40 final size:42
Alignment explanation
Indices: 2185873--2185980 Score: 105
Period size: 43 Copynumber: 2.6 Consensus size: 42
2185863 GATGGAAAGC
* * * *
2185873 CGTCCTCATCGCTTAGGAACCGTGTCATCC-A-CTAACCAGAT
1 CGTCCTCATCACGTAGGAACCGTGTCAACCTAGATAACCAG-T
* **
2185914 C-TCCTCATCACGTAGGAGCCACGTCAACCTTAGATAACCAGT
1 CGTCCTCATCACGTAGGAACCGTGTCAACC-TAGATAACCAGT
*
2185956 CGTCCGCATCACGTAGGAACCGTGT
1 CGTCCTCATCACGTAGGAACCGTGT
2185981 TATCATCCCT
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
40 22 0.42
41 1 0.02
42 3 0.06
43 26 0.50
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22
Consensus pattern (42 bp):
CGTCCTCATCACGTAGGAACCGTGTCAACCTAGATAACCAGT
Found at i:2186031 original size:131 final size:133
Alignment explanation
Indices: 2185854--2186196 Score: 390
Period size: 131 Copynumber: 2.6 Consensus size: 133
2185844 TTAAAACATT
* * * * * *
2185854 ATCCCTAAAGATGGAAAGCCGTCCTCATCGCTTAGGAACCGTGTCATCCACTAACCAGATCTCCT
1 ATCCCTAAAGATGGACAGTCATCCTCATCACATAGGAACAGTGTCATCCACT-ACCAGATCTCCT
* * ** * *
2185919 CATCACGTAGGAGCCACGTCAACCTTAGATAACCAGTCGTCCGCATCACGTAGGAACCGT-GT-T
65 CATCACGTAGGAGCCACGTCAACCTTAGATAAACAGCCGTCCGCATCACACAAGAACCATAGTAT
2185982 -ATC
130 CATC
* * * *
2185985 ATCCCTAAAGATGGCCAGTCATCCTCATCACATCGGAACAGTGTCATCCCCCTACCAGATATCCT
1 ATCCCTAAAGATGGACAGTCATCCTCATCACATAGGAACAGTGTCAT-CCACTACCAGATCTCCT
** * *
2186050 CATCACGTAGGAGCTGCGTCAACCTTAGATAAACAGCCGTCCTCATCACACAAGAACCATATTAT
65 CATCACGTAGGAGCCACGTCAACCTTAGATAAACAGCCGTCCGCATCACACAAGAACCATAGTAT
2186115 CATC
130 CATC
* * * *
2186119 ATCCCTAAAGAT-GATCAGTCATCCTCATCTCGTAGAAACCA-TGTCATCCACCGACCAGATCTC
1 ATCCCTAAAGATGGA-CAGTCATCCTCATCACATAGGAA-CAGTGTCATCCA-CTACCAGATCTC
2186182 CTCATCACGTAGGAG
63 CTCATCACGTAGGAG
2186197 TCGTGTCACC
Statistics
Matches: 177, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
131 101 0.57
132 5 0.03
133 4 0.02
134 65 0.37
135 2 0.01
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.22
Consensus pattern (133 bp):
ATCCCTAAAGATGGACAGTCATCCTCATCACATAGGAACAGTGTCATCCACTACCAGATCTCCTC
ATCACGTAGGAGCCACGTCAACCTTAGATAAACAGCCGTCCGCATCACACAAGAACCATAGTATC
ATC
Found at i:2192334 original size:37 final size:37
Alignment explanation
Indices: 2192293--2192364 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
2192283 ACAAATGGTC
* *
2192293 GTCTCACTAAAGACAATTTTTCTCAAAAATAAATTTT
1 GTCTCACTAAAGACAATTTCTCTCAAAAAAAAATTTT
** *
2192330 GTCTCACTTGAGACAATTTCTCTTAAAAAAAAATT
1 GTCTCACTAAAGACAATTTCTCTCAAAAAAAAATT
2192365 CATCTCGCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (37 bp):
GTCTCACTAAAGACAATTTCTCTCAAAAAAAAATTTT
Found at i:2192471 original size:30 final size:30
Alignment explanation
Indices: 2192437--2192494 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2192427 AACCAAAAAC
* *
2192437 CTTTGAGATTGTTTCTCTTGAAACAAAAGT
1 CTTTGAGATTGTTTCCCTTGAAAAAAAAGT
*
2192467 CTTTGAGTTTGTTTCCCTTGAAAAAAAA
1 CTTTGAGATTGTTTCCCTTGAAAAAAAA
2192495 TTGTCTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (30 bp):
CTTTGAGATTGTTTCCCTTGAAAAAAAAGT
Found at i:2192985 original size:134 final size:131
Alignment explanation
Indices: 2192643--2193002 Score: 344
Period size: 131 Copynumber: 2.7 Consensus size: 131
2192633 TTGAAACATT
* * * * *
2192643 ATCCCTAAAGATGAACAGCCATCCTCATCGCTTAGGAACTGTGTCATCCACTAACCAGATATCCC
1 ATCCCTAAAGATGAACAGTCATCCTCATCGCATAGGAACCGTGTCATCCACCAACCAGATATCCT
* * * * ** * *
2192708 CATAATGTAGGAGCCGCGTCAACCTTAGATAACCAGTCTTCCTCATCACATAGGAACCATGTTAT
66 CATCACGAAGGAGCCGTGTCAACCTTAGATAACCAACCATCCACATCACATAGGAACCATGTTAT
2192773 C
131 C
** ** ** ** * * *
2192774 ATCCCTAAAGATGGCCAGTTGTCCTCATTACATATAAACCGTGTCATCCCCCTACCATATATCCT
1 ATCCCTAAAGATGAACAGTCATCCTCATCGCATAGGAACCGTGTCATCCACCAACCAGATATCCT
* * * * * *
2192839 CATCGC-ATAGGAGACGTGCCAACCTTAGATAACCAACCATCCACATCGCGTAGGAACCGTGTTA
66 CATCACGA-AGGAGCCGTGTCAACCTTAGATAACCAACCATCCACATCACATAGGAACCATG-T-
2192903 TCATC
128 T-ATC
* * * * * *
2192908 ATCCCTAAAGATGATCAATCATCCTCATCGCGTAGGAACCATGTCATCCACCGACCAGATCTCCT
1 ATCCCTAAAGATGAACAGTCATCCTCATCGCATAGGAACCGTGTCATCCACCAACCAGATATCCT
*
2192973 CATCACGAAGGAGCCGTGTCACCCTTAGAT
66 CATCACGAAGGAGCCGTGTCAACCTTAGAT
2193003 GACTAGAACT
Statistics
Matches: 175, Mismatches: 49, Indels: 7
0.76 0.21 0.03
Matches are distributed among these distances:
131 95 0.54
132 1 0.01
133 1 0.01
134 77 0.44
135 1 0.01
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGAACAGTCATCCTCATCGCATAGGAACCGTGTCATCCACCAACCAGATATCCT
CATCACGAAGGAGCCGTGTCAACCTTAGATAACCAACCATCCACATCACATAGGAACCATGTTAT
C
Found at i:2193195 original size:3 final size:3
Alignment explanation
Indices: 2193187--2193234 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
2193177 TTAAAAATAT
* *
2193187 TTA TTA TTA TTA TT- TTA TTA TTA TAA TAA TTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
2193232 TTA
1 TTA
2193235 CATTTTACAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2194063 original size:14 final size:14
Alignment explanation
Indices: 2194042--2194091 Score: 93
Period size: 14 Copynumber: 3.6 Consensus size: 14
2194032 AAACAGCAGT
2194042 CGAC-GTCGAGTAG
1 CGACGGTCGAGTAG
2194055 CGACGGTCGAGTAG
1 CGACGGTCGAGTAG
2194069 CGACGGTCGAGTAG
1 CGACGGTCGAGTAG
2194083 CGACGGTCG
1 CGACGGTCG
2194092 GTTTATGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 4 0.11
14 32 0.89
ACGTcount: A:0.20, C:0.24, G:0.42, T:0.14
Consensus pattern (14 bp):
CGACGGTCGAGTAG
Found at i:2199789 original size:21 final size:20
Alignment explanation
Indices: 2199761--2199799 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2199751 CATTGCATGA
2199761 ATTTATGGCCTCAATAAACG
1 ATTTATGGCCTCAATAAACG
*
2199781 ATTTCATGGCCTGAATAAA
1 ATTT-ATGGCCTCAATAAA
2199800 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (20 bp):
ATTTATGGCCTCAATAAACG
Found at i:2215909 original size:22 final size:21
Alignment explanation
Indices: 2215883--2215989 Score: 90
Period size: 23 Copynumber: 4.8 Consensus size: 21
2215873 TTAGTGCAGA
2215883 GGGAATCGATACCCCCTTGAAG
1 GGGAA-CGATACCCCCTTGAAG
*
2215905 GGGAACTGATTCCCCCCTTGAAG
1 GGGAAC-GA-TACCCCCTTGAAG
*
2215928 GGGAACTGATTCCCCCTTTGAAG
1 GGGAAC-GATACCCCC-TTGAAG
* **
2215951 GGGAACCGATTCCCCC-ACACAG
1 GGGAA-CGATACCCCCTTGA-AG
2215973 GGGAATCGATACCCCCT
1 GGGAA-CGATACCCCCT
2215990 GAGGGTTCTG
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.03
22 29 0.40
23 41 0.56
24 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.19
Consensus pattern (21 bp):
GGGAACGATACCCCCTTGAAG
Found at i:2215924 original size:23 final size:23
Alignment explanation
Indices: 2215894--2215966 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
2215884 GGAATCGATA
2215894 CCCCCTTGAAGGGGAACTGATTC
1 CCCCCTTGAAGGGGAACTGATTC
2215917 CCCCCTTGAAGGGGAACTGATTC
1 CCCCCTTGAAGGGGAACTGATTC
* *
2215940 CCCCTTTGAAGGGGAACCGATTC
1 CCCCCTTGAAGGGGAACTGATTC
2215963 CCCC
1 CCCC
2215967 ACACAGGGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.21, C:0.34, G:0.25, T:0.21
Consensus pattern (23 bp):
CCCCCTTGAAGGGGAACTGATTC
Found at i:2215988 original size:45 final size:44
Alignment explanation
Indices: 2215883--2215989 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 44
2215873 TTAGTGCAGA
*
2215883 GGGAATCGATACCCCC-TTGAAGGGGAACTGATTCCCCCCTTGAAG
1 GGGAATCGATACCCCCTTTGAAGGGGAACCGATTCCCCCC-T-AAG
*
2215928 GGGAA-CTGATTCCCCCTTTGAAGGGGAACCGATTCCCCCAC-ACAG
1 GGGAATC-GATACCCCCTTTGAAGGGGAACCGATTCCCCC-CTA-AG
2215973 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
2215990 GAGGGTTCTG
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
44 2 0.04
45 29 0.54
46 22 0.41
47 1 0.02
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.19
Consensus pattern (44 bp):
GGGAATCGATACCCCCTTTGAAGGGGAACCGATTCCCCCCTAAG
Found at i:2217576 original size:18 final size:18
Alignment explanation
Indices: 2217555--2217595 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2217545 AGAACAGCAC
*
2217555 GAGGAACAAGCTCCACCA
1 GAGGAACAAGCACCACCA
*
2217573 GAGGAACAAGCACGACCA
1 GAGGAACAAGCACCACCA
2217591 GAGGA
1 GAGGA
2217596 TCAAATGCCT
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:0.41, C:0.27, G:0.29, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACCACCA
Found at i:2222224 original size:28 final size:28
Alignment explanation
Indices: 2222184--2222246 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
2222174 CAGGTTCGGA
2222184 TCGGGTCGGGTTTTTTTAAGTATGATAT
1 TCGGGTCGGGTTTTTTTAAGTATGATAT
*
2222212 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTATGATAT
*
2222240 TTGGGTC
1 TCGGGTC
2222247 AAGTTTGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.14, C:0.08, G:0.32, T:0.46
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTATGATAT
Found at i:2222791 original size:18 final size:17
Alignment explanation
Indices: 2222753--2222798 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2222743 TTTCAGATTT
2222753 AGATTCCAATTCCTAAC
1 AGATTCCAATTCCTAAC
* *
2222770 AGATTTCAATTCCTTCAC
1 AGATTCCAATTCC-TAAC
*
2222788 AGATTCTAATT
1 AGATTCCAATT
2222799 TCCTCAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.37
Consensus pattern (17 bp):
AGATTCCAATTCCTAAC
Found at i:2224374 original size:2 final size:2
Alignment explanation
Indices: 2224367--2224402 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2224357 ATTTTTAAAC
*
2224367 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2224403 TCTTTTCACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2225501 original size:19 final size:19
Alignment explanation
Indices: 2225477--2225513 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2225467 AGTTTTAAAA
*
2225477 CAAAATAAAATTTAGATAC
1 CAAAATAAAATATAGATAC
*
2225496 CAAAATAGAATATAGATA
1 CAAAATAAAATATAGATA
2225514 ATAGTTTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (19 bp):
CAAAATAAAATATAGATAC
Found at i:2225807 original size:121 final size:120
Alignment explanation
Indices: 2225648--2225893 Score: 404
Period size: 121 Copynumber: 2.0 Consensus size: 120
2225638 GGGAAAGGAG
* *
2225648 AATTTTACTCTCACGTGTATGGAACCCGTAACTTAAAAAAATGAAAAGTACTAACCGAAAGCTTT
1 AATTATACTCCCACGTGTATGGAACCCGTAACTTAAAAAAA--AAAAGTACTAACCGAAAGCTTT
*
2225713 TAACAATTTATTGTAAAGATTATTGAT-AAACAAATAATAACTTTGAACATAAGAGA
64 TAACAATTTATTGTAAAGATTATTGATAAAACAAATAAAAACTTTGAACATAAGAGA
* *
2225769 AATTATACTCCCACGTGTATTGAACCCGTAACTTAAAAAAAAAAATTACTAACCGAAAGCTTTTA
1 AATTATACTCCCACGTGTATGGAACCCGTAACTTAAAAAAAAAAAGTACTAACCGAAAGCTTTTA
*
2225834 ACAATTTATTGTAAAGATTATTGATAAAAATAAATAAAAACTTTGAACATAAGAGA
66 ACAATTTATTGTAAAGATTATTGAT-AAAACAAATAAAAACTTTGAACATAAGAGA
2225890 AATT
1 AATT
2225894 CAGTAATTTT
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
119 48 0.41
121 69 0.59
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (120 bp):
AATTATACTCCCACGTGTATGGAACCCGTAACTTAAAAAAAAAAAGTACTAACCGAAAGCTTTTA
ACAATTTATTGTAAAGATTATTGATAAAACAAATAAAAACTTTGAACATAAGAGA
Found at i:2226453 original size:1 final size:1
Alignment explanation
Indices: 2226449--2226473 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2226439 TCTATGCAAG
2226449 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
2226474 GTATTAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2227546 original size:18 final size:19
Alignment explanation
Indices: 2227512--2227547 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2227502 TTTTAGGGTA
*
2227512 TGTTGTAGTTCCATAAATT
1 TGTTGTAATTCCATAAATT
2227531 TGTTGTAATT-CATAAAT
1 TGTTGTAATTCCATAAAT
2227548 ATCGTTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (19 bp):
TGTTGTAATTCCATAAATT
Found at i:2227554 original size:19 final size:19
Alignment explanation
Indices: 2227513--2227554 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2227503 TTTAGGGTAT
* *
2227513 GTTGTAGTTCCATAAATTT
1 GTTGTAATTCCATAAATTC
2227532 GTTGTAATT-CATAAATATC
1 GTTGTAATTCCATAAAT-TC
2227551 GTTG
1 GTTG
2227555 ATTTTCTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.45
Consensus pattern (19 bp):
GTTGTAATTCCATAAATTC
Found at i:2230302 original size:16 final size:17
Alignment explanation
Indices: 2230275--2230310 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2230265 ATATGAGAAA
2230275 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
2230292 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
2230308 AAA
1 AAA
2230311 ATAACATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:2235477 original size:16 final size:16
Alignment explanation
Indices: 2235456--2235486 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2235446 CTTCTATGTA
2235456 ATCGTTTCATTTTTTC
1 ATCGTTTCATTTTTTC
2235472 ATCGTTTCATTTTTT
1 ATCGTTTCATTTTTT
2235487 TCCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.06, T:0.65
Consensus pattern (16 bp):
ATCGTTTCATTTTTTC
Found at i:2240361 original size:18 final size:19
Alignment explanation
Indices: 2240335--2240374 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2240325 TCGAAAGGAC
*
2240335 TGAACTAAATGATAAGA-T
1 TGAACTAAATAATAAGACT
*
2240353 TGAATTAAATAATAAGACT
1 TGAACTAAATAATAAGACT
2240372 TGA
1 TGA
2240375 TGGTAGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (19 bp):
TGAACTAAATAATAAGACT
Found at i:2241516 original size:24 final size:24
Alignment explanation
Indices: 2241489--2241576 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
2241479 TTCTATTATA
* *
2241489 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGAACTGGATTCTGATCGG
* *
2241513 ATACTTGAACTGGATTCTGATTGA
1 ATACTTGAACTGGATTCTGATCGG
* *
2241537 ATACTTGAACTGGATTTTGATCTG
1 ATACTTGAACTGGATTCTGATCGG
*
2241561 ATACTTGACCTGGATT
1 ATACTTGAACTGGATT
2241577 ATTTTATGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (24 bp):
ATACTTGAACTGGATTCTGATCGG
Found at i:2241791 original size:2 final size:2
Alignment explanation
Indices: 2241784--2241810 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2241774 CGGATGGGGG
2241784 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2241811 GTTTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2248294 original size:47 final size:46
Alignment explanation
Indices: 2248225--2248316 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 46
2248215 ATAACATCTC
*
2248225 TGAAAATATATTAAAGTTACTTAAACCCCCACCAAAATCCATATTTT
1 TGAAAATAGATTAAAGTTACTTAAACCCCCA-CAAAATCCATATTTT
2248272 TGAAAATAGATTAAAGTTACTTAAACCCCCACAAAATCCATATTT
1 TGAAAATAGATTAAAGTTACTTAAACCCCCACAAAATCCATATTT
2248317 GGTTTTCACA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 14 0.32
47 30 0.68
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.30
Consensus pattern (46 bp):
TGAAAATAGATTAAAGTTACTTAAACCCCCACAAAATCCATATTTT
Found at i:2249277 original size:15 final size:15
Alignment explanation
Indices: 2249259--2249288 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2249249 TAAAGCAACA
2249259 TTTAAAAAATATAAT
1 TTTAAAAAATATAAT
2249274 TTTAAAAAATATAAT
1 TTTAAAAAATATAAT
2249289 CATAATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTAAAAAATATAAT
Found at i:2251389 original size:36 final size:35
Alignment explanation
Indices: 2251307--2251447 Score: 151
Period size: 35 Copynumber: 4.0 Consensus size: 35
2251297 CTTAAATCTG
* * * *
2251307 TAAGGAATTACCAGTTCGA-CCAGTCTGAACATATA
1 TAAGGAATTACCAGTTTGATCGAG-CTGAACCTACA
* * * *
2251342 TAAGGAATTACCAATTTAATCGAGCTGAACCTGCCG
1 TAAGGAATTACCAGTTTGATCGAGCTGAACCT-ACA
*
2251378 TAAGGAATTACCAGTTTGATCG-GTCTGAACCTATA
1 TAAGGAATTACCAGTTTGATCGAG-CTGAACCTACA
*
2251413 TAAGGAATTATCAGTTTGATCGAGCTGAACCTACA
1 TAAGGAATTACCAGTTTGATCGAGCTGAACCTACA
2251448 GAGACTTCAT
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
35 55 0.63
36 32 0.37
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (35 bp):
TAAGGAATTACCAGTTTGATCGAGCTGAACCTACA
Found at i:2251422 original size:71 final size:71
Alignment explanation
Indices: 2251306--2251444 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 71
2251296 CCTTAAATCT
2251306 GTAAGGAATTACCAGTTCGACCAGTCTGAACATATATAAGGAATTACCAATTTAATCGAGCTGAA
1 GTAAGGAATTACCAGTTCGACCAGTCTGAACATATATAAGGAATTACCAATTTAATCGAGCTGAA
2251371 CCTGCC
66 CCTGCC
* * * * * * *
2251377 GTAAGGAATTACCAGTTTGATCGGTCTGAACCTATATAAGGAATTATCAGTTTGATCGAGCTGAA
1 GTAAGGAATTACCAGTTCGACCAGTCTGAACATATATAAGGAATTACCAATTTAATCGAGCTGAA
2251442 CCT
66 CCT
2251445 ACAGAGACTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (71 bp):
GTAAGGAATTACCAGTTCGACCAGTCTGAACATATATAAGGAATTACCAATTTAATCGAGCTGAA
CCTGCC
Found at i:2253114 original size:18 final size:18
Alignment explanation
Indices: 2253091--2253126 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2253081 ACGATCAGGC
2253091 CGGTCAAAGTCAACAGTT
1 CGGTCAAAGTCAACAGTT
*
2253109 CGGTCAAAGTTAACAGTT
1 CGGTCAAAGTCAACAGTT
2253127 AGACCAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (18 bp):
CGGTCAAAGTCAACAGTT
Found at i:2253215 original size:20 final size:20
Alignment explanation
Indices: 2253161--2253217 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
2253151 AGTCAATGGG
2253161 TCAGGTCGGGTTGACTCAGT
1 TCAGGTCGGGTTGACTCAGT
* *
2253181 TCAAGTCGAGTTGACTCAGT
1 TCAGGTCGGGTTGACTCAGT
** *
2253201 TTGGGTCGGGCTGACTC
1 TCAGGTCGGGTTGACTC
2253218 GATTCGGACC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.16, C:0.21, G:0.33, T:0.30
Consensus pattern (20 bp):
TCAGGTCGGGTTGACTCAGT
Found at i:2255235 original size:22 final size:22
Alignment explanation
Indices: 2255156--2255235 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
2255146 TAAATCATGG
* * * *
2255156 AAGTACCTCAGCACTAATACTA
1 AAGTGCCTTAGCACTGATACAA
* *
2255178 AAGTGCCTTAGAATTGATACAA
1 AAGTGCCTTAGCACTGATACAA
** *
2255200 AAGTGTGTTCGCACTGATACAA
1 AAGTGCCTTAGCACTGATACAA
*
2255222 AAGTGCCATAGCAC
1 AAGTGCCTTAGCAC
2255236 ATGAGAAACG
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGATACAA
Found at i:2260733 original size:137 final size:137
Alignment explanation
Indices: 2260477--2260736 Score: 335
Period size: 137 Copynumber: 1.9 Consensus size: 137
2260467 TACAATGTAA
* * * * * * *
2260477 ATGATGGTTATCAATTGATTTTGTTTAATTCATATGTTGCATATTCGTATCTGTACTATGTGTAC
1 ATGAAGGTTATCAATCGATTTTGTTTAATGCATATGTTACATATTCGTATCAGTACTATATATAC
* * * *
2260542 TTTTGACACTAGATGTGGAACCATGGTATTCATAATAAGTTTGTGAATTACCATTTTGACATATA
66 TTTCGACACTAGATGTGCAACCATAGAATTCATAATAAGTTTGTGAATTACCATTTTGACATATA
2260607 TTTGTGT
131 TTTGTGT
* * *
2260614 ATGAAGGTTATCAATCGATTTTGTTTAATGCATATTTTACATTTTCGTTTCAGTACTATATATAC
1 ATGAAGGTTATCAATCGATTTTGTTTAATGCATATGTTACATATTCGTATCAGTACTATATATAC
* **
2260679 TTTCGGCACTATG-TGTGCTTCCATAGAATTCATAATAAGTTTGTGAAATT-CCATTTTG
66 TTTCGACACTA-GATGTGCAACCATAGAATTCATAATAAGTTTGTG-AATTACCATTTTG
2260737 GCACTTAAGT
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
137 99 0.95
138 5 0.05
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.44
Consensus pattern (137 bp):
ATGAAGGTTATCAATCGATTTTGTTTAATGCATATGTTACATATTCGTATCAGTACTATATATAC
TTTCGACACTAGATGTGCAACCATAGAATTCATAATAAGTTTGTGAATTACCATTTTGACATATA
TTTGTGT
Found at i:2267745 original size:137 final size:136
Alignment explanation
Indices: 2267584--2267841 Score: 360
Period size: 137 Copynumber: 1.9 Consensus size: 136
2267574 TGTATATGAT
* * *
2267584 GGTTATCAATCGATTTTGTTTAATGCATATGTTGCATTTTTT-TCTCAGTACTATGTGTAATTTC
1 GGTTATCAATCGATTTTGTTTAATGCATATGTTG--TTTTTTCTATCAATACTATATGTAATTTC
* * *
2267648 AGCACTA-GATGTGCAACCATGGTATTCATAATGAGTTTGTG-AATTACCATTTTGACATACATT
64 AGCACTATG-TGTGCAACCATGGAATTCATAATAAGTTTGTGAAATT-CCATTTCGACATACATT
2267711 TGTGAATTAA
127 TGTGAATTAA
* * *
2267721 GGTTATCAATCGATTTTGTTTAATGCATATGTTGTTTTTTCGTATCAATATTATATGTACTTTCG
1 GGTTATCAATCGATTTTGTTTAATGCATATGTTGTTTTTTC-TATCAATACTATATGTAATTTCA
*
2267786 GCACTATGTGTGCATCCATGGAATTCATAATAAGTTTGTGAAATTCCATTTCGACA
65 GCACTATGTGTGCAACCATGGAATTCATAATAAGTTTGTGAAATTCCATTTCGACA
2267842 CTTAGGTGCA
Statistics
Matches: 107, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
135 6 0.06
137 96 0.90
138 5 0.05
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (136 bp):
GGTTATCAATCGATTTTGTTTAATGCATATGTTGTTTTTTCTATCAATACTATATGTAATTTCAG
CACTATGTGTGCAACCATGGAATTCATAATAAGTTTGTGAAATTCCATTTCGACATACATTTGTG
AATTAA
Found at i:2270729 original size:58 final size:58
Alignment explanation
Indices: 2270649--2271269 Score: 848
Period size: 58 Copynumber: 10.7 Consensus size: 58
2270639 TGACAATAAA
* * * * *
2270649 TGTGCAAAAAAGTTAAGAAATTCATATTGAGTGTATGAATTTCTGTATTGAGCATTTCG
1 TGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCG
* * *
2270708 TGCGCAAAATGTTAAGAAATTCATAC-AATGTGTATGAATTTCCGTATTGGACACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAA-GTGTATGAATTTCTGTATTGGGCACTTCG
* * *
2270766 TGTGCAAAATGTTAAGATATTCATACTAAGTGTATGAGTTTCCGTATTGGGCACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCG
* *
2270824 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGACACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCG
* * *
2270882 TGTGCAAAATGTTAAGAAACTCATACTAAGTGTATGGATTTCCT-TATTGAGCACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTT-CTGTATTGGGCACTTCG
* * *
2270940 TGTTCAAAATGTTAAGAAATTTATACTAAGTGTATGAATTTCTGTATTGGGCACTTCA
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCG
*
2270998 AGTGC--AATGTTAAGAAATTCATACTAAGTGTATGAATTT-TCGTATTGGGCACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGCACTTCG
* * *
2271054 TGT-CAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTATATTGGACACTTCA
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCG
* *
2271111 TGTGCAAAATGTTAAGAAATTCATACTGAGTGTATGAATTTATGTATTGGGCACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCG
*
2271169 TGTGCAAAAATGTTAAGAAATTCATAC-AATGTGTATGAATTT-TCGTATTGGGCACTTTG
1 TGTGC-AAAATGTTAAGAAATTCATACTAA-GTGTATGAATTTCT-GTATTGGGCACTTCG
*
2271228 TGTGC-AAATCGTTAAGAGA-TCTATACTAAGTGTATGAATTTC
1 TGTGCAAAAT-GTTAAGAAATTC-ATACTAAGTGTATGAATTTC
2271270 CATATGGAAA
Statistics
Matches: 504, Mismatches: 42, Indels: 32
0.87 0.07 0.06
Matches are distributed among these distances:
55 2 0.00
56 49 0.10
57 58 0.12
58 334 0.66
59 61 0.12
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (58 bp):
TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCG
Found at i:2271830 original size:2 final size:2
Alignment explanation
Indices: 2271823--2271907 Score: 97
Period size: 2 Copynumber: 43.5 Consensus size: 2
2271813 AGGAATTGTT
* *
2271823 TA TA TA TA TA TA TA TA TA TA TCA -A T- TGA -A T- TG TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA TA TA TA TA TA TA
*
2271863 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2271905 TA T
1 TA T
2271908 GATGTGACAT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
1 4 0.05
2 68 0.93
3 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2277994 original size:58 final size:58
Alignment explanation
Indices: 2277924--2278602 Score: 1028
Period size: 58 Copynumber: 11.7 Consensus size: 58
2277914 TGGCACTAAA
** *
2277924 TGTGCAAAAATGTTAAGAAATTCGCACTAAGTGTATGAATTTTCGTATTGGGCACTTCG
1 TGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
* * * *
2277983 TGTGGAAAATGTTAAGAAATTCATACTAAGTGTATAAATTTCCGTATTGGGTACTTCA
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
* * *
2278041 TGCGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGTCACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
*
2278099 TATGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
* * * * *
2278157 TGTGC--AATGTTAAGAAATTCATACTAAGTGTAAGAATTTCTGTATTGGACAGTTTG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
*
2278213 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGCCACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
* *
2278271 TGTGCAAAATGTTAAGAAATTCATACTAAGTCTATGAATTTCCGTATTGGGCACTTCA
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
* * * *
2278329 TGTGCAAAATGTTAAGAAATTTATACTAAGTGTATGAATTTTCATATTGGGAACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
2278387 TGT-CAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
2278444 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTA-GAAATTTCCGTATTGGGCACTTCG
1 TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATG-AATTTCCGTATTGGGCACTTCG
* * * *
2278502 TGTGCAAAAATGTTAAGAAACT-ATACTAAGTGTATGAATTTTCGTATTGGACACTTTG
1 TGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
*
2278560 TGTGC-AAATCGTTAAGAGATTCATACTAAGTGTATGAATTTCC
1 TGTGCAAAAT-GTTAAGAAATTCATACTAAGTGTATGAATTTCC
2278603 ATATGGGAAA
Statistics
Matches: 563, Mismatches: 49, Indels: 17
0.90 0.08 0.03
Matches are distributed among these distances:
56 55 0.10
57 63 0.11
58 425 0.75
59 20 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (58 bp):
TGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
Found at i:2278337 original size:230 final size:230
Alignment explanation
Indices: 2277931--2278611 Score: 1032
Period size: 230 Copynumber: 3.0 Consensus size: 230
2277921 AAATGTGCAA
** *
2277931 AAATGTTAAGAAATTCGCACTAAGTGTATGAATTT-TCGTATTGGGCACTTCGTGTGGAAAATGT
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGCACTTCGTGTGCAAAATGT
* * * *
2277995 TAAGAAATTCATACTAAGTGTATAAATTTCCGTATTGGGTACTTCATGCGCAAAATGTTAAGAAA
65 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAAATGTTAAGAAA
* *
2278060 TTCATACTAAGTGTATGAATTTTCGTATTGGTCACTTCGTATGCAAAATGTTAAGAAATTCATAC
130 TTCATACTAAGTGTATGAATTTTCGTATTGGACACTTCGTGTGCAAAATGTTAAGAAATTCATAC
* *
2278125 TAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGC
195 TAAGTGTATGAATTTCCATATTGGGAACTTCGTGT-C
* * * *
2278162 -AATGTTAAGAAATTCATACTAAGTGTAAGAATTTCTGTATTGGACAGTTTGTGTGCAAAATGTT
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTGCAAAATGTT
*
2278226 AAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGCCACTTCGTGTGCAAAATGTTAAGAAAT
66 AAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAAATGTTAAGAAAT
* * * * *
2278291 TCATACTAAGTCTATGAATTTCCGTATTGGGCACTTCATGTGCAAAATGTTAAGAAATTTATACT
131 TCATACTAAGTGTATGAATTTTCGTATTGGACACTTCGTGTGCAAAATGTTAAGAAATTCATACT
*
2278356 AAGTGTATGAATTTTCATATTGGGAACTTCGTGTC
196 AAGTGTATGAATTTCCATATTGGGAACTTCGTGTC
*
2278391 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAAATGT
1 -AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTGCAAAATGT
2278456 TAAGAAATTCATACTAAGTGTA-GAAATTTCCGTATTGGGCACTTCGTGTGCAAAAATGTTAAGA
65 TAAGAAATTCATACTAAGTGTATG-AATTTCCGTATTGGGCACTTCGTGTGC-AAAATGTTAAGA
* * *
2278520 AACT-ATACTAAGTGTATGAATTTTCGTATTGGACACTTTGTGTGC-AAATCGTTAAGAGATTCA
128 AATTCATACTAAGTGTATGAATTTTCGTATTGGACACTTCGTGTGCAAAAT-GTTAAGAAATTCA
2278583 TACTAAGTGTATGAATTTCCATA-TGGGAA
192 TACTAAGTGTATGAATTTCCATATTGGGAA
2278612 ATATGTGTAT
Statistics
Matches: 408, Mismatches: 36, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
229 1 0.00
230 216 0.53
231 176 0.43
232 15 0.04
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (230 bp):
AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTGCAAAATGTT
AAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTGTGCAAAATGTTAAGAAAT
TCATACTAAGTGTATGAATTTTCGTATTGGACACTTCGTGTGCAAAATGTTAAGAAATTCATACT
AAGTGTATGAATTTCCATATTGGGAACTTCGTGTC
Found at i:2278938 original size:4 final size:4
Alignment explanation
Indices: 2278919--2279018 Score: 128
Period size: 4 Copynumber: 25.0 Consensus size: 4
2278909 ACTGTTTAAA
* * * *
2278919 ATAT ATAT AAAA ATAT ATAT ATAA ATAA ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
2278967 ATAA ATAT ATAT ATAA ATAA ATAT ATAT ATAT ATAT ATAT GTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
2279015 ATAT
1 ATAT
2279019 GATTTGACAC
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 84 1.00
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:2284203 original size:26 final size:26
Alignment explanation
Indices: 2284152--2284203 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
2284142 ATATAATCAT
*
2284152 AAATTATATTTTAAAACTAAATTATTA
1 AAATTATATTTTAAAAC-AAAATATTA
*
2284179 AAATTTTATTTTAAATA-AAAATATT
1 AAATTATATTTTAAA-ACAAAATATT
2284204 TTTATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 14 0.64
28 1 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATTATATTTTAAAACAAAATATTA
Found at i:2285590 original size:21 final size:22
Alignment explanation
Indices: 2285554--2285594 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2285544 TTAAAAATTA
2285554 TAAAGGTAGTACCGATACTCGT
1 TAAAGGTAGTACCGATACTCGT
*
2285576 TAAAGG-AGTATCGATACTC
1 TAAAGGTAGTACCGATACTC
2285595 CCTGTCTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (22 bp):
TAAAGGTAGTACCGATACTCGT
Found at i:2289583 original size:21 final size:22
Alignment explanation
Indices: 2289542--2289583 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2289532 TCAAACCATT
*
2289542 TAAATTGTAAACAATTTATAAA
1 TAAATTGTAAACAATTCATAAA
*
2289564 TAAATTGTACA-AATTCATAA
1 TAAATTGTAAACAATTCATAA
2289584 TTCATTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
TAAATTGTAAACAATTCATAAA
Found at i:2290309 original size:60 final size:60
Alignment explanation
Indices: 2290232--2290418 Score: 243
Period size: 60 Copynumber: 3.1 Consensus size: 60
2290222 CGTAGTGTAG
* * * *
2290232 GAGCCACTTGAGAGGAGTGCCCCCAAGTCCATAAAGACTTACCCAATGCACAAAGTAAAT
1 GAGCCACCTGAGGGGAGTGCCCCCAAGTCCATAAGGACTTACCCAATGCACAAAGAAAAT
* * * *
2290292 GAGCCACCTGAGGGGAGT-CCCCCAGGTTCATAAGGGCTTACCCAATACACAAAGAAAAT
1 GAGCCACCTGAGGGGAGTGCCCCCAAGTCCATAAGGACTTACCCAATGCACAAAGAAAAT
* * *
2290351 GAGCCACTTGAGGGGAATGCCCCC-AGTTCCATAAGGACTTACCCAATGCATAAAGAAAAT
1 GAGCCACCTGAGGGGAGTGCCCCCAAG-TCCATAAGGACTTACCCAATGCACAAAGAAAAT
*
2290411 GACCCACC
1 GAGCCACC
2290419 CTAAAAAGTG
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
59 52 0.48
60 56 0.52
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (60 bp):
GAGCCACCTGAGGGGAGTGCCCCCAAGTCCATAAGGACTTACCCAATGCACAAAGAAAAT
Found at i:2293572 original size:11 final size:11
Alignment explanation
Indices: 2293544--2293577 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2293534 ATGTATAGTA
2293544 GTATAAAACATC
1 GTATAAAA-ATC
*
2293556 GTATAAAAATT
1 GTATAAAAATC
2293567 GTATAAAAATC
1 GTATAAAAATC
2293578 ATTTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (11 bp):
GTATAAAAATC
Found at i:2296048 original size:30 final size:30
Alignment explanation
Indices: 2296014--2296078 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
2296004 AAATTACCAC
* * *
2296014 TTTGGTCC-TTTAACTTTCCCAATTTTTTAT
1 TTTGGTCCATATAACTTT-CAAATTTTATAT
2296044 TTTGG-CCATATAACTTTCAAATTTTATAT
1 TTTGGTCCATATAACTTTCAAATTTTATAT
2296073 TTTGGT
1 TTTGGT
2296079 ACTTGTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.22, C:0.15, G:0.09, T:0.54
Consensus pattern (30 bp):
TTTGGTCCATATAACTTTCAAATTTTATAT
Found at i:2297912 original size:65 final size:65
Alignment explanation
Indices: 2297861--2297986 Score: 182
Period size: 65 Copynumber: 1.9 Consensus size: 65
2297851 CATTAATTGC
* *
2297861 ATTCGATGTTTCAAAACAGTCATGAGTGCATCGATGCATGG-TCTGTGCATCGGTAAACAAAATC
1 ATTCGATGTTTCAAAACAGTCAAGAGTGCATCGATGCATGGCT-TGTGCATCGATAAACAAAATC
2297925 A
65 A
* * * *
2297926 ATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTTGTGCATCGGTACACAAA
1 ATTCGATGTTTCAAAACAGTCAAGAGTGCATCGATGCATGGCTTGTGCATCGATAAACAAA
2297987 CTGCATTCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
65 55 0.98
66 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (65 bp):
ATTCGATGTTTCAAAACAGTCAAGAGTGCATCGATGCATGGCTTGTGCATCGATAAACAAAATCA
Found at i:2298364 original size:12 final size:13
Alignment explanation
Indices: 2298334--2298363 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2298324 TTTAATATTT
2298334 TTTTTGAAAATAA
1 TTTTTGAAAATAA
*
2298347 TTTTTGAAAGTAA
1 TTTTTGAAAATAA
2298360 TTTT
1 TTTT
2298364 GTAAACTTAC
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:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TTTTTGAAAATAA
Found at i:2300043 original size:22 final size:20
Alignment explanation
Indices: 2300006--2300045 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
2299996 TTGTTTATCC
*
2300006 TATTTTCCTAATTTATTTAT
1 TATTTTCCTAAATTATTTAT
2300026 TATTTTCCTTTAAATTATTT
1 TATTTTCC--TAAATTATTT
2300046 TCTTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTTTCCTAAATTATTTAT
Found at i:2300052 original size:14 final size:15
Alignment explanation
Indices: 2300024--2300052 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2300014 TAATTTATTT
2300024 ATTATTTTCCTTTAA
1 ATTATTTTCCTTTAA
2300039 ATTATTTT-CTTTAA
1 ATTATTTTCCTTTAA
2300053 TTAGAACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATTTTCCTTTAA
Found at i:2310634 original size:42 final size:41
Alignment explanation
Indices: 2310552--2310668 Score: 119
Period size: 42 Copynumber: 2.8 Consensus size: 41
2310542 TAAGAAAACA
** * * *
2310552 AAATCCTTCAGGTCA-TAGTAAGTCATTCGATCGTGATGATT
1 AAATCCTTTGGGTCACTA-TAAGTCTTTCGAGCATGATGATT
*
2310593 AAATCCTTTGGGTCACTACTAAGTCTTTCGAGCATGGTGATT
1 AAATCCTTTGGGTCACTA-TAAGTCTTTCGAGCATGATGATT
* * *
2310635 AAGTCCTTTGGGCCATCTATAAGACTTTCGAGCA
1 AAATCCTTTGGGTCA-CTATAAGTCTTTCGAGCA
2310669 AGATCTTTGA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 13 0.20
42 48 0.75
43 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (41 bp):
AAATCCTTTGGGTCACTATAAGTCTTTCGAGCATGATGATT
Found at i:2310994 original size:44 final size:44
Alignment explanation
Indices: 2310946--2311108 Score: 191
Period size: 44 Copynumber: 3.7 Consensus size: 44
2310936 TTCGCTCGAG
* * *
2310946 ACAGAGAGAGTTGTGTCAACAACAACATTTCACTCGATTCCATA
1 ACAGAGGGAGTTGGGTCAACATCAACATTTCACTCGATTCCATA
* * * * * *
2310990 ACAGAGGGAATTGGGTTAATATCAATATTTCACTCGATTTCAAA
1 ACAGAGGGAGTTGGGTCAACATCAACATTTCACTCGATTCCATA
* * *
2311034 ACAGAGTGAGTTGGGTCAACATCAACATTGCACTCAATTCCATA
1 ACAGAGGGAGTTGGGTCAACATCAACATTTCACTCGATTCCATA
* * *
2311078 ACAAAGGGAGTTGGTTCAATATCAACATTTC
1 ACAGAGGGAGTTGGGTCAACATCAACATTTC
2311109 GCTTGTTTTC
Statistics
Matches: 96, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 96 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (44 bp):
ACAGAGGGAGTTGGGTCAACATCAACATTTCACTCGATTCCATA
Found at i:2311119 original size:88 final size:88
Alignment explanation
Indices: 2310946--2311108 Score: 238
Period size: 88 Copynumber: 1.9 Consensus size: 88
2310936 TTCGCTCGAG
* * * *
2310946 ACAGAGAGAGTTGTGTCAACAACAACATTTCACTCGATTCCATAACAGAGGGAATTGGGTTAATA
1 ACAGAGAGAGTTGGGTCAACAACAACATTGCACTCAATTCCATAACAAAGGGAATTGGGTTAATA
*
2311011 TCAATATTTCACTCGATTTCAAA
66 TCAACATTTCACTCGATTTCAAA
* * *
2311034 ACAGAGTGAGTTGGGTCAACATCAACATTGCACTCAATTCCATAACAAAGGGAGTT-GGTTCAAT
1 ACAGAGAGAGTTGGGTCAACAACAACATTGCACTCAATTCCATAACAAAGGGAATTGGGTT-AAT
2311098 ATCAACATTTC
65 ATCAACATTTC
2311109 GCTTGTTTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
87 4 0.06
88 62 0.94
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (88 bp):
ACAGAGAGAGTTGGGTCAACAACAACATTGCACTCAATTCCATAACAAAGGGAATTGGGTTAATA
TCAACATTTCACTCGATTTCAAA
Found at i:2311142 original size:88 final size:88
Alignment explanation
Indices: 2310962--2311145 Score: 194
Period size: 88 Copynumber: 2.1 Consensus size: 88
2310952 AGAGTTGTGT
* * * * *
2310962 CAACAACAACATTTCACTCGATTCCATAACAGAGGGAATTGGGTTAATATCAATATTTCACTCGA
1 CAACATCAACATTGCACTCAATTCCATAACAAAGGGAATTGGGTTAATATCAACATTTCACTCGA
* ***
2311027 TTTCAAAACAGAGTGAGTTGGGT
66 TTTCAAAACAGAGTAAGTTGAAA
* * *
2311050 CAACATCAACATTGCACTCAATTCCATAACAAAGGGAGTT-GGTTCAATATCAACATTTCGCTTG
1 CAACATCAACATTGCACTCAATTCCATAACAAAGGGAATTGGGTT-AATATCAACATTTCACTCG
* *
2311114 TTTTCATCACACA-AG-AAGTTGAAA
65 ATTTCA--AAACAGAGTAAGTTGAAA
2311138 CAACATCA
1 CAACATCA
2311146 GTATTACTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
87 4 0.05
88 69 0.87
89 2 0.03
90 4 0.05
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (88 bp):
CAACATCAACATTGCACTCAATTCCATAACAAAGGGAATTGGGTTAATATCAACATTTCACTCGA
TTTCAAAACAGAGTAAGTTGAAA
Found at i:2313971 original size:20 final size:20
Alignment explanation
Indices: 2313946--2313983 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2313936 CTGATCATTA
*
2313946 ATATGATGTTATCATGAACT
1 ATATGATATTATCATGAACT
2313966 ATATGATATTATCATGAA
1 ATATGATATTATCATGAA
2313984 TGATTTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (20 bp):
ATATGATATTATCATGAACT
Found at i:2315161 original size:124 final size:124
Alignment explanation
Indices: 2315009--2315259 Score: 502
Period size: 124 Copynumber: 2.0 Consensus size: 124
2314999 ATTCGAAACA
2315009 TTTCATAACCCAAAATAGGTAAATTTCTAGTTCTTTCACGAATTACATATTTATAACATTTATTA
1 TTTCATAACCCAAAATAGGTAAATTTCTAGTTCTTTCACGAATTACATATTTATAACATTTATTA
2315074 TAAAATAAGTAATCAGAGAAAATCAAAATATAATATTTCAACTTCTCTTTAAAATTTGG
66 TAAAATAAGTAATCAGAGAAAATCAAAATATAATATTTCAACTTCTCTTTAAAATTTGG
2315133 TTTCATAACCCAAAATAGGTAAATTTCTAGTTCTTTCACGAATTACATATTTATAACATTTATTA
1 TTTCATAACCCAAAATAGGTAAATTTCTAGTTCTTTCACGAATTACATATTTATAACATTTATTA
2315198 TAAAATAAGTAATCAGAGAAAATCAAAATATAATATTTCAACTTCTCTTTAAAATTTGG
66 TAAAATAAGTAATCAGAGAAAATCAAAATATAATATTTCAACTTCTCTTTAAAATTTGG
2315257 TTT
1 TTT
2315260 GGCAATAACA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 127 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (124 bp):
TTTCATAACCCAAAATAGGTAAATTTCTAGTTCTTTCACGAATTACATATTTATAACATTTATTA
TAAAATAAGTAATCAGAGAAAATCAAAATATAATATTTCAACTTCTCTTTAAAATTTGG
Found at i:2315972 original size:58 final size:58
Alignment explanation
Indices: 2315864--2316100 Score: 275
Period size: 58 Copynumber: 4.1 Consensus size: 58
2315854 CTAACCCGAG
* * * * *
2315864 TATGACACGTAAGGTTGTACCCACCATGTGCACTAGTTATACTTTAGTGCAGTCCCAAA
1 TATGACACATAAGGTCGTGCCCA-CATATGCACTAGTTATACTTTAGTGCAATCCCAAA
* * *
2315923 TATGATACATAAGGTCGTGCCCAC-TAATGCACTAGTCATACTTTAGTGCAATCCCGAA
1 TATGACACATAAGGTCGTGCCCACAT-ATGCACTAGTTATACTTTAGTGCAATCCCAAA
* * ***
2315981 TATAACACATAAGGTC-TGCCCAACATATGCAATAGTTATACTTTAGTGCAAT-CTTGA
1 TATGACACATAAGGTCGTGCCC-ACATATGCACTAGTTATACTTTAGTGCAATCCCAAA
*
2316038 -ATGACACATAAGGTCGTGCCAACCATATGCACTAGTTATACTTTAGTGCAATCCCCAAA
1 TATGACACATAAGGTCGTGCCCA-CATATGCACTAGTTATACTTTAGTGCAAT-CCCAAA
2316097 TATG
1 TATG
2316101 TAGCCTGCTG
Statistics
Matches: 149, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
56 15 0.10
57 40 0.27
58 69 0.46
59 22 0.15
60 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (58 bp):
TATGACACATAAGGTCGTGCCCACATATGCACTAGTTATACTTTAGTGCAATCCCAAA
Found at i:2318954 original size:54 final size:54
Alignment explanation
Indices: 2318872--2318980 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
2318862 GAACACATTA
2318872 GTAACGTGGATAAAAGTGGTTCATGGAAGCATTGAAAGTGGATTGGGAGCCTTT
1 GTAACGTGGATAAAAGTGGTTCATGGAAGCATTGAAAGTGGATTGGGAGCCTTT
2318926 GTAACGTGGATAAAAGTGGTTCATGGAAGCATTGAAAGTGGATTGGGAGCCTTT
1 GTAACGTGGATAAAAGTGGTTCATGGAAGCATTGAAAGTGGATTGGGAGCCTTT
2318980 G
1 G
2318981 CTTAATCGGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.28
Consensus pattern (54 bp):
GTAACGTGGATAAAAGTGGTTCATGGAAGCATTGAAAGTGGATTGGGAGCCTTT
Found at i:2319140 original size:17 final size:18
Alignment explanation
Indices: 2319102--2319145 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
2319092 CCCAATACAT
2319102 AACCCATTTTACAATAAA
1 AACCCATTTTACAATAAA
2319120 AACCCATTTTACAAT-AA
1 AACCCATTTTACAATAAA
2319137 AACCCATTT
1 AACCCATTT
2319146 ATCCATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (18 bp):
AACCCATTTTACAATAAA
Found at i:2321967 original size:13 final size:13
Alignment explanation
Indices: 2321949--2321985 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2321939 TGAGTCCTAA
2321949 CATTTCATAAAAT
1 CATTTCATAAAAT
2321962 CATTTCATAAAAT
1 CATTTCATAAAAT
2321975 CATTTCA-AAAA
1 CATTTCATAAAA
2321986 CTCCATCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (13 bp):
CATTTCATAAAAT
Found at i:2327714 original size:20 final size:20
Alignment explanation
Indices: 2327664--2327715 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
2327654 GTCCTCAGGG
2327664 TTGTATATTGGGCTATTGTCTA
1 TTGTATA-T-GGCTATTGTCTA
*
2327686 TTGTTTATGGCTATTGTCTA
1 TTGTATATGGCTATTGTCTA
2327706 -TGCTATATGG
1 TTG-TATATGG
2327716 TTTATTGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 18 0.67
21 1 0.04
22 6 0.22
ACGTcount: A:0.17, C:0.10, G:0.23, T:0.50
Consensus pattern (20 bp):
TTGTATATGGCTATTGTCTA
Found at i:2327835 original size:44 final size:45
Alignment explanation
Indices: 2327744--2327919 Score: 284
Period size: 44 Copynumber: 4.0 Consensus size: 45
2327734 GTAAGCATGC
*
2327744 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTGTATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTGTATTGGTA
* *
2327789 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTCTATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTGTATTGGTA
2327833 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTGTATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTGTATTGGTA
* * *
2327877 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTGG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTGTATTGG
2327920 ATATGATGGT
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 82 0.67
45 40 0.33
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTGTATTGGTA
Found at i:2337115 original size:11 final size:10
Alignment explanation
Indices: 2337094--2337150 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
2337084 ACTTTTTTTA
*
2337094 AAAAATAAAT
1 AAAAATGAAT
2337104 AAAAATGCAAT
1 AAAAATG-AAT
2337115 -AAAATGAATT
1 AAAAATGAA-T
2337125 AAAAATGAAT
1 AAAAATGAAT
* *
2337135 AAAATTCAAT
1 AAAAATGAAT
2337145 AAAAAT
1 AAAAAT
2337151 ATAATGTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.68
11 11 0.28
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (10 bp):
AAAAATGAAT
Found at i:2337150 original size:20 final size:20
Alignment explanation
Indices: 2337095--2337150 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2337085 CTTTTTTTAA
*
2337095 AAAATAAATAAAAATGCAAT
1 AAAATCAATAAAAATGCAAT
*
2337115 AAAATGAATTAAAAATG-AAT
1 AAAATCAA-TAAAAATGCAAT
2337135 AAAATTCAATAAAAAT
1 AAAA-TCAATAAAAAT
2337151 ATAATGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAATCAATAAAAATGCAAT
Found at i:2338126 original size:10 final size:10
Alignment explanation
Indices: 2338101--2338151 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
2338091 TTTACATTAT
*
2338101 ATTTTTATTG
1 ATTTTTATTC
*
2338111 AATTTTATTC
1 ATTTTTATTC
2338121 ATTTTTAATT-
1 ATTTTT-ATTC
2338131 ATTTTGTATTGC
1 ATTTT-TATT-C
2338143 ATTTTTATT
1 ATTTTTATT
2338152 TGTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 21 0.62
11 8 0.24
12 5 0.15
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:2338126 original size:21 final size:22
Alignment explanation
Indices: 2338101--2338149 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
2338091 TTTACATTAT
2338101 ATTTTT-ATTGAATTT-TATT-C
1 ATTTTTAATT-AATTTGTATTGC
*
2338121 ATTTTTAATTATTTTGTATTGC
1 ATTTTTAATTAATTTGTATTGC
2338143 ATTTTTA
1 ATTTTTA
2338150 TTTGTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 10 0.40
21 7 0.28
22 8 0.32
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.65
Consensus pattern (22 bp):
ATTTTTAATTAATTTGTATTGC
Found at i:2345329 original size:44 final size:44
Alignment explanation
Indices: 2345263--2345351 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
2345253 AAATTATTAT
2345263 GCTTTAGGAAATAAGTTAGAAAT-ATTGGTAATAACTCCAACATA
1 GCTTTAGGAAATAAGTTAGAAATGA-TGGTAATAACTCCAACATA
* * *
2345307 GCTTTAGGAAATAAGTTGGAAATGATGGTAATGACTTCAACATA
1 GCTTTAGGAAATAAGTTAGAAATGATGGTAATAACTCCAACATA
2345351 G
1 G
2345352 ATAAAATAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 40 0.98
45 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.29
Consensus pattern (44 bp):
GCTTTAGGAAATAAGTTAGAAATGATGGTAATAACTCCAACATA
Found at i:2348101 original size:20 final size:21
Alignment explanation
Indices: 2348078--2348118 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2348068 GGCTCCTAGC
*
2348078 ATCATTTCCATGT-AAATTAA
1 ATCATTTCCATATCAAATTAA
2348098 ATCATTTCCATATCAAATTAA
1 ATCATTTCCATATCAAATTAA
2348119 TCCAAATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.39
Consensus pattern (21 bp):
ATCATTTCCATATCAAATTAA
Found at i:2348803 original size:24 final size:24
Alignment explanation
Indices: 2348776--2348821 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2348766 TAGGATATTA
2348776 TTTTAAATA-GTATTTTAGTTTATC
1 TTTT-AATAGGTATTTTAGTTTATC
**
2348800 TTTTTTTAGGTATTTTAGTTTA
1 TTTTAATAGGTATTTTAGTTTA
2348822 AATAGTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.24, C:0.02, G:0.11, T:0.63
Consensus pattern (24 bp):
TTTTAATAGGTATTTTAGTTTATC
Found at i:2349776 original size:19 final size:20
Alignment explanation
Indices: 2349752--2349789 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2349742 AATTTAATCG
*
2349752 AATATATAAT-TTAAAATTC
1 AATATAAAATATTAAAATTC
2349771 AATATAAAATATTAAAATT
1 AATATAAAATATTAAAATT
2349790 TATTAACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATAAAATATTAAAATTC
Found at i:2355503 original size:20 final size:20
Alignment explanation
Indices: 2355469--2355544 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
2355459 AAACCCCGAC
*
2355469 GAGTGAATCGATACACTGCA
1 GAGTGTATCGATACACTGCA
* *
2355489 GAGTGTATTGGTACACTGCA
1 GAGTGTATCGATACACTGCA
2355509 GAGTGTATCGATACACTGCA
1 GAGTGTATCGATACACTGCA
2355529 GAGTGTATCGATACAC
1 GAGTGTATCGATACAC
2355545 ATTCAAGGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (20 bp):
GAGTGTATCGATACACTGCA
Found at i:2355616 original size:14 final size:15
Alignment explanation
Indices: 2355597--2355627 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2355587 ATAGCGAGGG
2355597 TGTATCGATACA-TA
1 TGTATCGATACACTA
2355611 TGTATCGATACACTA
1 TGTATCGATACACTA
2355626 TG
1 TG
2355628 CACGAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (15 bp):
TGTATCGATACACTA
Found at i:2358368 original size:43 final size:45
Alignment explanation
Indices: 2358245--2358369 Score: 159
Period size: 47 Copynumber: 2.8 Consensus size: 45
2358235 TATAAAATCT
*
2358245 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAACTA
1 CTTACCATTTAAT-TCATAAGCTCGTAAGCTTATTTTACCAAACTA
*
2358290 CTTACCATTTAAATTCTATAAGCTCGTAAGCTTATTTTATCAATA-TA
1 CTTACCATTT-AATTC-ATAAGCTCGTAAGCTTATTTTACCAA-ACTA
*
2358337 CTTGCCA-TT-ATTCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATTCATAAGCTCGTAAGCTTATTT
2358370 GCATACTTAC
Statistics
Matches: 73, Mismatches: 3, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
43 20 0.27
44 4 0.05
45 10 0.14
46 3 0.04
47 35 0.48
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTAATTCATAAGCTCGTAAGCTTATTTTACCAAACTA
Found at i:2358377 original size:38 final size:42
Alignment explanation
Indices: 2358245--2358383 Score: 133
Period size: 47 Copynumber: 3.2 Consensus size: 42
2358235 TATAAAATCT
* * *
2358245 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAACTA
1 CTTACCA-TTATTCTATAAGCTCGTAAGCTTATTTTAGC-AA-TA
*
2358290 CTTACCATTTAAATTCTATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCA-TT--ATTCTATAAGCTCGTAAGCTTATTTTAGC-A-ATA
*
2358337 CTTGCCATTATTC-ATAAGCTCGTAAGCTTA-TTT-GC-ATA
1 CTTACCATTATTCTATAAGCTCGTAAGCTTATTTTAGCAATA
2358375 CTTACCATT
1 CTTACCATT
2358384 TATTAACCAT
Statistics
Matches: 85, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
38 11 0.13
41 1 0.01
42 3 0.04
43 17 0.20
44 4 0.05
45 10 0.12
46 2 0.02
47 36 0.42
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (42 bp):
CTTACCATTATTCTATAAGCTCGTAAGCTTATTTTAGCAATA
Found at i:2364566 original size:18 final size:19
Alignment explanation
Indices: 2364516--2364573 Score: 82
Period size: 20 Copynumber: 3.1 Consensus size: 19
2364506 CTGTTCACAC
*
2364516 AGTAGCAGTACTATTCATA
1 AGTATCAGTACTATTCATA
*
2364535 TAGTATCGGTACTATTCATA
1 -AGTATCAGTACTATTCATA
2364555 AGTAT-AGTACTATTCATA
1 AGTATCAGTACTATTCATA
2364573 A
1 A
2364574 AAATATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
18 13 0.37
19 5 0.14
20 17 0.49
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (19 bp):
AGTATCAGTACTATTCATA
Found at i:2364809 original size:21 final size:19
Alignment explanation
Indices: 2364785--2364842 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 19
2364775 ATGTTTAATG
2364785 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
*
2364804 ACAAAAGGATACAAATTGTT-
1 A-AAAA-GATACCAATTGTTA
*
2364824 AAAAAGATACCTATTGTTA
1 AAAAAGATACCAATTGTTA
2364843 CTAATTGTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 11 0.33
19 5 0.15
20 5 0.15
21 12 0.36
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:2364839 original size:18 final size:18
Alignment explanation
Indices: 2364785--2364842 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
2364775 ATGTTTAATG
2364785 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
*
2364803 AACAAAAGGATACAAATTGTT
1 -A-AAAA-GATACCAATTGTT
*
2364824 AAAAAGATACCTATTGTT
1 AAAAAGATACCAATTGTT
2364842 A
1 A
2364843 CTAATTGTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 5 0.15
21 12 0.35
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:2367514 original size:19 final size:20
Alignment explanation
Indices: 2367490--2367529 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2367480 AATTTAATCG
*
2367490 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
2367509 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
2367529 A
1 A
2367530 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:2371340 original size:25 final size:25
Alignment explanation
Indices: 2371312--2371359 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2371302 TTGTTCAATT
2371312 TTTATTTTCAATTTTATTTTTCTAA
1 TTTATTTTCAATTTTATTTTTCTAA
***
2371337 TTTATTTTTGTTTTTATTTTTCT
1 TTTATTTTCAATTTTATTTTTCT
2371360 TTGATTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTATTTTCAATTTTATTTTTCTAA
Found at i:2371345 original size:14 final size:13
Alignment explanation
Indices: 2371305--2371370 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 13
2371295 TTTCCGTTTG
2371305 TTCAATTTT-TATT
1 TTCAATTTTAT-TT
2371318 TTCAATTTTATTT
1 TTCAATTTTATTT
2371331 TTCTAA-TTTATTT
1 TTC-AATTTTATTT
**
2371344 TT-GTTTTTATTT
1 TTCAATTTTATTT
*
2371356 TTC--TTTGATTT
1 TTCAATTTTATTT
2371367 TTCA
1 TTCA
2371371 TGTATCCCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
11 10 0.22
12 9 0.20
13 23 0.51
14 3 0.07
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (13 bp):
TTCAATTTTATTT
Found at i:2373593 original size:24 final size:24
Alignment explanation
Indices: 2373566--2373623 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
2373556 AATATATTAA
2373566 TTTAGGAATTATCTTTAGATTATT
1 TTTAGGAATTATCTTTAGATTATT
*
2373590 TTTAGGAATTATCTTTAGCTTATT
1 TTTAGGAATTATCTTTAGATTATT
2373614 TTTAGGAATT
1 TTTAGGAATT
2373624 TGAAGGCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (24 bp):
TTTAGGAATTATCTTTAGATTATT
Found at i:2374701 original size:16 final size:16
Alignment explanation
Indices: 2374680--2374717 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
2374670 TAAAATAAAT
2374680 TTAAAATTTATTTTAG
1 TTAAAATTTATTTTAG
2374696 TTAAAATTTATTTTAG
1 TTAAAATTTATTTTAG
*
2374712 TCAAAA
1 TTAAAA
2374718 AGTCCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (16 bp):
TTAAAATTTATTTTAG
Done.