Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_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: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 17
Found at i:2195211 original size:2 final size:2
Alignment explanation
Indices: 2195204--2195234 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2195194 ATACCTCATA
2195204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2195235 ACAAAATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2195974 original size:19 final size:19
Alignment explanation
Indices: 2195952--2196014 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
2195942 GATCAAATTA
2195952 AATAACATCTTAAAAATAT
1 AATAACATCTTAAAAATAT
* **
2195971 AATACCAGGTACCCAAAAATATAT
1 AATAACA--T--CTTAAAA-ATAT
2195995 AATAACATCTTAAAAATAT
1 AATAACATCTTAAAAATAT
2196014 A
1 A
2196015 TTTTAATACA
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
19 11 0.33
20 5 0.15
21 1 0.03
22 1 0.03
23 5 0.15
24 10 0.30
ACGTcount: A:0.56, C:0.14, G:0.03, T:0.27
Consensus pattern (19 bp):
AATAACATCTTAAAAATAT
Found at i:2197316 original size:22 final size:23
Alignment explanation
Indices: 2197285--2197331 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2197275 TAATCGCGAG
2197285 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* *
2197307 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
2197330 TT
1 TT
2197332 ATTTAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Found at i:2200091 original size:17 final size:16
Alignment explanation
Indices: 2200062--2200127 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
2200052 TCTTCTCTCA
2200062 CCTTTTCTTTCCTTCT
1 CCTTTTCTTTCCTTCT
2200078 CCTTTTCTTTTCCTTCT
1 CCTTTTC-TTTCCTTCT
* * * *
2200095 -CTTTCCTCCTCTTTTT
1 CCTTTTCT-TTCCTTCT
*
2200111 CCTTTCCTTTCCTTCT
1 CCTTTTCTTTCCTTCT
2200127 C
1 C
2200128 TCTCTCTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
15 1 0.03
16 23 0.57
17 16 0.40
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
CCTTTTCTTTCCTTCT
Found at i:2200092 original size:27 final size:27
Alignment explanation
Indices: 2200062--2200120 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
2200052 TCTTCTCTCA
* *
2200062 CCTTTTCTTTCCTTCTCCTTTTCTTTT
1 CCTTTTCTTTCCTCCTCCTTTTCCTTT
* *
2200089 CCTTCTCTTTCCTCCTCTTTTTCCTTT
1 CCTTTTCTTTCCTCCTCCTTTTCCTTT
2200116 CCTTT
1 CCTTT
2200121 CCTTCTCTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (27 bp):
CCTTTTCTTTCCTCCTCCTTTTCCTTT
Found at i:2200113 original size:22 final size:22
Alignment explanation
Indices: 2200085--2200144 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
2200075 TCTCCTTTTC
2200085 TTTTCCTTCTCTTTCCTCCTCT
1 TTTTCCTTCTCTTTCCTCCTCT
*
2200107 TTTTCCTT-TCCTTTCCTTCTCT
1 TTTTCCTTCT-CTTTCCTCCTCT
* *
2200129 CTCT-CTTCTC-TTCCTC
1 TTTTCCTTCTCTTTCCTC
2200145 TTTCTCCTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
20 5 0.16
21 5 0.16
22 22 0.69
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTCCTTCTCTTTCCTCCTCT
Found at i:2200148 original size:32 final size:31
Alignment explanation
Indices: 2200077--2200148 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
2200067 TCTTTCCTTC
* *
2200077 TCCT-TTTCTTTTCCTTCTCTTTCCTCCTCT
1 TCCTCTTTCCTTTCCTTCTCTCTCCTCCTCT
** *
2200107 TTTTCCTTTCCTTTCCTTCTCTCTCTCTTCTCT
1 TCCT-CTTTCCTTTCCTTCTCTCTC-CTCCTCT
2200140 TCCTCTTTC
1 TCCTCTTTC
2200149 TCCTCCTCCT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
30 2 0.06
32 22 0.69
33 8 0.25
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (31 bp):
TCCTCTTTCCTTTCCTTCTCTCTCCTCCTCT
Found at i:2205438 original size:2 final size:2
Alignment explanation
Indices: 2205431--2205459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2205421 TTTTCTTTAA
2205431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2205460 ACATAAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2206507 original size:17 final size:17
Alignment explanation
Indices: 2206485--2206541 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
2206475 CTATTTTAAA
2206485 TATTTTAATAATATTAT
1 TATTTTAATAATATTAT
* *
2206502 TATTTTGATAAGTAATTAA
1 TATTTTAATAA-T-ATTAT
*
2206521 TATAATTAATAATA-TAT
1 TAT-TTTAATAATATTAT
2206538 TATT
1 TATT
2206542 CTTATATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
17 15 0.48
18 2 0.06
19 8 0.26
20 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
TATTTTAATAATATTAT
Found at i:2206562 original size:33 final size:37
Alignment explanation
Indices: 2206489--2206569 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 37
2206479 TTTAAATATT
2206489 TTAATAATATTATTATTTTGATAAGTAATTAATATAA
1 TTAATAATATTATTATTTTGATAAGTAATTAATATAA
*
2206526 TTAATAATA-TATTATTCTT-AT-ATTAA-T-ATATAA
1 TTAATAATATTATTATT-TTGATAAGTAATTAATATAA
*
2206559 TTAATATTATT
1 TTAATAATATT
2206570 CATATAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 14 0.35
34 2 0.05
35 4 0.10
36 9 0.22
37 11 0.28
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (37 bp):
TTAATAATATTATTATTTTGATAAGTAATTAATATAA
Found at i:2206583 original size:42 final size:39
Alignment explanation
Indices: 2206489--2206598 Score: 95
Period size: 42 Copynumber: 2.8 Consensus size: 39
2206479 TTTAAATATT
* *
2206489 TTAATAATATTATTATTTTGAT--AA-GTAATTAATATAA
1 TTAATAATA-TATTATTTTAATAAAATATAATTAATATAA
* *
2206526 TTAATAATATATTATTCTTATATTAATATATAATTAATATTA
1 TTAATAATATATTATT-TTA-A-TAAAATATAATTAATATAA
2206568 TTCATATAAT-T-TTATTTTAATAAAATATAAT
1 TT-A-ATAATATATTATTTTAATAAAATATAAT
2206599 ATTTTTAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
36 7 0.12
37 11 0.18
38 1 0.02
39 11 0.18
40 1 0.02
41 4 0.07
42 18 0.30
43 2 0.03
44 5 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (39 bp):
TTAATAATATATTATTTTAATAAAATATAATTAATATAA
Found at i:2206596 original size:39 final size:42
Alignment explanation
Indices: 2206514--2206598 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
2206504 TTTTGATAAG
*
2206514 TAATTAATATAATTAATAATATATTATTCTTATATTAATATA
1 TAATTAATATAATTAATAATATATTATTCTTATATTAAAATA
*
2206556 TAATTAATATTATTCATATAAT-T-TTATT-TTA-A-TAAAATA
1 TAATTAATATAATT-A-ATAATATATTATTCTTATATTAAAATA
2206595 TAAT
1 TAAT
2206599 ATTTTTAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
39 10 0.26
40 1 0.03
41 3 0.08
42 18 0.46
43 2 0.05
44 5 0.13
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (42 bp):
TAATTAATATAATTAATAATATATTATTCTTATATTAAAATA
Found at i:2215880 original size:18 final size:18
Alignment explanation
Indices: 2215857--2215894 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2215847 ACAGCAGCCA
*
2215857 CCGCAGCCATTTATGATG
1 CCGCAGCCATATATGATG
2215875 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
2215893 CC
1 CC
2215895 TCCGCCTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:2216424 original size:26 final size:24
Alignment explanation
Indices: 2216353--2216424 Score: 60
Period size: 26 Copynumber: 3.0 Consensus size: 24
2216343 TTATATTTGT
2216353 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
* * *
2216378 ATTT--TTTATTATATCT-CATTTA
1 ATTTACTTTATTTTGT-TAAATTTA
2216400 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
2216425 GTTAGACTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 11
0.67 0.12 0.21
Matches are distributed among these distances:
22 4 0.11
23 11 0.31
24 3 0.09
25 5 0.14
26 12 0.34
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:2219822 original size:13 final size:15
Alignment explanation
Indices: 2219785--2219826 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2219775 TATTTTTTTA
2219785 AATAATCATAATAAAC
1 AATAAT-ATAATAAAC
2219801 AATAAATATAATAAA-
1 AAT-AATATAATAAAC
2219816 AATATATATAA
1 AATA-ATATAA
2219827 CAAAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 9 0.38
16 11 0.46
17 3 0.12
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAATATAATAAAC
Found at i:2219824 original size:15 final size:15
Alignment explanation
Indices: 2219792--2219831 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2219782 TTAAATAATC
2219792 ATAATAAACAATAAAT
1 ATAATAAA-AATAAAT
*
2219808 ATAATAAAAATATAT
1 ATAATAAAAATAAAT
*
2219823 ATAACAAAA
1 ATAATAAAA
2219832 TTTATAACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (15 bp):
ATAATAAAAATAAAT
Found at i:2229189 original size:15 final size:15
Alignment explanation
Indices: 2229169--2229207 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2229159 GATCGATGTC
2229169 AGTTCAGGTCAAAAT
1 AGTTCAGGTCAAAAT
*
2229184 AGTTCATGTCAAAAT
1 AGTTCAGGTCAAAAT
*
2229199 AGTTTAGGT
1 AGTTCAGGT
2229208 TCGGAGCAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (15 bp):
AGTTCAGGTCAAAAT
Found at i:2238351 original size:24 final size:24
Alignment explanation
Indices: 2238324--2238400 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
2238314 TTTTATTTGG
*
2238324 ATTTTGATATGATATTTGACATGA
1 ATTTTGATATGATACTTGACATGA
* * *
2238348 ATTTTTATATATGATACTTGACCTGG
1 A-TTTT-GATATGATACTTGACATGA
* * *
2238374 ATTTTGATCTGCTACTTGACGTGA
1 ATTTTGATATGATACTTGACATGA
2238398 ATT
1 ATT
2238401 ATTTTTTGAT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
24 18 0.43
25 8 0.19
26 16 0.38
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.45
Consensus pattern (24 bp):
ATTTTGATATGATACTTGACATGA
Found at i:2239318 original size:2 final size:2
Alignment explanation
Indices: 2239313--2239351 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2239303 ATGAAATAAT
2239313 TA TA 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 TA TA T
2239352 GTTCCAAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2239621 original size:21 final size:22
Alignment explanation
Indices: 2239596--2239651 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
2239586 GTATATAGTT
* *
2239596 TATATAATTATATTA-ATGAAC
1 TATATAATTATAGTATATAAAC
2239617 TATATAATTCATTAGTATATAAAC
1 TATATAATT-A-TAGTATATAAAC
2239641 TATAT-ATTATA
1 TATATAATTATA
2239652 AAGTTCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 11 0.37
22 2 0.07
23 7 0.23
24 10 0.33
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (22 bp):
TATATAATTATAGTATATAAAC
Found at i:2239716 original size:31 final size:31
Alignment explanation
Indices: 2239574--2239717 Score: 125
Period size: 31 Copynumber: 4.6 Consensus size: 31
2239564 GTTTATCTTA
*
2239574 ATAAACTATAAAGTATATAGTTTA-TA-TA-
1 ATAAACTATAAAGTATATAGTTCATTAGTAT
* * * * *
2239602 ATTATATTAATGAACTATATAATTCATTAGTAT
1 A-TAAACT-ATAAAGTATATAGTTCATTAGTAT
* * *
2239635 ATAAACTATATATTATAAAGTTCATTAGTATAT
1 ATAAACTATAAAGTATATAGTTCATTAG--TAT
*
2239668 ATAAACTAGATAA-TATATAGTTCATTAGTAT
1 ATAAACTATA-AAGTATATAGTTCATTAGTAT
2239699 ATAAACTATAAAGTATATA
1 ATAAACTATAAAGTATATA
2239718 TAATCTATAT
Statistics
Matches: 90, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.01
29 4 0.04
30 15 0.17
31 36 0.40
32 6 0.07
33 27 0.30
34 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (31 bp):
ATAAACTATAAAGTATATAGTTCATTAGTAT
Found at i:2239717 original size:33 final size:32
Alignment explanation
Indices: 2239617--2239719 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 32
2239607 ATTAATGAAC
*
2239617 TATATAATTCATTAGTATATAAACTATATAT-
1 TATATAGTTCATTAGTATATAAACTATATATA
* *
2239648 TATAAAGTTCATTAGTATATATAAACTAGATA-A
1 TATATAGTTCATTAG--TATATAAACTATATATA
*
2239681 TATATAGTTCATTAGTATATAAACTATAAAGTA
1 TATATAGTTCATTAGTATATAAACTATATA-TA
2239714 TATATA
1 TATATA
2239720 ATCTATATAG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 26 0.43
33 35 0.57
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.41
Consensus pattern (32 bp):
TATATAGTTCATTAGTATATAAACTATATATA
Found at i:2239757 original size:117 final size:114
Alignment explanation
Indices: 2239617--2239877 Score: 310
Period size: 117 Copynumber: 2.3 Consensus size: 114
2239607 ATTAATGAAC
*
2239617 TATATAATTCATTAG-TATATAAACTATATATTATAAAGTTCATTAGTATATATAAACTAGATAA
1 TATATAGTTCATTAGTTATATAAACTATATATTATAAAGTTCATTAGTATATATAAACTAGATAA
*** * * *
2239681 TATATAGTTCATTA-GTATATAAACTATAAAGTATATATAATCTATATAGT
66 TATATA-AAAATTATATATATAAACTATAAAGTATATACAAACTATATA-T
* * * * * *
2239731 TCATGTAGTTCATTAGTTTATATAAACTATATATTATATAGTTTATTGGTATGTATAAACTATAT
1 T-ATATAGTTCATTAG-TTATATAAACTATATATTATAAAGTTCATTAGTATATATAAACTAGAT
** **
2239796 GGTATATAAAAATTATATATATAAACTATATGGTATATACAAACTATATAT
64 AATATATAAAAATTATATATATAAACTATAAAGTATATACAAACTATATAT
2239847 TATATAGTTCATTAGTATATATAAACTATAT
1 TATATAGTTCATTAGT-TATATAAACTATAT
2239878 GGTATATATA
Statistics
Matches: 124, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
114 2 0.02
115 39 0.31
116 6 0.05
117 77 0.62
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (114 bp):
TATATAGTTCATTAGTTATATAAACTATATATTATAAAGTTCATTAGTATATATAAACTAGATAA
TATATAAAAATTATATATATAAACTATAAAGTATATACAAACTATATAT
Found at i:2239819 original size:31 final size:31
Alignment explanation
Indices: 2239784--2239846 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
2239774 TATTGGTATG
*
2239784 TATAAACTATATGGTATATAAAAATTATATA
1 TATAAACTATATGGTATATAAAAACTATATA
*
2239815 TATAAACTATATGGTATATACAAACTATATA
1 TATAAACTATATGGTATATAAAAACTATATA
2239846 T
1 T
2239847 TATATAGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (31 bp):
TATAAACTATATGGTATATAAAAACTATATA
Found at i:2239884 original size:33 final size:34
Alignment explanation
Indices: 2239828--2239987 Score: 114
Period size: 33 Copynumber: 4.7 Consensus size: 34
2239818 AAACTATATG
* *
2239828 GTATATACAAACTATATATTATATAGT-TCATTA
1 GTATATATAAACTATATAGTATATAGTATCATTA
* *
2239861 GTATATATAAACTATATGGTATATA-TAAACTATATA
1 GTATATATAAACTATATAGTATATAGT-ATC-AT-TA
* ** * * * *
2239897 TTATATAGTTCATTAGTAT-GTATAAACTATATATTA
1 GTATATA-TAAACTA-TATAGTATATAGTAT-CATTA
* *
2239933 -TATATATAAACTATATATTATATAGT-TTATTA
1 GTATATATAAACTATATAGTATATAGTATCATTA
2239965 GTATATATAAACTATATAGTATA
1 GTATATATAAACTATATAGTATA
2239988 AATTAATAAT
Statistics
Matches: 99, Mismatches: 18, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
32 6 0.06
33 47 0.47
34 11 0.11
35 8 0.08
36 10 0.10
37 13 0.13
38 4 0.04
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (34 bp):
GTATATATAAACTATATAGTATATAGTATCATTA
Found at i:2239897 original size:53 final size:51
Alignment explanation
Indices: 2239807--2239987 Score: 283
Period size: 51 Copynumber: 3.5 Consensus size: 51
2239797 GTATATAAAA
* *
2239807 ATTA-TATATATAAACTATATGGTATATACAAACTATATATTATATAGTTC
1 ATTAGTATATATAAACTATATAGTATATATAAACTATATATTATATAGTTC
*
2239857 ATTAGTATATATAAACTATATGGTATATATAAACTATATATTATATAGTTC
1 ATTAGTATATATAAACTATATAGTATATATAAACTATATATTATATAGTTC
* * *
2239908 ATTAGTATGTATAAACTATATATTATATATATAAACTATATATTATATAGTTT
1 ATTAGTATATATAAACTATATA--GTATATATAAACTATATATTATATAGTTC
2239961 ATTAGTATATATAAACTATATAGTATA
1 ATTAGTATATATAAACTATATAGTATA
2239988 AATTAATAAT
Statistics
Matches: 121, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
50 4 0.03
51 69 0.57
53 48 0.40
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (51 bp):
ATTAGTATATATAAACTATATAGTATATATAAACTATATATTATATAGTTC
Found at i:2239901 original size:18 final size:18
Alignment explanation
Indices: 2239696--2239987 Score: 160
Period size: 18 Copynumber: 17.1 Consensus size: 18
2239686 AGTTCATTAG
*
2239696 TATATAAACTATAAAGTA
1 TATATAAACTATATAGTA
*
2239714 TATATAATCTATATAGT-
1 TATATAAACTATATAGTA
* ** *
2239731 TCATGT-AGTTCAT-TAGTT
1 T-ATATAAACT-ATATAGTA
2239749 TATATAAACTATATA-T-
1 TATATAAACTATATAGTA
*** *
2239765 TATATAGTTTAT-TGGTA
1 TATATAAACTATATAGTA
* *
2239782 TGTATAAACTATATGGTA
1 TATATAAACTATATAGTA
2239800 TATA-AAA--AT-TA-TA
1 TATATAAACTATATAGTA
*
2239813 TATATAAACTATATGGTA
1 TATATAAACTATATAGTA
*
2239831 TATACAAACTATATA-T-
1 TATATAAACTATATAGTA
**
2239847 TATAT-AGTTCAT-TAGTA
1 TATATAAACT-ATATAGTA
*
2239864 TATATAAACTATATGGTA
1 TATATAAACTATATAGTA
2239882 TATATAAACTATATA-T-
1 TATATAAACTATATAGTA
**
2239898 TATAT-AGTTCAT-TAGTA
1 TATATAAACT-ATATAGTA
* *
2239915 TGTATAAACTATATATTATA
1 TATATAAACTATATA--GTA
2239935 TATATAAACTATATA-T-
1 TATATAAACTATATAGTA
***
2239951 TATATAGTTTAT-TAGTA
1 TATATAAACTATATAGTA
2239968 TATATAAACTATATAGTA
1 TATATAAACTATATAGTA
2239986 TA
1 TA
2239988 AATTAATAAT
Statistics
Matches: 205, Mismatches: 41, Indels: 56
0.68 0.14 0.19
Matches are distributed among these distances:
13 6 0.03
14 4 0.02
15 13 0.06
16 37 0.18
17 50 0.24
18 79 0.39
20 16 0.08
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (18 bp):
TATATAAACTATATAGTA
Found at i:2239950 original size:84 final size:83
Alignment explanation
Indices: 2239632--2239987 Score: 362
Period size: 82 Copynumber: 4.2 Consensus size: 83
2239622 AATTCATTAG
* * * *
2239632 TATATAAACTATATATTATAAAGTTCATTAGTATATATAAACTAGATAATATATAGTTCATTA-G
1 TATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATATTATATAGTTCATTATA
*
2239696 TATATAAACTATAAAGTA
66 TATATAAACTATATAGTA
* * * *
2239714 TATATAATCTATATAGTTCATGTAGTTCATTAGTTTATATAAACTATATATTATATAGTTTATTG
1 TATATAAACTATATA-TT-ATATAGTTCATTAGTATATATAAACTATATATTATATAGTTCATT-
* * *
2239779 GTATGTATAAACTATATGGTA
63 ATATATATAAACTATATAGTA
* * ** * *
2239800 TATAAAAATTATATA-TATA-AACT-ATATGGTATATACAAACTATATATTATATAGTTCATTAG
1 TATATAAACTATATATTATATAGTTCAT-TAGTATATATAAACTATATATTATATAGTTCATTA-
*
2239862 TATATATAAACTATATGGTA
64 TATATATAAACTATATAGTA
* * *
2239882 TATATAAACTATATATTATATAGTTCATTAGTATGTATAAACTATATATTATATA-TATAAACTA
1 TATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATATTATATAGT-T-CATTA
* * *
2239946 TATATTATATAGTTTATTAGTA
64 TATA-TATAAACTATA-TAGTA
*
2239968 TATATAAACTATATAGTATA
1 TATATAAACTATATATTATA
2239988 AATTAATAAT
Statistics
Matches: 223, Mismatches: 38, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
81 2 0.01
82 78 0.35
83 9 0.04
84 71 0.32
85 13 0.06
86 50 0.22
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.43
Consensus pattern (83 bp):
TATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATATTATATAGTTCATTATA
TATATAAACTATATAGTA
Found at i:2239951 original size:20 final size:20
Alignment explanation
Indices: 2239917--2239956 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2239907 CATTAGTATG
2239917 TATAAACTATATATTATATA
1 TATAAACTATATATTATATA
2239937 TATAAACTATATATTATATA
1 TATAAACTATATATTATATA
2239957 GTTTATTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAAACTATATATTATATA
Found at i:2240478 original size:2 final size:2
Alignment explanation
Indices: 2240471--2240497 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2240461 ATTATAATTG
2240471 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
2240498 ATACCTCCCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2241759 original size:9 final size:8
Alignment explanation
Indices: 2241745--2241862 Score: 50
Period size: 9 Copynumber: 14.2 Consensus size: 8
2241735 TTATTCTAAC
2241745 TATATAGTA
1 TATATA-TA
*
2241754 TATATAAA
1 TATATATA
2241762 CTATATAGTA
1 -TATATA-TA
*
2241772 TATATAAA
1 TATATATA
*
2241780 CTATATGGTA
1 -TATAT-ATA
*
2241790 TATATAAA
1 TATATATA
2241798 CTATATAT-
1 -TATATATA
2241806 TATATAGT-
1 TATATA-TA
2241814 TA-AT-TA
1 TATATATA
2241820 GTATATATA
1 -TATATATA
*
2241829 AACTATATA
1 TA-TATATA
2241838 -ATATATA
1 TATATATA
*
2241845 TAAACTATA
1 TATA-TATA
2241854 TAT-TATA
1 TATATATA
2241861 TA
1 TA
2241863 GTTCATTAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 28
0.69 0.09 0.23
Matches are distributed among these distances:
5 1 0.01
7 22 0.26
8 12 0.14
9 48 0.56
10 2 0.02
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (8 bp):
TATATATA
Found at i:2241765 original size:18 final size:18
Alignment explanation
Indices: 2241742--2241862 Score: 160
Period size: 18 Copynumber: 6.9 Consensus size: 18
2241732 AATTTATTCT
2241742 AACTATATAGTATATATA
1 AACTATATAGTATATATA
2241760 AACTATATAGTATATATA
1 AACTATATAGTATATATA
*
2241778 AACTATATGGTATATATA
1 AACTATATAGTATATATA
2241796 AACTATATA-T-TATAT-
1 AACTATATAGTATATATA
**
2241811 AGTTA-ATTAGTATATATA
1 AACTATA-TAGTATATATA
*
2241829 AACTATATAATATATATA
1 AACTATATAGTATATATA
*
2241847 AACTATATATTATATA
1 AACTATATAGTATATA
2241863 GTTCATTAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
14 1 0.01
15 5 0.06
16 6 0.07
17 6 0.07
18 71 0.79
19 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
AACTATATAGTATATATA
Found at i:2241832 original size:51 final size:51
Alignment explanation
Indices: 2241767--2241870 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
2241757 ATAAACTATA
**
2241767 TAGTATATATAAACTATATGGTATATATAAACTATATATTATATAGTTAAT
1 TAGTATATATAAACTATATAATATATATAAACTATATATTATATAGTTAAT
*
2241818 TAGTATATATAAACTATATAATATATATAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATAATATATATAAACTATATATTATATAGTTAAT
2241869 TA
1 TA
2241871 ATTTTTAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (51 bp):
TAGTATATATAAACTATATAATATATATAAACTATATATTATATAGTTAAT
Found at i:2242764 original size:2 final size:2
Alignment explanation
Indices: 2242757--2242793 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2242747 CCGGTTAGTT
2242757 TA 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 TA T
2242794 CCAATTACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2243982 original size:34 final size:33
Alignment explanation
Indices: 2243919--2244030 Score: 145
Period size: 34 Copynumber: 3.3 Consensus size: 33
2243909 GATTATATAC
*
2243919 ATATATATAATATTTTATATTTTTATATTAATTAT
1 ATATATATAATA-TATATA-TTTTATATTAATTAT
2243954 ATATATATAATATATAATATTTTATATTAATTAT
1 ATATATATAATATAT-ATATTTTATATTAATTAT
* * *
2243988 ATATATAATATTTTATATTTTTTATATTAATTAT
1 ATATAT-ATAATATATATATTTTATATTAATTAT
2244022 ATA-ATATAA
1 ATATATATAA
2244031 ACCCTAAACC
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
32 3 0.04
33 2 0.03
34 43 0.61
35 22 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
ATATATATAATATATATATTTTATATTAATTAT
Found at i:2244782 original size:3 final size:3
Alignment explanation
Indices: 2244752--2244798 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
2244742 TTTTATTTAT
* *
2244752 TTA TTA ATA CTA TTA TTA GTTA TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
2244797 TT
1 TT
2244799 TACAATTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2246126 original size:35 final size:34
Alignment explanation
Indices: 2246065--2246131 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
2246055 CATATTTCTA
*
2246065 GTTATTTTATTTTAGTCCTTAATATTATTTAGGG
1 GTTATTTTATTTTAGTACTTAATATTATTTAGGG
*
2246099 GTTATTTCTATTTCTAGTACTT-GTATTATTTAG
1 GTTATTT-TATTT-TAGTACTTAATATTATTTAG
2246132 TAATTTCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 7 0.24
35 15 0.52
36 7 0.24
ACGTcount: A:0.22, C:0.07, G:0.13, T:0.57
Consensus pattern (34 bp):
GTTATTTTATTTTAGTACTTAATATTATTTAGGG
Found at i:2246411 original size:30 final size:30
Alignment explanation
Indices: 2246168--2246418 Score: 256
Period size: 30 Copynumber: 8.4 Consensus size: 30
2246158 ATTTTATTTG
*
2246168 TATTTTAGTCCCTTAAGTTTCTATTTTTAC
1 TATTTTAGTCCTTTAAGTTTCTATTTTTAC
* * * *
2246198 CAATTTAGTCCCTTAACTTT-TATTTTTAC
1 TATTTTAGTCCTTTAAGTTTCTATTTTTAC
* * *
2246227 TATTTTAGTCCTTTAGGTTTATATTTTTGC
1 TATTTTAGTCCTTTAAGTTTCTATTTTTAC
* *
2246257 T-GTTTAGTTCTTTAAGTTTCTATTTTTAC
1 TATTTTAGTCCTTTAAGTTTCTATTTTTAC
*
2246286 TATTTTAG-CCTTTTAAGTTTCTATTTATAC
1 TATTTTAGTCC-TTTAAGTTTCTATTTTTAC
** *
2246316 TATTTTAACCCTTTAAGTTTCTATTTTTAA
1 TATTTTAGTCCTTTAAGTTTCTATTTTTAC
* * * * *
2246346 TATTTTAGTCTTTTAAATTCCTGTTTGTAC
1 TATTTTAGTCCTTTAAGTTTCTATTTTTAC
* * *
2246376 TATTTTGGTCCTTTAAGTTGCTATTTTTCC
1 TATTTTAGTCCTTTAAGTTTCTATTTTTAC
* *
2246406 CATTTTGGTCCTT
1 TATTTTAGTCCTT
2246419 GTAATTTTAA
Statistics
Matches: 181, Mismatches: 36, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
29 49 0.27
30 130 0.72
31 2 0.01
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.57
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAGTTTCTATTTTTAC
Found at i:2247387 original size:16 final size:17
Alignment explanation
Indices: 2247368--2247399 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2247358 TTTTAAACTA
2247368 ATTGATTTTT-GATTTT
1 ATTGATTTTTAGATTTT
2247384 ATTGATTTTTAGATTT
1 ATTGATTTTTAGATTT
2247400 GAGCAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (17 bp):
ATTGATTTTTAGATTTT
Found at i:2252673 original size:14 final size:14
Alignment explanation
Indices: 2252654--2252681 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2252644 CGTCATCTTT
2252654 GTCGTTTCTCTTGA
1 GTCGTTTCTCTTGA
2252668 GTCGTTTCTCTTGA
1 GTCGTTTCTCTTGA
2252682 TGAAACACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.21, T:0.50
Consensus pattern (14 bp):
GTCGTTTCTCTTGA
Found at i:2252742 original size:28 final size:29
Alignment explanation
Indices: 2252682--2252775 Score: 104
Period size: 28 Copynumber: 3.3 Consensus size: 29
2252672 TTTCTCTTGA
* *
2252682 TGAAACACATCATCTTGAGTTTATTT-TTCT
1 TGAAACAAATCAT-TTGAGTCTATTTCTT-T
2252712 TGAAACAAATCA-TTGAGTCTATTTCTTT
1 TGAAACAAATCATTTGAGTCTATTTCTTT
** *
2252740 TGAAACAAAT-ATTTGAGTCGGTTTCTCT
1 TGAAACAAATCATTTGAGTCTATTTCTTT
2252768 TGAAACAA
1 TGAAACAA
2252776 TAATCCCTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
27 1 0.02
28 43 0.75
29 2 0.04
30 11 0.19
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (29 bp):
TGAAACAAATCATTTGAGTCTATTTCTTT
Found at i:2253112 original size:136 final size:131
Alignment explanation
Indices: 2252778--2253146 Score: 409
Period size: 131 Copynumber: 2.8 Consensus size: 131
2252768 TGAAACAATA
* * *
2252778 ATCCCTAAAGATGACCAAGCCGTCCTCATTACGTAGGAACAATGTCATCCACCGACTAGACCTCC
1 ATCCCTAAAGATGACCAAGCCGTCCTCATCACATAGGAACAATGTCATCCACCGACCAGACCTCC
* ** * * * * *
2252843 TCATCACGTAGGAGTCGCATCAACCTTATATTACCTGCCGTTCTCATCACGTAGGAACCATGTTA
66 TCATCACGTAGGAGCCGTGTC-ACCTTAGATAACCAGCCGTCCTAATCACGTAGGAACCATGTTA
2252908 TC
130 TC
** * ** * ** *
2252910 ATCCCTAAAGATGGTCTA-CTATCCTCATCATATAGGAACCGTATCATCCACCGACCAGACCTCC
1 ATCCCTAAAGATGACCAAGCCGTCCTCATCACATAGGAACAATGTCATCCACCGACCAGACCTCC
* *
2252974 TCAACACGTAGGAGCCGTGTCACCTGTAGATAACCAGTCGTCCTAATCACGTAGGAACCGA-GTT
66 TCATCACGTAGGAGCCGTGTCACCT-TAGATAACCAGCCGTCCTAATCACGTAGGAACC-ATGTT
2253038 ATCACC
129 AT---C
* * * *
2253044 ATTCCCTAAAGATGACCAAGCCGTCCTCATCACATAGGAACAATGTTATTCACTGACCAGATCTC
1 A-TCCCTAAAGATGACCAAGCCGTCCTCATCACATAGGAACAATGTCATCCACCGACCAGACCTC
*
2253109 CTCATCACGTAGGAGCCGTGTCACCTTTAGATGACCAG
65 CTCATCACGTAGGAGCCGTGTCACC-TTAGATAACCAG
2253147 AACTTTCATC
Statistics
Matches: 192, Mismatches: 37, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
130 4 0.02
131 86 0.45
132 16 0.08
134 2 0.01
135 14 0.07
136 69 0.36
137 1 0.01
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGACCAAGCCGTCCTCATCACATAGGAACAATGTCATCCACCGACCAGACCTCC
TCATCACGTAGGAGCCGTGTCACCTTAGATAACCAGCCGTCCTAATCACGTAGGAACCATGTTAT
C
Found at i:2253336 original size:3 final size:3
Alignment explanation
Indices: 2253330--2253420 Score: 130
Period size: 3 Copynumber: 30.0 Consensus size: 3
2253320 TTTTTATTTA
* * *
2253330 ATT ATT AAT ACT ATT ATT AGTT AAT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
2253375 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
2253421 TACAATTACA
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
2 1 0.01
3 73 0.91
4 6 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2254879 original size:30 final size:30
Alignment explanation
Indices: 2254844--2255017 Score: 122
Period size: 30 Copynumber: 5.8 Consensus size: 30
2254834 TTATTTATAT
*
2254844 TTTAGTCCCTTAAGTTTCTATTTTTACCAG
1 TTTAGTCCCTTAAGTTTCTATTTTTACTAG
* * * *
2254874 TTTAGTCCCTTAACTTTTTGTTTTTACTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTACTAG
** * *
2254904 TTTAGTCATTTAGGTTTCTATTTTTA-TTG
1 TTTAGTCCCTTAAGTTTCTATTTTTACTAG
* * * * *
2254933 TTTTGTCCTTTAAGTTTCTGTTTTTAATAT
1 TTTAGTCCCTTAAGTTTCTATTTTTACTAG
* * *
2254963 TTTAGTCCTTTAAATTCCT-TTTTGTACTA-
1 TTTAGTCCCTTAAGTTTCTATTTT-TACTAG
* *
2254992 TTTCGATCCTTTAAGTTGT-TATTTTT
1 TTTAG-TCCCTTAAGTT-TCTATTTTT
2255018 CCCATTTTGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
29 31 0.27
30 78 0.69
31 4 0.04
ACGTcount: A:0.18, C:0.14, G:0.10, T:0.59
Consensus pattern (30 bp):
TTTAGTCCCTTAAGTTTCTATTTTTACTAG
Found at i:2256362 original size:24 final size:24
Alignment explanation
Indices: 2256308--2256362 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
2256298 TTTTATGTTT
* *
2256308 TAAAAAATTATAAAATTTTACAAA
1 TAAAAATTTATAAAAATTTACAAA
2256332 -AATAAATTTATAAAAATTTA-AGAA
1 TAA-AAATTTATAAAAATTTACA-AA
2256356 TAAAAAT
1 TAAAAAT
2256363 ATATTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 3 0.12
24 21 0.81
25 2 0.08
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAAATTTATAAAAATTTACAAA
Found at i:2262079 original size:21 final size:21
Alignment explanation
Indices: 2262037--2262079 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2262027 TTTCTGGGCT
* *
2262037 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
2262058 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
2262079 A
1 A
2262080 ACGAGTATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2262997 original size:30 final size:31
Alignment explanation
Indices: 2262952--2263023 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 31
2262942 TGTCGAGACA
* * *
2262952 TATGGACAGTATACCTATGTTC-TAAGGAAC
1 TATGGATAGTTTACCTAGGTTCTTAAGGAAC
** *
2262982 TATGGATAGTTTACCTAGGTTCTTCGGGACC
1 TATGGATAGTTTACCTAGGTTCTTAAGGAAC
2263013 TATGGATAGTT
1 TATGGATAGTT
2263024 ACCGAGGATC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 19 0.54
31 16 0.46
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (31 bp):
TATGGATAGTTTACCTAGGTTCTTAAGGAAC
Found at i:2263026 original size:30 final size:30
Alignment explanation
Indices: 2263009--2263171 Score: 317
Period size: 30 Copynumber: 5.4 Consensus size: 30
2262999 GGTTCTTCGG
*
2263009 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2263039 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2263069 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2263099 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2263129 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2263159 GACCTCTGGATAG
1 GACCTCTGGATAG
2263172 GTCCTTCGGA
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 132 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:2266465 original size:21 final size:21
Alignment explanation
Indices: 2266423--2266465 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2266413 TTTCTGGGCT
* *
2266423 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
2266444 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
2266465 A
1 A
2266466 ACGAGTATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2267409 original size:30 final size:30
Alignment explanation
Indices: 2267348--2267419 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
2267338 CTAAGGAACA
* * *
2267348 TATGGATAGTTTACCTAGGTTCTTCGGGACC
1 TATGGATAG-TTACCGAGGATCTTCAGGACC
* *
2267379 TATGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTCAGGACC
*
2267409 TCTGGATAGTT
1 TATGGATAGTT
2267420 GTGATATGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 26 0.74
31 9 0.26
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTCAGGACC
Found at i:2267531 original size:170 final size:170
Alignment explanation
Indices: 2267249--2267589 Score: 682
Period size: 170 Copynumber: 2.0 Consensus size: 170
2267239 GCCCATATTA
2267249 TGTGATATGAGAGCTAGGGTATAGTTGGTATGCCAAGAGTCAAAGAACTACCTATGTCTGTCGAG
1 TGTGATATGAGAGCTAGGGTATAGTTGGTATGCCAAGAGTCAAAGAACTACCTATGTCTGTCGAG
2267314 ACATATGGACAGTATACCTATGTTCTAAGGAACATATGGATAGTTTACCTAGGTTCTTCGGGACC
66 ACATATGGACAGTATACCTATGTTCTAAGGAACATATGGATAGTTTACCTAGGTTCTTCGGGACC
2267379 TATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGT
131 TATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGT
2267419 TGTGATATGAGAGCTAGGGTATAGTTGGTATGCCAAGAGTCAAAGAACTACCTATGTCTGTCGAG
1 TGTGATATGAGAGCTAGGGTATAGTTGGTATGCCAAGAGTCAAAGAACTACCTATGTCTGTCGAG
2267484 ACATATGGACAGTATACCTATGTTCTAAGGAACATATGGATAGTTTACCTAGGTTCTTCGGGACC
66 ACATATGGACAGTATACCTATGTTCTAAGGAACATATGGATAGTTTACCTAGGTTCTTCGGGACC
2267549 TATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGT
131 TATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGT
2267589 T
1 T
2267590 ACCGAGGATC
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 171 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (170 bp):
TGTGATATGAGAGCTAGGGTATAGTTGGTATGCCAAGAGTCAAAGAACTACCTATGTCTGTCGAG
ACATATGGACAGTATACCTATGTTCTAAGGAACATATGGATAGTTTACCTAGGTTCTTCGGGACC
TATGGATAGTTACCGAGGATCTTTATGACCTCTGGATAGT
Found at i:2267579 original size:30 final size:30
Alignment explanation
Indices: 2267545--2267707 Score: 317
Period size: 30 Copynumber: 5.4 Consensus size: 30
2267535 GGTTCTTCGG
*
2267545 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2267575 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2267605 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2267635 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2267665 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2267695 GACCTCTGGATAG
1 GACCTCTGGATAG
2267708 GTCCTTCGGA
Statistics
Matches: 132, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 132 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:2272840 original size:18 final size:18
Alignment explanation
Indices: 2272817--2272855 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2272807 CGGTTGGTAA
2272817 AGAGAGTCTTGATTTTTC
1 AGAGAGTCTTGATTTTTC
*
2272835 AGAGAGTTTTGATTTTTC
1 AGAGAGTCTTGATTTTTC
2272853 AGA
1 AGA
2272856 AACTTTAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44
Consensus pattern (18 bp):
AGAGAGTCTTGATTTTTC
Found at i:2273050 original size:20 final size:20
Alignment explanation
Indices: 2273027--2273078 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2273017 AACGCGATCC
2273027 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2273047 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2273067 CCAAAATCGCAA
1 CCAGAATCGCAA
2273079 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2273159 original size:20 final size:20
Alignment explanation
Indices: 2273134--2273327 Score: 85
Period size: 20 Copynumber: 9.7 Consensus size: 20
2273124 GATTTTCCAT
* *
2273134 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2273154 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2273174 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2273194 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
2273214 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
2273234 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
2273254 TATCGCAACGCGTATC-CATA
1 AATCGCAACGCG-AACACATA
** *
2273274 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2273295 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2273315 AATCGCAACGCGA
1 AATCGCAACGCGA
2273328 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2273179 original size:40 final size:39
Alignment explanation
Indices: 2273130--2273327 Score: 173
Period size: 40 Copynumber: 5.0 Consensus size: 39
2273120 TTGCGATTTT
* * *
2273130 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATACGTAAATCGCAACGCGAA
* * *
2273168 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATACGTAAATCGCAACGCG-AA
* ** * *
2273209 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATACGTAAATCGCAACGCG-AA
* * * * **
2273249 CCGTATATCGCAACGCGTATCCATAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATACGTAAATCGCAACGCGAA
* *
2273288 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATACGTAAATCGCAACGCGA
2273328 TATTTAAAGC
Statistics
Matches: 130, Mismatches: 25, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 93 0.72
41 32 0.25
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATACGTAAATCGCAACGCGAA
Found at i:2273217 original size:60 final size:60
Alignment explanation
Indices: 2273153--2273326 Score: 240
Period size: 60 Copynumber: 2.9 Consensus size: 60
2273143 GCGAATATGA
* * *
2273153 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCAT
* *** * *
2273213 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCAT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCAT
**
2273273 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCG
2273327 ATATTTAAAG
Statistics
Matches: 96, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 65 0.68
61 31 0.32
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCAT
Found at i:2273745 original size:33 final size:33
Alignment explanation
Indices: 2273706--2273776 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2273696 TTCACTTAGA
*
2273706 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2273739 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2273772 TTTCA
1 TTTCA
2273777 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2273915 original size:14 final size:14
Alignment explanation
Indices: 2273896--2273950 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2273886 AGAATGACTG
2273896 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2273910 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2273929 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2273943 TCGCAACG
1 TCGCAACG
2273951 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2273933 original size:33 final size:33
Alignment explanation
Indices: 2273896--2273966 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2273886 AGAATGACTG
**
2273896 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2273929 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2273962 TCGCA
1 TCGCA
2273967 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2273984 original size:19 final size:18
Alignment explanation
Indices: 2273962--2274054 Score: 76
Period size: 14 Copynumber: 5.5 Consensus size: 18
2273952 GAAACCAAAA
*
2273962 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
2273981 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
2273995 TCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
2274013 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
* *
2274027 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATT
2274046 TCGCGTTGC
1 TCGCGTTGC
2274055 TATTCTCTCG
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.33
15 4 0.07
16 2 0.03
17 6 0.10
18 10 0.17
19 18 0.30
ACGTcount: A:0.10, C:0.26, G:0.23, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:2274003 original size:14 final size:14
Alignment explanation
Indices: 2273984--2274072 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
2273974 TTTCATTTCG
2273984 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2273998 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
2274016 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2274030 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
*
2274047 CGCGTTGCTATTCTCT
1 --CGTTGCGATTCTCT
2274063 CGTTGCGATT
1 CGTTGCGATT
2274073 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.44
15 4 0.06
16 5 0.08
17 8 0.13
18 11 0.18
19 7 0.11
ACGTcount: A:0.09, C:0.26, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2274060 original size:33 final size:33
Alignment explanation
Indices: 2273967--2274080 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
2273957 CAAAATCGCA
2273967 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2274000 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* * *
2274032 TTGCGATTGTCATCTCGCGTTGCTATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2274065 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2274081 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
32 32 0.43
33 43 0.57
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2275961 original size:90 final size:92
Alignment explanation
Indices: 2275766--2276139 Score: 670
Period size: 90 Copynumber: 4.1 Consensus size: 92
2275756 TAGATTGCTT
*
2275766 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-GTGTATTCTTTAACACTGTGAAATAGTA
2275831 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2275859 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-TGTATTCTTTAACACTGTGAAATA-TAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACGTGTATTCTTTAACACTGTGAAATAGTAT
2275921 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
2275948 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT---ACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-GTGTATTCTTTAACACTGTGAAATAGTA
2276010 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2276038 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC-GTGTATTCTTTAACACTGTGAAATAGTA
2276103 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2276131 AGTAAATTT
1 AGTAAATTT
2276140 ATCCATTCAA
Statistics
Matches: 273, Mismatches: 1, Indels: 14
0.95 0.00 0.05
Matches are distributed among these distances:
89 44 0.16
90 134 0.49
92 41 0.15
93 54 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACGTGTATTCTTTAACACTGTGAAATAGTAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2276082 original size:182 final size:181
Alignment explanation
Indices: 2275766--2276141 Score: 684
Period size: 182 Copynumber: 2.1 Consensus size: 181
2275756 TAGATTGCTT
2275766 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-A-ACTGTGAAATAGTA
2275831 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
64 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
2275896 TATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
129 TATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2275948 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-ACTGTGAAATAGTATT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACTGTGAAATAGTATT
2276012 TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
66 TGTCTTTGTTTTGTCTTTTGGTTGAAAGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAAC--T
2276077 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
128 GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2276131 AGTAAATTTAT
1 AGTAAATTTAT
2276142 CCATTCAAGT
Statistics
Matches: 188, Mismatches: 2, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
179 45 0.24
180 32 0.17
182 71 0.38
183 40 0.21
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (181 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACTGTGAAATAGTATT
TGTCTTTGTTTTGTCTTTTGGTTGAAAGTAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTA
TTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2276223 original size:19 final size:19
Alignment explanation
Indices: 2276183--2276311 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2276173 TAGTTTACTT
* *
2276183 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2276203 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2276222 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2276241 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2276255 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2276274 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2276288 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2276307 TCGCA
1 TCGCA
2276312 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2276262 original size:33 final size:32
Alignment explanation
Indices: 2276219--2276311 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2276209 CGCGAAACCA
**
2276219 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2276251 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2276284 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2276312 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2276309 original size:52 final size:52
Alignment explanation
Indices: 2276183--2276311 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2276173 TAGTTTACTT
**
2276183 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2276235 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2276288 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2276312 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2276329 original size:19 final size:18
Alignment explanation
Indices: 2276307--2276425 Score: 110
Period size: 19 Copynumber: 6.8 Consensus size: 18
2276297 GAAACCAAAA
*
2276307 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
2276326 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
*
2276342 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
*
2276359 TCGCGTTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
2276375 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
*
2276392 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
2276411 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
2276426 AAGTTTCGTG
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 16 0.19
16 10 0.12
17 10 0.12
19 47 0.57
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:2276348 original size:14 final size:14
Alignment explanation
Indices: 2276329--2276385 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2276319 TTTCATTTCG
2276329 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
2276343 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
2276360 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
2276376 CGTTGCGATT
1 CGTTGCGATT
2276386 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2276354 original size:33 final size:33
Alignment explanation
Indices: 2276312--2276404 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
2276302 CAAAATCGCA
*
2276312 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
**
2276345 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2276378 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2276405 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2276433 original size:20 final size:19
Alignment explanation
Indices: 2276307--2276441 Score: 105
Period size: 19 Copynumber: 7.6 Consensus size: 19
2276297 GAAACCAAAA
*
2276307 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
2276326 TCGCGTTGCGA--TT-CTT
1 TCGCGTTGCGATTTTAGTT
*
2276342 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
*
2276359 TCGCGTTGCGATTCT-G--
1 TCGCGTTGCGATTTTAGTT
2276375 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
2276392 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
2276411 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-AGTT
*
2276431 TCGTGTTGCGA
1 TCGCGTTGCGA
2276442 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 7, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
14 19 0.20
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAGTT
Found at i:2278381 original size:14 final size:14
Alignment explanation
Indices: 2278362--2278397 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2278352 ATTGTTTAAT
2278362 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2278376 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2278390 TGATTTGT
1 TGATTTGT
2278398 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2278580 original size:20 final size:19
Alignment explanation
Indices: 2278504--2278586 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
2278494 AAAAATGACT
2278504 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2278523 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2278542 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2278556 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2278576 ATCGCAATGCG
1 ATCGCAATGCG
2278587 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 1 0.02
17 3 0.05
19 28 0.50
20 13 0.23
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2278639 original size:19 final size:19
Alignment explanation
Indices: 2278615--2278938 Score: 387
Period size: 19 Copynumber: 18.4 Consensus size: 19
2278605 GATTATCTCG
2278615 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2278634 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2278653 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2278667 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2278685 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2278704 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2278722 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2278741 TTGCGA--TT-ATGTCG--
1 TTGCGATTTTCATTTCGCA
2278755 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2278774 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2278793 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2278812 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2278826 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2278845 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2278864 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2278878 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2278898 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2278912 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2278931 TTGCGATT
1 TTGCGATT
2278939 GTATTTTCCG
Statistics
Matches: 267, Mismatches: 11, Indels: 54
0.80 0.03 0.16
Matches are distributed among these distances:
14 35 0.13
15 3 0.01
16 33 0.12
17 22 0.08
18 27 0.10
19 135 0.51
20 12 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2278650 original size:52 final size:52
Alignment explanation
Indices: 2278593--2278910 Score: 446
Period size: 52 Copynumber: 6.0 Consensus size: 52
2278583 TGCGTTTATA
*
2278593 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2278645 ATTTCGCATTGCGATTCTTTCGTTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
2278696 ATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTATGTC
1 ATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * * *
2278754 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTT
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2278804 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2278856 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2278909 AT
1 AT
2278911 GTTGGGATTT
Statistics
Matches: 237, Mismatches: 17, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
50 8 0.03
51 42 0.18
52 124 0.52
53 22 0.09
54 2 0.01
55 6 0.03
56 21 0.09
57 3 0.01
58 9 0.04
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2278809 original size:71 final size:71
Alignment explanation
Indices: 2278593--2278871 Score: 440
Period size: 71 Copynumber: 4.0 Consensus size: 71
2278583 TGCGTTTATA
2278593 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
2278658 ATTCTTT
66 ATT-TTT
** * * *
2278665 CGTT-GCGATTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCATTGC
1 ATTTCGC-ATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
*
2278726 GATTTTA
65 GATTTTT
*
2278733 ATTTCGCATTGCGATTATGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
2278798 ATTTTT
66 ATTTTT
*
2278804 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
2278869 ATT
66 ATT
2278872 CTCTCGTTGC
Statistics
Matches: 187, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
68 8 0.04
69 25 0.13
70 55 0.29
71 93 0.50
72 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (71 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTTTT
Found at i:2278882 original size:33 final size:33
Alignment explanation
Indices: 2278845--2278938 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 33
2278835 TCATTTCGCA
2278845 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCAT-G
*
2278878 TTGCGATTTTCATTTCCGCATTGCGATTTTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCATG
* *
2278912 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
2278939 GTATTTTCCG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 26 0.46
34 29 0.52
35 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCATG
Found at i:2278903 original size:34 final size:33
Alignment explanation
Indices: 2278634--2278938 Score: 164
Period size: 33 Copynumber: 8.8 Consensus size: 33
2278624 TCATTTCGCA
*
2278634 TTGCGATTTTCATTTCGCATTGCGATTCT-TTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCAT-G
*
2278667 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCA--T-G
* *
2278702 CATTGCGA-TTTCATTTCGCATTGCGATTTTAAT-
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCATG
* * *
2278735 TT-CGCA-TTGCGATTAT-GTCGTTGCGATTTTCATTTCG
1 TTGCG-ATTTTC-ATT-TCG-CATTGCGATTCTCA--T-G
* *
2278772 CATTGCGATTTTCATTTCGCATTGCGATTTTTAT-
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCATG
* * * *
2278806 TT-CGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 TTGCG-ATTTTC-ATT-TCGCATTGCGATTCTCA--T-G
2278843 CATTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCAT-G
*
2278878 TTGCGATTTTCATTTCCGCATTGCGATTTTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCATG
* *
2278912 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
2278939 GTATTTTCCG
Statistics
Matches: 221, Mismatches: 20, Indels: 62
0.73 0.07 0.20
Matches are distributed among these distances:
30 2 0.01
31 11 0.05
32 31 0.14
33 59 0.27
34 29 0.13
35 10 0.05
36 1 0.00
37 29 0.13
38 26 0.12
39 13 0.06
40 10 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCATG
Found at i:2281235 original size:12 final size:12
Alignment explanation
Indices: 2281218--2281242 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2281208 TCTTCGGGGA
2281218 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2281230 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2281242 C
1 C
2281243 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2282173 original size:20 final size:20
Alignment explanation
Indices: 2282145--2282513 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
2282135 AAATTTCAGT
* * * *
2282145 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2282165 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2282185 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
2282205 GTTGCGATTTACAGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2282225 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2282245 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2282265 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2282285 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2282305 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2282325 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
2282345 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2282365 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2282385 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2282405 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2282425 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2282445 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2282465 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2282485 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2282505 GTTGCGATT
1 GTTGCGATT
2282514 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2282594 original size:20 final size:20
Alignment explanation
Indices: 2282569--2282620 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2282559 AAGAATCGCG
*
2282569 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2282589 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
2282609 TTGCGATTCTGG
1 TTGCGATTCTGG
2282621 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:2283749 original size:19 final size:19
Alignment explanation
Indices: 2283727--2283766 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2283717 AAAATAAGGA
2283727 AAATGAAATAAA-AAAGAAT
1 AAAT-AAATAAATAAAGAAT
*
2283746 AAATAAATAAATAAATAAT
1 AAATAAATAAATAAAGAAT
2283765 AA
1 AA
2283767 CATATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
AAATAAATAAATAAAGAAT
Found at i:2283860 original size:25 final size:22
Alignment explanation
Indices: 2283832--2283925 Score: 81
Period size: 22 Copynumber: 4.2 Consensus size: 22
2283822 TGAAAGGAAT
2283832 TAAATAAAGACAAAATAGAATGAGA
1 TAAATAAAGA-AAAATAGAAT-A-A
2283857 TAAATAAAGAAAAA-AG-ATAAA
1 TAAATAAAGAAAAATAGAAT-AA
2283878 TAAA-ATAAGAAAAATA-AATCAA
1 TAAATA-AAGAAAAATAGAAT-AA
*
2283900 TAAATAAAG-AAAATAAAATAAA
1 TAAATAAAGAAAAATAGAAT-AA
2283922 TAAA
1 TAAA
2283926 CCAAAACAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
20 1 0.02
21 19 0.31
22 24 0.39
23 3 0.05
24 4 0.07
25 10 0.16
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (22 bp):
TAAATAAAGAAAAATAGAATAA
Found at i:2283876 original size:17 final size:17
Alignment explanation
Indices: 2283854--2283917 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
2283844 AAATAGAATG
2283854 AGATAAATAAAGAAA-AA
1 AGATAAATAAA-AAAGAA
2283871 AGATAAATAAAATAAGAA
1 AGATAAATAAAA-AAGAA
* * *
2283889 AAATAAATCAATAAATAA
1 AGATAAAT-AAAAAAGAA
2283907 AGA-AAATAAAA
1 AGATAAATAAAA
2283918 TAAATAAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.10
17 17 0.44
18 15 0.38
19 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (17 bp):
AGATAAATAAAAAAGAA
Found at i:2283880 original size:4 final size:4
Alignment explanation
Indices: 2283856--2283925 Score: 50
Period size: 4 Copynumber: 16.2 Consensus size: 4
2283846 ATAGAATGAG
* * * *
2283856 ATAA ATAA AGAA AAAA GATAA ATAAA ATAA GAAAA ATAA ATCA ATAA ATAA
1 ATAA ATAA ATAA ATAA -ATAA AT-AA ATAA -ATAA ATAA ATAA ATAA ATAA
*
2283907 AGAAA ATAAA ATAA ATAA A
1 A-TAA AT-AA ATAA ATAA A
2283926 CCAAAACAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
4 35 0.67
5 17 0.33
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (4 bp):
ATAA
Found at i:2283913 original size:9 final size:9
Alignment explanation
Indices: 2283856--2283925 Score: 60
Period size: 9 Copynumber: 8.0 Consensus size: 9
2283846 ATAGAATGAG
2283856 ATAAATAAA
1 ATAAATAAA
*
2283865 GA-AAA-AAG
1 -ATAAATAAA
2283873 ATAAATAAA
1 ATAAATAAA
2283882 ATAAGA-AAA
1 ATAA-ATAAA
*
2283891 ATAAAT-CA
1 ATAAATAAA
2283899 ATAAATAAA
1 ATAAATAAA
2283908 GA-AAATAAA
1 -ATAAATAAA
2283917 ATAAATAAA
1 ATAAATAAA
2283926 CCAAAACAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
7 1 0.02
8 14 0.29
9 31 0.63
10 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (9 bp):
ATAAATAAA
Found at i:2283921 original size:18 final size:18
Alignment explanation
Indices: 2283875--2283956 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 18
2283865 GAAAAAAGAT
2283875 AAATAAAATAAGA-AAAA
1 AAATAAAATAAGATAAAA
*
2283892 TAAAT-CAATAA-ATAAAGA
1 -AAATAAAATAAGATAAA-A
2283910 AAATAAAATAA-ATAAACCA
1 AAATAAAATAAGATAAA--A
*
2283929 AAACAAAA-AAGGATAAAA
1 AAATAAAATAA-GATAAAA
2283947 AAATAAAATA
1 AAATAAAATA
2283957 CACACATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.02
17 12 0.23
18 25 0.48
19 9 0.17
20 5 0.10
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (18 bp):
AAATAAAATAAGATAAAA
Found at i:2285389 original size:18 final size:16
Alignment explanation
Indices: 2285366--2285415 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
2285356 GGTTAATAAA
2285366 ATAATAATACATATATAT
1 ATAAT-ATA-ATATATAT
2285384 ATAATATAATATATA-
1 ATAATATAATATATAT
* *
2285399 AAAATAT-ATATGTAT
1 ATAATATAATATATAT
2285414 AT
1 AT
2285416 TTCGGTTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 6 0.21
15 7 0.25
16 7 0.25
17 3 0.11
18 5 0.18
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATAATATAATATATAT
Found at i:2285404 original size:10 final size:12
Alignment explanation
Indices: 2285361--2285408 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2285351 ACTTTGGTTA
*
2285361 ATAAAATAATA-
1 ATAATATAATAT
2285372 ATACATAT-ATAT
1 ATA-ATATAATAT
2285384 ATAATATAATAT
1 ATAATATAATAT
2285396 ATAA-A-AATAT
1 ATAATATAATAT
2285406 ATA
1 ATA
2285409 TGTATATTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
10 8 0.24
11 11 0.33
12 14 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:2285405 original size:26 final size:26
Alignment explanation
Indices: 2285359--2285409 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2285349 CAACTTTGGT
*
2285359 TAATAAAATAATAATACATATATATA
1 TAATAAAATAATAATAAATATATATA
*
2285385 TAATATAATATATAA-AAATATATAT
1 TAATAAAATA-ATAATAAATATATAT
2285410 GTATATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TAATAAAATAATAATAAATATATATA
Found at i:2286387 original size:106 final size:106
Alignment explanation
Indices: 2286061--2286433 Score: 471
Period size: 106 Copynumber: 3.5 Consensus size: 106
2286051 GTATTGCTTC
* * *
2286061 GAGTCTAATATCCTTC-ATCGTGAAGTTGAAATTGGCTCT-AGAACTGGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGA-AACTGGGAAGTTGTTTGTTGAC
* * *
2286124 AGTTAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTC
64 AGTCAGTCGTCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * * * **
2286167 GAGTCTAATATCCTTCGCTGTGAGGTTGAAATTGACTCTGAATGAAACTGAAGAAGTTGTGCGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAACTG-GGAAGTTGTTTGTT
* *
2286232 AACAGTCAGCCGTCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
61 GACAGTCAGTCGTCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
* * *
2286278 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAG
* * * * *
2286343 CCAGTCGTCCCTTCGTTGTGAAGTTGAGATTATGTTGTCTT
66 TCAGTCGTCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
2286384 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAA
2286434 ACCCCTTCGT
Statistics
Matches: 230, Mismatches: 30, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
106 130 0.57
107 9 0.04
110 6 0.03
111 85 0.37
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAGTTGTTTGTTGACAG
TCAGTCGTCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTT
Found at i:2287518 original size:5 final size:5
Alignment explanation
Indices: 2287508--2287552 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
2287498 CCCACCTTAT
*
2287508 TTTTC TTTTC TTTTTC TTTTC TTTTT TTTTCC TTTT- TTTTC TTTT
1 TTTTC TTTTC -TTTTC TTTTC TTTTC TTTT-C TTTTC TTTTC TTTT
2287553 TTCAATTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 4 0.11
5 22 0.63
6 9 0.26
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:2287529 original size:16 final size:17
Alignment explanation
Indices: 2287508--2287553 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 17
2287498 CCCACCTTAT
2287508 TTTTCTTTTCTTTTT-C
1 TTTTCTTTTCTTTTTCC
2287524 TTTTCTTTT-TTTTTCC
1 TTTTCTTTTCTTTTTCC
2287540 TTTT-TTTTCTTTTT
1 TTTTCTTTTCTTTTT
2287554 TCAATTTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTCC
Found at i:2287553 original size:10 final size:10
Alignment explanation
Indices: 2287507--2287554 Score: 69
Period size: 10 Copynumber: 4.6 Consensus size: 10
2287497 GCCCACCTTA
2287507 TTTTTCTTTTC
1 TTTTT-TTTTC
2287518 TTTTTCTTTTC
1 TTTTT-TTTTC
2287529 TTTTTTTTTC
1 TTTTTTTTTC
*
2287539 CTTTTTTTTC
1 TTTTTTTTTC
2287549 TTTTTT
1 TTTTTT
2287555 CAATTTAGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
10 19 0.54
11 16 0.46
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:2288479 original size:53 final size:53
Alignment explanation
Indices: 2288375--2288488 Score: 117
Period size: 53 Copynumber: 2.1 Consensus size: 53
2288365 CATATTATTA
* *
2288375 TTATTATTATTCATATTTTATTGTATATACATGTATTATTATTTTACTATTTAC
1 TTATT-TTATTCATATGTTATTGTATATACATGTATTATTATTTTAATATTTAC
* * **
2288429 TTATTTTATTTATATGTTATAT-TATATATAT-TATT-TTATTTCTTAATATTTTT
1 TTATTTTATTCATATGTTAT-TGTATATACATGTATTATTA-TT-TTAATATTTAC
2288482 TTATTTT
1 TTATTTT
2288489 TTAGTTTACA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
51 3 0.06
52 6 0.12
53 36 0.71
54 6 0.12
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (53 bp):
TTATTTTATTCATATGTTATTGTATATACATGTATTATTATTTTAATATTTAC
Found at i:2288509 original size:2 final size:2
Alignment explanation
Indices: 2288504--2288547 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2288494 TTACAAGCTA
2288504 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
2288546 AT
1 AT
2288548 TTATCCTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2288577 original size:4 final size:4
Alignment explanation
Indices: 2288568--2288637 Score: 50
Period size: 4 Copynumber: 16.2 Consensus size: 4
2288558 TTTGTTTTGG
* * *
2288568 TTTA TTTA TTTTA TTTTC TTTA TTTA TTGA TTTA TTTT TCTTA TTTTA
1 TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T-TTA -TTTA
* *
2288616 TTTA TTTGT TTTC TTTA TTTA T
1 TTTA TTT-A TTTA TTTA TTTA T
2288638 CTCATTCTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
4 36 0.68
5 16 0.30
6 1 0.02
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2288582 original size:9 final size:9
Alignment explanation
Indices: 2288568--2288622 Score: 62
Period size: 9 Copynumber: 6.2 Consensus size: 9
2288558 TTTGTTTTGG
2288568 TTTATTTAT
1 TTTATTTAT
2288577 TTTATTT-T
1 TTTATTTAT
2288585 CTTTATTTA-
1 -TTTATTTAT
*
2288594 TTGATTTAT
1 TTTATTTAT
2288603 TTT-TCTTAT
1 TTTAT-TTAT
2288612 TTTATTTAT
1 TTTATTTAT
2288621 TT
1 TT
2288623 GTTTTCTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 9 0.23
9 29 0.74
10 1 0.03
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:2289353 original size:13 final size:13
Alignment explanation
Indices: 2289335--2289359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2289325 TTCACTTAAG
2289335 GCTCTAAACCCGA
1 GCTCTAAACCCGA
2289348 GCTCTAAACCCG
1 GCTCTAAACCCG
2289360 TTTTAAATGG
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:0.28, C:0.40, G:0.16, T:0.16
Consensus pattern (13 bp):
GCTCTAAACCCGA
Found at i:2300100 original size:4 final size:4
Alignment explanation
Indices: 2300076--2300144 Score: 50
Period size: 4 Copynumber: 16.2 Consensus size: 4
2300066 ATAGAATGAG
* * *
2300076 ATAA ATAA AGAA AAAA GATAA ATAA ACTAA GA-AA ATAA ATCA ATAA ATAA
1 ATAA ATAA ATAA ATAA -ATAA ATAA A-TAA -ATAA ATAA ATAA ATAA ATAA
*
2300126 AGAAA ATAAA ATAA ATAA A
1 A-TAA AT-AA ATAA ATAA A
2300145 CCAAAACAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
3 1 0.02
4 37 0.71
5 13 0.25
6 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (4 bp):
ATAA
Found at i:2300100 original size:21 final size:21
Alignment explanation
Indices: 2300053--2300171 Score: 82
Period size: 21 Copynumber: 5.3 Consensus size: 21
2300043 GAAATGAATA
*
2300053 AAATAAAGACAAAATAGAATGAGAT
1 AAATAAAGA-AAAA-AG-AT-AAAT
2300078 AAATAAAGAAAAAAGATAAAT
1 AAATAAAGAAAAAAGATAAAT
*
2300099 AAACT-AAGAAAATAA-ATCAAT
1 AAA-TAAAGAAAA-AAGATAAAT
*
2300120 AAATAAAGAAAATAAAATAAAT
1 AAATAAAGAAAA-AAGATAAAT
* *
2300142 AAACCAAAACAAAAAAGGATAAA-
1 AAA--TAAAGAAAAAA-GATAAAT
2300165 AAATAAA
1 AAATAAA
2300172 ATATACACAC
Statistics
Matches: 80, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.01
21 34 0.43
22 13 0.16
23 7 0.09
24 16 0.20
25 9 0.11
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.14
Consensus pattern (21 bp):
AAATAAAGAAAAAAGATAAAT
Found at i:2300134 original size:9 final size:9
Alignment explanation
Indices: 2300039--2300144 Score: 51
Period size: 9 Copynumber: 11.8 Consensus size: 9
2300029 AAGATAGTGA
*
2300039 AAATGAAAT
1 AAATAAAAT
*
2300048 GAATAAAAT
1 AAATAAAAT
*
2300057 AAAGACAAAAT
1 -AA-ATAAAAT
* *
2300068 AGAATGAGAT
1 A-AATAAAAT
2300078 AAATAAAGA-
1 AAATAAA-AT
*
2300087 AAA-AAGAT
1 AAATAAAAT
*
2300095 AAATAAACT
1 AAATAAAAT
*
2300104 -AAGAAAAT
1 AAATAAAAT
*
2300112 AAAT-CAAT
1 AAATAAAAT
2300120 AAATAAAGA-
1 AAATAAA-AT
2300129 AAATAAAAT
1 AAATAAAAT
2300138 AAATAAA
1 AAATAAA
2300145 CCAAAACAAA
Statistics
Matches: 70, Mismatches: 17, Indels: 20
0.65 0.16 0.19
Matches are distributed among these distances:
7 1 0.01
8 19 0.27
9 34 0.49
10 9 0.13
11 7 0.10
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:2301608 original size:23 final size:23
Alignment explanation
Indices: 2301582--2301626 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2301572 ACTTTGGTTA
2301582 ATAAAATAATA-ATACATATATAT
1 ATAAAATAATATATA-ATATATAT
*
2301605 ATAATATAATATATAATATATA
1 ATAAAATAATATATAATATATA
2301627 AAAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATAAAATAATATATAATATATAT
Found at i:2301618 original size:12 final size:12
Alignment explanation
Indices: 2301582--2301624 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
2301572 ACTTTGGTTA
*
2301582 ATAAAATAATA-
1 ATAATATAATAT
2301593 ATACATAT-ATAT
1 ATA-ATATAATAT
2301605 ATAATATAATAT
1 ATAATATAATAT
2301617 ATAATATA
1 ATAATATA
2301625 TAAAAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:2302475 original size:2 final size:2
Alignment explanation
Indices: 2302468--2302502 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2302458 CTTTACTTGT
*
2302468 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2302503 GGTTAGGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2302919 original size:7 final size:7
Alignment explanation
Indices: 2302907--2302933 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2302897 ATAGCTCAGA
2302907 CTATAGC
1 CTATAGC
2302914 CTATAGC
1 CTATAGC
2302921 CTATAGC
1 CTATAGC
2302928 CTATAG
1 CTATAG
2302934 GTTCGCCCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (7 bp):
CTATAGC
Found at i:2305619 original size:28 final size:28
Alignment explanation
Indices: 2305582--2305638 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2305572 AAGCTTTGCT
2305582 TGAAGGCTATGTGAGATCGATCCAATGC
1 TGAAGGCTATGTGAGATCGATCCAATGC
2305610 TGAAGGCTATGTGAGATCGATCCAATGC
1 TGAAGGCTATGTGAGATCGATCCAATGC
2305638 T
1 T
2305639 TCAATTGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (28 bp):
TGAAGGCTATGTGAGATCGATCCAATGC
Found at i:2305864 original size:94 final size:94
Alignment explanation
Indices: 2305701--2305907 Score: 353
Period size: 94 Copynumber: 2.2 Consensus size: 94
2305691 ATGATATACC
* *
2305701 TGATGGCTATGTGAGGACCATGAGATCATTCAGCAGCTTAGTGGTAATTGTACCGATGCGTTGTG
1 TGATGGTTATGTGAGGACCATGAGATCATTCAGCAGCTTAGTGGTAATTGTACCGATGCGTTGTA
* *
2305766 ACTTCGGGTTCCCTCAGTTAACTAGTGTG
66 ACTTCAGGTTCCCTCAGTTAACTAGTCTG
* *
2305795 TGATGGTTAAGTGAGGACCATGAGATCATTCAGCAGCTTAGTGGTAATTGTACCGATGTGTTGTA
1 TGATGGTTATGTGAGGACCATGAGATCATTCAGCAGCTTAGTGGTAATTGTACCGATGCGTTGTA
2305860 ACTTCAGGTTCCCTCAGTTAACTAGTCTG
66 ACTTCAGGTTCCCTCAGTTAACTAGTCTG
2305889 TGATGGTTATGTGA-GACCA
1 TGATGGTTATGTGAGGACCA
2305908 GATATTAGTT
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 5 0.05
94 101 0.95
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (94 bp):
TGATGGTTATGTGAGGACCATGAGATCATTCAGCAGCTTAGTGGTAATTGTACCGATGCGTTGTA
ACTTCAGGTTCCCTCAGTTAACTAGTCTG
Found at i:2311520 original size:3 final size:3
Alignment explanation
Indices: 2311512--2311561 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
2311502 ATCAATAATT
* *
2311512 TAA TAA TAA TAA TAA TAA TAA TAA TAG TTA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2311559 TAA
1 TAA
2311562 CATATGTGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2311795 original size:82 final size:82
Alignment explanation
Indices: 2311689--2312377 Score: 925
Period size: 82 Copynumber: 8.4 Consensus size: 82
2311679 TCATAGGAAA
* * *
2311689 TCTGCTCCACTCTTCTTTCAGGGGAGATCGGAGTTGATATGTTCCTCTTTTTCGGGTAGTCAGAT
1 TCTGCTCCACTATTCTTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGAT
* * *
2311754 GAATTTTGGAAGATAGA
66 CAATTTTGGAAGACAGG
* * * * * *
2311771 TCTACTCCAGTCTTCTCTCAGGGGATATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCATAT
1 TCTGCTCCACTATTCTTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGAT
2311836 CAATTTTGGAAGAC-GG
66 CAATTTTGGAAGACAGG
* * * * *
2311852 TTCTGCTCCACTATTCTTTCAAGGGAGATTAGACTTGATTTGTTCCTCTTTTTTGGGTAGTCAAA
1 -TCTGCTCCACTATTCTTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGA
**
2311917 TCAATTTTGGAAGATGGG
65 TCAATTTTGGAAGACAGG
* * * * *
2311935 TCTGCTCCACTAGTCTTACAGGGAAGATCAAACTTGATTTGTTCCTCTTTTTCGGGTAGTCAGAT
1 TCTGCTCCACTATTCTTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGAT
2312000 CAATTTTGGAAGACAGG
66 CAATTTTGGAAGACAGG
* *
2312017 TCTACTCCACTATTCTTTCAGGGAAGATCAGACTTGA-ATTGTTCCTCTTTTTCGGGTAGTCAGA
1 TCTGCTCCACTATTCTTTCAGGGGAGATCAGACTTGATA-TGTTCCTCTTTTTCGGGTAGTCAGA
*
2312081 TCAATTTTGGAAGACGGG
65 TCAATTTTGGAAGACAGG
* * *
2312099 TCTACTCCACTATTCTTTTAGGGGAGATCAGACTTGATATGTTCATCTTTTTCGGGTAGTCAGAT
1 TCTGCTCCACTATTCTTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGAT
*
2312164 CAATGTTGGAAGACAGG
66 CAATTTTGGAAGACAGG
* * *
2312181 TATGCTCCACTATTCTTTCAGGGGAGATCAGACTTGATTTGTTCCTCTATTTCGGGTAGTCAGAT
1 TCTGCTCCACTATTCTTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGAT
* *
2312246 CAATTTTAGAAGACCGG
66 CAATTTTGGAAGACAGG
* * * * *
2312263 TCTGCTCAACTATTCTTTCAGGGGAGATTAGACTTGATTTGTTCCACTTTTTCAGGTAGTCAGAT
1 TCTGCTCCACTATTCTTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGAT
*
2312328 CAATTTTGGAAGACGGG
66 CAATTTTGGAAGACAGG
* * * *
2312345 TCTGCTCTACTCTTCTTTCA-AGGAGATAAGACT
1 TCTGCTCCACTATTCTTTCAGGGGAGATCAGACT
2312378 CAAAAAATCT
Statistics
Matches: 540, Mismatches: 63, Indels: 9
0.88 0.10 0.01
Matches are distributed among these distances:
81 12 0.02
82 525 0.97
83 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (82 bp):
TCTGCTCCACTATTCTTTCAGGGGAGATCAGACTTGATATGTTCCTCTTTTTCGGGTAGTCAGAT
CAATTTTGGAAGACAGG
Found at i:2312699 original size:89 final size:89
Alignment explanation
Indices: 2312518--2312701 Score: 219
Period size: 89 Copynumber: 2.1 Consensus size: 89
2312508 TATAAATATT
* * *
2312518 AAATCAGAAATAAGAAGAATCTACTCCTCTACTCTTTCGAGCAGATCAGAATCAAGATTGATTTG
1 AAATCTGAAATAAGAAGAATCTACTCCTATACTCTTCCGAGCAGATCAGAATCAAGATTGATTTG
* *
2312583 CTTCGCTACTCTTTTGGGAATACC
66 CTTCGCTACTCTTTTAGGAAGACC
* * * * * * *
2312607 AAATCTGAAATAAGAAGAATTTGCTCTTATACTCTTCCGGGGAGATCAGACTCGAGATTGATTTG
1 AAATCTGAAATAAGAAGAATCTACTCCTATACTCTTCCGAGCAGATCAGAATCAAGATTGATTTG
*
2312672 CTTCGCT-C-CTTCTTCAGGAAGATC
66 CTTCGCTACTCTT-TT-AGGAAGACC
2312696 AAATCT
1 AAATCT
2312702 AACCTAATTT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
87 3 0.04
88 3 0.04
89 74 0.93
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (89 bp):
AAATCTGAAATAAGAAGAATCTACTCCTATACTCTTCCGAGCAGATCAGAATCAAGATTGATTTG
CTTCGCTACTCTTTTAGGAAGACC
Found at i:2312950 original size:42 final size:41
Alignment explanation
Indices: 2312881--2312976 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 41
2312871 TTACGGACGG
* *
2312881 CCCGAAGGACTTATTATCTTGCTCGAAAGACTTACAGATGA
1 CCCGAAGGACTTATCATCATGCTCGAAAGACTTACAGATGA
* **
2312922 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGA
1 CCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACAGATGA
*
2312964 CCCAAAGGACTTA
1 CCCGAAGGACTTA
2312977 CAAATTTTGG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 12 0.26
42 35 0.74
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (41 bp):
CCCGAAGGACTTATCATCATGCTCGAAAGACTTACAGATGA
Found at i:2313362 original size:42 final size:42
Alignment explanation
Indices: 2313278--2313384 Score: 137
Period size: 42 Copynumber: 2.6 Consensus size: 42
2313268 GCCTGAAGGT
* * *
2313278 CTTACAGATGGCCCAAAGGACTT-ATCATCTTGCCGTATAGA
1 CTTACAGATGGCCCAAAGGATTTAATCATCATGCCGTAAAGA
*
2313319 CTTACAGATGACCCAAAGGATTTAATCATCATGCTCG-AAAGA
1 CTTACAGATGGCCCAAAGGATTTAATCATCATGC-CGTAAAGA
* *
2313361 CTTACTGATGGCCCGAAGGATTTA
1 CTTACAGATGGCCCAAAGGATTTA
2313385 CCAATTTCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
41 21 0.37
42 34 0.60
43 2 0.04
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (42 bp):
CTTACAGATGGCCCAAAGGATTTAATCATCATGCCGTAAAGA
Found at i:2314945 original size:36 final size:37
Alignment explanation
Indices: 2314879--2314948 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
2314869 TTCCTGGATG
*
2314879 ATATGGGCATTCAAAAATGCCATAACATTTATTATTA
1 ATATGGGCATTCAAAAATGCCATAAAATTTATTATTA
*
2314916 ATATGGG-ACTTC-AAAATGCCCTAAAATTTATTA
1 ATATGGGCA-TTCAAAAATGCCATAAAATTTATTA
2314949 CATCTAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 20 0.67
37 10 0.33
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (37 bp):
ATATGGGCATTCAAAAATGCCATAAAATTTATTATTA
Found at i:2319769 original size:44 final size:44
Alignment explanation
Indices: 2319706--2319796 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
2319696 AAAGTGATAT
*
2319706 AAACAAATTAATACGAATAA-AAAATTAATAATCTAATGAAAAAC
1 AAACAAATTAATACAAATAACAAAATTAA-AATCTAATGAAAAAC
* * * * *
2319750 AAACAAGTTAGTACAAATAACAAACTTAAAATCTAATGTAACAC
1 AAACAAATTAATACAAATAACAAAATTAAAATCTAATGAAAAAC
2319794 AAA
1 AAA
2319797 AATGTAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
44 33 0.82
45 7 0.17
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.22
Consensus pattern (44 bp):
AAACAAATTAATACAAATAACAAAATTAAAATCTAATGAAAAAC
Found at i:2322542 original size:3 final size:3
Alignment explanation
Indices: 2322536--2322564 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2322526 TTAATAATTT
2322536 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
2322565 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2325069 original size:11 final size:11
Alignment explanation
Indices: 2325053--2325077 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2325043 ATTTTAATAG
2325053 TTTTTCTTTTT
1 TTTTTCTTTTT
2325064 TTTTTCTTTTT
1 TTTTTCTTTTT
2325075 TTT
1 TTT
2325078 ATCGAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:2326748 original size:59 final size:58
Alignment explanation
Indices: 2326586--2326899 Score: 219
Period size: 59 Copynumber: 5.3 Consensus size: 58
2326576 ACCGAATGGA
* * * * * *
2326586 GCACTTTGTGTGCTAAAACGATAAGGAAA-CTATACTGAGTGTATAGATTTTCATAT-GG
1 GCACTTAGTGTGCTAAAATGGTAAGGAAATC-ATACT-AATGTATGGATTTCCATATAGG
* * * **
2326644 AGCACTTAGTGTGCT-AAATGATAAAGAAATCATATTAAAAATATGGATTTCCATATAGG
1 -GCACTTAGTGTGCTAAAATGGTAAGGAAATCATACT-AATGTATGGATTTCCATATAGG
* * * **
2326703 GCATGTTA-TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAA
1 GCA-CTTAGTGTGCTAAAATGGTAAGGAAATCATACT-AATGTATGGATTTCCATATAGG
* * * * * *
2326762 GCACTAAGGGTGCTATAA-GGATAAGAAAATCATACTAATGGTATGGATTTTCACATAGG
1 GCACTTAGTGTGCTAAAATGG-TAAGGAAATCATACTAAT-GTATGGATTTCCATATAGG
* ** **
2326821 GCATTTTA-TGTGCTAAAATGGTAACAAAATCATACTAATGGTATGGATTTTTGA-ATAGG
1 GCA-CTTAGTGTGCTAAAATGGTAAGGAAATCATACTAAT-GTATGGA-TTTCCATATAGG
* *
2326880 GAACTTCGTGTGCTAAAATG
1 GCACTTAGTGTGCTAAAATG
2326900 AAAGAGGAAG
Statistics
Matches: 204, Mismatches: 40, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
58 47 0.23
59 148 0.73
60 9 0.04
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (58 bp):
GCACTTAGTGTGCTAAAATGGTAAGGAAATCATACTAATGTATGGATTTCCATATAGG
Found at i:2326838 original size:118 final size:117
Alignment explanation
Indices: 2326594--2326870 Score: 317
Period size: 118 Copynumber: 2.4 Consensus size: 117
2326584 GAGCACTTTG
* * * * * ** * *
2326594 TGTGCTAAAACGATAAGGAAA-CTATACTGAGTGTATAGATTTTCATATGGAGCACTTAGTGTGC
1 TGTGCTAAAATGGTAAGGAAATC-ATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGTGC
* * *
2326658 TAAATGATAAAGAAATCATATTAAAAATATGGATTTCCATATAGGGCATGTTA
65 TAAAGGATAAAGAAATCATACTAAAAATATGGATTTCCACATAGGGCATGTTA
2326711 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGTGCT
*** * *
2326776 ATAAGGAT-AAGAAAATCATACTAATGGTATGGATTTTCACATAGGGCATTTTA
66 A-AAGGATAAAG-AAATCATACTAAAAATATGGATTTCCACATAGGGCATGTTA
** *
2326829 TGTGCTAAAATGGTAACAAAATCATACT-AATGGTATGGATTT
1 TGTGCTAAAATGGTAAGGAAATCATACTGAGT-GTATGGATTT
2326871 TTGAATAGGG
Statistics
Matches: 136, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
117 60 0.44
118 76 0.56
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAAGGGTGCT
AAAGGATAAAGAAATCATACTAAAAATATGGATTTCCACATAGGGCATGTTA
Done.