Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_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: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 23
Found at i:3623879 original size:21 final size:21
Alignment explanation
Indices: 3623855--3623903 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3623845 CTCTCTGATG
3623855 AACACTCTTCATGCTATTCAC
1 AACACTCTTCATGCTATTCAC
* *
3623876 AACACTCTTCATGTTGTTCAC
1 AACACTCTTCATGCTATTCAC
3623897 ATACACT
1 A-ACACT
3623904 AACATTCCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.35
Consensus pattern (21 bp):
AACACTCTTCATGCTATTCAC
Found at i:3625590 original size:6 final size:6
Alignment explanation
Indices: 3625581--3625606 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3625571 AAATAATAAT
3625581 ATATTA ATATTA ATATTA ATATTA AT
1 ATATTA ATATTA ATATTA ATATTA AT
3625607 CACACTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:3630796 original size:94 final size:95
Alignment explanation
Indices: 3630671--3630850 Score: 281
Period size: 94 Copynumber: 1.9 Consensus size: 95
3630661 AAAAGGAAAG
* * * * * * *
3630671 TATCGATACCATGGATTCCAGAATGTCGAAATGGTATCGATATTGAAAGTGAGTATCGGTACCAT
1 TATCGATACCATAGATTCCAGAATGTAGAAATGGTATCGATACTAAAAGGGAGTATCGATACCAC
*
3630736 AGTATAGAAGTATCGGTACAAGGAGAAAAA
66 AGTATAGAAGTATCGATACAAGGAGAAAAA
3630766 TATCGATACCATAGA-TCCAGAATGTAGAAATGGTATCGATACTAAAAGGGAGTATCGATACCAC
1 TATCGATACCATAGATTCCAGAATGTAGAAATGGTATCGATACTAAAAGGGAGTATCGATACCAC
3630830 AGTATAGAAGTATCGATACAA
66 AGTATAGAAGTATCGATACAA
3630851 TGGTAGAGGT
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
94 63 0.82
95 14 0.18
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.24
Consensus pattern (95 bp):
TATCGATACCATAGATTCCAGAATGTAGAAATGGTATCGATACTAAAAGGGAGTATCGATACCAC
AGTATAGAAGTATCGATACAAGGAGAAAAA
Found at i:3630864 original size:94 final size:94
Alignment explanation
Indices: 3630666--3630868 Score: 275
Period size: 94 Copynumber: 2.1 Consensus size: 94
3630656 TACCAAAAAG
* * * * * *
3630666 GAAAGTATCGATACCATGGATTCCAGAATGTCGAAATGGTATCGATATTGAAAGTGAGTATCGGT
1 GAAAGTATCGATACCATAGATTCCAGAATGTAGAAATGGTATCGATACTAAAAGGGAGTATCGAT
* *
3630731 ACCATAGTATAGAAGTATCGGTACAAGGA
66 ACCACAGTATAGAAGTATCGATACAAGGA
*
3630760 GAAAAATATCGATACCATAGA-TCCAGAATGTAGAAATGGTATCGATACTAAAAGGGAGTATCGA
1 G-AAAGTATCGATACCATAGATTCCAGAATGTAGAAATGGTATCGATACTAAAAGGGAGTATCGA
3630824 TACCACAGTATAGAAGTATCGATACAATGGTA
65 TACCACAGTATAGAAGTATCGATACAA-GG-A
*
3630856 G-AGGTATCGATAC
1 GAAAGTATCGATAC
3630869 TATTGAGCCA
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
94 74 0.78
95 19 0.20
96 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (94 bp):
GAAAGTATCGATACCATAGATTCCAGAATGTAGAAATGGTATCGATACTAAAAGGGAGTATCGAT
ACCACAGTATAGAAGTATCGATACAAGGA
Found at i:3643760 original size:19 final size:19
Alignment explanation
Indices: 3643736--3643773 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3643726 AAATAATATC
*
3643736 CTAAAACTTAATTAAAATA
1 CTAAAACCTAATTAAAATA
*
3643755 CTAAAACCTATTTAAAATA
1 CTAAAACCTAATTAAAATA
3643774 AAATAGAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:3647969 original size:21 final size:21
Alignment explanation
Indices: 3647921--3647985 Score: 103
Period size: 21 Copynumber: 3.0 Consensus size: 21
3647911 TGGCAGATTG
* *
3647921 CCCAGAGGGAACCGATTCCCC
1 CCCAGGGGGTACCGATTCCCC
3647942 TCCCAGGGGGTACCGATTCCCC
1 -CCCAGGGGGTACCGATTCCCC
3647964 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACCGATTCCCC
3647985 C
1 C
3647986 TTGTATAACG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 22 0.54
22 19 0.46
ACGTcount: A:0.17, C:0.43, G:0.26, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACCGATTCCCC
Found at i:3653414 original size:45 final size:44
Alignment explanation
Indices: 3653338--3653436 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 44
3653328 TTTGTGCACA
*
3653338 ATGCATCAATACACTATGAATGTGCATCGATGCA-TCCCTTTGAAT
1 ATGCATCAATACACTATGAATGTGCACCGATGCACT-CC-TTGAAT
* *
3653383 TTGCATCGATACA-TCATGAA-GATGCACCGATGCACTCCTTGAAT
1 ATGCATCAATACACT-ATGAATG-TGCACCGATGCACTCCTTGAAT
3653427 ATGCATCAAT
1 ATGCATCAAT
3653437 GCACAATGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
44 16 0.35
45 29 0.63
46 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.29
Consensus pattern (44 bp):
ATGCATCAATACACTATGAATGTGCACCGATGCACTCCTTGAAT
Found at i:3667470 original size:17 final size:17
Alignment explanation
Indices: 3667448--3667489 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
3667438 TCAAGTTATT
*
3667448 CCACATTTTAGGTTTCA
1 CCACATTTTAGGTTGCA
3667465 CCACATTTTAGGTTGCA
1 CCACATTTTAGGTTGCA
*
3667482 GCACATTT
1 CCACATTT
3667490 GTACCACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (17 bp):
CCACATTTTAGGTTGCA
Found at i:3676942 original size:38 final size:38
Alignment explanation
Indices: 3676880--3676968 Score: 162
Period size: 38 Copynumber: 2.4 Consensus size: 38
3676870 TTTTGTTCGG
3676880 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCAA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
*
3676917 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAG
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
3676955 GTCGGGTCGGGTTT
1 GTCGGGTCGGGTTT
3676969 GGGTTTAGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 11 0.22
38 39 0.78
ACGTcount: A:0.12, C:0.11, G:0.38, T:0.38
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
Found at i:3677564 original size:16 final size:18
Alignment explanation
Indices: 3677543--3677621 Score: 121
Period size: 16 Copynumber: 4.6 Consensus size: 18
3677533 ATATGGAATT
3677543 AGATTCTAATTCC-T-AC
1 AGATTCTAATTCCTTCAC
3677559 AGATTCTAATTCCTTCAC
1 AGATTCTAATTCCTTCAC
3677577 AGATTCTAATT-CTT-AC
1 AGATTCTAATTCCTTCAC
*
3677593 AGATTCCAATTCCTTCAC
1 AGATTCTAATTCCTTCAC
3677611 AGATTCTAATT
1 AGATTCTAATT
3677622 ATCTCATAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
16 25 0.44
17 7 0.12
18 25 0.44
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.39
Consensus pattern (18 bp):
AGATTCTAATTCCTTCAC
Found at i:3677581 original size:34 final size:34
Alignment explanation
Indices: 3677543--3677621 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
3677533 ATATGGAATT
*
3677543 AGATTCTAATTCCTACAGATTCTAATTCCTTCAC
1 AGATTCTAATTCCTACAGATTCCAATTCCTTCAC
*
3677577 AGATTCTAATTCTTACAGATTCCAATTCCTTCAC
1 AGATTCTAATTCCTACAGATTCCAATTCCTTCAC
3677611 AGATTCTAATT
1 AGATTCTAATT
3677622 ATCTCATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.39
Consensus pattern (34 bp):
AGATTCTAATTCCTACAGATTCCAATTCCTTCAC
Found at i:3680172 original size:30 final size:30
Alignment explanation
Indices: 3680101--3680182 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 30
3680091 TTCAAAAGTT
*
3680101 ACAATTTGATAAATTTAATAATCATTTGGTA
1 ACAATTTGATAAATTTAATGATCATTT-GTA
3680132 ACAATTTGATAAATTTAATGATCATTT-TA
1 ACAATTTGATAAATTTAATGATCATTTGTA
* *
3680161 TATATTTTGATAAATTTAATGA
1 -ACAATTTGATAAATTTAATGA
3680183 CCAAAATGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
29 2 0.04
30 19 0.40
31 26 0.55
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (30 bp):
ACAATTTGATAAATTTAATGATCATTTGTA
Found at i:3680346 original size:30 final size:29
Alignment explanation
Indices: 3680293--3680398 Score: 113
Period size: 30 Copynumber: 3.6 Consensus size: 29
3680283 ATCCTTTTAG
* *
3680293 TCATTAAACTTTCAAATGTTATAAAATAT
1 TCATTAAATTTTCAAATGTTATAAAATAA
*
3680322 TCATAAAATTTTCAAATAGTTATAAAATAA
1 TCATTAAATTTTCAAAT-GTTATAAAATAA
* * * *
3680352 CCATTAAATTTATCAACTGTTATATAATAG
1 TCATTAAATTT-TCAAATGTTATAAAATAA
*
3680382 TCATTAAACTTATCAAA
1 TCATTAAA-TTTTCAAA
3680399 ATTTATTACT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
29 15 0.24
30 41 0.65
31 7 0.11
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (29 bp):
TCATTAAATTTTCAAATGTTATAAAATAA
Found at i:3682231 original size:2 final size:2
Alignment explanation
Indices: 3682226--3682258 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3682216 ATTGTGTGTG
3682226 TA TA TA 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 TA TA TA T
3682259 CTATCTGATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3682790 original size:42 final size:42
Alignment explanation
Indices: 3682698--3682830 Score: 158
Period size: 42 Copynumber: 3.1 Consensus size: 42
3682688 ATAGTTCAAG
* * * * *
3682698 ATCTATAGTAGCGTTTTTGGAACAAACGCCACAAAAAGTTGAT
1 ATCTATAGCAGCATTTTTGGAACAAACGCCGC-AAAAGGTCAT
* * * *
3682741 ATCTATAGCGGTATTTTTGGAACATACGCCGCAAAAGGTCAG
1 ATCTATAGCAGCATTTTTGGAACAAACGCCGCAAAAGGTCAT
* *
3682783 ATCTATAGCAGCGTTTTTGAAACAAACGCCGCAAAAGGTCAT
1 ATCTATAGCAGCATTTTTGGAACAAACGCCGCAAAAGGTCAT
3682825 ATCTAT
1 ATCTAT
3682831 CACTACAAGA
Statistics
Matches: 75, Mismatches: 15, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
42 49 0.65
43 26 0.35
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (42 bp):
ATCTATAGCAGCATTTTTGGAACAAACGCCGCAAAAGGTCAT
Found at i:3683691 original size:3 final size:3
Alignment explanation
Indices: 3683685--3683785 Score: 202
Period size: 3 Copynumber: 33.7 Consensus size: 3
3683675 TTTTTATCCA
3683685 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3683733 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3683781 TAT TA
1 TAT TA
3683786 AATATATTAA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3696932 original size:16 final size:16
Alignment explanation
Indices: 3696911--3696948 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3696901 TACAATTCTA
3696911 TTATTTCA-AGTTCAAT
1 TTATTTCAGAG-TCAAT
*
3696927 TTATTTGAGAGTCAAT
1 TTATTTCAGAGTCAAT
3696943 TTATTT
1 TTATTT
3696949 TTGAAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.53
Consensus pattern (16 bp):
TTATTTCAGAGTCAAT
Found at i:3697826 original size:84 final size:84
Alignment explanation
Indices: 3697685--3698114 Score: 670
Period size: 84 Copynumber: 5.1 Consensus size: 84
3697675 AAATAAGTGT
* *
3697685 TCTGATTTAGCAGAACCAATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAG
1 TCTGATTTGGTAGAACCAATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAG
3697750 TATTCTTTGAGTTATCTGA
66 TATTCTTTGAGTTATCTGA
* *
3697769 TCTGATTTGGTAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAG
1 TCTGATTTGGTAGAACCAATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAG
*
3697834 TGTTCTTTGAGTTATCTGA
66 TATTCTTTGAGTTATCTGA
** *
3697853 TCTGATTTGGCGGAACCAATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTTGAAG
1 TCTGATTTGGTAGAACCAATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAG
3697918 TATTCTTTGAGTTATCTGA
66 TATTCTTTGAGTTATCTGA
*
3697937 TCTG-GTTGG-ACGGAACCAATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGA
1 TCTGATTTGGTA--GAACCAATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGA
* *
3698000 AGTGTTCTTTGAATTATCTGA
64 AGTATTCTTTGAGTTATCTGA
* * *
3698021 TTTGGTTTGGTA-AACC-ATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAT
1 TCTGATTTGGTAGAACCAATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAG
*
3698084 TATTCTTTGAGTTATTTGA
66 TATTCTTTGAGTTATCTGA
*
3698103 TCTGGTTTGGTA
1 TCTGATTTGGTA
3698115 AAAATTACAG
Statistics
Matches: 319, Mismatches: 23, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
82 73 0.23
83 8 0.03
84 233 0.73
85 4 0.01
86 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (84 bp):
TCTGATTTGGTAGAACCAATCATTGAATTTAGAAGATGAATGTGCTCAATAGCATCTTCTGGAAG
TATTCTTTGAGTTATCTGA
Found at i:3698921 original size:113 final size:112
Alignment explanation
Indices: 3698722--3699343 Score: 862
Period size: 113 Copynumber: 5.6 Consensus size: 112
3698712 TTCCAGTTCG
3698722 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-TTCATAATGAGAAGAATTTGTTC
* * * *
3698786 -ACCATTTT-GCTTAAATCTATCACTTGATGGATTATCTTTTCCAGAGAA
65 AACC-TTTTACCTGAATTC-ATCACTTGATGGATTAGCTTTTCCAGAGAA
3698834 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AATTCATAATGAGAAGAATTTGTTC
*** *
3698899 AACCTTTTGTTTGAATTCATCACTTGATGGATTAACTTTTCCAGAGAA
65 AACCTTTTACCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGAA
*
3698947 GGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT--GAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-TTCATAATGAGAAGAATTTGTTC
* * * * *
3699010 AACCTTTTACCTGAGTCCATCATTTGATGGATCAGCCTTTCC--AGAA
65 AACCTTTTACCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGAA
3699056 AGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAG--TTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAATTTGTTCA
* *
3699118 ACCTTTTACCTGAATTCATCAATTGATGGATTATCTTTTCCAGAGAA
66 ACCTTTTACCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGAA
3699165 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AATTCATAATGAGAAGAATTTGTTC
* * * * *
3699230 AACCTTTTACCTGAGTCCATCATTTGATGGATCAGCCTTTCCAGAGAA
65 AACCTTTTACCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGAA
* *
3699278 AGTTCATAAT--G-AGAACTCATCTGAAGAA-GAAGAAG--TTCATAATAAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAATTTGTTCA
*
3699337 ACTTTTT
66 ACCTTTT
3699344 GCATAATTCT
Statistics
Matches: 466, Mismatches: 31, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
105 8 0.02
106 28 0.06
107 49 0.11
108 7 0.02
109 76 0.16
110 24 0.05
111 47 0.10
112 31 0.07
113 186 0.40
114 10 0.02
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (112 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAATTTGTTCA
ACCTTTTACCTGAATTCATCACTTGATGGATTAGCTTTTCCAGAGAA
Found at i:3699116 original size:331 final size:328
Alignment explanation
Indices: 3698722--3699343 Score: 968
Period size: 331 Copynumber: 1.9 Consensus size: 328
3698712 TTCCAGTTCG
3698722 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC-
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
* * *
3698786 ACCATTTTGCTTAAA-TCTATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAG
66 ACC-TTTTACCTAAATTC-ATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAG
***
3698850 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAAT
129 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
* * * *
3698915 TCATCACTTGATGGATTAACTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
194 CCATCACTTGATGGATCAACCTTTCCAGAGAAAGTTCATAAT--G-AGAACTCATCT---GAA-G
*
3698980 AAGAAGAAGTTCATAAT-GAAGAATTTGTTCAACCTTTTACCTGAGTCCATCATTTGATGGATCA
252 AAGAAGAAGTTCATAATAGAAGAACTTGTTCAACCTTTTACCTGAGTCCATCATTTGATGGATCA
3699044 GCCTTTCCAGAA
317 GCCTTTCCAGAA
3699056 AGTTCATAATGAGAAGAACTCATCTG-A-A-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
*
3699118 ACCTTTTACCTGAATTCATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTACCTAAATTCATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
*
3699183 CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAGTCC
131 CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
* *
3699248 ATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAACTCATCTGAAGAAGAAGAAG
196 ATCACTTGATGGATCAACCTTTCCAGAGAAAGTTCATAATGAGAACTCATCTGAAGAAGAAGAAG
*
3699313 TTCATAATAAGAAGAACTTGTTCAACTTTTT
261 TTCATAAT-AGAAGAACTTGTTCAACCTTTT
3699344 GCATAATTCT
Statistics
Matches: 268, Mismatches: 16, Indels: 16
0.89 0.05 0.05
Matches are distributed among these distances:
324 18 0.07
325 3 0.01
326 19 0.07
328 11 0.04
329 1 0.00
331 183 0.68
332 6 0.02
333 1 0.00
334 26 0.10
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (328 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
ACCTTTTACCTAAATTCATCAATTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
ATCACTTGATGGATCAACCTTTCCAGAGAAAGTTCATAATGAGAACTCATCTGAAGAAGAAGAAG
TTCATAATAGAAGAACTTGTTCAACCTTTTACCTGAGTCCATCATTTGATGGATCAGCCTTTCCA
GAA
Found at i:3699134 original size:218 final size:220
Alignment explanation
Indices: 3698722--3699343 Score: 943
Period size: 218 Copynumber: 2.8 Consensus size: 220
3698712 TTCCAGTTCG
3698722 AGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT-AGAAGAATTTGTTC
* * * * * * * * *
3698786 -ACCATTTTGCTTAAATCTATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAG
65 AACC-TTTTACCTGAGTCCATCATTTGATGGATCAGCCTTTCCA-AGAAAGTTCATAATGAGAAG
***
3698850 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAAT
128 AACTCATCTGAAGAA-GAAGAAG---TTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAAT
*
3698915 TCATCACTTGATGGATTAACTTTTCCAGAGAA
189 TCATCAATTGATGGATTAACTTTTCCAGAGAA
*
3698947 GGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT-GAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAGAAGAATTTGTTCA
3699011 ACCTTTTACCTGAGTCCATCATTTGATGGATCAGCCTTTCC-AGAAAGTTCATAATGAGAAGAAC
66 ACCTTTTACCTGAGTCCATCATTTGATGGATCAGCCTTTCCAAGAAAGTTCATAATGAGAAGAAC
3699075 TCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAA
131 TCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAA
*
3699140 TTGATGGATTATCTTTTCCAGAGAA
196 TTGATGGATTAACTTTTCCAGAGAA
*
3699165 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT-AGAAGAATTTGTTC
3699230 AACCTTTTACCTGAGTCCATCATTTGATGGATCAGCCTTTCCAGAGAAAGTTCATAAT--G-AGA
65 AACCTTTTACCTGAGTCCATCATTTGATGGATCAGCCTTTCCA-AGAAAGTTCATAATGAGAAGA
* * *
3699292 ACTCATCTGAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
129 ACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
3699344 GCATAATTCT
Statistics
Matches: 371, Mismatches: 20, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
218 114 0.31
219 52 0.14
220 56 0.15
221 7 0.02
222 49 0.13
224 42 0.11
225 31 0.08
226 20 0.05
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (220 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAGAAGAATTTGTTCA
ACCTTTTACCTGAGTCCATCATTTGATGGATCAGCCTTTCCAAGAAAGTTCATAATGAGAAGAAC
TCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAA
TTGATGGATTAACTTTTCCAGAGAA
Found at i:3699664 original size:3 final size:3
Alignment explanation
Indices: 3699658--3699745 Score: 151
Period size: 3 Copynumber: 29.7 Consensus size: 3
3699648 TTTTTATCCA
*
3699658 TAT TAT TAT TA- TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
3699705 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3699746 AATATATTAA
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
2 2 0.02
3 79 0.98
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3710872 original size:20 final size:21
Alignment explanation
Indices: 3710819--3710875 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3710809 CAAAACAATG
3710819 AAGGGATCGATCCTTTCTTGA
1 AAGGGATCGATCCTTTCTTGA
*
3710840 AAGGGATCAATCCTTT-TT-A
1 AAGGGATCGATCCTTTCTTGA
*
3710859 AAGGGGATTGATCCTTT
1 AA-GGGATCGATCCTTT
3710876 GAAAAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.09
20 14 0.44
21 15 0.47
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (21 bp):
AAGGGATCGATCCTTTCTTGA
Found at i:3710948 original size:20 final size:21
Alignment explanation
Indices: 3710892--3710970 Score: 63
Period size: 22 Copynumber: 3.8 Consensus size: 21
3710882 TTAAAACGTT
*
3710892 GGGATCGATCCTTTCTGATCAA
1 GGGATCGATCCTTTTTGA-CAA
** *
3710914 GGGATTAATCTTTTTTGA-AA
1 GGGATCGATCCTTTTTGACAA
**
3710934 GGGATCGATCC-TTTTCCCTAA
1 GGGATCGATCCTTTTTGAC-AA
*
3710955 GGGATCGATCATTTTT
1 GGGATCGATCCTTTTT
3710971 CTAGAAAACT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.09
20 10 0.23
21 12 0.27
22 18 0.41
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (21 bp):
GGGATCGATCCTTTTTGACAA
Found at i:3722182 original size:307 final size:306
Alignment explanation
Indices: 3721629--3722198 Score: 944
Period size: 307 Copynumber: 1.9 Consensus size: 306
3721619 GCTTCATGAC
* * *
3721629 AAAATTTCCCTATCAAGGAAATAATTGTCAGCCATTCTTCAGATAGTTCTTTTATCAATCTCAGA
1 AAAATTTCCCCATCAAGGAAATAATTGTCAGCCATTCTTCAAATAGTTATTTTATCAATCTCAGA
* * *
3721694 TGCACATGGAGGATATGTTTGATACTTGATATATTGCATAATATCATGGTACCATGGTTGACCAT
66 TGCACATGGAGGACATGTTTGATACTTGATATATTGCAGAATATCATGGTACCATGGCTGACCAT
*
3721759 CTGTTTCTTCCTCTATGCTATAATATAATGATGGGGTTTTATACGCTTGCATTTTGATTAGCATC
131 CTGTTTCTTCCTCTATGCTATAATATAATGATGGGGTTTTATACACTTGCATTTTGATTAGCATC
3721824 ATGTCAGCCTACCTATTTGCTTTAAACATGGCAGTTAACATAGCCAAAGCATCATCCATTTGATT
196 ATGTCAGCCTACCTATTTGCTTTAAACATGGCAGTTAACATAGCCAAAGCATCATCCATTTGATT
3721889 GTCATCACACATTTCAAAAGAACTTGATCACTGCCCCTTTTATACA
261 GTCATCACACATTTCAAAAGAACTTGATCACTGCCCCTTTTATACA
*
3721935 AAAATTTCCCCGTCAAGGAAATAATTGTCAGCCATTCTTCAAATAGTTATTTTATCAATCTCAGA
1 AAAATTTCCCCATCAAGGAAATAATTGTCAGCCATTCTTCAAATAGTTATTTTATCAATCTCAGA
* * * *
3722000 TGCACATGGAGGACATTTTTTTATACTTGATATATTGTAGAATATCATGGTATCATGGCTGACCA
66 TGCACATGGAGGACA-TGTTTGATACTTGATATATTGCAGAATATCATGGTACCATGGCTGACCA
* *
3722065 TCTGTTTCTTCCTTTATGCTATGATA-ATATGATGGGGTTTTATACACTTGCATTTTGATTAGCA
130 TCTGTTTCTTCCTCTATGCTATAATATA-ATGATGGGGTTTTATACACTTGCATTTTGATTAGCA
* * * * *
3722129 TCATGTCAGCCTTCTTATTTGCTTTGAACATGGTAGTTAACGTAGCCAAAGCATCATCCATTTGA
194 TCATGTCAGCCTACCTATTTGCTTTAAACATGGCAGTTAACATAGCCAAAGCATCATCCATTTGA
3722194 TTGTC
259 TTGTC
3722199 TTCTCGAATG
Statistics
Matches: 243, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
306 76 0.31
307 167 0.69
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (306 bp):
AAAATTTCCCCATCAAGGAAATAATTGTCAGCCATTCTTCAAATAGTTATTTTATCAATCTCAGA
TGCACATGGAGGACATGTTTGATACTTGATATATTGCAGAATATCATGGTACCATGGCTGACCAT
CTGTTTCTTCCTCTATGCTATAATATAATGATGGGGTTTTATACACTTGCATTTTGATTAGCATC
ATGTCAGCCTACCTATTTGCTTTAAACATGGCAGTTAACATAGCCAAAGCATCATCCATTTGATT
GTCATCACACATTTCAAAAGAACTTGATCACTGCCCCTTTTATACA
Found at i:3730278 original size:305 final size:305
Alignment explanation
Indices: 3729727--3730299 Score: 932
Period size: 305 Copynumber: 1.9 Consensus size: 305
3729717 TTGCTTCATG
* * *
3729727 ACAAAATTTCCCTATCAAGGAAATAATTGTCAGCCATTCTTCAGATAGTTCTTTTATCAATCTCA
1 ACAAAATTTCCCCATCAAGGAAATAATTGTCAGCCATTCTTCAAATAGTTATTTTATCAATCTCA
* *
3729792 GATGCACATGGAGGACATGTTTGATACTTGATATATTGCACAATATCATGGTACCATGGTTGAGC
66 GATGCACATGGAGGACATGTTTGATACTTGATATATTGCACAATATCATGGTACCATGGCTGACC
* * *
3729857 ATCTGTTTCTTCCTCTATGCTATAATATAATGATGGGGTTTTATACGCTTGCATTTTGATTAGCA
131 ATCTATTTCTTCCTCTATGCTATAATATAATGATGGGGTTTCATACACTTGCATTTTGATTAGCA
*
3729922 TCATGTCAGCCTACCTATTTGCTTTAAACATGGCAGTTAACATAGCCAAAGCATCATCCATTTGA
196 TCATGTCAGCCTACCTATTTGCTTTAAACATGGCAGTAAACATAGCCAAAGCATCATCCATTTGA
3729987 TTGTCATCACACATTTCAAAAGAACTTGATCACTGCCCCTTCTAT
261 TTGTCATCACACATTTCAAAAGAACTTGATCACTGCCCCTTCTAT
*
3730032 ACAAAATTTCCCCGTCAAGGAAATAATTGTCAGCCATTCTTCAAATAGTTATTTTATCAATCTCA
1 ACAAAATTTCCCCATCAAGGAAATAATTGTCAGCCATTCTTCAAATAGTTATTTTATCAATCTCA
* * * * *
3730097 GATGCACATGGAGGACATTTTTTATACTTGATATATTGTAGAATATCATGGTATCATGGCTGACC
66 GATGCACATGGAGGACATGTTTGATACTTGATATATTGCACAATATCATGGTACCATGGCTGACC
* *
3730162 ATCTATTTCTTCCTTTATTCTATAATA-ATATGATGGGGTTTCATACACTTGCATTTTGATTAGC
131 ATCTATTTCTTCCTCTATGCTATAATATA-ATGATGGGGTTTCATACACTTGCATTTTGATTAGC
* * * * *
3730226 ATCATGTCAGCCTTCTTATTTGCTTTGAACATGGTAGTAAACGTAGCCAAAGCATCATCCATTTG
195 ATCATGTCAGCCTACCTATTTGCTTTAAACATGGCAGTAAACATAGCCAAAGCATCATCCATTTG
3730291 ATTGTCATC
260 ATTGTCATC
3730300 TCGAATGAGA
Statistics
Matches: 245, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
304 1 0.00
305 244 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (305 bp):
ACAAAATTTCCCCATCAAGGAAATAATTGTCAGCCATTCTTCAAATAGTTATTTTATCAATCTCA
GATGCACATGGAGGACATGTTTGATACTTGATATATTGCACAATATCATGGTACCATGGCTGACC
ATCTATTTCTTCCTCTATGCTATAATATAATGATGGGGTTTCATACACTTGCATTTTGATTAGCA
TCATGTCAGCCTACCTATTTGCTTTAAACATGGCAGTAAACATAGCCAAAGCATCATCCATTTGA
TTGTCATCACACATTTCAAAAGAACTTGATCACTGCCCCTTCTAT
Found at i:3732754 original size:15 final size:15
Alignment explanation
Indices: 3732736--3732766 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3732726 AAATTCTAAA
3732736 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
3732751 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
3732766 T
1 T
3732767 CTATCTGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:3738814 original size:38 final size:38
Alignment explanation
Indices: 3738763--3738850 Score: 158
Period size: 38 Copynumber: 2.3 Consensus size: 38
3738753 TTCGCACCTC
* *
3738763 TGAATGATTCAGTGTTGGCTGATTCAGCAAAACAGTGT
1 TGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTGT
3738801 TGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTGT
1 TGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTGT
3738839 TGAATGATTCAG
1 TGAATGATTCAG
3738851 CACAAAGTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (38 bp):
TGAATGATTCAGTGCTGACTGATTCAGCAAAACAGTGT
Found at i:3738941 original size:56 final size:56
Alignment explanation
Indices: 3738881--3738992 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
3738871 ATTCAGAGCC
* * *
3738881 ATTATCAAACAGCATGTCATATTCAGAGTTAATTCATACAGAGCATCTGAATCATT
1 ATTATCAAACAGCATGTCACATTCAGAGCTAATTCATACAGAACATCTGAATCATT
3738937 ATTATCAAACAGCATGTCACATTCAGAGCTAATTCATACAGAACATCTGAATCATT
1 ATTATCAAACAGCATGTCACATTCAGAGCTAATTCATACAGAACATCTGAATCATT
3738993 CAGCATTTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (56 bp):
ATTATCAAACAGCATGTCACATTCAGAGCTAATTCATACAGAACATCTGAATCATT
Found at i:3739022 original size:15 final size:16
Alignment explanation
Indices: 3738984--3739024 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3738974 ACAGAACATC
*
3738984 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
3739000 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
3739016 T-AATCATTC
1 TGAATCATTC
3739025 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:3754005 original size:22 final size:21
Alignment explanation
Indices: 3753979--3754036 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
3753969 ATAGGGCAGA
3753979 GGGAATCGATACCCCCT-TGAAG
1 GGGAATCGATACCCCCTCT--AG
* *
3754001 GGGAACCGAT-TCCCCTCTAG
1 GGGAATCGATACCCCCTCTAG
3754021 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
3754037 CTGGGGTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 11 0.37
21 9 0.30
22 10 0.33
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGAATCGATACCCCCTCTAG
Found at i:3761918 original size:60 final size:58
Alignment explanation
Indices: 3761825--3761945 Score: 206
Period size: 60 Copynumber: 2.1 Consensus size: 58
3761815 AATAGATGGA
*
3761825 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAAGGCAAACTCGATAATATGTCTC
1 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATG-AAAAGGAAAACTCGATAATATGT-TC
*
3761885 TAAGTGTCCTATTGAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGTTC
1 TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGTTC
3761943 TAA
1 TAA
3761946 CCAACCCTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
58 5 0.08
59 22 0.37
60 32 0.54
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (58 bp):
TAAGTGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATGTTC
Found at i:3764766 original size:7 final size:7
Alignment explanation
Indices: 3764754--3764800 Score: 58
Period size: 7 Copynumber: 6.3 Consensus size: 7
3764744 TAACGATCAC
3764754 TTTAATT
1 TTTAATT
3764761 TTTAATT
1 TTTAATT
3764768 TTTATATAT
1 TTTA-AT-T
3764777 TTTAATT
1 TTTAATT
*
3764784 TTAAATAT
1 TTTAAT-T
3764792 TTTAATT
1 TTTAATT
3764799 TT
1 TT
3764801 AAATAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 20 0.57
8 10 0.29
9 5 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTAATT
Found at i:3764782 original size:23 final size:21
Alignment explanation
Indices: 3764755--3764802 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
3764745 AACGATCACT
* *
3764755 TTAATTTTTAATTTTTATATATT
1 TTAATTTTAAATATTT-TA-ATT
3764778 TTAATTTTAAATATTTTAATT
1 TTAATTTTAAATATTTTAATT
3764799 TTAA
1 TTAA
3764803 ATAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 2 0.09
23 14 0.61
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTAATTTTAAATATTTTAATT
Found at i:3764791 original size:15 final size:15
Alignment explanation
Indices: 3764760--3764805 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
3764750 TCACTTTAAT
*
3764760 TTTTAATTTTTATATA
1 TTTTAA-TTTTAAATA
3764776 TTTTAATTTTAAATA
1 TTTTAATTTTAAATA
3764791 TTTTAATTTTAAATA
1 TTTTAATTTTAAATA
3764806 AAATAATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 23 0.79
16 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAATTTTAAATA
Found at i:3765298 original size:19 final size:18
Alignment explanation
Indices: 3765263--3765312 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
3765253 CTTTATACAG
* *
3765263 TATTGTTATTGTTAATAGA
1 TATTGATATTATTAATA-A
3765282 GTATTGAT-TTATTAATAA
1 -TATTGATATTATTAATAA
3765300 TATTGATATTATT
1 TATTGATATTATT
3765313 TACTTTGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.26
18 6 0.22
19 8 0.30
20 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
TATTGATATTATTAATAA
Found at i:3768364 original size:18 final size:18
Alignment explanation
Indices: 3768341--3768376 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3768331 ATTCTAATAA
3768341 TTGAATCGAATATAAAAT
1 TTGAATCGAATATAAAAT
*
3768359 TTGAATCTAATATAAAAT
1 TTGAATCGAATATAAAAT
3768377 CTTAAAATTC
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:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (18 bp):
TTGAATCGAATATAAAAT
Found at i:3768903 original size:20 final size:22
Alignment explanation
Indices: 3768860--3768906 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
3768850 AAAATTAAAA
* *
3768860 ATATAAATAAAATGCAATGCAT
1 ATATAAATAAAATACAATGAAT
3768882 ATATAAAT-AAATAC-ATGAAT
1 ATATAAATAAAATACAATGAAT
3768902 ATATA
1 ATATA
3768907 GTTGAACAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 5 0.22
22 8 0.35
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (22 bp):
ATATAAATAAAATACAATGAAT
Found at i:3771701 original size:12 final size:13
Alignment explanation
Indices: 3771684--3771716 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3771674 AATGGGCAAA
*
3771684 TTTGAAAACT-AT
1 TTTGAAAACTAAG
3771696 TTTGAAAACTAAG
1 TTTGAAAACTAAG
3771709 TTTGAAAA
1 TTTGAAAA
3771717 TCATAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACTAAG
Found at i:3772271 original size:21 final size:21
Alignment explanation
Indices: 3772207--3772279 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
3772197 CGATATCAGG
3772207 GTATCGATACC-CATTGAAGCA
1 GTATCGATACCTC-TTGAAGCA
*
3772228 GTATC-AGTA-CTGTT-AAGAACA
1 GTATCGA-TACCTCTTGAAG--CA
3772249 GTATCGATACCTCTTGAAGCA
1 GTATCGATACCTCTTGAAGCA
3772270 GTATCGATAC
1 GTATCGATAC
3772280 TATGCTAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
19 3 0.07
20 4 0.09
21 28 0.65
22 5 0.12
23 3 0.07
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (21 bp):
GTATCGATACCTCTTGAAGCA
Found at i:3779019 original size:24 final size:25
Alignment explanation
Indices: 3778977--3779032 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
3778967 TTTTTTAATT
*
3778977 TTATTAATTTAATTTAATATATAAAA
1 TTATTAA-TTAATTAAATATATAAAA
* *
3779003 TTATTAA-TAATTAAATATGTAATA
1 TTATTAATTAATTAAATATATAAAA
3779027 TTATTA
1 TTATTA
3779033 TATATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 20 0.74
26 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTATTAATTAATTAAATATATAAAA
Found at i:3779531 original size:28 final size:27
Alignment explanation
Indices: 3779490--3779566 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 27
3779480 CCTTACGATT
* *
3779490 CCTTAATTTCTATATTTATAATTAGTTC
1 CCTTAATTTTTATATTTATAATTAG-AC
* *
3779518 TCTTAATTTTTATATTTATAGTTAGAC
1 CCTTAATTTTTATATTTATAATTAGAC
*
3779545 CCTTTAATTTTTACATTTATAA
1 CC-TTAATTTTTATATTTATAA
3779567 ATGAGGTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 2 0.05
28 39 0.95
ACGTcount: A:0.30, C:0.12, G:0.04, T:0.55
Consensus pattern (27 bp):
CCTTAATTTTTATATTTATAATTAGAC
Found at i:3780577 original size:129 final size:127
Alignment explanation
Indices: 3780346--3780596 Score: 448
Period size: 129 Copynumber: 2.0 Consensus size: 127
3780336 TTTAAATTTT
*
3780346 TTCATTAAATTTAATATATTTAATTTTTTTGTTACTCTGTTTTTTTCACTAACAACTATTTAAAT
1 TTCATTAAATTTAATATATTTAATTTTTTTGTTACTATGTTTTTTTCACTAACAACTATTTAAAT
* *
3780411 TGATTGTTATATAGATATAAAATGATTTTTTTGGGTAAAAATTTTATTTTTTTAAAAAAAAA
66 TGATTGTTATATAGATACAAAATGATTTTTTTAGGTAAAAATTTTATTTTTTTAAAAAAAAA
*
3780473 TTCATTAAATTTAATATATTTAATTTTTTTTGTTACTATGCTTTTTTTCACTAACGACTATTTAA
1 TTCATTAAATTTAATATATTTAA-TTTTTTTGTTACTATG-TTTTTTTCACTAACAACTATTTAA
3780538 ATTGATTGTTATATAGATACAAAATGATTTTTTTAGGTAAAAATTTTATTTTTTTAAAA
64 ATTGATTGTTATATAGATACAAAATGATTTTTTTAGGTAAAAATTTTATTTTTTTAAAA
3780597 TGACATCATT
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
127 23 0.19
128 15 0.13
129 80 0.68
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (127 bp):
TTCATTAAATTTAATATATTTAATTTTTTTGTTACTATGTTTTTTTCACTAACAACTATTTAAAT
TGATTGTTATATAGATACAAAATGATTTTTTTAGGTAAAAATTTTATTTTTTTAAAAAAAAA
Found at i:3781666 original size:23 final size:24
Alignment explanation
Indices: 3781637--3781686 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3781627 AAACATTTTT
*
3781637 AAAGGAGTTGA-TTTTTCTTTTAA
1 AAAGGAGCTGATTTTTTCTTTTAA
*
3781660 AAAGGAGCTGATTTTTTGTTTTAA
1 AAAGGAGCTGATTTTTTCTTTTAA
3781684 AAA
1 AAA
3781687 AAGTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (24 bp):
AAAGGAGCTGATTTTTTCTTTTAA
Found at i:3798463 original size:20 final size:19
Alignment explanation
Indices: 3798410--3798465 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
3798400 CCACATGCAC
3798410 ATGAAGTTTTGAAACTTTG
1 ATGAAGTTTTGAAACTTTG
* *
3798429 AGGAAAATTTTGAAACTTTG
1 ATG-AAGTTTTGAAACTTTG
*
3798449 ATGAGAGTTTCGAAACT
1 ATGA-AGTTTTGAAACT
3798466 ATTGTGAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (19 bp):
ATGAAGTTTTGAAACTTTG
Found at i:3798674 original size:20 final size:21
Alignment explanation
Indices: 3798625--3798675 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3798615 TAGTGTTTTT
3798625 CATATTTTAAAAGCTTTAAAA
1 CATATTTTAAAAGCTTTAAAA
* *
3798646 GACATTTTAAACA-CTTT-AAA
1 CATATTTTAAA-AGCTTTAAAA
3798666 CATATTTTAA
1 CATATTTTAA
3798676 TTAACTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 11 0.44
21 13 0.52
22 1 0.04
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (21 bp):
CATATTTTAAAAGCTTTAAAA
Found at i:3800223 original size:107 final size:107
Alignment explanation
Indices: 3800071--3800284 Score: 428
Period size: 107 Copynumber: 2.0 Consensus size: 107
3800061 CTTGTACTTC
3800071 GGCAACCGGTACGCATGGGAACATTTCTGCGACATATCCGATGCTCGTGTGCTGGCAGAGCAGCA
1 GGCAACCGGTACGCATGGGAACATTTCTGCGACATATCCGATGCTCGTGTGCTGGCAGAGCAGCA
3800136 AATATGGGCTGCCGTAACCGACGGCGCCAAGAACCAAGCTTT
66 AATATGGGCTGCCGTAACCGACGGCGCCAAGAACCAAGCTTT
3800178 GGCAACCGGTACGCATGGGAACATTTCTGCGACATATCCGATGCTCGTGTGCTGGCAGAGCAGCA
1 GGCAACCGGTACGCATGGGAACATTTCTGCGACATATCCGATGCTCGTGTGCTGGCAGAGCAGCA
3800243 AATATGGGCTGCCGTAACCGACGGCGCCAAGAACCAAGCTTT
66 AATATGGGCTGCCGTAACCGACGGCGCCAAGAACCAAGCTTT
3800285 CAATTGTACT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (107 bp):
GGCAACCGGTACGCATGGGAACATTTCTGCGACATATCCGATGCTCGTGTGCTGGCAGAGCAGCA
AATATGGGCTGCCGTAACCGACGGCGCCAAGAACCAAGCTTT
Found at i:3801905 original size:43 final size:42
Alignment explanation
Indices: 3801858--3801997 Score: 109
Period size: 43 Copynumber: 3.3 Consensus size: 42
3801848 TGACAACATA
* **
3801858 TAGCGACGTTTGTTGAACAAACGCCGTAAAAGGTATTGATATT
1 TAGCGACGTTTGTAGAA-AAACGCCACAAAAGGTATTGATATT
* * *
3801901 TAGCGGCGTTTTGTAGAAAAACGCCACAATAGGTGTTGATATT
1 TAGCGACG-TTTGTAGAAAAACGCCACAAAAGGTATTGATATT
* * * * * * ** *
3801944 TAACGACATTTGGCAGACAAACGCCGCAATAGGCGTTGATGTT
1 TAGCGACGTTT-GTAGAAAAACGCCACAAAAGGTATTGATATT
*
3801987 TAGCGGCGTTT
1 TAGCGACGTTT
3801998 TCTTCACAAA
Statistics
Matches: 78, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
42 3 0.04
43 67 0.86
44 8 0.10
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (42 bp):
TAGCGACGTTTGTAGAAAAACGCCACAAAAGGTATTGATATT
Found at i:3802007 original size:43 final size:43
Alignment explanation
Indices: 3801874--3802141 Score: 165
Period size: 43 Copynumber: 6.3 Consensus size: 43
3801864 CGTTTGTTGA
* * * * * **
3801874 ACAAACGCCGTAAAAGGTATTGATATTTAGCGGCGTTTTGTAG
1 ACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTCTTC
* * * * * * * **
3801917 AAAAACGCCACAATAGGTGTTGATATTTAACGACATTTGGC-AG
1 ACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTT-TCTTC
** *
3801960 ACAAACGCCGCAATAGGCGTTGATGTTTAGCGGCGTTTTCTTC
1 ACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTCTTC
* * * * *
3802003 ACAAACGCCGCAGTAGATGTTTATTTTTACCAGC-TTTT-TTCC
1 ACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTCTT-C
*
3802045 TACAAACGCCGCAGA-AGATGTTGATATTTAGCGGCGTTTTCCT-
1 -ACAAACGCCGCA-ATAGATGTTGATATTTAGCGGCGTTTTCTTC
* *
3802088 ACAAACGCCGCAATATG-TCTTGAGATTTCA-CGGCGTTTT-TATC
1 ACAAACGCCGCAATA-GATGTTGATATTT-AGCGGCGTTTTCT-TC
*
3802131 ATAAACGCCGC
1 ACAAACGCCGC
3802142 TAAATGTATG
Statistics
Matches: 176, Mismatches: 37, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
41 3 0.02
42 38 0.22
43 130 0.74
44 4 0.02
45 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (43 bp):
ACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTCTTC
Found at i:3802122 original size:42 final size:42
Alignment explanation
Indices: 3801985--3802126 Score: 119
Period size: 42 Copynumber: 3.3 Consensus size: 42
3801975 GGCGTTGATG
* * * * **
3801985 TTTAGCGGCGTTTTCTTCACAAACGCCGCAGTAGATGTTTATT
1 TTTAGCGGCGTTTTCCT-ACAAACGCCGCAGAAGATCTTGAGA
* * * * *
3802028 TTTACCAGCTTTTTTCCTACAAACGCCGCAGAAGATGTTGATA
1 TTTAGCGGC-GTTTTCCTACAAACGCCGCAGAAGATCTTGAGA
3802071 TTTAGCGGCGTTTTCCTACAAACGCCGCA-ATATG-TCTTGAGA
1 TTTAGCGGCGTTTTCCTACAAACGCCGCAGA-A-GATCTTGAGA
3802113 TTTCA-CGGCGTTTT
1 TTT-AGCGGCGTTTT
3802127 TATCATAAAC
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
41 1 0.01
42 38 0.46
43 38 0.46
44 6 0.07
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (42 bp):
TTTAGCGGCGTTTTCCTACAAACGCCGCAGAAGATCTTGAGA
Found at i:3802543 original size:21 final size:21
Alignment explanation
Indices: 3802480--3802588 Score: 94
Period size: 21 Copynumber: 5.2 Consensus size: 21
3802470 TGATATATTA
* * *
3802480 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * * *
3802501 CCTCTCTCTGTGCTGCCACTG
1 CTTCTCTCTCTGCTTCCGCTG
*
3802522 CTTCTCTCTCTACTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* **
3802543 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
*
3802564 CTGCTCTCTCTGCTTCC-CTTG
1 CTTCTCTCTCTGCTTCCGC-TG
3802585 CTTC
1 CTTC
3802589 ATTTTCCGCT
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 1 0.01
21 71 0.99
ACGTcount: A:0.03, C:0.41, G:0.17, T:0.39
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:3807489 original size:40 final size:42
Alignment explanation
Indices: 3807427--3807521 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 42
3807417 ATATTTAACA
* *
3807427 TTTTGCGGCGTTTTTAAGAAAAACGCCACTA-T-ATCACATAC
1 TTTTGTGGCGTTTATAAGAAAAACGCCACTATTGATCA-ATAC
*
3807468 TTTTGTGGCGTTTATAA-AAAAACGCCACTATTGATTAATAC
1 TTTTGTGGCGTTTATAAGAAAAACGCCACTATTGATCAATAC
*
3807509 TATTGTGGCGTTT
1 TTTTGTGGCGTTT
3807522 GTCTAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 13 0.27
41 32 0.67
42 3 0.06
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (42 bp):
TTTTGTGGCGTTTATAAGAAAAACGCCACTATTGATCAATAC
Found at i:3811447 original size:26 final size:26
Alignment explanation
Indices: 3811415--3811474 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
3811405 TACCTCATTA
3811415 TTCTTCTTGTTTTTCTTTTCTTTATC
1 TTCTTCTTGTTTTTCTTTTCTTTATC
*
3811441 TTCTTCTTGTTTTTCTTTTCTTTATT
1 TTCTTCTTGTTTTTCTTTTCTTTATC
3811467 TTCTTCTT
1 TTCTTCTT
3811475 CTTCATTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (26 bp):
TTCTTCTTGTTTTTCTTTTCTTTATC
Found at i:3812368 original size:64 final size:63
Alignment explanation
Indices: 3812295--3812457 Score: 177
Period size: 64 Copynumber: 2.6 Consensus size: 63
3812285 ATTGTTTGAA
* ** *
3812295 GGTGTATCGATGCACAGGTAGTGCATCGATGCACCCTTTTAATCTAA-AAACATCGAATGCAATT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCACCC-AGTAAT-AAACAAACATCGAATGCAATT
* * * *
3812359 GGTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAAACAAACATCGAATGTATTT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCA-CCCAGTAATAAACAAACATCGAATGCAATT
** *
3812423 TATGCACCGATGCACAGGTAGTGCATCGATGCACC
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCACC
3812458 GATAGGGAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
63 8 0.10
64 67 0.82
65 7 0.09
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (63 bp):
GGTGCATCGATGCACAGGTAGTGCATCGATGCACCCAGTAATAAACAAACATCGAATGCAATT
Found at i:3813417 original size:103 final size:103
Alignment explanation
Indices: 3813233--3813450 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
3813223 GTCGAGGGTC
* * *
3813233 TATGTAGTTCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCGGGTGAGACACATAC
* *
3813298 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
3813336 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCGGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCGGGTGAGACACATAC
*
3813401 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
3813439 TATGTGGTCCTT
1 TATGTGGTCCTT
3813451 ATAGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCGGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:3813533 original size:23 final size:23
Alignment explanation
Indices: 3813457--3813534 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
3813447 CCTTATAGAC
*
3813457 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * * *
3813481 ATTCTACGCGGCACTCCGGTACA
1 ATTATATGTGGCACTACGGTGCA
* *
3813504 ATTATATGTGGCACTTCGATGCA
1 ATTATATGTGGCACTACGGTGCA
3813527 ATTATATG
1 ATTATATG
3813535 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 39 0.93
24 3 0.07
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:3818272 original size:64 final size:65
Alignment explanation
Indices: 3818199--3818488 Score: 254
Period size: 64 Copynumber: 4.5 Consensus size: 65
3818189 ATTGTTTGAA
* * * *
3818199 GGTGTATCGATGCACAGGTAGTGCATCGATGCACT-CTTTTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCACTCCCTGTAAT-AAACAAACATCGAATGCAAT
3818262 T
65 T
* * * * * *
3818263 GGTGCATCGATGCATAAGGCA-TGCATCGATGCA-TCCCCGTAATAAACAAACATCAAATGTATT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCACTCCCTGTAATAAACAAACATCGAATGCAAT
3818326 T
65 T
** * * * * *
3818327 TATGCACCGATGCACAGGTAGTGCATCGATGTACT-CTTTTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCACTCCCTGTAAT-AAACAAACATCGAATGCAAT
3818390 T
65 T
* * * * *
3818391 GGTGCATCGATGCATAAGGCA-TGCATCGATGCA-TCCCAGTAATAAACAAACATCGAATGTATT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCACTCCCTGTAATAAACAAACATCGAATGCAAT
3818454 T
65 T
** * *
3818455 TATGCACCGATGCACAGGTAGTGTATCGATGCAC
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCAC
3818489 CGATAGGGAA
Statistics
Matches: 174, Mismatches: 41, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
63 14 0.08
64 149 0.86
65 11 0.06
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (65 bp):
GGTGCATCGATGCACAGGTAGTGCATCGATGCACTCCCTGTAATAAACAAACATCGAATGCAATT
Found at i:3818364 original size:128 final size:128
Alignment explanation
Indices: 3818206--3818488 Score: 530
Period size: 128 Copynumber: 2.2 Consensus size: 128
3818196 GAAGGTGTAT
3818206 CGATGCACAGGTAGTGCATCGATGCACTCTTTTAATCTAAAAACATCGAATGCAATTGGTGCATC
1 CGATGCACAGGTAGTGCATCGATGCACTCTTTTAATCTAAAAACATCGAATGCAATTGGTGCATC
*
3818271 GATGCATAAGGCATGCATCGATGCATCCCCGTAATAAACAAACATCAAATGTATTTTATGCAC
66 GATGCATAAGGCATGCATCGATGCATCCCAGTAATAAACAAACATCAAATGTATTTTATGCAC
*
3818334 CGATGCACAGGTAGTGCATCGATGTACTCTTTTAATCTAAAAACATCGAATGCAATTGGTGCATC
1 CGATGCACAGGTAGTGCATCGATGCACTCTTTTAATCTAAAAACATCGAATGCAATTGGTGCATC
*
3818399 GATGCATAAGGCATGCATCGATGCATCCCAGTAATAAACAAACATCGAATGTATTTTATGCAC
66 GATGCATAAGGCATGCATCGATGCATCCCAGTAATAAACAAACATCAAATGTATTTTATGCAC
*
3818462 CGATGCACAGGTAGTGTATCGATGCAC
1 CGATGCACAGGTAGTGCATCGATGCAC
3818489 CGATAGGGAA
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 150 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (128 bp):
CGATGCACAGGTAGTGCATCGATGCACTCTTTTAATCTAAAAACATCGAATGCAATTGGTGCATC
GATGCATAAGGCATGCATCGATGCATCCCAGTAATAAACAAACATCAAATGTATTTTATGCAC
Found at i:3819499 original size:103 final size:103
Alignment explanation
Indices: 3819274--3819491 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
3819264 GTCGAGGGTC
3819274 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTAGTGAGACACATAC
*
3819339 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
* * *
3819377 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATTTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTAGTGAGACACATAC
*
3819442 TTGATCCTTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
3819480 TATGTGGTCCTT
1 TATGTGGTCCTT
3819492 ATAGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTAGTGAGACACATAC
TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:3819574 original size:23 final size:23
Alignment explanation
Indices: 3819498--3819575 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
3819488 CCTTATAGAC
* *
3819498 ATTATTATATGGCACTACGGTCCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
3819522 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
3819545 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
3819568 ATTATATG
1 ATTATATG
3819576 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:3825325 original size:17 final size:18
Alignment explanation
Indices: 3825292--3825325 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3825282 CCGCTACTAG
3825292 TGAACCGGTCGGAACCGC
1 TGAACCGGTCGGAACCGC
*
3825310 TGAACCGTTC-GAACCG
1 TGAACCGGTCGGAACCG
3825326 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.32, G:0.29, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCGGAACCGC
Found at i:3842397 original size:13 final size:15
Alignment explanation
Indices: 3842381--3842412 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
3842371 GCTCTCTCAA
3842381 TTCTCTC-TATT-TT
1 TTCTCTCGTATTATT
3842394 TTCTCTCGTATTATT
1 TTCTCTCGTATTATT
3842409 TTCT
1 TTCT
3842413 TTTGCTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 4 0.24
15 6 0.35
ACGTcount: A:0.09, C:0.22, G:0.03, T:0.66
Consensus pattern (15 bp):
TTCTCTCGTATTATT
Found at i:3842488 original size:2 final size:2
Alignment explanation
Indices: 3842481--3842549 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
3842471 TGCTTTGCTC
3842481 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
3842523 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 A
3842550 CATGAAATAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3861410 original size:28 final size:29
Alignment explanation
Indices: 3861373--3861428 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
3861363 TATGAGAAGT
3861373 TGTCCTTTAT-TACATTT-TATAAAAAAAA
1 TGTCCTTTATATA-ATTTATATAAAAAAAA
3861401 TGTCCTTTATCATAATTTATATAAAAAA
1 TGTCCTTTAT-ATAATTTATATAAAAAA
3861429 GTATACTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 10 0.40
29 4 0.16
30 11 0.44
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (29 bp):
TGTCCTTTATATAATTTATATAAAAAAAA
Found at i:3861514 original size:29 final size:29
Alignment explanation
Indices: 3861440--3861505 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
3861430 TATACTTTAT
**
3861440 TTTATAAA-AAGTTTTACACTTTATTATAA
1 TTTATAAACAA-TTTTGTACTTTATTATAA
3861469 TTTATAAACAATTTTGTACTTTATTATAA
1 TTTATAAACAATTTTGTACTTTATTATAA
*
3861498 TTTTTAAA
1 TTTATAAA
3861506 ACCTTTTGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 31 0.94
30 2 0.06
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (29 bp):
TTTATAAACAATTTTGTACTTTATTATAA
Found at i:3866306 original size:26 final size:26
Alignment explanation
Indices: 3866260--3866326 Score: 88
Period size: 24 Copynumber: 2.7 Consensus size: 26
3866250 TAATTTTAAC
3866260 ATTAATTTTTTAA-A-TAAATTAAAT
1 ATTAATTTTTTAATATTAAATTAAAT
* *
3866284 ATTAATTTTTTAATATTATATTAGAT
1 ATTAATTTTTTAATATTAAATTAAAT
3866310 ATTAA--TTTTAATATTAA
1 ATTAATTTTTTAATATTAA
3866327 TTTTTTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 24 0.63
25 1 0.03
26 13 0.34
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
ATTAATTTTTTAATATTAAATTAAAT
Found at i:3866317 original size:62 final size:62
Alignment explanation
Indices: 3866230--3866384 Score: 240
Period size: 62 Copynumber: 2.5 Consensus size: 62
3866220 TTATATTTAA
* * *
3866230 TTTT-ATAGTATATTTGATTTTAATTTTAACATTAATTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTAGATATTAATTTTAACATTAATTTTTTAAATAAATTAAATATTAATT
*
3866291 TTTTAATATTATATTAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTAGATATTAATTTTAACATTAATTTTTTAAATAAATTAAATATTAATT
3866353 TTTTAATATTATATTATAGATATTTAATTTTA
1 TTTTAATATTATA-T-TAGATA-TTAATTTTA
3866385 TATCATATAA
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 4 0.05
62 66 0.77
63 1 0.01
64 6 0.07
65 9 0.10
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (62 bp):
TTTTAATATTATATTAGATATTAATTTTAACATTAATTTTTTAAATAAATTAAATATTAATT
Found at i:3866323 original size:38 final size:37
Alignment explanation
Indices: 3866281--3866363 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 37
3866271 AAATAAATTA
* *
3866281 AATATTAATTTTTTAATATTATATTAGATATTAA-TTTT
1 AATATTAATTTTTTAA-A-TAAATTAAATATTAATTTTT
3866319 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTT
1 AATATTAATTTTTTAAATAAATTAAATATTAA-TTTTT
3866357 AATATTA
1 AATATTA
3866364 TATTATAGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
36 13 0.32
37 1 0.02
38 27 0.66
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
AATATTAATTTTTTAAATAAATTAAATATTAATTTTT
Found at i:3866439 original size:20 final size:19
Alignment explanation
Indices: 3866379--3866440 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
3866369 TAGATATTTA
*
3866379 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
3866398 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
3866416 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
3866436 ATTTT
1 ATTTT
3866441 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:3866938 original size:31 final size:31
Alignment explanation
Indices: 3866903--3866962 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3866893 TAGTTGTATG
* *
3866903 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
3866934 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
3866963 CTTTTACGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:3868869 original size:28 final size:29
Alignment explanation
Indices: 3868813--3868869 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
3868803 AAAATAAATT
*
3868813 ACCAAAATAGAATTAACAGAAACTTAAGG
1 ACCAAAATAGAATAAACAGAAACTTAAGG
*
3868842 ACCAAAATAGAA-AAATAGAAACTTAAGG
1 ACCAAAATAGAATAAACAGAAACTTAAGG
3868870 GATTAAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.58, C:0.12, G:0.14, T:0.16
Consensus pattern (29 bp):
ACCAAAATAGAATAAACAGAAACTTAAGG
Found at i:3870416 original size:9 final size:10
Alignment explanation
Indices: 3870402--3870449 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 10
3870392 TAGTTATTAC
3870402 TAATAAAAT-
1 TAATAAAATA
3870411 TAATAATAATAA
1 TAATAA-AAT-A
3870423 TAATAAAATA
1 TAATAAAATA
3870433 TAATAATAAATA
1 TAAT-A-AAATA
3870445 TAATA
1 TAATA
3870450 TTTTTGTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
9 6 0.18
10 8 0.24
11 5 0.15
12 15 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAATAAAATA
Found at i:3870417 original size:12 final size:12
Alignment explanation
Indices: 3870397--3870442 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 12
3870387 TAATTTAGTT
*
3870397 ATTACTAATAAA
1 ATTAATAATAAA
3870409 ATTAATAAT--A
1 ATTAATAATAAA
3870419 A-TAATAATAAA
1 ATTAATAATAAA
3870430 ATATAATAATAAA
1 AT-TAATAATAAA
3870443 TATAATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
9 7 0.24
10 2 0.07
11 2 0.07
12 8 0.28
13 10 0.34
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
ATTAATAATAAA
Found at i:3870419 original size:3 final size:3
Alignment explanation
Indices: 3870402--3870441 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
3870392 TAGTTATTAC
3870402 TAA TAA -AA TTAA TAA TAA TAA TAA TAA -AA T-A TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3870442 ATATAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.18
3 25 0.76
4 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3870443 original size:12 final size:13
Alignment explanation
Indices: 3870419--3870449 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3870409 ATTAATAATA
3870419 ATAATAATAAAAT
1 ATAATAATAAAAT
3870432 ATAATAAT-AAAT
1 ATAATAATAAAAT
3870444 ATAATA
1 ATAATA
3870450 TTTTTGTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATAAAAT
Found at i:3870951 original size:130 final size:129
Alignment explanation
Indices: 3870764--3871105 Score: 375
Period size: 130 Copynumber: 2.6 Consensus size: 129
3870754 TATGAAAACA
* * * * * ***
3870764 ACTGGTTATCTAGGGGTGACACGGCTCTTACGTGATGAGGAGGTATGGTATGGGGATGACATGGT
1 ACTGGTTATC-AGGGGTGACACGACTCCTACGTAATGAGGAAGTATGGTACGGGGATGACACAAT
* * ** *
3870829 TCTTACGTAATGAGGATGATAGGCCATCTTTAGGGATGATAACATGGTTCGC-ACGTGATGAGGA
65 TCCTACGTAATGAGGATGATAGGCCACCTTTAGGGATGATAACACAGTTC-CTACATGATGAGGA
3870893 C
129 C
* *
3870894 GACTGGTTATCAGGGGTGACATGACTCCTACGTAATGAGGAAGTCTGGT-CGGTGGATGACACAA
1 -ACTGGTTATCAGGGGTGACACGACTCCTACGTAATGAGGAAGTATGGTACGG-GGATGACACAA
*
3870958 TTCCTACGTGATGAGGATGATAGGCCACCTTTAGGGATGATAACACAGTTCCTACATGATGAGGA
64 TTCCTACGTAATGAGGATGATAGGCCACCTTTAGGGATGATAACACAGTTCCTACATGATGAGGA
3871023 C
129 C
* * * * * * *
3871024 AGTTGGTTATCAGGGGTGACACGACTCCTACGTGATTTATGAGGTCTAGT-CAGGGGATGACACA
1 A-CTGGTTATCAGGGGTGACACGACTCCTACGT-AATGAGGAAGTATGGTAC-GGGGATGACACA
**
3871088 ATTCCTACGCGATGAGGA
63 ATTCCTACGTAATGAGGA
3871106 CGACATGCCA
Statistics
Matches: 182, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
129 4 0.02
130 127 0.70
131 49 0.27
132 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (129 bp):
ACTGGTTATCAGGGGTGACACGACTCCTACGTAATGAGGAAGTATGGTACGGGGATGACACAATT
CCTACGTAATGAGGATGATAGGCCACCTTTAGGGATGATAACACAGTTCCTACATGATGAGGAC
Found at i:3871437 original size:65 final size:61
Alignment explanation
Indices: 3871266--3871480 Score: 263
Period size: 62 Copynumber: 3.4 Consensus size: 61
3871256 GATGGTAAAT
* * *
3871266 TTTGTTTCCAAAGAAACAGACTCAATGATTTTTCTCAAAAGAAACTGTCTCGAGAGACAAAA
1 TTTGTTT-CAAAGAAACAGACTCAAAGATTTTTTTCAAAAGAAATTGTCTCGAGAGACAAAA
* * *
3871328 TTTGTTTCAAAGGAAA-AAACTCAGAGATTTTTTCTCAAATGAAATTGTCTCAAGAGAGACCAAA
1 TTTGTTTCAAA-GAAACAGACTCAAAGATTTTTT-TCAAAAGAAATTGTCTC--GAGAGA-CAAA
3871392 A
61 A
* *
3871393 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTTAAAAGAAATTGTCTCGAGAGATAAAA
1 TTTGTTT-CAAAGAAACAGACTCAAAGATTTTTTTCAAAAGAAATTGTCTCGAGAGACAAAA
*
3871455 TTTATTTCAAGAGAAACA-ACTCAAAG
1 TTTGTTTCAA-AGAAACAGACTCAAAG
3871481 GATACTGATA
Statistics
Matches: 133, Mismatches: 12, Indels: 17
0.82 0.07 0.10
Matches are distributed among these distances:
61 28 0.21
62 43 0.32
63 6 0.05
64 6 0.05
65 31 0.23
66 19 0.14
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (61 bp):
TTTGTTTCAAAGAAACAGACTCAAAGATTTTTTTCAAAAGAAATTGTCTCGAGAGACAAAA
Found at i:3873098 original size:2 final size:2
Alignment explanation
Indices: 3873091--3873125 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3873081 ATTGTATGTG
3873091 TA TA TA TA 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 TA TA TA TA T
3873126 TCTGAGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3875776 original size:30 final size:30
Alignment explanation
Indices: 3875740--3875797 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
3875730 ACGAAATATT
3875740 ACAAACACAAA-AAAAAAAT-AAGTTAGTAAC
1 ACAAACA-AAAGAAAAAAATGAA-TTAGTAAC
*
3875770 ACAAACAAAAGAGAAAAATGAATTAGTA
1 ACAAACAAAAGAAAAAAATGAATTAGTA
3875798 CCAACAAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 20 0.80
31 2 0.08
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (30 bp):
ACAAACAAAAGAAAAAAATGAATTAGTAAC
Found at i:3877441 original size:31 final size:31
Alignment explanation
Indices: 3877398--3877480 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
3877388 CATACATAAG
* *
3877398 GGATTAAAATAGAATAATAAAAAAATTTAAA
1 GGATCAAAATAGAATAATAAAAAAACTTAAA
*
3877429 GGATCAAAATAGAAT--TAACAGAAACTTAAA
1 GGATCAAAATAGAATAATAA-AAAAACTTAAA
* *
3877459 -GACCAAAATAGAAAAATAAAAA
1 GGATCAAAATAGAATAATAAAAA
3877481 CTTAAGGGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
29 15 0.35
30 11 0.26
31 17 0.40
ACGTcount: A:0.64, C:0.06, G:0.11, T:0.19
Consensus pattern (31 bp):
GGATCAAAATAGAATAATAAAAAAACTTAAA
Found at i:3877582 original size:29 final size:28
Alignment explanation
Indices: 3877424--3877584 Score: 103
Period size: 29 Copynumber: 5.6 Consensus size: 28
3877414 ATAAAAAAAT
* * *
3877424 TTAAAGGATCAAAATAGAATTAACAGAAAC
1 TTAAAGGA-CTAAATAGAA-AAATAGAAAC
* *
3877454 TTAAA-GACCAAAATAGAAAAATAAAAAC
1 TTAAAGGA-CTAAATAGAAAAATAGAAAC
* * * *
3877482 TTAAGGGATTTAA-A-AAAAATACAATCAC
1 TTAAAGGACTAAATAGAAAAATAGAA--AC
* * *
3877510 TTAAAGGACTAAAATAGAAAAACATAAAT
1 TTAAAGGACT-AAATAGAAAAATAGAAAC
* *
3877539 TTAGAGGATTAAAATAGCAAAAATAGAAAC
1 TTAAAGGACT-AAATAG-AAAAATAGAAAC
3877569 TTAAAGGACTAAATAG
1 TTAAAGGACTAAATAG
3877585 TAATTACAAA
Statistics
Matches: 102, Mismatches: 22, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
26 9 0.09
27 1 0.01
28 23 0.23
29 38 0.37
30 23 0.23
31 8 0.08
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.20
Consensus pattern (28 bp):
TTAAAGGACTAAATAGAAAAATAGAAAC
Found at i:3878680 original size:18 final size:18
Alignment explanation
Indices: 3878657--3878706 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
3878647 AACACATATG
* *
3878657 TCCCGAAGGATCGCTATA
1 TCCCGAAGGACCACTATA
3878675 TCCCGAAGGACCACTATA
1 TCCCGAAGGACCACTATA
3878693 TCCCGAAGGACCAC
1 TCCCGAAGGACCAC
3878707 ATAGAATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.30, C:0.34, G:0.20, T:0.16
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:3878690 original size:64 final size:64
Alignment explanation
Indices: 3878611--3878730 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 64
3878601 GTAGAATTTG
*
3878611 TCCCGAATGACCACTATATCCCAAAGGACCACATAGAACACATATGTCCCGAAGGATCGCTATA
1 TCCCGAAGGACCACTATATCCCAAAGGACCACATAGAACACATATGTCCCGAAGGATCGCTATA
* *
3878675 TCCCGAAGGACCACTATATCCCGAAGGACCACATAGAATACATATGTCCCGAAGGA
1 TCCCGAAGGACCACTATATCCCAAAGGACCACATAGAACACATATGTCCCGAAGGA
3878731 CCACGTAGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.17
Consensus pattern (64 bp):
TCCCGAAGGACCACTATATCCCAAAGGACCACATAGAACACATATGTCCCGAAGGATCGCTATA
Found at i:3879585 original size:19 final size:19
Alignment explanation
Indices: 3879561--3879611 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
3879551 TCTATGCTAG
3879561 GGTACCGATACCCTACCCC
1 GGTACCGATACCCTACCCC
3879580 GGTACCGATACCCTACCCC
1 GGTACCGATACCCTACCCC
*
3879599 GGTATCGATACCC
1 GGTACCGATACCC
3879612 AAATTAGCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.43, G:0.18, T:0.18
Consensus pattern (19 bp):
GGTACCGATACCCTACCCC
Found at i:3881768 original size:19 final size:18
Alignment explanation
Indices: 3881732--3881771 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3881722 ATTTAGTTAT
*
3881732 TAATAATAAAATTGATAA
1 TAATAATAAAATTAATAA
*
3881750 TAATAATTAAATATAATAA
1 TAATAATAAAAT-TAATAA
3881769 TAA
1 TAA
3881772 ATATAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TAATAATAAAATTAATAA
Found at i:3881774 original size:12 final size:13
Alignment explanation
Indices: 3881749--3881779 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3881739 AAAATTGATA
3881749 ATAATAATTAAAT
1 ATAATAATTAAAT
3881762 ATAATAA-TAAAT
1 ATAATAATTAAAT
3881774 ATAATA
1 ATAATA
3881780 TTTTTGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATAATTAAAT
Found at i:3892084 original size:12 final size:12
Alignment explanation
Indices: 3892067--3892131 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
3892057 AAAAAAATTA
3892067 ATTAAATAAAAT
1 ATTAAATAAAAT
3892079 ATTAAAATAGTTAAAT
1 ATT-AAATA---AAAT
3892095 AATTAAATAAAAT
1 -ATTAAATAAAAT
* *
3892108 ACT-AACAAAAT
1 ATTAAATAAAAT
*
3892119 ATTAAATATAAT
1 ATTAAATAAAAT
3892131 A
1 A
3892132 AAATATACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
11 9 0.21
12 12 0.29
13 9 0.21
16 9 0.21
17 3 0.07
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:3892130 original size:33 final size:31
Alignment explanation
Indices: 3892061--3892136 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 31
3892051 AACAGCAAAA
*
3892061 AAAT-TAATTAAATAAAATATTAAAATAGTT
1 AAATATAATTAAATAAAATATCAAAATAGTT
3892091 -AA-ATAATTAAATAAAATACTAACAAAATA-TT
1 AAATATAATTAAATAAAATA-T--CAAAATAGTT
*
3892122 AAATATAATAAAATA
1 AAATATAATTAAATA
3892137 TACCTTAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
29 17 0.45
30 1 0.03
31 2 0.05
32 8 0.21
33 10 0.26
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (31 bp):
AAATATAATTAAATAAAATATCAAAATAGTT
Found at i:3892136 original size:17 final size:18
Alignment explanation
Indices: 3892104--3892137 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3892094 TAATTAAATA
3892104 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
3892122 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
3892138 ACCTTAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:3894870 original size:75 final size:76
Alignment explanation
Indices: 3894667--3894899 Score: 191
Period size: 75 Copynumber: 3.2 Consensus size: 76
3894657 CATGTTTGGG
* * * * * *
3894667 CTAAATTTCCTGCACCTGAAA-CTCAAGGTAT-GCCCTGTGAACTCCCTGGAAA-CAACATGTTT
1 CTAAATTTCCTGGACC-CAAATCCCAAGCTATAGCCCTGTGAACCCCCT-GAAATCAACATGTTC
3894729 GGGAAACAA---T
64 GGGAAACAAGCTT
* * * * * * *
3894739 -TAAGTTTCCTGGACCCCAATCTCAAGCTATA-CCCTCTGAACCCCTTGGAATTAACATGTTCGG
1 CTAAATTTCCTGGACCCAAATCCCAAGCTATAGCCCTGTGAACCCCCTGAAATCAACATGTTCGG
3894802 GAAACAAGCTT
66 GAAACAAGCTT
* * * *
3894813 CTAAATTTCCTGGTCCTAAATCCCAGGCT-TAGCCCTGTGAACCCCCTCAAATCAACATGTTC-G
1 CTAAATTTCCTGGACCCAAATCCCAAGCTATAGCCCTGTGAACCCCCTGAAATCAACATGTTCGG
*
3894876 AAAAGC-AGTCTT
66 GAAA-CAAG-CTT
3894888 CTAAATTTCCTG
1 CTAAATTTCCTG
3894900 AACCTGATCC
Statistics
Matches: 128, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
70 5 0.04
71 51 0.40
74 9 0.07
75 63 0.49
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (76 bp):
CTAAATTTCCTGGACCCAAATCCCAAGCTATAGCCCTGTGAACCCCCTGAAATCAACATGTTCGG
GAAACAAGCTT
Found at i:3898419 original size:21 final size:21
Alignment explanation
Indices: 3898393--3898475 Score: 157
Period size: 21 Copynumber: 3.9 Consensus size: 21
3898383 AAACAACAGA
3898393 GAGTATCGATACTTCTTTAAT
1 GAGTATCGATACTTCTTTAAT
3898414 GAGTATCGATACTTCTTTAAT
1 GAGTATCGATACTTCTTTAAT
3898435 GAGTATCGATACTTCTTTAAT
1 GAGTATCGATACTTCTTTAAT
3898456 GAGTATCGATACTTCCTTTA
1 GAGTATCGATACTT-CTTTA
3898476 TAATATTTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 56 0.92
22 5 0.08
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (21 bp):
GAGTATCGATACTTCTTTAAT
Found at i:3899952 original size:20 final size:19
Alignment explanation
Indices: 3899915--3899964 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
3899905 CTTTAAATCA
*
3899915 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAA-TCCATTTTG
3899935 TTTTTCAAAATCCAATTTTG
1 TTTTTCAAAATCC-ATTTTG
*
3899955 -CTTTCAAAAT
1 TTTTTCAAAAT
3899965 AAAATCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTTTCAAAATCCATTTTG
Found at i:3900460 original size:3 final size:3
Alignment explanation
Indices: 3900452--3900504 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
3900442 GTTTACCTCA
* * * *
3900452 TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC ATC TTC ATC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
3900499 ATC TTC
1 TTC TTC
3900505 ATTTACCATC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.06, C:0.30, G:0.02, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:3901804 original size:21 final size:22
Alignment explanation
Indices: 3901770--3901810 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3901760 CGAGGATAGG
* *
3901770 GAGTATCTATACTT-CTTTAAT
1 GAGTATCAACACTTACTTTAAT
3901791 GAGTATCAACACTTACTTTA
1 GAGTATCAACACTTACTTTA
3901811 TAATATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (22 bp):
GAGTATCAACACTTACTTTAAT
Found at i:3902060 original size:11 final size:11
Alignment explanation
Indices: 3902044--3902101 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
3902034 ACAATATCGG
3902044 TAGTATTCATA
1 TAGTATTCATA
*
3902055 TAGTA-TC-GA
1 TAGTATTCATA
*
3902064 TACTATTCATA
1 TAGTATTCATA
*
3902075 TAGTA-TC-GA
1 TAGTATTCATA
*
3902084 TACTATTCATA
1 TAGTATTCATA
3902095 TAGTATT
1 TAGTATT
3902102 GGTACTATGT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
9 10 0.29
10 8 0.23
11 17 0.49
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (11 bp):
TAGTATTCATA
Found at i:3902109 original size:20 final size:20
Alignment explanation
Indices: 3902047--3902100 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
3902037 ATATCGGTAG
3902047 TATTCATATAGTATCGATAC
1 TATTCATATAGTATCGATAC
3902067 TATTCATATAGTATCGATAC
1 TATTCATATAGTATCGATAC
3902087 TATTCATATAGTAT
1 TATTCATATAGTAT
3902101 TGGTACTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (20 bp):
TATTCATATAGTATCGATAC
Found at i:3912168 original size:12 final size:12
Alignment explanation
Indices: 3912153--3912208 Score: 67
Period size: 12 Copynumber: 4.3 Consensus size: 12
3912143 TATATATATA
*
3912153 TATGCGTGTGTG
1 TATGTGTGTGTG
3912165 TATGTGTGTGTG
1 TATGTGTGTGTG
3912177 TATGTGTATGTGTGTG
1 TA--TG--TGTGTGTG
3912193 TATGTGTGTGTG
1 TATGTGTGTGTG
3912205 TATG
1 TATG
3912209 CGTATGTGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
12 25 0.64
14 4 0.10
16 10 0.26
ACGTcount: A:0.11, C:0.02, G:0.39, T:0.48
Consensus pattern (12 bp):
TATGTGTGTGTG
Found at i:3912170 original size:6 final size:6
Alignment explanation
Indices: 3912161--3912217 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
3912151 TATATGCGTG
* *
3912161 TGTGTA TGTGTG TGTGTA TGTGTA TGTG-- TGTGTA TGTGTG TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
*
3912207 TGCGTA TGTGT
1 TGTGTA TGTGT
3912218 GTATTAACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
4 4 0.09
6 39 0.91
ACGTcount: A:0.11, C:0.02, G:0.39, T:0.49
Consensus pattern (6 bp):
TGTGTA
Found at i:3912171 original size:10 final size:10
Alignment explanation
Indices: 3912158--3912203 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
3912148 ATATATATGC
3912158 GTGTGTGTAT
1 GTGTGTGTAT
3912168 GTGTGTG--T
1 GTGTGTGTAT
*
3912176 GTATGTGTAT
1 GTGTGTGTAT
3912186 GTGTGTGTAT
1 GTGTGTGTAT
3912196 GTGTGTGT
1 GTGTGTGT
3912204 GTATGCGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.22
10 25 0.78
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (10 bp):
GTGTGTGTAT
Found at i:3912197 original size:28 final size:28
Alignment explanation
Indices: 3912158--3912219 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
3912148 ATATATATGC
*
3912158 GTGTGTGTATGTGTGTGTGTATGTGTAT
1 GTGTGTGTATGTGTGTGTGTATGCGTAT
3912186 GTGTGTGTATGTGTGTGTGTATGCGTAT
1 GTGTGTGTATGTGTGTGTGTATGCGTAT
3912214 GTGTGT
1 GTGTGT
3912220 ATTAACCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.10, C:0.02, G:0.40, T:0.48
Consensus pattern (28 bp):
GTGTGTGTATGTGTGTGTGTATGCGTAT
Found at i:3913348 original size:23 final size:23
Alignment explanation
Indices: 3913316--3913359 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3913306 GCCCAACAAC
*
3913316 AGCTTCTAGAAGGCTCAATCAGT
1 AGCTTCTAGAAGACTCAATCAGT
* *
3913339 AGCTTTTAGAAGATTCAATCA
1 AGCTTCTAGAAGACTCAATCA
3913360 ATACCGGGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (23 bp):
AGCTTCTAGAAGACTCAATCAGT
Found at i:3914214 original size:18 final size:19
Alignment explanation
Indices: 3914193--3914228 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3914183 GAATTTATTT
3914193 TTTTAATTT-ATCATTTTA
1 TTTTAATTTAATCATTTTA
*
3914211 TTTTATTTTAATCATTTT
1 TTTTAATTTAATCATTTT
3914229 TATTACTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTAATTTAATCATTTTA
Found at i:3919529 original size:18 final size:19
Alignment explanation
Indices: 3919495--3919533 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3919485 TTACTTTTAA
3919495 TTTTTAGTTTTCAATTCCGT
1 TTTTTAGTTTTCAATT-CGT
3919515 TTTTTA-TTTTC-ATTCGT
1 TTTTTAGTTTTCAATTCGT
3919532 TT
1 TT
3919534 ATTTTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 3 0.16
19 5 0.26
20 6 0.32
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTTTAGTTTTCAATTCGT
Found at i:3921652 original size:8 final size:8
Alignment explanation
Indices: 3921639--3921670 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3921629 ATTAGTGATC
3921639 AAATTTAA
1 AAATTTAA
3921647 AAATTTAA
1 AAATTTAA
3921655 AAATTTAA
1 AAATTTAA
*
3921663 AGATTTAA
1 AAATTTAA
3921671 TGCTACAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
AAATTTAA
Found at i:3924130 original size:19 final size:20
Alignment explanation
Indices: 3924106--3924178 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
3924096 AACTAATTTT
3924106 GGTATCGATACC-ATATAGG
1 GGTATCGATACCTATATAGG
* *
3924125 GGTATCAATACCATATTATAGT
1 GGTATCGATACC-TA-TATAGG
* *
3924147 GGTATCGATACCTATGGTAAG
1 GGTATCGATACCTAT-ATAGG
3924168 GGTATCGATAC
1 GGTATCGATAC
3924179 GGGGCCATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 11 0.25
20 1 0.02
21 16 0.36
22 16 0.36
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (20 bp):
GGTATCGATACCTATATAGG
Found at i:3924204 original size:96 final size:96
Alignment explanation
Indices: 3924051--3924269 Score: 239
Period size: 96 Copynumber: 2.3 Consensus size: 96
3924041 ACCTAATGAT
* * *
3924051 GTGGTATCAATACC-ATGGTGAGGGTAT-GATACCGGGTAACATCGAAACTAATTTTGGTATCGA
1 GTGGTATCGATACCTATGGTAAGGGTATCGATACCGGGCAACATCGAAACTAATTTTGGTATCGA
* *
3924114 TACCATATA-GGGGTATCAATACCATATTATA
66 TA-CATATAGGGGGTATCAATACCATAGTAGA
* * * * * *
3924145 GTGGTATCGATACCTATGGTAAGGGTATCGATACGGGGCCATATCGAATCTAATTTTGGTTTTGA
1 GTGGTATCGATACCTATGGTAAGGGTATCGATACCGGGCAACATCGAAACTAATTTTGGTATCGA
* * * *
3924210 TACTTGTAGGGGGTATCGATACCATAGTAGG
66 TACATATAGGGGGTATCAATACCATAGTAGA
* * *
3924241 GTAGTATCGATA-CTATAGTAGGGGTATCG
1 GTGGTATCGATACCTATGGTAAGGGTATCG
3924270 TTACTGAAGG
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
94 13 0.12
95 31 0.30
96 60 0.58
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (96 bp):
GTGGTATCGATACCTATGGTAAGGGTATCGATACCGGGCAACATCGAAACTAATTTTGGTATCGA
TACATATAGGGGGTATCAATACCATAGTAGA
Found at i:3924269 original size:20 final size:20
Alignment explanation
Indices: 3924219--3924274 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 20
3924209 ATACTTGTAG
*
3924219 GGGGTATCGATACCATAGTA
1 GGGGTATCGATACTATAGTA
3924239 GGGTAGTATCGATACTATAGTA
1 GGG--GTATCGATACTATAGTA
*
3924261 GGGGTATCGTTACT
1 GGGGTATCGATACT
3924275 GAAGGGCCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.41
22 19 0.59
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (20 bp):
GGGGTATCGATACTATAGTA
Found at i:3924898 original size:79 final size:79
Alignment explanation
Indices: 3924677--3924906 Score: 334
Period size: 79 Copynumber: 2.9 Consensus size: 79
3924667 GAAAAGAATG
* * * *
3924677 TAAAAGAATAATGCATATGGGTGCATTATTGGCGTGAAAGGATGCTATAACTGAAATGTATATGA
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
*
3924742 GTATATTGTCAGCA
66 GTACATTGTCAGCA
* * *
3924756 TAAAAGAATAATGCATATGGGTACATTATTGGCATGAAAGGATGCCATAGCTAAAATATATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
3924821 GTACATTGTCAGCA
66 GTACATTGTCAGCA
* * * * *
3924835 TAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAAGATGCCAGAGTTGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
*
3924900 GTGCATT
66 GTACATT
3924907 ATCAACAGAA
Statistics
Matches: 134, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 134 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
GTACATTGTCAGCA
Found at i:3924930 original size:45 final size:44
Alignment explanation
Indices: 3924848--3925031 Score: 170
Period size: 45 Copynumber: 4.1 Consensus size: 44
3924838 AAGAATAATA
*** * *
3924848 CATATGGGTGCATTATTGGCATGAAAAGATGCCAGAGTTGAAATG
1 CATATGGGTGCATTATCAACA-GAAAATATGCTAGAGTTGAAATG
*
3924893 CATATGGGTGCATTATCAACAGAAAAATATGCTAGAGTTGAGATG
1 CATATGGGTGCATTATCAACAG-AAAATATGCTAGAGTTGAAATG
* * * * * * *
3924938 TATATGGGTACATTATCAATATAAAAGTATACTATAGTTGAAATA
1 CATATGGGTGCATTATCAACAGAAAA-TATGCTAGAGTTGAAATG
* * * * *
3924983 CATATAGGTGCAATATCAACAGAAAATATGTTATAGTTTAAAATG
1 CATATGGGTGCATTATCAACAGAAAATATGCTAGAG-TTGAAATG
3925028 CATA
1 CATA
3925032 ATGATGTATT
Statistics
Matches: 112, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
44 13 0.12
45 99 0.88
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (44 bp):
CATATGGGTGCATTATCAACAGAAAATATGCTAGAGTTGAAATG
Found at i:3925043 original size:90 final size:89
Alignment explanation
Indices: 3924883--3925052 Score: 191
Period size: 90 Copynumber: 1.9 Consensus size: 89
3924873 AAGATGCCAG
* * * * * *
3924883 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATGCTAGAGTTGAGATGTATATGGGTA
1 AGTTGAAATACATATAGGTGCAATATCAACAGAAAAATATGCTAGAGTTAAAATGCATATGGGTA
* *
3924948 CATTATCAATATAAAAGTATACTAT
66 -ATTATAAACATAAAAGTATACTAT
* * *
3924973 AGTTGAAATACATATAGGTGCAATATCAACAG-AAAATATGTTATAGTTTAAAATGCATAATGAT
1 AGTTGAAATACATATAGGTGCAATATCAACAGAAAAATATGCTAGAG-TTAAAATGCAT-ATG-G
3925037 GT-ATTATAAACATAAA
63 GTAATTATAAACATAAA
3925053 CGAAGGTTAC
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
89 12 0.18
90 49 0.74
91 3 0.05
92 2 0.03
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (89 bp):
AGTTGAAATACATATAGGTGCAATATCAACAGAAAAATATGCTAGAGTTAAAATGCATATGGGTA
ATTATAAACATAAAAGTATACTAT
Found at i:3931155 original size:22 final size:20
Alignment explanation
Indices: 3931109--3931161 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
3931099 AACCTAATTT
*
3931109 TGGTATCGATACCATATAGG
1 TGGTATCGATACCATATAAG
*
3931129 T-GTATCGGTACCATAGTATAG
1 TGGTATCGATACCATA-TA-AG
3931150 TGGTATCGATAC
1 TGGTATCGATAC
3931162 TTATGGTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 13 0.48
20 3 0.11
21 2 0.07
22 9 0.33
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (20 bp):
TGGTATCGATACCATATAAG
Found at i:3931273 original size:20 final size:20
Alignment explanation
Indices: 3931225--3931277 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
3931215 ACTGGTAGGG
* *
3931225 GGTATCAATACCATAGTAGG
1 GGTATCGATACCATAGTAGA
3931245 GTAGTATCGATACCATAGTAGA
1 G--GTATCGATACCATAGTAGA
3931267 GGTATCGATAC
1 GGTATCGATAC
3931278 TGAAGGGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.38
22 18 0.62
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCATAGTAGA
Found at i:3931811 original size:79 final size:79
Alignment explanation
Indices: 3931680--3931922 Score: 405
Period size: 79 Copynumber: 3.1 Consensus size: 79
3931670 AAAATGAATG
* *
3931680 TAAAAGAATAATGTATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
*
3931745 GTACATTGTCAGCA
66 GTACATTGTCAACA
3931759 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
3931824 GTACATTGTCAACA
66 GTACATTGTCAACA
* * *
3931838 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGTTGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
* *
3931903 GTGCATTATCAACA
66 GTACATTGTCAACA
*
3931917 AAAAAG
1 TAAAAG
3931923 TATGCTAGAA
Statistics
Matches: 155, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 155 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
GTACATTGTCAACA
Found at i:3931946 original size:45 final size:45
Alignment explanation
Indices: 3931847--3932034 Score: 189
Period size: 45 Copynumber: 4.2 Consensus size: 45
3931837 ATAAAAGAAT
*** ** * *
3931847 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAGAGTTGA
*
3931892 AATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAGAATTGA
1 AATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAGAGTTGA
* * * * ** * *
3931937 GATGTATATGGGTACATTATCAACATAAAAGTATATTATAGTTAA
1 AATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAGAGTTGA
* * *
3931982 AATGCATATGGGTGCATTATCAACAAAAAAG-ATGTTATAGTTTAA
1 AATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAGAG-TTGA
3932027 AATGCATA
1 AATGCATA
3932035 ATGATGTATT
Statistics
Matches: 120, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
44 8 0.07
45 112 0.93
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAGAGTTGA
Found at i:3932046 original size:45 final size:45
Alignment explanation
Indices: 3931886--3932051 Score: 156
Period size: 45 Copynumber: 3.7 Consensus size: 45
3931876 AGGATGCCAG
* * ** *
3931886 AGTTGAAATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAG
1 AGTTAAAATGCATATGGATGCATTATCAACAAAAAAGTATATTAT
* * * * * * *
3931931 AATTGAGATGTATATGGGTACATTATCAACATAAAAGTATATTAT
1 AGTTAAAATGCATATGGATGCATTATCAACAAAAAAGTATATTAT
* *
3931976 AGTTAAAATGCATATGGGTGCATTATCAACAAAAAAG-ATGTTAT
1 AGTTAAAATGCATATGGATGCATTATCAACAAAAAAGTATATTAT
* *
3932020 AGTTTAAAATGCATAAT-GATGTATTATAAACA
1 AG-TTAAAATGCAT-ATGGATGCATTATCAACA
3932052 TAAACGGAGG
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
44 8 0.08
45 91 0.90
46 2 0.02
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.31
Consensus pattern (45 bp):
AGTTAAAATGCATATGGATGCATTATCAACAAAAAAGTATATTAT
Found at i:3932046 original size:90 final size:89
Alignment explanation
Indices: 3931886--3932055 Score: 209
Period size: 90 Copynumber: 1.9 Consensus size: 89
3931876 AGGATGCCAG
* * * *
3931886 AGTTGAAATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAGAATTGAGATGTATATGGGTA
1 AGTTAAAATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAGAATTAAAATGCATATGGGTA
*
3931951 CATTATCAACATAAAAGTATATTAT
66 -ATTATAAACATAAAAGTATATTAT
* * * *
3931976 AGTTAAAATGCATATGGGTGCATTATCAACAAAAAAG-ATGTTATAGTTTAAAATGCATAATGAT
1 AGTTAAAATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAGA-ATTAAAATGCAT-ATG-G
3932040 GT-ATTATAAACATAAA
63 GTAATTATAAACATAAA
3932056 CGGAGGTTAC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
89 6 0.09
90 57 0.84
91 3 0.04
92 2 0.03
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (89 bp):
AGTTAAAATGCATATGGGTGCATTATCAACAAAAAAGTATGCTAGAATTAAAATGCATATGGGTA
ATTATAAACATAAAAGTATATTAT
Found at i:3932515 original size:20 final size:20
Alignment explanation
Indices: 3932492--3932531 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3932482 ATGGGTGTTA
* *
3932492 CAATGTAAATGGACTCTTTT
1 CAATATAAATGGACTATTTT
*
3932512 CAATATTAATGGACTATTTT
1 CAATATAAATGGACTATTTT
3932532 ATGGGTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (20 bp):
CAATATAAATGGACTATTTT
Found at i:3932658 original size:15 final size:16
Alignment explanation
Indices: 3932624--3932661 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3932614 ATGAAATGTG
* *
3932624 TAATATACTAATTGTT
1 TAATATACTAATTATC
3932640 TAATAT-CTAATTATC
1 TAATATACTAATTATC
3932655 TAATATA
1 TAATATA
3932662 TGCAATGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (16 bp):
TAATATACTAATTATC
Found at i:3934296 original size:30 final size:31
Alignment explanation
Indices: 3934237--3934300 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
3934227 ATGCTTTAAA
3934237 ACTCTTCTCAAAGCGCCTTTTTCGGGTTTTC
1 ACTCTTCTCAAAGCGCCTTTTTCGGGTTTTC
*
3934268 ACTCTTCTCAAAGCTCCTTTTT-GGGTTTTC
1 ACTCTTCTCAAAGCGCCTTTTTCGGGTTTTC
3934298 ACT
1 ACT
3934301 TTGGTGTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.44
Consensus pattern (31 bp):
ACTCTTCTCAAAGCGCCTTTTTCGGGTTTTC
Found at i:3934405 original size:16 final size:16
Alignment explanation
Indices: 3934383--3934417 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3934373 TTTCGTTTAT
*
3934383 TTTTTTCTTTATTCTTC
1 TTTTTCCTTT-TTCTTC
3934400 TTTTTCCTTTTTCTTC
1 TTTTTCCTTTTTCTTC
3934416 TT
1 TT
3934418 CTAAACTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTCCTTTTTCTTC
Done.