Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 19 of 190
Found at i:2837045 original size:20 final size:18
Alignment explanation
Indices: 2837008--2837046 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2836998 AAAATAAAAA
*
2837008 AAAATTAAATATTGATTT
1 AAAATTAAATATTAATTT
2837026 AAAATTATAATATTTAATTT
1 AAAATTA-AATA-TTAATTT
2837046 A
1 A
2837047 GTTTGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AAAATTAAATATTAATTT
Found at i:2838955 original size:10 final size:10
Alignment explanation
Indices: 2838870--2838939 Score: 63
Period size: 10 Copynumber: 6.7 Consensus size: 10
2838860 TTTTTTTATT
*
2838870 TTTATTTTGA
1 TTTATTTAGA
2838880 TCTTATTTTAAGA
1 T-TTA-TTT-AGA
*
2838893 TTCATTT-GTA
1 TTTATTTAG-A
2838903 TTTATTTAGA
1 TTTATTTAGA
2838913 TTTATTTAGA
1 TTTATTTAGA
2838923 TTT-TTTATGA
1 TTTATTTA-GA
2838933 TTTATTT
1 TTTATTT
2838940 GTTTAAATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
9 5 0.10
10 27 0.54
11 10 0.20
12 5 0.10
13 3 0.06
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.64
Consensus pattern (10 bp):
TTTATTTAGA
Found at i:2838972 original size:14 final size:14
Alignment explanation
Indices: 2838922--2838973 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2838912 ATTTATTTAG
* *
2838922 ATTTTTTATGATTT
1 ATTTATTATAATTT
*
2838936 ATTTGTT-TAAATTT
1 ATTTATTAT-AATTT
2838950 ATTTAATTATAATTT
1 ATTT-ATTATAATTT
2838965 ATTTATTAT
1 ATTTATTAT
2838974 TTATAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 1 0.03
14 19 0.59
15 11 0.34
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (14 bp):
ATTTATTATAATTT
Found at i:2839042 original size:23 final size:23
Alignment explanation
Indices: 2838960--2839043 Score: 96
Period size: 23 Copynumber: 3.5 Consensus size: 23
2838950 ATTTAATTAT
*
2838960 AATTTATTTATTATTTATAAATA
1 AATTTATTTAATATTTATAAATA
* *
2838983 TATTTGTTTATATATGTTTATAAATA
1 AATTTATTTA-ATA--TTTATAAATA
* *
2839009 TATTTATTTAATATTTATGAATA
1 AATTTATTTAATATTTATAAATA
2839032 AATTTATTTAAT
1 AATTTATTTAAT
2839044 TTAACTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
23 28 0.54
24 2 0.04
25 3 0.06
26 19 0.37
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTTATTTAATATTTATAAATA
Found at i:2843022 original size:12 final size:12
Alignment explanation
Indices: 2843007--2843038 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2842997 ACCACCCCCA
2843007 CCACCAGGAGAT
1 CCACCAGGAGAT
2843019 CCACCAGGAGAT
1 CCACCAGGAGAT
*
2843031 CTACCAGG
1 CCACCAGG
2843039 GGACCTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.34, G:0.25, T:0.09
Consensus pattern (12 bp):
CCACCAGGAGAT
Found at i:2847123 original size:21 final size:21
Alignment explanation
Indices: 2847099--2847149 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2847089 TTCATGATTA
*
2847099 AAATATTAAAATTAAATCAAT
1 AAATATTAAAATAAAATCAAT
* *
2847120 AAATATAAAAATAAAATTAAT
1 AAATATTAAAATAAAATCAAT
2847141 AAATTATTA
1 AAA-TATTA
2847150 TTATATGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATTAAAATAAAATCAAT
Found at i:2848495 original size:29 final size:29
Alignment explanation
Indices: 2848451--2848519 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
2848441 GTATTATTCG
* *
2848451 ATTTTTAAAAATTTAATATGTT-TAGTATT
1 ATTTTTAAAAAATTAATAT-TTATAATATT
*
2848480 ATTTTAAAAAAATTAATATTTATAATATT
1 ATTTTTAAAAAATTAATATTTATAATATT
2848509 ATTTTTAAAAA
1 ATTTTTAAAAA
2848520 TTTTAGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 2 0.06
29 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTTTTAAAAAATTAATATTTATAATATT
Found at i:2848529 original size:28 final size:27
Alignment explanation
Indices: 2848451--2848529 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 27
2848441 GTATTATTCG
*
2848451 ATTTTTAAAAATTTAATATGTT-TAGTATT
1 ATTTTTAAAAATTT--TAT-TTATAATATT
* *
2848480 ATTTTAAAAAAATTAATATTTATAATATT
1 ATTTT-TAAAAATT-TTATTTATAATATT
2848509 ATTTTTAAAAATTTTAGTTTA
1 ATTTTTAAAAATTTTA-TTTA
2848530 ATCGTTAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 2 0.05
28 13 0.32
29 19 0.46
30 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (27 bp):
ATTTTTAAAAATTTTATTTATAATATT
Found at i:2848615 original size:30 final size:29
Alignment explanation
Indices: 2848548--2848626 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
2848538 TAATGCACGT
* *
2848548 AGATTAAATTTCTTAAAAATAATACTATAG
1 AGATTAAATTT-TTAAAAATAATACTACAA
*
2848578 AGATTAAATTTATTAAAAATAATATTACAA
1 AGATTAAATTT-TTAAAAATAATACTACAA
**
2848608 ATCTTAAATTTTTAAAAAT
1 AGATTAAATTTTTAAAAAT
2848627 CAAAAAGTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 8 0.19
30 35 0.81
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (29 bp):
AGATTAAATTTTTAAAAATAATACTACAA
Found at i:2849936 original size:20 final size:21
Alignment explanation
Indices: 2849901--2849957 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
2849891 ATAATCCTAT
* *
2849901 TTTAAAATTTGTTTATATTCA
1 TTTAGAATTCGTTTATATTCA
*
2849922 TTTAG-ATTCGTTTATATTCG
1 TTTAGAATTCGTTTATATTCA
*
2849942 TTTAGAATTTGTTTAT
1 TTTAGAATTCGTTTAT
2849958 TATTTATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (21 bp):
TTTAGAATTCGTTTATATTCA
Found at i:2851004 original size:29 final size:29
Alignment explanation
Indices: 2850962--2851022 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
2850952 ACTCACAAAC
2850962 ATTCAAACATATATATCTATAAGACCTAA
1 ATTCAAACATATATATCTATAAGACCTAA
2850991 ATTCAAACATATATATCTATAAGACCTAA
1 ATTCAAACATATATATCTATAAGACCTAA
2851020 ATT
1 ATT
2851023 TTTAGTAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (29 bp):
ATTCAAACATATATATCTATAAGACCTAA
Found at i:2853235 original size:18 final size:19
Alignment explanation
Indices: 2853192--2853245 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
2853182 ATATATTTAA
2853192 AGATGATACATTT-ATGGT
1 AGATGATACATTTGATGGT
*
2853210 A-AGGGATACATTTGAT-GT
1 AGA-TGATACATTTGATGGT
2853228 AGATGATACATTTG-TGGT
1 AGATGATACATTTGATGGT
2853246 GGATAATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 2 0.07
18 25 0.83
19 3 0.10
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (19 bp):
AGATGATACATTTGATGGT
Found at i:2853599 original size:6 final size:6
Alignment explanation
Indices: 2853588--2853636 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
2853578 CAAAATTCGT
* *
2853588 ACCATC ACCATC ATCATC ACCATC ACCAAC ACCATC ACCATC ACCATC
1 ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC
2853636 A
1 A
2853637 TCTGAACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.37, C:0.47, G:0.00, T:0.16
Consensus pattern (6 bp):
ACCATC
Found at i:2868947 original size:39 final size:39
Alignment explanation
Indices: 2868904--2868981 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
2868894 TTTCAAACAA
2868904 ATACTTACTATTCCAATTAGAAAGACAAGCTATAGGACT
1 ATACTTACTATTCCAATTAGAAAGACAAGCTATAGGACT
*
2868943 ATACTTACTATTTCAATTAGAAAGACAAGCTATAGGACT
1 ATACTTACTATTCCAATTAGAAAGACAAGCTATAGGACT
2868982 TACCCTGCAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (39 bp):
ATACTTACTATTCCAATTAGAAAGACAAGCTATAGGACT
Found at i:2870812 original size:17 final size:17
Alignment explanation
Indices: 2870787--2870823 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2870777 AAAGACCAAA
2870787 AAAAAAAAAAAAGAAAG
1 AAAAAAAAAAAAGAAAG
* *
2870804 AAAAGAAAAACAGAAAG
1 AAAAAAAAAAAAGAAAG
2870821 AAA
1 AAA
2870824 GCTGAAGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAGAAAG
Found at i:2871649 original size:17 final size:17
Alignment explanation
Indices: 2871629--2871662 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2871619 AAATATCATT
2871629 AAATAAAAATTAATAAA
1 AAATAAAAATTAATAAA
**
2871646 AAATATGAATTAATAAA
1 AAATAAAAATTAATAAA
2871663 TTAAAAATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATAAAAATTAATAAA
Found at i:2871923 original size:356 final size:358
Alignment explanation
Indices: 2871269--2871955 Score: 1215
Period size: 356 Copynumber: 1.9 Consensus size: 358
2871259 ACATTAAAAA
* *
2871269 ATTAAATAAAAATTAATAAAAAATCTGAATTAATAAATTAAAAAATGTTATTACATATATCAAGT
1 ATTAAATAAAAATTAATAAAAAATATGAATTAATAAATTAAAAAATGTTATTACATAAATCAAGT
2871334 AACCCAAATTTAGAAATATTTTAATATATTTTTAAATAAATATTTTATTACAAATTTGATAAAAT
66 AACCCAAATTTAGAAATATTTTAATATATTTTTAAATAAATATTTTATTACAAATTTGATAAAAT
2871399 TTTTACATTTAAATAAATACCAATTAAATTTCAAATATAAATGATACTTTAAATCATTTTTATAT
131 TTTTACATTTAAATAAATACCAATTAAATTTCAAATATAAATGATACTTTAAATCATTTTTATAT
*
2871464 ATTATTGATTTTTTCATAAATTTTATTAATTTATCAATTTAAATTTAAAAATTATCAAATACATT
196 ATTATTAATTTTTTCATAAATTTTATTAATTTATCAATTTAAATTTAAAAATTATCAAATACATT
* * *
2871529 TGCAATAAAATTTTTCAATTTTATAAGTAAAATTAAAATATT-G-ATATATATTTTTAATGTATA
261 TGCAATAAAATTTTTCAATTTCATAAATAAAATTAAAATATTAGCATATATA-TTTTAATATATA
2871592 TTTAAAAAAATAACAAAATAATTTAAAAAATATC
325 TTTAAAAAAATAACAAAATAATTTAAAAAATATC
2871626 ATTAAATAAAAATTAATAAAAAATATGAATTAATAAATT-AAAAATGTTATTACATAAATCAAGT
1 ATTAAATAAAAATTAATAAAAAATATGAATTAATAAATTAAAAAATGTTATTACATAAATCAAGT
2871690 AACCCAAAATTTAGAAATATTTTAATATATTTTTAAATAAATATTTTATTACAAATTTGATAAAA
66 AACCC-AAATTTAGAAATATTTTAATATATTTTTAAATAAATATTTTATTACAAATTTGATAAAA
* *
2871755 TTTTTGCA-TTAAATAAATACTAATTAAATTTCAAATATAAATGATACTTTAAATCATTTTTATA
130 TTTTTACATTTAAATAAATACCAATTAAATTTCAAATATAAATGATACTTTAAATCATTTTTATA
*
2871819 T-TTATTAATTTTTTCATAAATTTTATTGATTTATCAATTTAAATTTAATAAATTATCAAATACA
195 TATTATTAATTTTTTCATAAATTTTATTAATTTATCAATTTAAATTTAA-AAATTATCAAATACA
2871883 TTTGCAATGAAAA-TTTTCAATTTCATAAATAAAATTAAAATATTAGCATATATATTTTAATATA
259 TTTGCAAT-AAAATTTTTCAATTTCATAAATAAAATTAAAATATTAGCATATATATTTTAATATA
2871947 TATTTAAAA
323 TATTTAAAA
2871956 GATTATAATA
Statistics
Matches: 316, Mismatches: 9, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
355 45 0.14
356 137 0.43
357 127 0.40
358 7 0.02
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (358 bp):
ATTAAATAAAAATTAATAAAAAATATGAATTAATAAATTAAAAAATGTTATTACATAAATCAAGT
AACCCAAATTTAGAAATATTTTAATATATTTTTAAATAAATATTTTATTACAAATTTGATAAAAT
TTTTACATTTAAATAAATACCAATTAAATTTCAAATATAAATGATACTTTAAATCATTTTTATAT
ATTATTAATTTTTTCATAAATTTTATTAATTTATCAATTTAAATTTAAAAATTATCAAATACATT
TGCAATAAAATTTTTCAATTTCATAAATAAAATTAAAATATTAGCATATATATTTTAATATATAT
TTAAAAAAATAACAAAATAATTTAAAAAATATC
Found at i:2872031 original size:25 final size:24
Alignment explanation
Indices: 2871984--2872035 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
2871974 CATTTTAATT
* *
2871984 TTATTTATATAATTAAAATTTTTTA
1 TTATTAATATAATTAAAA-ATTTTA
2872009 TTATTAATAT-ATTAAATAATTTTA
1 TTATTAATATAATTAAA-AATTTTA
2872033 TTA
1 TTA
2872036 AATCTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTAATATAATTAAAAATTTTA
Found at i:2872904 original size:20 final size:19
Alignment explanation
Indices: 2872868--2872907 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2872858 TTTTATTAAA
*
2872868 AAAATTAATATTATTATTT
1 AAAATTAATATGATTATTT
*
2872887 AAAATTAATCATGCTTATTT
1 AAAATTAAT-ATGATTATTT
2872907 A
1 A
2872908 TTTAGTAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (19 bp):
AAAATTAATATGATTATTT
Found at i:2873942 original size:22 final size:23
Alignment explanation
Indices: 2873903--2873947 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2873893 ATTTATTAAA
** *
2873903 TTTAAAATTATTTAATATTAATT
1 TTTAAAATTAAATAATATGAATT
2873926 TTTAAAATTAAAT-ATATGAATT
1 TTTAAAATTAAATAATATGAATT
2873948 AATCGATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTAAAATTAAATAATATGAATT
Found at i:2875071 original size:24 final size:23
Alignment explanation
Indices: 2875044--2875099 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
2875034 ATAAATTTTT
2875044 TTATTTTATTAAATTT-ATATATAA
1 TTATTTTATTAAATTTAAT-TAT-A
*
2875068 TTATTATTA-TAATTTTAATTATA
1 TTATT-TTATTAAATTTAATTATA
2875091 TTATTTTAT
1 TTATTTTAT
2875100 ATTATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 3 0.11
23 6 0.21
24 14 0.50
25 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTTTATTAAATTTAATTATA
Found at i:2875112 original size:13 final size:13
Alignment explanation
Indices: 2875072--2875121 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
2875062 ATATAATTAT
*
2875072 TATTATAATTTTA
1 TATTATATTTTTA
2875085 -ATTATATTATTTTA
1 TATTATA-T-TTTTA
2875099 TATTATATTTTTA
1 TATTATATTTTTA
2875112 TATTATATTT
1 TATTATATTT
2875122 ATATCATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.18
13 15 0.45
14 6 0.18
15 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTATATTTTTA
Found at i:2875124 original size:11 final size:11
Alignment explanation
Indices: 2875086--2875130 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
2875076 ATAATTTTAA
2875086 TTATATTAT-T
1 TTATATTATAT
2875096 TTATATTATATTT
1 TTATATTATA--T
2875109 TTATATTATAT
1 TTATATTATAT
*
2875120 TTATATCATAT
1 TTATATTATAT
2875131 CATCATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
10 9 0.29
11 11 0.35
13 11 0.35
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTATAT
Found at i:2875138 original size:24 final size:24
Alignment explanation
Indices: 2875088--2875145 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
2875078 AATTTTAATT
* ** *
2875088 ATATTAT-TTTATATTATATTTTT
1 ATATTATATTTATATCATATCATC
2875111 ATATTATATTTATATCATATCATC
1 ATATTATATTTATATCATATCATC
*
2875135 ATATAATATTT
1 ATATTATATTT
2875146 TAAATTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (24 bp):
ATATTATATTTATATCATATCATC
Found at i:2875625 original size:13 final size:13
Alignment explanation
Indices: 2875603--2875644 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
2875593 AATAATTTTA
* *
2875603 AATATGATATGAT
1 AATATAATATAAT
2875616 AATATAATATAAT
1 AATATAATATAAT
*
2875629 AATATATTATAA-
1 AATATAATATAAT
2875641 AATA
1 AATA
2875645 ATAAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (13 bp):
AATATAATATAAT
Found at i:2875668 original size:27 final size:28
Alignment explanation
Indices: 2875614--2875670 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
2875604 ATATGATATG
* *
2875614 ATAATATAATATAATAATATATTATAAA
1 ATAATATAAAATAAAAATATATTATAAA
* *
2875642 ATAATA-AAAATAAAAATATTTTTTAAA
1 ATAATATAAAATAAAAATATATTATAAA
2875669 AT
1 AT
2875671 TTTATATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATAATATAAAATAAAAATATATTATAAA
Found at i:2879397 original size:11 final size:11
Alignment explanation
Indices: 2879383--2879426 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
2879373 AAATTTTAAA
2879383 TTATATTATTT
1 TTATATTATTT
*
2879394 TTATATATTTTAT
1 TTATAT-TATT-T
2879407 TTATATTATTT
1 TTATATTATTT
2879418 TTATATTAT
1 TTATATTAT
2879427 ATGATCGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATATTATTT
Found at i:2879402 original size:13 final size:13
Alignment explanation
Indices: 2879384--2879423 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2879374 AATTTTAAAT
2879384 TATATTATTTTTA
1 TATATTATTTTTA
*
2879397 TATATT-TTATT-
1 TATATTATTTTTA
2879408 TATATTATTTTTA
1 TATATTATTTTTA
2879421 TAT
1 TAT
2879424 TATATGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 6 0.26
12 8 0.35
13 9 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATATTATTTTTA
Found at i:2879406 original size:15 final size:14
Alignment explanation
Indices: 2879377--2879428 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
2879367 TTTTAAAAAT
* *
2879377 TTTAAATTATATTA
1 TTTATATTATTTTA
*
2879391 TTTTTATATATTTTA
1 TTTATAT-TATTTTA
2879406 TTTATATTATTTTTA
1 TTTATATTA-TTTTA
2879421 TATTATAT
1 T-TTATAT
2879429 GATCGTATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 7 0.23
15 18 0.58
16 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATATTATTTTA
Found at i:2886871 original size:17 final size:18
Alignment explanation
Indices: 2886844--2886887 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2886834 TATAAAAGAT
* *
2886844 AAATTAATTTTAT-TTAT
1 AAATTATTTTTATATTAA
*
2886861 ATATTATTTTTATATTAA
1 AAATTATTTTTATATTAA
2886879 AAATTATTT
1 AAATTATTT
2886888 AAAAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AAATTATTTTTATATTAA
Found at i:2887536 original size:119 final size:117
Alignment explanation
Indices: 2887389--2887629 Score: 428
Period size: 119 Copynumber: 2.0 Consensus size: 117
2887379 ATGCTCTTAA
* *
2887389 TTTATGTCATAAAAATTTTAATTTATAAATATTTATTTAATTATTTTTAATAAAAAATTTATAAA
1 TTTATGTAATAAAAATTTTAATTTATAAATATTTATTTAATTATTTTTAATAAAAAAATTATAAA
*
2887454 TTCAATTTAAGTCTCTCTCGTTAATTAAACATAGCATCTTCTTTGATACTTTT
66 TTCAATTTAAGTCTCTCTCGTTAATTAAACATAACATCTTCTTTGAT-CTTTT
2887507 TTTATGTAATAAAAAATTTTAATTTATAAATATTTATTTAATTATTTTTAATAAAAAAATTATAA
1 TTTATGTAAT-AAAAATTTTAATTTATAAATATTTATTTAATTATTTTTAATAAAAAAATTATAA
*
2887572 ATTCAATTTAAGTCTCTCTCGTTAATTAAACATAACATCTTCTTTGATTTTTT
65 ATTCAATTTAAGTCTCTCTCGTTAATTAAACATAACATCTTCTTTGATCTTTT
2887625 TTTAT
1 TTTAT
2887630 AGGAAAAAAA
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
118 18 0.15
119 100 0.85
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (117 bp):
TTTATGTAATAAAAATTTTAATTTATAAATATTTATTTAATTATTTTTAATAAAAAAATTATAAA
TTCAATTTAAGTCTCTCTCGTTAATTAAACATAACATCTTCTTTGATCTTTT
Found at i:2887655 original size:119 final size:119
Alignment explanation
Indices: 2887413--2887662 Score: 362
Period size: 119 Copynumber: 2.1 Consensus size: 119
2887403 ATTTTAATTT
*
2887413 ATAAATATTTATTTAATTATTTTTAATAAAAAATTTATAAATTCAATTTAAGTCTCTCTCGTTAA
1 ATAAATATTTATTTAATTATTTTTAATAAAAAAATTATAAATTCAATTTAAGTCTCTCTCGTTAA
* *** **
2887478 TTAAACATAGCATCTTCTTTGATACTTTTTTTATGTAATAAAAAATTTTAATTT
66 TTAAACATAACATCTTCTTTGATACTTTTTTTATGTAATAAAAAATAAAAATAG
2887532 ATAAATATTTATTTAATTATTTTTAATAAAAAAATTATAAATTCAATTTAAGTCTCTCTCGTTAA
1 ATAAATATTTATTTAATTATTTTTAATAAAAAAATTATAAATTCAATTTAAGTCTCTCTCGTTAA
* *
2887597 TTAAACATAACATCTTCTTTGAT-TTTTTTTTATAG-GA-AAAAAATAAAAGAGTAG
66 TTAAACATAACATCTTCTTTGATACTTTTTTTAT-GTAATAAAAAATAAAA-A-TAG
2887651 ATAAATTATTTA
1 ATAAA-TATTTA
2887663 ATTTTTTAAG
Statistics
Matches: 118, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
117 8 0.07
118 11 0.09
119 93 0.79
120 6 0.05
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (119 bp):
ATAAATATTTATTTAATTATTTTTAATAAAAAAATTATAAATTCAATTTAAGTCTCTCTCGTTAA
TTAAACATAACATCTTCTTTGATACTTTTTTTATGTAATAAAAAATAAAAATAG
Found at i:2887723 original size:24 final size:28
Alignment explanation
Indices: 2887673--2887725 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
2887663 ATTTTTTAAG
2887673 TTAAAATAAAATATATCGTATATGATAAT
1 TTAAAATAAAATATATC-TATATGATAAT
2887702 TTAAAAT-AAATA-AT-TATA-GATAAT
1 TTAAAATAAAATATATCTATATGATAAT
2887726 ATATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 6 0.25
25 4 0.17
27 2 0.08
28 5 0.21
29 7 0.29
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (28 bp):
TTAAAATAAAATATATCTATATGATAAT
Found at i:2889449 original size:16 final size:16
Alignment explanation
Indices: 2889428--2889458 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2889418 TTATAAAAAT
*
2889428 TTAAAATATATATAAA
1 TTAAAAAATATATAAA
2889444 TTAAAAAATATATAA
1 TTAAAAAATATATAA
2889459 TTTCATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAAAAATATATAAA
Found at i:2889589 original size:25 final size:26
Alignment explanation
Indices: 2889540--2889590 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
2889530 TTTAATGTTT
* *
2889540 AAACTTAATTTAAACTAAATAAAATA
1 AAACTTAATCTAAACTAAACAAAATA
*
2889566 AAAC-TAATCTAAACTAAACCAAATA
1 AAACTTAATCTAAACTAAACAAAATA
2889591 TTATAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (26 bp):
AAACTTAATCTAAACTAAACAAAATA
Found at i:2889623 original size:9 final size:8
Alignment explanation
Indices: 2889608--2889633 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2889598 TTTGAATCAA
2889608 ATTTTTTT
1 ATTTTTTT
2889616 ATTTTTTT
1 ATTTTTTT
2889624 ATTTTTTT
1 ATTTTTTT
2889632 AT
1 AT
2889634 CGTTTCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:2890286 original size:18 final size:20
Alignment explanation
Indices: 2890258--2890297 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
2890248 ATTTAATTTG
*
2890258 AATCAAATTT-ATTTTAAAA
1 AATCAAATTTAAATTTAAAA
2890277 AATC-AATTTAAATTTAAAA
1 AATCAAATTTAAATTTAAAA
2890296 AA
1 AA
2890298 ATTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATCAAATTTAAATTTAAAA
Found at i:2890953 original size:14 final size:14
Alignment explanation
Indices: 2890945--2890984 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
2890935 AATATTATTT
2890945 TTTAAATATAAATA
1 TTTAAATATAAATA
2890959 TTTAAATATATAATTA
1 TTTAAATATA-AA-TA
*
2890975 TATAAATATA
1 TTTAAATATA
2890985 TATAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 2 0.09
16 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAATATAAATA
Found at i:2890966 original size:8 final size:8
Alignment explanation
Indices: 2890950--2890986 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
2890940 TATTTTTTAA
2890950 ATATAAAT
1 ATATAAAT
*
2890958 ATTTAAAT
1 ATATAAAT
*
2890966 ATATAATT
1 ATATAAAT
2890974 ATATAAAT
1 ATATAAAT
2890982 ATATA
1 ATATA
2890987 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAAAT
Found at i:2890993 original size:14 final size:14
Alignment explanation
Indices: 2890947--2890994 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2890937 TATTATTTTT
* *
2890947 TAAATATAAATATT
1 TAAATATATATATA
2890961 TAAATATATAATTATA
1 TAAATATAT-A-TATA
*
2890977 TAAATATATATAAA
1 TAAATATATATATA
2890991 TAAA
1 TAAA
2890995 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 15 0.52
15 2 0.07
16 12 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATATATATA
Found at i:2890999 original size:26 final size:24
Alignment explanation
Indices: 2890950--2891000 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
2890940 TATTTTTTAA
* *
2890950 ATATAAATATTTAAATATATAATT
1 ATATAAATATTTAAATAAAAAATT
2890974 ATATAAATATATATAAATAAAAAATT
1 ATATAAATAT-T-TAAATAAAAAATT
2891000 A
1 A
2891001 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 1 0.04
26 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATAAATATTTAAATAAAAAATT
Found at i:2891376 original size:31 final size:31
Alignment explanation
Indices: 2891303--2891377 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
2891293 ATTCTTAATT
*
2891303 TTTTTTTATTTTTTTAAGATGTCTTAAATTA
1 TTTTTTTATTTTTTTAAGATGTCTTAAACTA
* * *
2891334 TCTTTTAATTTTTTTAATAT-T-TTAAAACTA
1 TTTTTTTATTTTTTTAAGATGTCTT-AAACTA
2891364 TTTTTGTTATTTTT
1 TTTTT-TTATTTTT
2891378 ATATTTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 2 0.06
30 10 0.28
31 24 0.67
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (31 bp):
TTTTTTTATTTTTTTAAGATGTCTTAAACTA
Found at i:2901187 original size:18 final size:18
Alignment explanation
Indices: 2901147--2901188 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2901137 AGTTTATAAA
*
2901147 TCAA-TTAAATTAAGCTT
1 TCAATTTAAATTAAACTT
* *
2901164 TGAATTTAAATTAAATTT
1 TCAATTTAAATTAAACTT
2901182 TCAATTT
1 TCAATTT
2901189 TTTTTATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (18 bp):
TCAATTTAAATTAAACTT
Found at i:2904100 original size:29 final size:29
Alignment explanation
Indices: 2904023--2904114 Score: 80
Period size: 28 Copynumber: 3.1 Consensus size: 29
2904013 AAAGGTTAAG
* *
2904023 AATTTATTTAAACATAAATTAAAAATTTAAA
1 AATTTATTT-AA-ATAAAATAAAAATATAAA
* * **
2904054 ATTTTA-TTAGATGCAATAAAAATATAAA
1 AATTTATTTAAATAAAATAAAAATATAAA
2904082 AATTTATTTAAATAAAATAATAAA-ATTAAA
1 AATTTATTTAAATAAAATAA-AAATA-TAAA
2904112 AAT
1 AAT
2904115 GCTTCTAATT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
28 19 0.40
29 12 0.25
30 12 0.25
31 5 0.10
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (29 bp):
AATTTATTTAAATAAAATAAAAATATAAA
Found at i:2907004 original size:13 final size:13
Alignment explanation
Indices: 2906971--2907006 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
2906961 CATGCATTCA
*
2906971 AAATGATCATAAC
1 AAATGATTATAAC
2906984 AAATGATTATAAC
1 AAATGATTATAAC
2906997 AAATGATTAT
1 AAATGATTAT
2907007 CGACAGAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
AAATGATTATAAC
Found at i:2907913 original size:14 final size:14
Alignment explanation
Indices: 2907894--2907927 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2907884 GATTTAAAAT
2907894 AATAATATTTTATA
1 AATAATATTTTATA
*
2907908 AATAATTTTTTATA
1 AATAATATTTTATA
*
2907922 ATTAAT
1 AATAAT
2907928 TGTGTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATAATATTTTATA
Found at i:2921511 original size:62 final size:62
Alignment explanation
Indices: 2921414--2921534 Score: 197
Period size: 62 Copynumber: 2.0 Consensus size: 62
2921404 TCGGATCTAG
* * *
2921414 CTTTCCTAGTATAAGTATTGACATAATATCGAAAAGGCAGAAATTAACATGAATAAGAGTCA
1 CTTTCCTAGTATAAATATTGACATAATATAGAAAAGGCAGAAACTAACATGAATAAGAGTCA
* *
2921476 CTTTCCTATTATAAATATTGAGATAATATAGAAAAGGCAGAAACTAACATGAATAAGAG
1 CTTTCCTAGTATAAATATTGACATAATATAGAAAAGGCAGAAACTAACATGAATAAGAG
2921535 CTACTTAAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (62 bp):
CTTTCCTAGTATAAATATTGACATAATATAGAAAAGGCAGAAACTAACATGAATAAGAGTCA
Found at i:2925574 original size:14 final size:14
Alignment explanation
Indices: 2925555--2925581 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2925545 TATAAAAAAT
2925555 AAAAATTATAGATG
1 AAAAATTATAGATG
2925569 AAAAATTATAGAT
1 AAAAATTATAGAT
2925582 TACATATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (14 bp):
AAAAATTATAGATG
Found at i:2926732 original size:22 final size:22
Alignment explanation
Indices: 2926689--2926734 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2926679 AAAAATTTAT
* *
2926689 AAAATTTTTAATATCTATATTA
1 AAAATATTTAATATCAATATTA
2926711 AAAATATTTAATA-CAATAATTA
1 AAAATATTTAATATCAAT-ATTA
2926733 AA
1 AA
2926735 TATTTGTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATATTTAATATCAATATTA
Found at i:2937847 original size:101 final size:101
Alignment explanation
Indices: 2937668--2937871 Score: 372
Period size: 101 Copynumber: 2.0 Consensus size: 101
2937658 CTTGATATGA
*
2937668 GATAGTTGTCTTAACTTCTAATGATTGCATTGAAGAATTGGTGTCCTTAGTTCAAGAATGGCAAT
1 GATAGTTGTCTTAACTTCTAATGATTGCATTGAAGAATTGGTGTCCTTACTTCAAGAATGGCAAT
*
2937733 TAAATCATTTAATTTCATTAATATAGCTGATGCATT
66 TAAATCATATAATTTCATTAATATAGCTGATGCATT
*
2937769 GATAGTTGTCTTAACTTCTAATGATTGTATTGAAGAATTGGTGTCCTTACTTCAAGAATGGCAAT
1 GATAGTTGTCTTAACTTCTAATGATTGCATTGAAGAATTGGTGTCCTTACTTCAAGAATGGCAAT
*
2937834 TAAGTCATATAATTTCATTAATATAGCTGATGCATT
66 TAAATCATATAATTTCATTAATATAGCTGATGCATT
2937870 GA
1 GA
2937872 AAAATGTGCT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (101 bp):
GATAGTTGTCTTAACTTCTAATGATTGCATTGAAGAATTGGTGTCCTTACTTCAAGAATGGCAAT
TAAATCATATAATTTCATTAATATAGCTGATGCATT
Found at i:2937951 original size:17 final size:17
Alignment explanation
Indices: 2937929--2937971 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2937919 ATTTCCTAGC
* * *
2937929 AAAAGAAAGAGAGACAT
1 AAAAGAAAAAGACAAAT
2937946 AAAAGAAAAAGACAAAT
1 AAAAGAAAAAGACAAAT
2937963 AAAAGAAAA
1 AAAAGAAAA
2937972 GATCCATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAGAAAAAGACAAAT
Found at i:2939276 original size:21 final size:20
Alignment explanation
Indices: 2939236--2939277 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2939226 AATTTATTGA
* *
2939236 TAAAATATTAAAATTTTAAT
1 TAAAATATTAAAAATATAAT
2939256 TAAAATAATTAAAAATATAAT
1 TAAAAT-ATTAAAAATATAAT
2939277 T
1 T
2939278 TTAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAATATTAAAAATATAAT
Found at i:2947774 original size:22 final size:23
Alignment explanation
Indices: 2947740--2947782 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2947730 TAAAACAAAC
*
2947740 AACATATTAAATTAAAATAATTT
1 AACAGATTAAATTAAAATAATTT
*
2947763 AACAGATT-AATTAAACTAAT
1 AACAGATTAAATTAAAATAAT
2947783 AAAAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (23 bp):
AACAGATTAAATTAAAATAATTT
Found at i:2956476 original size:32 final size:31
Alignment explanation
Indices: 2956440--2956509 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
2956430 TATATAACAG
*
2956440 AAATGGAAAAATCT-AAGATTCCAAAGCAGCAA
1 AAATGGAAAAATCTAAAGATACCAAA-CAG-AA
*
2956472 AAATGG--AAATCTAAAGATACCCAACAGAA
1 AAATGGAAAAATCTAAAGATACCAAACAGAA
2956501 AAATGGAAA
1 AAATGGAAA
2956510 CTTTCAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
29 8 0.24
30 9 0.27
31 10 0.30
32 6 0.18
ACGTcount: A:0.56, C:0.14, G:0.16, T:0.14
Consensus pattern (31 bp):
AAATGGAAAAATCTAAAGATACCAAACAGAA
Found at i:2956507 original size:29 final size:30
Alignment explanation
Indices: 2956448--2956509 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
2956438 AGAAATGGAA
*
2956448 AAATCTAAGATTCCAAAGCAGCAAAAATGG
1 AAATCTAAGATACCAAAGCAGCAAAAATGG
*
2956478 AAATCTAAAGATACCCAA-CAG-AAAAATGG
1 AAATCT-AAGATACCAAAGCAGCAAAAATGG
2956507 AAA
1 AAA
2956510 CTTTCAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 11 0.38
30 9 0.31
31 9 0.31
ACGTcount: A:0.55, C:0.16, G:0.15, T:0.15
Consensus pattern (30 bp):
AAATCTAAGATACCAAAGCAGCAAAAATGG
Found at i:2956759 original size:2 final size:2
Alignment explanation
Indices: 2956752--2956776 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2956742 AAATACACAA
2956752 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2956777 CACACACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2957443 original size:20 final size:21
Alignment explanation
Indices: 2957406--2957448 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2957396 AGATTTCTTC
*
2957406 TTATCCTTTTCCTTTTCTTTT
1 TTATCCTTTTCCTATTCTTTT
*
2957427 TTATTCTTTT-CTATTCTTTT
1 TTATCCTTTTCCTATTCTTTT
2957447 TT
1 TT
2957449 TTATTCTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATCCTTTTCCTATTCTTTT
Found at i:2957449 original size:21 final size:21
Alignment explanation
Indices: 2957406--2957460 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
2957396 AGATTTCTTC
* *
2957406 TTATCCTTTTCCTTTTC-TTTT
1 TTATTCTTTT-CTATTCTTTTT
2957427 TTATTCTTTTCTATTCTTTTTT
1 TTATTCTTTTCTATTC-TTTTT
*
2957449 TTATTCTATTCT
1 TTATTCTTTTCT
2957461 TTGTGCTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.17
21 9 0.31
22 15 0.52
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATTCTTTTCTATTCTTTTT
Found at i:2958999 original size:19 final size:19
Alignment explanation
Indices: 2958975--2959012 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2958965 CATGATTATG
*
2958975 TTGTGTTTAAAGTTATCTA
1 TTGTGTTTAAAATTATCTA
2958994 TTGTGTTTAAAATTATCTA
1 TTGTGTTTAAAATTATCTA
2959013 AGTTTGTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (19 bp):
TTGTGTTTAAAATTATCTA
Found at i:2964276 original size:48 final size:47
Alignment explanation
Indices: 2964219--2964318 Score: 137
Period size: 48 Copynumber: 2.1 Consensus size: 47
2964209 TTCTTTTTGG
* *
2964219 ATTTATAAATTTTTCACCATTTGGGTCAATTTAAAAATATTTTTTTTA
1 ATTTCTAAATTTTTCACCATCTGGGTCAATTTAAAAA-ATTTTTTTTA
* * *
2964267 ATTTCTAAATTTTTCATCATCTGGGTCTATTTAGAAAATTTTTTTTA
1 ATTTCTAAATTTTTCACCATCTGGGTCAATTTAAAAAATTTTTTTTA
*
2964314 TTTTC
1 ATTTC
2964319 GGAAAGAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 14 0.30
48 32 0.70
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (47 bp):
ATTTCTAAATTTTTCACCATCTGGGTCAATTTAAAAAATTTTTTTTA
Found at i:2964773 original size:26 final size:26
Alignment explanation
Indices: 2964744--2964797 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
2964734 AAATTTTGAC
**
2964744 AAAATTTTTCACTTAAAAATTTTATA
1 AAAATTTACCACTTAAAAATTTTATA
* *
2964770 AAAATTTACCATTTAAAATTTTTATA
1 AAAATTTACCACTTAAAAATTTTATA
2964796 AA
1 AA
2964798 TTTCATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAATTTACCACTTAAAAATTTTATA
Found at i:2964834 original size:180 final size:180
Alignment explanation
Indices: 2964494--2964853 Score: 408
Period size: 180 Copynumber: 2.0 Consensus size: 180
2964484 AAAATTTTAT
* ** *
2964494 TTTGAAAAGAATACAATTACTTTTATTGAAATTTCATATAAATTATTCCATTATTTATGACAAAT
1 TTTGAAAAAAATACAATTACTTTTATTGAAATTTCATATAAATTATTCCACAATTTAGGACAAAT
* * * *
2964559 TTAGAGAAATTTTTCACCTAAAGATTTCTTAAAAATTTATCATTTGAAATTCTTAAGAATCTCAT
66 TTAGAAAAATTTTTCACCTAAAAATTTCTTAAAAATTTACCATTTAAAATTCTTAAGAATCTCAT
* **
2964624 CCTTAGGTAATTTGTATTTAATTCCAAAA-T-TTATTTTTTATTTTTTTG
131 CATTAGGTAATTAATATTTAATTCCAAAATTATTATTTTTTATTTTTTTG
* * * * * *
2964672 TTTGAAAAAAATATTAATTA-TTGTTATTGAAATTTTATCTAAATTATTTCACAATTTGGGATAA
1 TTTGAAAAAAATA-CAATTACTT-TTATTGAAATTTCATATAAATTATTCCACAATTTAGGACAA
* * *
2964736 ATTTTGACAAAATTTTTCACTTAAAAATTT-TATAAAAATTTACCATTTAAAATTTTTATA-AAT
64 ATTTAGA-AAAATTTTTCACCTAAAAATTTCT-TAAAAATTTACCATTTAAAATTCTTA-AGAAT
* * *
2964799 TTCATCATT-GGATAATTAATATTTATTTTCAAAATTTATTATTTTTTATTTTTTT
126 CTCATCATTAGG-TAATTAATATTTAATTCCAAAA-TTATTATTTTTTATTTTTTT
2964854 CTAAATTTAA
Statistics
Matches: 150, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
178 14 0.09
179 47 0.31
180 70 0.47
181 1 0.01
182 1 0.01
183 17 0.11
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (180 bp):
TTTGAAAAAAATACAATTACTTTTATTGAAATTTCATATAAATTATTCCACAATTTAGGACAAAT
TTAGAAAAATTTTTCACCTAAAAATTTCTTAAAAATTTACCATTTAAAATTCTTAAGAATCTCAT
CATTAGGTAATTAATATTTAATTCCAAAATTATTATTTTTTATTTTTTTG
Found at i:2968249 original size:2 final size:2
Alignment explanation
Indices: 2968195--2968233 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2968185 CCTGCACTGC
*
2968195 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2968234 CACACATAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2971629 original size:2 final size:2
Alignment explanation
Indices: 2971622--2971670 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2971612 AGTGAGGATG
2971622 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2971664 GA GA GA G
1 GA GA GA G
2971671 GGAAGGGGGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2974330 original size:14 final size:15
Alignment explanation
Indices: 2974313--2974343 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2974303 GTGGTTCTCT
2974313 TTGGA-TCGATCTTC
1 TTGGATTCGATCTTC
2974327 TTGGATTCGATCTTC
1 TTGGATTCGATCTTC
2974342 TT
1 TT
2974344 TTCATCGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
TTGGATTCGATCTTC
Found at i:2974889 original size:3 final size:3
Alignment explanation
Indices: 2974883--2974917 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2974873 AAATTAAATA
2974883 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2974918 AAATGCTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2975156 original size:50 final size:50
Alignment explanation
Indices: 2975102--2975776 Score: 623
Period size: 49 Copynumber: 13.8 Consensus size: 50
2975092 TTGAAAGTTT
* * * * *
2975102 AAAAAGCTCCTCTCAGTAGAGGCTCAACAA-TTAAAAATTTTTTTTTTTGA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TTCTTATCTTGA
* ** * * *
2975152 AAAAA-CTCTTCTCAATAGAGGCTCAACAACTTTTAAATCTCATATCATGA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TCTTATCTTGA
* *
2975202 AAAAGGGCTCCTCTCAGCAGAAGCTCAACAACTTTAAAAGTT-TTATCTTGA
1 AAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TTCTTATCTTGA
** * * *
2975253 AAAGGGTTCATCTCAGCAGAAGCTCAACAACTTTAAAATT-TTCATCTTG-
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTT-ATCTTGA
* * * *
2975302 AAAAAGTTCCTCTCCGCAGAGTCTCAACAACTTTTAAAATTCTTATATTGA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAAC-TTTAAAATTCTTATCTTGA
** * * * * * *
2975353 AAAGGGCTCATCTTAGCAGAGGATCAATAACTTTAAAATTCTCATATT-A
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTGA
* * * * * * *
2975402 GAAAAGCTTCTCTCAACAGAGGCTCAAAAACTTTAGAATTCTCATCTTGG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTGA
* *
2975452 AAAAA-CTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTGTTATTTTG-
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTGA
* * * *
2975500 AAAAAGCTCCTCTCAGTAGAAGCTCAACAACTTTAAAATTCTCATTTTG-
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTGA
*
2975549 AAAAAGCTCCTCTCAACAGAGGCTC-ACAACTTTAAAATTCTTATCTTGA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTGA
** * * *
2975598 AAAGGGCTCATCTCGGCAGAGGTTCAACAACTTTAAAATTCTTATCTTGA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTGA
** * * * *
2975648 AAAGGGCTCATCTCAGCAGATGCTCAATAACTTTAAAAAT-TTA--TT--
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTGA
* * * *
2975693 AAAAAGCTCATATCAGCAGAGGCTCAATAACTTTAAAA-TCTCATC-TG-
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTGA
*
2975740 -AAAAGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
2975777 ATCTCATATA
Statistics
Matches: 523, Mismatches: 85, Indels: 38
0.81 0.13 0.06
Matches are distributed among these distances:
44 1 0.00
45 36 0.07
46 35 0.07
47 2 0.00
48 26 0.05
49 209 0.40
50 151 0.29
51 34 0.07
52 28 0.05
53 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.30
Consensus pattern (50 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATCTTGA
Found at i:2988038 original size:207 final size:209
Alignment explanation
Indices: 2987655--2988046 Score: 460
Period size: 207 Copynumber: 1.9 Consensus size: 209
2987645 AATTTAACTA
* * * * * *
2987655 TATTGAAGATTTTCTATAAATATTCCAATACGCTGGTAATATTTTACAGAAAAATCTTCTCACTT
1 TATTGAAAATTTTCTATAAATACTCCAATACACAGGTAATATTTTACAGAAAAATATTCTCACCT
* * * * *
2987720 AGAGATTTCTTAAAGCATCTCTACTCGGAATACTTTTAGAATCCCATCATTGGATTAAATTTCTT
66 AGAGATTTCATAAAGCATCACTACTCGGAATACCTTTAGAATCCCATCATCGGATAAAATTTCTT
*
2987785 TCCTTCCTATTTTTATTACTTATATTTAGTTTATTAATCAATTTTTAT-TTATTACTAACAAAAA
131 TCCTTCATATTTTTATTACTTATATTTAG-TTATTAATCAATTTTTATATTATTACTAACAAAAA
2987849 AGAAAATCTGTACTG
195 AGAAAATCTGTACTG
* * *
2987864 TATTGAAAATTTTTTATAAATACTCTAATACACAGGTAGTA-TTTA-A-AACAAATATTCTCACC
1 TATTGAAAATTTTCTATAAATACTCCAATACACAGGTAATATTTTACAGAA-AAATATTCTCACC
* * *
2987926 TAGAGATTTCAT-AGGCATCACTACTCGGAATACCTTT-GAATCTCATCGTCGGATAAAAATTTT
65 TAGAGATTTCATAAAGCATCACTACTCGGAATACCTTTAGAATCCCATCATCGGAT-AAAA-TTT
* **
2987989 CTTTTCTTACAT-TTTTTATTACTT-TAGTATTA-TTATTAAATTTATTTTTATATTATTA
128 CTTTCCTT-CATATTTTTATTACTTATA-T-TTAGTTATT-AATCAATTTTTATATTATTA
2988047 TTTTTATAGT
Statistics
Matches: 154, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
205 14 0.09
206 34 0.22
207 57 0.37
208 15 0.10
209 34 0.22
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (209 bp):
TATTGAAAATTTTCTATAAATACTCCAATACACAGGTAATATTTTACAGAAAAATATTCTCACCT
AGAGATTTCATAAAGCATCACTACTCGGAATACCTTTAGAATCCCATCATCGGATAAAATTTCTT
TCCTTCATATTTTTATTACTTATATTTAGTTATTAATCAATTTTTATATTATTACTAACAAAAAA
GAAAATCTGTACTG
Found at i:2988049 original size:14 final size:13
Alignment explanation
Indices: 2988029--2988063 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
2988019 TATTATTAAA
*
2988029 TTTATTTTTATAT
1 TTTATTTTTATAG
2988042 TATTATTTTTATAG
1 T-TTATTTTTATAG
2988056 TTTATTTT
1 TTTATTTT
2988064 AAAAATTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTATTTTTATAG
Found at i:2989605 original size:17 final size:17
Alignment explanation
Indices: 2989575--2989613 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2989565 CATAACCCTA
2989575 TATATATATATATATAT
1 TATATATATATATATAT
* *
2989592 TATATTTATTTATATAT
1 TATATATATATATATAT
2989609 T-TATA
1 TATATA
2989614 AGTCATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:2990829 original size:14 final size:14
Alignment explanation
Indices: 2990795--2990855 Score: 65
Period size: 13 Copynumber: 4.5 Consensus size: 14
2990785 AATTAATTAT
*
2990795 ACAAAAT-AGAAAA
1 ACAAAATAAAAAAA
*
2990808 CCAAAATAAAAATAA
1 ACAAAATAAAAA-AA
2990823 A-AAAATAAAAAAA
1 ACAAAATAAAAAAA
2990836 ACAAAA-AAAAAAA
1 ACAAAATAAAAAAA
*
2990849 AGAAAAT
1 ACAAAAT
2990856 GGCAAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 21 0.52
14 17 0.43
15 2 0.05
ACGTcount: A:0.82, C:0.07, G:0.03, T:0.08
Consensus pattern (14 bp):
ACAAAATAAAAAAA
Found at i:2990833 original size:9 final size:9
Alignment explanation
Indices: 2990815--2990855 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
2990805 AAACCAAAAT
2990815 AAAAAT-AA
1 AAAAATAAA
2990823 AAAAATAAA
1 AAAAATAAA
*
2990832 AAAAACAAA
1 AAAAATAAA
2990841 AAAAA-AAA
1 AAAAATAAA
2990849 AGAAAAT
1 A-AAAAT
2990856 GGCAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 10 0.34
9 19 0.66
ACGTcount: A:0.88, C:0.02, G:0.02, T:0.07
Consensus pattern (9 bp):
AAAAATAAA
Found at i:2992186 original size:20 final size:19
Alignment explanation
Indices: 2992157--2992194 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2992147 AATAAAAAAA
2992157 AAATCTAAACCTTAAAATT
1 AAATCTAAACCTTAAAATT
*
2992176 AAATCTCAAACCTTCAAAT
1 AAATCT-AAACCTTAAAAT
2992195 CCTATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATCTAAACCTTAAAATT
Found at i:2992205 original size:28 final size:28
Alignment explanation
Indices: 2992160--2992403 Score: 136
Period size: 28 Copynumber: 8.5 Consensus size: 28
2992150 AAAAAAAAAA
* * *
2992160 TCTAAACCTTAAAATTAAATCTCAAACC
1 TCTAAACCCTAAAATTAAACCCCAAACC
* *
2992188 T-TCAAATCCTATAATTAAACCCCAAACC
1 TCT-AAACCCTAAAATTAAACCCCAAACC
* *
2992216 TCTAAACCCTAAAATTAAACCCTAAATAC
1 TCTAAACCCTAAAATTAAACCCCAAA-CC
** ** *
2992245 TCTAAACCCTAAAACCAAAACTTCAAACA
1 TCTAAACCCTAAAA-TTAAACCCCAAACC
* * * *
2992274 TC-AAACCTTAAAATCAAATCCCTAAAACA
1 TCTAAACCCTAAAATTAAA-CCC-CAAACC
* * * *
2992303 TCAAAATCCTAAAATCAAAACCCTAAATCC
1 TCTAAACCCTAAAAT-TAAACCCCAAA-CC
** **
2992333 TCTAAACCCTAAAACCAAAACTTCAAACC
1 TCTAAACCCTAAAA-TTAAACCCCAAACC
* *
2992362 TC-AAACCCTAAAATCAAAACCCCAAATC
1 TCTAAACCCTAAAAT-TAAACCCCAAACC
*
2992390 TC-AAACTCTAAAAT
1 TCTAAACCCTAAAAT
2992404 AAAAAACCTA
Statistics
Matches: 167, Mismatches: 38, Indels: 22
0.74 0.17 0.10
Matches are distributed among these distances:
27 4 0.02
28 87 0.52
29 32 0.19
30 41 0.25
31 3 0.02
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (28 bp):
TCTAAACCCTAAAATTAAACCCCAAACC
Found at i:2992252 original size:16 final size:15
Alignment explanation
Indices: 2992203--2992402 Score: 102
Period size: 14 Copynumber: 13.8 Consensus size: 15
2992193 ATCCTATAAT
* *
2992203 TAAACCCCAAACCTC
1 TAAACCCTAAAACTC
2992218 TAAACCCTAAAA-T-
1 TAAACCCTAAAACTC
2992231 TAAACCCTAAATACTC
1 TAAACCCTAAA-ACTC
2992247 TAAACCCTAAAAC-C
1 TAAACCCTAAAACTC
* * *
2992261 -AAAACTTCAAACATC
1 TAAACCCTAAAAC-TC
*
2992276 -AAACCTTAAAA-TC
1 TAAACCCTAAAACTC
2992289 -AAATCCCTAAAACATC
1 TAAA-CCCTAAAAC-TC
* *
2992305 AAAATCCTAAAA-TC
1 TAAACCCTAAAACTC
* *
2992319 AAAACCCTAAATCCTC
1 TAAACCCTAAA-ACTC
2992335 TAAACCCTAAAAC-C
1 TAAACCCTAAAACTC
* * *
2992349 -AAAACTTCAAAC-C
1 TAAACCCTAAAACTC
2992362 TCAAACCCTAAAA-TC
1 T-AAACCCTAAAACTC
* * *
2992377 AAAACCCCAAATCTC
1 TAAACCCTAAAACTC
*
2992392 -AAACTCTAAAA
1 TAAACCCTAAAA
2992403 TAAAAAACCT
Statistics
Matches: 145, Mismatches: 25, Indels: 31
0.72 0.12 0.15
Matches are distributed among these distances:
13 35 0.24
14 40 0.28
15 35 0.24
16 32 0.22
17 3 0.02
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (15 bp):
TAAACCCTAAAACTC
Found at i:2992339 original size:88 final size:86
Alignment explanation
Indices: 2992204--2992407 Score: 284
Period size: 88 Copynumber: 2.4 Consensus size: 86
2992194 TCCTATAATT
* * * *
2992204 AAACCCCAAACCTCTAAACCCTAAAATTAAACCCTAAATACTCTAAACCCTAAAACCAAAACTTC
1 AAACCCCAAAACTCAAAATCCTAAAATAAAACCCTAAATACTCTAAACCCTAAAACCAAAACTTC
*
2992269 AAACATCAAACCTTAAAATCA
66 AAACATCAAACCCTAAAATCA
* * *
2992290 AATCCCTAAAACATCAAAATCCTAAAATCAAAACCCTAAATCCTCTAAACCCTAAAACCAAAACT
1 AAACCCCAAAAC-TCAAAATCCTAAAAT-AAAACCCTAAATACTCTAAACCCTAAAACCAAAACT
*
2992355 TCAAACCTCAAACCCTAAAATCA
64 TCAAACATCAAACCCTAAAATCA
* *
2992378 AAACCCCAAATCTCAAACT-CTAAAATAAAA
1 AAACCCCAAAACTCAAAATCCTAAAATAAAA
2992408 AACCTAAACC
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
85 4 0.04
86 16 0.16
87 19 0.18
88 64 0.62
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (86 bp):
AAACCCCAAAACTCAAAATCCTAAAATAAAACCCTAAATACTCTAAACCCTAAAACCAAAACTTC
AAACATCAAACCCTAAAATCA
Found at i:2992408 original size:28 final size:28
Alignment explanation
Indices: 2992204--2992408 Score: 162
Period size: 28 Copynumber: 7.1 Consensus size: 28
2992194 TCCTATAATT
* *
2992204 AAACCCCAAACCTCTAAACCCTAAAAT-T
1 AAACCCCAAATCTC-AAACCCTAAAATCA
* *
2992232 AAACCCTAAATACTCTAAACCCTAAAACCA
1 AAACCCCAAAT-CTC-AAACCCTAAAATCA
** *
2992262 AAACTTCAAA-CATCAAACCTTAAAATCA
1 AAACCCCAAATC-TCAAACCCTAAAATCA
* * * *
2992290 AATCCCTAAAACATCAAAATCCTAAAATCA
1 AAACCCCAAATC-TC-AAACCCTAAAATCA
* *
2992320 AAACCCTAAATCCTCTAAACCCTAAAACCA
1 AAACCCCAAAT-CTC-AAACCCTAAAATCA
** *
2992350 AAACTTCAAACCTCAAACCCTAAAATCA
1 AAACCCCAAATCTCAAACCCTAAAATCA
* *
2992378 AAACCCCAAATCTCAAACTCTAAAATAA
1 AAACCCCAAATCTCAAACCCTAAAATCA
2992406 AAA
1 AAA
2992409 ACCTAAACCC
Statistics
Matches: 141, Mismatches: 30, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
28 67 0.48
29 24 0.17
30 49 0.35
31 1 0.01
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (28 bp):
AAACCCCAAATCTCAAACCCTAAAATCA
Found at i:2999115 original size:38 final size:37
Alignment explanation
Indices: 2999065--2999146 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 37
2999055 AACCTTGAGT
*
2999065 AAAAAAAAATATGGGACATCACAAAAAAAAAAAAAACA
1 AAAAAAAAATATGAGACATCACAAAAAAAAAAAAAA-A
*
2999103 AAAAAAAAATATGAGACATCACAAAAAAAAAAGAAAA
1 AAAAAAAAATATGAGACATCACAAAAAAAAAAAAAAA
2999140 AAAAAAA
1 AAAAAAA
2999147 GACATTTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
37 8 0.19
38 34 0.81
ACGTcount: A:0.77, C:0.09, G:0.07, T:0.07
Consensus pattern (37 bp):
AAAAAAAAATATGAGACATCACAAAAAAAAAAAAAAA
Found at i:3001208 original size:129 final size:128
Alignment explanation
Indices: 3000967--3001298 Score: 325
Period size: 129 Copynumber: 2.6 Consensus size: 128
3000957 GCCACTTTTA
* * *
3000967 AAAAGATTTTTAAATTCTTAAAGTTTCATTGCCTCTGATTATGAAGAGCATTCAAAGATTTTGAG
1 AAAAGATTTTTAAATTTTTAAAGTTTCATTACCTCTAATTATGAAGAGCATTCAAAGATTTTGAG
** * * *
3001032 ATTTGTAAGACCTTCGGACATAATCTCTACTACTTTTGAGCACAACTTTCAAGACCTCCGGAC
66 ATTTGTAAGACCTTAAGACATAATCTCTACAACCTTCGAGCACAACTTTCAAGACCTCCGGAC
* * *
3001095 AAAAGATTTTTAAATTTTTAAAAGTTTCATTACTTCTAATTATGAGGGGCATTCAAAGATTTTGA
1 AAAAGATTTTTAAATTTTT-AAAGTTTCATTACCTCTAATTATGAAGAGCATTCAAAGATTTTGA
** * * * * ** * *
3001160 GATTTGTAAGACCTCTAAG-TGTAATTTCTA-AAGCCTTCGGGCATAACTTTCAATATTTTCGGG
65 GATTTGTAAGACCT-TAAGACATAATCTCTACAA-CCTTCGAGCACAACTTTCAAGACCTCCGGA
3001223 C
128 C
* * * * * * *
3001224 AAAAGATTTTTAAATTTTCAAAG-TTCATAGATCTCTTATTA-GAAAAGCATCCAAAGATATT--
1 AAAAGATTTTTAAATTTTTAAAGTTTCAT-TACCTCTAATTATGAAGAGCATTCAAAGATTTTGA
*
3001285 GATTTCTAAGACCT
65 GATTTGTAAGACCT
3001299 CCGAGCATAA
Statistics
Matches: 168, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
125 13 0.08
127 20 0.12
128 31 0.18
129 102 0.61
130 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (128 bp):
AAAAGATTTTTAAATTTTTAAAGTTTCATTACCTCTAATTATGAAGAGCATTCAAAGATTTTGAG
ATTTGTAAGACCTTAAGACATAATCTCTACAACCTTCGAGCACAACTTTCAAGACCTCCGGAC
Found at i:3001419 original size:108 final size:109
Alignment explanation
Indices: 3001279--3001493 Score: 301
Period size: 108 Copynumber: 2.0 Consensus size: 109
3001269 AGCATCCAAA
*
3001279 GATATTGATTTCTAAGACCTCCGAGCATAAATTTGATTCGCAATATTGTCCCAATCGATTCATTA
1 GATATTGATTTCTAAGACCTCCGAGCATAAATTTGATTCACAATATTGTCCCAATCGATTCATTA
3001344 TTTTTGACTTATGTTATTA-TCCTGATCGATTCTGTAAGACCTCT
66 TTTTTGACTTATGTTATTATTCC-GATCGATTCTGTAAGACCTCT
* ** * * *
3001388 GATA-TGATTTCTAAGACCTCC-AGACATAAATTTGATTTACGGTGTTGTCTCGATCGATTCATT
1 GATATTGATTTCTAAGACCTCCGAG-CATAAATTTGATTCACAATATTGTCCCAATCGATTCATT
* * *
3001451 ATTTTTGACTTGTGTTGTTATTCCGGTCGATTCTGTAAGACCT
65 ATTTTTGACTTATGTTATTATTCCGATCGATTCTGTAAGACCT
3001494 TCGGGCATAA
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
107 2 0.02
108 85 0.90
109 7 0.07
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (109 bp):
GATATTGATTTCTAAGACCTCCGAGCATAAATTTGATTCACAATATTGTCCCAATCGATTCATTA
TTTTTGACTTATGTTATTATTCCGATCGATTCTGTAAGACCTCT
Found at i:3001580 original size:88 final size:87
Alignment explanation
Indices: 3001412--3001585 Score: 224
Period size: 88 Copynumber: 2.0 Consensus size: 87
3001402 GACCTCCAGA
* * * *** * *
3001412 CATAAATTTGATTTACGGTGTTGTCTCGATCGATTCATTATTTTTGACTTGTGTTGTTATTCCGG
1 CATAAATTTGATTCACGATGTTATCTCGATCGATTCATTATTTTTGACTTGCAATGTTATCCCAG
*
3001477 TCGATTCTGTAAGACCTTCGGG
66 TCGATTCTATAAGACCTTCGGG
* *
3001499 CATAAATTTGATTCGCGATGTTATCTCGATCGATT-TTTAATTTTTTGACTTGCAATGTTATCCC
1 CATAAATTTGATTCACGATGTTATCTCGATCGATTCATT-A-TTTTTGACTTGCAATGTTATCCC
3001563 AGTCGATTCTATAAGACCTTCGG
64 AGTCGATTCTATAAGACCTTCGG
3001586 ACATGATTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
86 2 0.03
87 32 0.43
88 40 0.54
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (87 bp):
CATAAATTTGATTCACGATGTTATCTCGATCGATTCATTATTTTTGACTTGCAATGTTATCCCAG
TCGATTCTATAAGACCTTCGGG
Found at i:3001821 original size:111 final size:110
Alignment explanation
Indices: 3001499--3001922 Score: 386
Period size: 110 Copynumber: 3.8 Consensus size: 110
3001489 GACCTTCGGG
* * *
3001499 CATAAATTTGATTCGCGATGTTA-TCTCGATCGATTTTTAATTTTTTGACTTGCAATGTTATCCC
1 CATAAATTCGATTCGCGATGTTATTC-CGATCGATTTTTAATTTTTTGACTTGCAGTGTTATCAC
* * * *
3001563 AGTCGATTCTATAAGACCTTCGGACATGATTTCTAAGACCTCTGGA
65 AGTCGATTTTGTAAGACCTCCGGACATGATTTCTAAGACCTCTGAA
* * * ***
3001609 CATAAATTCGATTCGCGATATTATTCCGATTGATTTTTAATTTTTTGACTTGCAGTATTATTTTA
1 CATAAATTCGATTCGCGATGTTATTCCGATCGATTTTTAATTTTTTGACTTGCAGTGTTATCACA
* ** * *
3001674 GTTGATTTTGTAAGACCTCCAAACATGATTTCTAAGACTTTTGAA
66 GTCGATTTTGTAAGACCTCCGGACATGATTTCTAAGACCTCTGAA
** * * *
3001719 CATAAATTCGATTTACGATGTTATTCCGATCGATTCGTTATTTTTTTAACTTGCAGTGTTATCAC
1 CATAAATTCGATTCGCGATGTTATTCCGATCGATT-TTTAATTTTTTGACTTGCAGTGTTATCAC
* * ** *
3001784 AATCAATTTTGTAAGACCTCCGGGTATGATTTCTAAGACCT-TCAA
65 AGTCGATTTTGTAAGACCTCCGGACATGATTTCTAAGACCTCTGAA
* * * * * * * * * * *
3001829 GCATAAATTTGATTTGTGGTATTATCCCGATCTATTCATTTTATTTTTCGACTTAC-GATGTTGT
1 -CATAAATTCGATTCGCGATGTTATTCCGATCGATT--TTTAATTTTTTGACTTGCAG-TGTTAT
* * * *
3001893 CTCAGTCGATTCTATAAGACCTCTGGACAT
62 CACAGTCGATTTTGTAAGACCTCCGGACAT
3001923 AAATTCGATT
Statistics
Matches: 249, Mismatches: 60, Indels: 8
0.79 0.19 0.03
Matches are distributed among these distances:
110 124 0.50
111 86 0.35
112 39 0.16
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (110 bp):
CATAAATTCGATTCGCGATGTTATTCCGATCGATTTTTAATTTTTTGACTTGCAGTGTTATCACA
GTCGATTTTGTAAGACCTCCGGACATGATTTCTAAGACCTCTGAA
Found at i:3002019 original size:22 final size:22
Alignment explanation
Indices: 3001994--3002043 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3001984 ATCGATTTTG
3001994 TAAGACCTCCGGACATGA-TTC
1 TAAGACCTCCGGACATGATTTC
* *
3002015 TTAAGACCTCTGGGCATGATTTC
1 -TAAGACCTCCGGACATGATTTC
3002038 TAAGAC
1 TAAGAC
3002044 TTCCAGGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (22 bp):
TAAGACCTCCGGACATGATTTC
Found at i:3002107 original size:37 final size:37
Alignment explanation
Indices: 3002066--3002149 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
3002056 ATTTGATTCG
* *
3002066 CGGTGTTATCTCGATTGATTTTTTATTTTTTGACTTA
1 CGGTGTTATCTCGATCGATTCTTTATTTTTTGACTTA
* *
3002103 CGGTGTTGTCTCGATCGATTCTTTATTTTTTGATTTA
1 CGGTGTTATCTCGATCGATTCTTTATTTTTTGACTTA
*
3002140 CGATGTTATC
1 CGGTGTTATC
3002150 CCAACCGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.15, C:0.13, G:0.18, T:0.54
Consensus pattern (37 bp):
CGGTGTTATCTCGATCGATTCTTTATTTTTTGACTTA
Found at i:3002159 original size:37 final size:37
Alignment explanation
Indices: 3002082--3002161 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 37
3002072 TATCTCGATT
* * * * * *
3002082 GATTTTTTATTTTTTGACTTACGGTGTTGTCTCGATC
1 GATTCTTTATTTTTTGACTTACGATGTTATCCCAACC
*
3002119 GATTCTTTATTTTTTGATTTACGATGTTATCCCAACC
1 GATTCTTTATTTTTTGACTTACGATGTTATCCCAACC
3002156 GATTCT
1 GATTCT
3002162 GTAAGACCTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.17, C:0.16, G:0.15, T:0.51
Consensus pattern (37 bp):
GATTCTTTATTTTTTGACTTACGATGTTATCCCAACC
Found at i:3002232 original size:169 final size:168
Alignment explanation
Indices: 3001951--3002267 Score: 381
Period size: 169 Copynumber: 1.9 Consensus size: 168
3001941 TATCCTGATT
* * * * * * * *
3001951 GATTCATTATTTTTTGACTTACGGTGTTGTTCTATCGATTTTGTAAGACCTCCGGACATGATTCT
1 GATTCATTATTTTTTGACTTACGATGTTATCCAACCGATTCTGTAAGACCTCCGAACATGATTCC
* * *
3002016 TAAGACCTCTGGGCATGATTTCTAAGACTTCCAGGCATAAATTTGATTCGCGGTGTTA-TCTCGA
66 TAAGACCTCTGGGCATGATTTCTAAAACCTCCAGGCATAAATTTGATTCACGGTGTTATTC-CGA
* *
3002080 TTGATTTTTTATTTTTTGACTTACGGTGTTGTCTCGATC
130 TCGATTCTTTATTTTTTGACTTACGGTGTTGTCTCGATC
* *
3002119 GATTCTTTATTTTTTGATTTACGATGTTATCCCAACCGATTCTGTAAGACCTCCGAACATGATTC
1 GATTCATTATTTTTTGACTTACGATGTTAT-CCAACCGATTCTGTAAGACCTCCGAACATGATTC
* * * * *
3002184 CTAAGACTTCTGGGCATGA-TTCTTAAAACCCTCGA-GTA-AAATTTTGATTTACGGTGTTGTTC
65 CTAAGACCTCTGGGCATGATTTC-TAAAA-CCTCCAGGCATAAA-TTTGATTCACGGTGTTATTC
3002246 CGATCGATTCTTTATTTTTTGA
127 CGATCGATTCTTTATTTTTTGA
3002268 TTTATGATGT
Statistics
Matches: 124, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
168 32 0.26
169 86 0.69
170 6 0.05
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (168 bp):
GATTCATTATTTTTTGACTTACGATGTTATCCAACCGATTCTGTAAGACCTCCGAACATGATTCC
TAAGACCTCTGGGCATGATTTCTAAAACCTCCAGGCATAAATTTGATTCACGGTGTTATTCCGAT
CGATTCTTTATTTTTTGACTTACGGTGTTGTCTCGATC
Found at i:3002330 original size:132 final size:132
Alignment explanation
Indices: 3002093--3002381 Score: 517
Period size: 132 Copynumber: 2.2 Consensus size: 132
3002083 ATTTTTTATT
*
3002093 TTTTGACTTACGGTGTTG-TCTCGATCGATTCTTTATTTTTTGATTTACGATGTTATCCCAACCG
1 TTTTGATTTACGGTGTTGTTC-CGATCGATTCTTTATTTTTTGATTTACGATGTTATCCCAACCG
* *
3002157 ATTCTGTAAGACCTCCGAACATGATTCCTAAGACTTCTGGGCATGATTCTTAAAACCCTCGAGTA
65 ATTCTGTAAGACCTCCAAACATGATTCCTAAGACTTCTGGGCATGATTCTTAAAACCCTCGAGCA
3002222 AAA
130 AAA
* *
3002225 TTTTGATTTACGGTGTTGTTCCGATCGATTCTTTATTTTTTGATTTATGATGTTATCTCAACCGA
1 TTTTGATTTACGGTGTTGTTCCGATCGATTCTTTATTTTTTGATTTACGATGTTATCCCAACCGA
3002290 TTCTGTAAGACCTCCAAACATGATTCCTAAGACTTCTGGGCATGATTCTTAAAACCCTCGAGCAA
66 TTCTGTAAGACCTCCAAACATGATTCCTAAGACTTCTGGGCATGATTCTTAAAACCCTCGAGCAA
3002355 AA
131 AA
3002357 TTTTGATTTACGGTGTTGTTCCGAT
1 TTTTGATTTACGGTGTTGTTCCGAT
3002382 GTTCCTAAGA
Statistics
Matches: 151, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
132 149 0.99
133 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (132 bp):
TTTTGATTTACGGTGTTGTTCCGATCGATTCTTTATTTTTTGATTTACGATGTTATCCCAACCGA
TTCTGTAAGACCTCCAAACATGATTCCTAAGACTTCTGGGCATGATTCTTAAAACCCTCGAGCAA
AA
Found at i:3002735 original size:26 final size:25
Alignment explanation
Indices: 3002688--3002742 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 25
3002678 ATAGTAATTT
** *
3002688 AAAAAAAAGTAAAAAATTAATTATATA
1 AAAAAAAACCAAAAAATAAATT-T-TA
3002715 AAAAAAAACCAAAAAA-AAATTTTA
1 AAAAAAAACCAAAAAATAAATTTTA
3002739 AAAA
1 AAAA
3002743 GTTAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 6 0.24
25 1 0.04
26 4 0.16
27 14 0.56
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (25 bp):
AAAAAAAACCAAAAAATAAATTTTA
Found at i:3003844 original size:12 final size:12
Alignment explanation
Indices: 3003829--3003924 Score: 61
Period size: 12 Copynumber: 7.9 Consensus size: 12
3003819 TAATTGTTTT
3003829 AATAATAATAAA
1 AATAATAATAAA
*
3003841 AATAAAATAGTAAA
1 AAT--AATAATAAA
*
3003855 AATAATGACTAAA
1 AATAAT-AATAAA
* *
3003868 AA-AATATTTAA
1 AATAATAATAAA
** *
3003879 AATGCT-TTAAA
1 AATAATAATAAA
* *
3003890 AAGAATAATAAT
1 AATAATAATAAA
*
3003902 AATAATAATAAT
1 AATAATAATAAA
3003914 AATAATAATAA
1 AATAATAATAA
3003925 TAATTTTTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
11 13 0.20
12 35 0.53
13 7 0.11
14 11 0.17
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:3003901 original size:3 final size:3
Alignment explanation
Indices: 3003893--3003928 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3003883 CTTTAAAAAG
3003893 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3003929 TTTTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3004207 original size:28 final size:28
Alignment explanation
Indices: 3004176--3004271 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
3004166 TAAAAAATAT
* * *
3004176 AAACCTTAAAATTAAATCTCAAACCTTC
1 AAACCCTAAAATTAAATCCCAAACCTCC
*
3004204 AAACCCTATAATTAAATCCCAAACCTCC
1 AAACCCTAAAATTAAATCCCAAACCTCC
* * *
3004232 AAACCCTAAAATTAAATCCTAAATACTCT
1 AAACCCTAAAATTAAATCCCAAA-CCTCC
3004261 AAACCCTAAAA
1 AAACCCTAAAA
3004272 CCAAACCTTC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 45 0.76
29 14 0.24
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (28 bp):
AAACCCTAAAATTAAATCCCAAACCTCC
Found at i:3004372 original size:28 final size:27
Alignment explanation
Indices: 3004348--3004409 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
3004338 ACTAAAACTT
3004348 CAAACCGCAAATCCTAAAATCAAAACCC
1 CAAACCGCAAA-CCTAAAATCAAAACCC
* * *
3004376 CAAATCTCAAACTCTAAAATCAAAAACC
1 CAAACCGCAAAC-CTAAAATCAAAACCC
*
3004404 TAAACC
1 CAAACC
3004410 CGAAAATTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.52, C:0.32, G:0.02, T:0.15
Consensus pattern (27 bp):
CAAACCGCAAACCTAAAATCAAAACCC
Found at i:3005992 original size:32 final size:35
Alignment explanation
Indices: 3005956--3006026 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 35
3005946 ATCATTATTA
*
3005956 TTATTATTGTGTATTAATATTTAT-T-TA-TTTAT
1 TTATTATTGTCTATTAATATTTATATGTATTTTAT
* * *
3005988 TTATTTTTTTCTGTTAATATTTATATGTATTTTAT
1 TTATTATTGTCTATTAATATTTATATGTATTTTAT
3006023 TTAT
1 TTAT
3006027 ATAGTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 20 0.62
33 1 0.03
34 2 0.06
35 9 0.28
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.68
Consensus pattern (35 bp):
TTATTATTGTCTATTAATATTTATATGTATTTTAT
Found at i:3006060 original size:17 final size:17
Alignment explanation
Indices: 3006040--3006083 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
3006030 GTTATATTTG
*
3006040 TTATTATTATGTTATCA
1 TTATTATTATATTATCA
*
3006057 TTATTATTATATTATTA
1 TTATTATTATATTATCA
*
3006074 TTATCATTAT
1 TTATTATTAT
3006084 CATTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (17 bp):
TTATTATTATATTATCA
Found at i:3006061 original size:14 final size:12
Alignment explanation
Indices: 3006051--3006083 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
3006041 TATTATTATG
3006051 TTATCATTATTA
1 TTATCATTATTA
3006063 TTAT-ATTATTA
1 TTATCATTATTA
3006074 TTATCATTAT
1 TTATCATTAT
3006084 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATCATTATTA
Found at i:3007014 original size:24 final size:23
Alignment explanation
Indices: 3006982--3007030 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
3006972 TTTTTTTTGT
*
3006982 TTTTATTTTCATTTATTTGTTTA
1 TTTTATTTTCATTTATTTATTTA
* *
3007005 TTTTATTTTTTATTTTTTTATTTA
1 TTTTA-TTTTCATTTATTTATTTA
3007029 TT
1 TT
3007031 AGATTAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTATTTTCATTTATTTATTTA
Found at i:3007238 original size:57 final size:57
Alignment explanation
Indices: 3007160--3007668 Score: 731
Period size: 57 Copynumber: 8.7 Consensus size: 57
3007150 AATAAAAATC
*
3007160 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC-C
1 AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCAA
*
3007217 AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAA
1 AAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC-AA
*
3007277 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC--
1 AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTCAA
*
3007334 AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAA
1 AAAAAATATTTTTGG-GAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC--AA
* *
3007395 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAA
1 AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAA-TTTCAA
3007455 AAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC-A
1 AAAAA-ATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCAA
* *
3007513 AAAAAATATTTTTGGGAAAAAGTTGAAAATATCAATTTTCCATAGAAATAAATTTCAA
1 AAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCAA
* *
3007571 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT-TA
1 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCAA
3007628 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCC
3007669 CTACACAAGA
Statistics
Matches: 417, Mismatches: 19, Indels: 32
0.89 0.04 0.07
Matches are distributed among these distances:
56 5 0.01
57 188 0.45
58 59 0.14
59 7 0.02
60 62 0.15
61 88 0.21
62 8 0.02
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (57 bp):
AAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCAA
Found at i:3007281 original size:117 final size:116
Alignment explanation
Indices: 3007160--3007668 Score: 766
Period size: 117 Copynumber: 4.4 Consensus size: 116
3007150 AATAAAAATC
*
3007160 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTC-CAAAAAAT
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCAAAAAAAAT
3007224 ATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAA
66 ATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC--A
*
3007277 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC--AAAAAA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTCAAAAAAAA
3007340 TATTTTT-GGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAA
65 TATTTTTGGGA-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC---A
* *
3007395 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAAAAAA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAA-TTTCAAAAAAA
*
3007460 TATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTCA
64 -ATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCA
* *
3007513 AAAAAATATTTTTG-GGAAAAAGTTGAAAATATCAATTTTCCATAGAAATAAATTTCAAAAAAAA
1 AAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCAAAAAAAA
*
3007577 TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT-A
65 TATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCA
3007628 AAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCC
3007669 CTACACAAGA
Statistics
Matches: 368, Mismatches: 10, Indels: 30
0.90 0.02 0.07
Matches are distributed among these distances:
114 2 0.01
115 80 0.22
116 19 0.05
117 109 0.30
118 98 0.27
119 7 0.02
121 9 0.02
122 42 0.11
124 2 0.01
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (116 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCAAAAAAAAT
ATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCA
Found at i:3007714 original size:6 final size:6
Alignment explanation
Indices: 3007703--3007731 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3007693 ATTCTTTTCT
3007703 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
3007732 TCTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
ATTTTG
Found at i:3012370 original size:2 final size:2
Alignment explanation
Indices: 3012363--3012390 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3012353 CGATTGACCA
3012363 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
3012391 CATAAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3018817 original size:12 final size:12
Alignment explanation
Indices: 3018791--3018832 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
3018781 TCGAGCCGTG
3018791 ATTTATTTTGA-T
1 ATTTATTTT-ATT
3018803 ATTTATTTTATT
1 ATTTATTTTATT
3018815 ATTT-TGTTTATT
1 ATTTAT-TTTATT
3018827 ATTTAT
1 ATTTAT
3018833 ATATTACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.07
12 24 0.89
13 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (12 bp):
ATTTATTTTATT
Found at i:3019065 original size:60 final size:59
Alignment explanation
Indices: 3018927--3019284 Score: 365
Period size: 60 Copynumber: 6.0 Consensus size: 59
3018917 ATTAATTTTT
* * * **
3018927 AAAATAAAAATTTTAAAAAAGTATTTTTGAGAAAAAGTTAAAAGTATCAATTTTT-TTTT
1 AAAAT-AAAATTTTAAAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAA
*
3018986 AAAATAAAGATTCTAAAAAAA-ATTTTTTGAGAAAAAAATTGATAA-TA-CTAATTTTTCTTAA
1 AAAATAAA-ATTTTAAAAAAATA-TTTTTGAG-AAAAAATTGA-AAGTATC-AATTTTTCTTAA
3019047 AAAATAAAATTTTCAAAAAAAATATTTTTGA-AAAAAAGTTGAAAGTATCAATTTTT-TTAA
1 AAAATAAAATTTT--AAAAAAATATTTTTGAGAAAAAA-TTGAAAGTATCAATTTTTCTTAA
* * *
3019107 AAAATAAAA-ATTAAAAAAATATATTTTAAGAAAAAATTGATAGTATCAATTTTTCTTAA
1 AAAATAAAATTTTAAAAAAATAT-TTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAA
** * * * *
3019166 AGGATAAAAATTTCAAAAAAGTATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAA
1 AAAAT-AAAATTTTAAAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTT-AA
* *
3019227 AATAA-AAATTTTTAAAGAAAA-ATATTTTAAGAAAAAATTGAAAGTATCAATTTTTCTT
1 AA-AATAAAATTTTAAA-AAAATAT-TTTTGAGAAAAAATTGAAAGTATCAATTTTTCTT
3019285 GTATAAAGGC
Statistics
Matches: 251, Mismatches: 27, Indels: 40
0.79 0.08 0.13
Matches are distributed among these distances:
57 10 0.04
58 26 0.10
59 39 0.16
60 87 0.35
61 72 0.29
62 16 0.06
63 1 0.00
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.37
Consensus pattern (59 bp):
AAAATAAAATTTTAAAAAAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAA
Found at i:3019093 original size:121 final size:117
Alignment explanation
Indices: 3018927--3019284 Score: 461
Period size: 121 Copynumber: 3.0 Consensus size: 117
3018917 ATTAATTTTT
*
3018927 AAAATAAAAATTTT-AAAAAAGTATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTTTTTAAAAT
1 AAAAT-AAAATTTTCAAAAAAGTATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTTTTAAAAAT
* *
3018991 AAAGATTCTAAAAAAAATTTTTTGAGAAAAAAATTGATAATA-CTAATTTTTCTTAA
65 AAA-ATT-TAAAAAAAATATTTTAAG-AAAAAATTGATAATATC-AATTTTTCTTAA
* * * *
3019047 AAAATAAAATTTTCAAAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTTTTAAAAAAT
1 AAAATAAAATTTTC-AAAAAAGTATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTTTTAAAAAT
* *
3019112 AAAAATTAAAAAAATATATTTTAAGAAAAAATTGATAGTATCAATTTTTCTTAA
65 AAAATTTAAAAAAA-ATATTTTAAGAAAAAATTGATAATATCAATTTTTCTTAA
** * * *
3019166 AGGATAAAAATTTCAAAAAAGTATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTGAAAATA
1 AAAATAAAATTTTCAAAAAAGTATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTTTTAAAAAT-
3019231 AAAATTTTTAAAGAAAAATATTTTAAGAAAAAATTGA-AAGTATCAATTTTTCTT
65 AAAA--TTTAAA-AAAAATATTTTAAGAAAAAATTGATAA-TATCAATTTTTCTT
3019285 GTATAAAGGC
Statistics
Matches: 209, Mismatches: 20, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
118 44 0.21
119 57 0.27
120 17 0.08
121 87 0.42
122 4 0.02
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.37
Consensus pattern (117 bp):
AAAATAAAATTTTCAAAAAAGTATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTTTTAAAAATA
AAATTTAAAAAAAATATTTTAAGAAAAAATTGATAATATCAATTTTTCTTAA
Found at i:3019264 original size:15 final size:14
Alignment explanation
Indices: 3019230--3019262 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3019220 TCTTGAAAAT
3019230 AAAAATTTTTAAAG
1 AAAAATTTTTAAAG
3019244 AAAAATATTTT-AAG
1 AAAAAT-TTTTAAAG
3019258 AAAAA
1 AAAAA
3019263 ATTGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (14 bp):
AAAAATTTTTAAAG
Found at i:3024677 original size:17 final size:17
Alignment explanation
Indices: 3024589--3024678 Score: 74
Period size: 17 Copynumber: 5.4 Consensus size: 17
3024579 AATTTAAAAA
*
3024589 TCTTGCGAATCTTCAAT
1 TCTTGCGAATCTTAAAT
* * * *
3024606 TTTTGTGAATCTTCAAC
1 TCTTGCGAATCTTAAAT
* *
3024623 TATTGCGAATCTTTAAT
1 TCTTGCGAATCTTAAAT
* **
3024640 TCTTGTGAATC-TATTT
1 TCTTGCGAATCTTAAAT
*
3024656 TCTTGCGAATCTAAAAT
1 TCTTGCGAATCTTAAAT
3024673 TCTTGC
1 TCTTGC
3024679 AAAATTTTGA
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
16 12 0.21
17 44 0.79
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (17 bp):
TCTTGCGAATCTTAAAT
Found at i:3024999 original size:25 final size:25
Alignment explanation
Indices: 3024964--3025015 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
3024954 CTTATTTGGT
3024964 TTAGTCCAAGTTATTCTTTTCAAAC
1 TTAGTCCAAGTTATTCTTTTCAAAC
*
3024989 TTAGTCTAAGTTATTCTTTTCAAAC
1 TTAGTCCAAGTTATTCTTTTCAAAC
3025014 TT
1 TT
3025016 CAGTTCAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (25 bp):
TTAGTCCAAGTTATTCTTTTCAAAC
Found at i:3025000 original size:110 final size:110
Alignment explanation
Indices: 3024878--3025100 Score: 304
Period size: 110 Copynumber: 2.0 Consensus size: 110
3024868 TATTCTTTGG
* * * *
3024878 CTTAGTCCAAGTTATTCTTTTCAGACTTCGGTTCAATCCACGACATTTTATTTTGGATTTCGACC
1 CTTAGTCCAAGTTATTCTTTTCAAACTTCAGTTCAATCCAAGACATTATATTTTGGATTTCGACC
* * ** *
3024943 TATGCTAGATCCTTAT-TTGGTTTAGTCCAAGTTATTCTTTTCAAA
66 TATGCTAAATCCTT-TCTCGACTTAGTCCAAGTTATTATTTTCAAA
* * * * *
3024988 CTTAGTCTAAGTTATTCTTTTCAAACTTCAGTTCAATCTAAGTCATTATGTTTTGGATTTCGACT
1 CTTAGTCCAAGTTATTCTTTTCAAACTTCAGTTCAATCCAAGACATTATATTTTGGATTTCGACC
3025053 TATGCTAAATCCTTTCTCGACTTAGTCCAAGTTATTATTTTCAAA
66 TATGCTAAATCCTTTCTCGACTTAGTCCAAGTTATTATTTTCAAA
3025098 CTT
1 CTT
3025101 TGGTTCAATC
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
109 1 0.01
110 97 0.99
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.44
Consensus pattern (110 bp):
CTTAGTCCAAGTTATTCTTTTCAAACTTCAGTTCAATCCAAGACATTATATTTTGGATTTCGACC
TATGCTAAATCCTTTCTCGACTTAGTCCAAGTTATTATTTTCAAA
Found at i:3025130 original size:85 final size:86
Alignment explanation
Indices: 3024987--3025305 Score: 273
Period size: 85 Copynumber: 3.8 Consensus size: 86
3024977 TTCTTTTCAA
* * * * * *
3024987 ACTT-AGTCTAAGTTATTCTTTTCAAACTTCAGTTCAATCTAAGTCATTATGTTTTGGATTTCGA
1 ACTTCAGTCCAAGTTATTATTTTCAAACTTCGGTTCAATCCAGGTCATTTTGTTTTGGATTTCGA
*
3025051 CTTATGCTAAATCCTTTCTCG
66 CCTATGCTAAATCCTTTCTCG
* * *
3025072 ACTT-AGTCCAAGTTATTATTTTCAAACTTTGGTTCAATCCAGGTCATTTTGTTTTGGATTTTGG
1 ACTTCAGTCCAAGTTATTATTTTCAAACTTCGGTTCAATCCAGGTCATTTTGTTTTGGATTTCGA
* * * *
3025136 CCCATGCT-CATTCTTTCTTTG
66 CCTATGCTAAATCCTTTC-TCG
* * * *
3025157 -GTTCAGTCCAA---ATTA-TTTCAGACTTCGATTCTATCCAGGTCATTTTGTTTTGGATTTC-A
1 ACTTCAGTCCAAGTTATTATTTTCAAACTTCGGTTCAATCCAGGTCATTTTGTTTTGGATTTCGA
* * *
3025216 GCCTATGCCAGATCCTTTTTC-
66 -CCTATGCTAAATCCTTTCTCG
* * * * * * *
3025237 AATTCAATTCAAGTTATT-TATTTCAAACTTTGGTTTAATCCAGATCATTTTGTTTTAGATTTCG
1 ACTTCAGTCCAAGTTATTAT-TTTCAAACTTCGGTTCAATCCAGGTCATTTTGTTTTGGATTTCG
*
3025301 GCCTA
65 ACCTA
3025306 CATTAGATCT
Statistics
Matches: 185, Mismatches: 38, Indels: 22
0.76 0.16 0.09
Matches are distributed among these distances:
81 53 0.29
82 10 0.05
84 12 0.06
85 110 0.59
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (86 bp):
ACTTCAGTCCAAGTTATTATTTTCAAACTTCGGTTCAATCCAGGTCATTTTGTTTTGGATTTCGA
CCTATGCTAAATCCTTTCTCG
Found at i:3025325 original size:166 final size:165
Alignment explanation
Indices: 3025029--3025380 Score: 412
Period size: 166 Copynumber: 2.1 Consensus size: 165
3025019 TTCAATCTAA
* * * * * * *
3025029 GTCATTATGTTTTGGATTTC-GACTTATGCTAAATCCTTTCTCGACTT-AGTCCAAGTTATTATT
1 GTCATTATGTTTTGGATTTCAG-CCTATGCCAGATCCTTTTTC-AATTCAATTCAAGTTATTATT
* * * *
3025092 TTCAAACTTTGGTTCAATCCAGGTCATTTTGTTTTGGATTTTGGCCCATGCTCATTCTTTCTTTG
64 TTCAAACTTTGGTTCAATCCAGATCATTTTGTTTTAGATTTCGGCCCAT-CTCAATCTTTCTTTG
* *
3025157 GTTCAGTCCAAATTATTTCAGAC-TTCGATTCTATCCAG
128 GTTCAGTCCAAATTATTTCAGACATTAG-TTCCATCCAG
*
3025195 GTCATTTTGTTTTGGATTTCAGCCTATGCCAGATCCTTTTTCAATTCAATTCAAGTTATT-TATT
1 GTCATTATGTTTTGGATTTCAGCCTATGCCAGATCCTTTTTCAATTCAATTCAAGTTATTAT-TT
*
3025259 TCAAACTTTGGTTTAATCCAGATCATTTTGTTTTAGATTTCGGCCTACAT-T-AGATC-TTCATT
65 TCAAACTTTGGTTCAATCCAGATCATTTTGTTTTAGATTTCGGCC--CATCTCA-ATCTTTC-TT
* **
3025321 TGGTTTAGTTTAAATTATTTCAGACATTAGTTCCATCCAG
126 TGGTTCAGTCCAAATTATTTCAGACATTAGTTCCATCCAG
3025361 GTCATTATGTTTTGGATTTC
1 GTCATTATGTTTTGGATTTC
3025381 GACATATGTC
Statistics
Matches: 159, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
165 8 0.05
166 144 0.91
167 4 0.03
168 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (165 bp):
GTCATTATGTTTTGGATTTCAGCCTATGCCAGATCCTTTTTCAATTCAATTCAAGTTATTATTTT
CAAACTTTGGTTCAATCCAGATCATTTTGTTTTAGATTTCGGCCCATCTCAATCTTTCTTTGGTT
CAGTCCAAATTATTTCAGACATTAGTTCCATCCAG
Found at i:3030054 original size:21 final size:21
Alignment explanation
Indices: 3030028--3030104 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
3030018 CCTGCTGAAA
*
3030028 GAAACCAGCAGTCTGTTACAG
1 GAAACCAGCAGTCTGCTACAG
*
3030049 GAAACCAGTAGTCTGCTACAG
1 GAAACCAGCAGTCTGCTACAG
* *
3030070 GAAACCAGCAGTCTGCTGCAA
1 GAAACCAGCAGTCTGCTACAG
*
3030091 GAAACCAGTAGTCT
1 GAAACCAGCAGTCT
3030105 ACTGCTGTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (21 bp):
GAAACCAGCAGTCTGCTACAG
Found at i:3031243 original size:16 final size:17
Alignment explanation
Indices: 3031210--3031244 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3031200 AACCGATCTT
*
3031210 AAAACTGATTATAATCG
1 AAAACCGATTATAATCG
3031227 AAAACCGATTA-AATCG
1 AAAACCGATTATAATCG
3031243 AA
1 AA
3031245 CCGAAATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.23
Consensus pattern (17 bp):
AAAACCGATTATAATCG
Found at i:3032726 original size:61 final size:60
Alignment explanation
Indices: 3032565--3033015 Score: 388
Period size: 61 Copynumber: 7.4 Consensus size: 60
3032555 ATAAAATTAA
* * *
3032565 AAAAAAAAAAATTACTTTATAGAAAAGTTAAAATTATCAATTTTTCAT-AAAAT-AAAATTT-
1 AAAAAAAAAAATT--TTTA-AGAAAAATTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTC
* * * *
3032625 TAAAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAGATTTC
1 AAAAAAAAAAATTTTTAAGAAAAA-TTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTC
*
3032686 AAAAAAAAAAATTTTTGAAGAAAAATTAAGAA-TA-CTAATTTTCCTTAAAAAGTAAAAATTTC
1 AAAAAAAAAAATTTTT-AAGAAAAATTAA-AAGTATC-AATTTTTCTTAAAAA-TAAAAATTTC
* * *
3032748 --AAGAAAACATTTTTATGAAAAAAGTTAAAAGTATCAATTTTTCTTAAAAAATAAAAATTTC
1 AAAAAAAAAAATTTTTAAG-AAAAA-TTAAAAGTATCAATTTTTCTT-AAAAATAAAAATTTC
**
3032809 -AAAAAAAGTATTTTTAAGAAAAAGTTGAAAA-TATCAA-TTTTCTTCAAAAATAAAAATTTC
1 AAAAAAAAAAATTTTTAAGAAAAA-TT-AAAAGTATCAATTTTTCTT-AAAAATAAAAATTTC
* * * *
3032869 AAAAAAAAAACA-TTTTAAGGAAAAATTGAGAGTATCAATCTTTCTTAAATGATAAAAATTTC
1 AAAAAAAAAA-ATTTTTAA-GAAAAATTAAAAGTATCAATTTTTCTTAAA-AATAAAAATTTC
* *** * * * *
3032931 --AAAGATGTATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTTT
1 AAAAAAAAAAATTTTT-AAGAAAAATTAAAAGTATCAATTTTTCTTAAAAATAAAAA-TTTC
* * *
3032991 AAAGAAAAATATTTTAAAGAAAAAT
1 AAAAAAAAAAATTTTTAAGAAAAAT
3033016 ATTTTAAGAA
Statistics
Matches: 322, Mismatches: 43, Indels: 51
0.77 0.10 0.12
Matches are distributed among these distances:
57 6 0.02
58 22 0.07
59 15 0.05
60 98 0.30
61 107 0.33
62 74 0.23
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.34
Consensus pattern (60 bp):
AAAAAAAAAAATTTTTAAGAAAAATTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTC
Found at i:3032860 original size:183 final size:182
Alignment explanation
Indices: 3032585--3033014 Score: 526
Period size: 183 Copynumber: 2.4 Consensus size: 182
3032575 ATTACTTTAT
* * *
3032585 AGAAAAGTTAAAATTATCAATTTTTC--ATAAAAT-AAAATTTTAAAAAAAATATTTTTGAGAAA
1 AGAAAAGTTAAAAGTATCAATTTTTCTTAAAAAATAAAAATTTTAAAAAAAATATTTTTAAGAAA
*
3032647 AAGTTAAAAGTATCAATTTTTCTTAAAAATAAAGATTTCAAAAAAAAAA-ATTTTTGAA-GAAAA
66 AAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAAAAAACA-TTTT-AAGGAAAA
3032710 ATTAAGAATA-CTAAT-TTTCCTTAAAA-AGTAAAAATTTCAAGAAAACAT-TTTTATGA
129 ATTAAGAATATC-AATCTTT-CTTAAAAGA-TAAAAATTTC-A-AAAACATATTTT-TGA
* *
3032766 A-AAAAGTTAAAAGTATCAATTTTTCTTAAAAAATAAAAATTTCAAAAAAAGTATTTTTAAGAAA
1 AGAAAAGTTAAAAGTATCAATTTTTCTTAAAAAATAAAAATTTTAAAAAAAATATTTTTAAGAAA
3032830 AAGTTGAAAA-TATCAA-TTTTCTTCAAAAATAAAAATTTCAAAAAAAAAACATTTTAAGGAAAA
66 AAGTT-AAAAGTATCAATTTTTCTT-AAAAATAAAAATTTCAAAAAAAAAACATTTTAAGGAAAA
* * * * **
3032893 ATTGAGAGTATCAATCTTTCTTAAATGATAAAAATTTCAAAGATGTATTTTTGA
129 ATTAAGAATATCAATCTTTCTTAAAAGATAAAAATTTCAAAAACATATTTTTGA
* * *
3032947 AGAAAAGTTGAAAGTATCAATTTTTCTT-GAAAATAAAAATTTTTAAAGAAAAATATTTTAAAGA
1 AGAAAAGTTAAAAGTATCAATTTTTCTTAAAAAATAAAAA-TTTTAAA-AAAAATATTTTTAAGA
3033011 AAAA
64 AAAA
3033015 TATTTTAAGA
Statistics
Matches: 218, Mismatches: 17, Indels: 26
0.84 0.07 0.10
Matches are distributed among these distances:
180 23 0.11
181 19 0.09
182 51 0.23
183 115 0.53
184 10 0.05
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.34
Consensus pattern (182 bp):
AGAAAAGTTAAAAGTATCAATTTTTCTTAAAAAATAAAAATTTTAAAAAAAATATTTTTAAGAAA
AAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAAAAAACATTTTAAGGAAAAAT
TAAGAATATCAATCTTTCTTAAAAGATAAAAATTTCAAAAACATATTTTTGA
Found at i:3032999 original size:122 final size:121
Alignment explanation
Indices: 3032585--3033014 Score: 434
Period size: 122 Copynumber: 3.6 Consensus size: 121
3032575 ATTACTTTAT
* * * * *
3032585 AGAAAAGTTAAAATTATCAATTTTTCAT-AAAAT-AAAATTTTAAA-AAAAATATTTT-TGAGAA
1 AGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTTAAAGAAAAACATTTTAAG-GAA
* **
3032646 AAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAGATTTCAAAAAAAAAAATTTTTGA
65 AAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTC-AAAAAAAGTATTTTTGA
* * * * *
3032704 AGAAAAATT--AAGAATACTAATTTTCCTTAAAAAGTAAAAA-TTTCAAG-AAAACATTTTTATG
1 AGAAAAGTTGAAAGTAT-C-AATTTTTCTTAAAAA-TAAAAATTTTAAAGAAAAACA-TTTTAAG
*
3032765 AAAAAAGTTAAAAGTATCAATTTTTCTTAAAAAATAAAAATTTCAAAAAAAGTATTTTT-A
62 GAAAAAGTTAAAAGTATCAATTTTTCTT-AAAAATAAAAATTTCAAAAAAAGTATTTTTGA
* * *
3032825 AGAAAAAGTTGAAAATATCAA-TTTTCTTCAAAAATAAAAATTTCAAAAAAAAAACATTTTAAGG
1 AG-AAAAGTTGAAAGTATCAATTTTTCTT-AAAAATAAAAATTT-TAAAGAAAAACATTTTAAGG
* * * * * *
3032889 AAAAA-TTGAGAGTATCAATCTTTCTTAAATGATAAAAATTTC-AAAGATGTATTTTTGA
63 AAAAAGTTAAAAGTATCAATTTTTCTTAAA-AATAAAAATTTCAAAAAAAGTATTTTTGA
* * *
3032947 AGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAAATTTTTAAAGAAAAATATTTTAAAGAA
1 AGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAA-TTTTAAAGAAAAACATTTTAAGGAA
3033012 AAA
65 AAA
3033015 TATTTTAAGA
Statistics
Matches: 259, Mismatches: 32, Indels: 38
0.79 0.10 0.12
Matches are distributed among these distances:
117 4 0.02
118 1 0.00
119 16 0.06
120 4 0.02
121 89 0.34
122 105 0.41
123 30 0.12
124 10 0.04
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.34
Consensus pattern (121 bp):
AGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTTAAAGAAAAACATTTTAAGGAAA
AAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTTCAAAAAAAGTATTTTTGA
Found at i:3033030 original size:15 final size:15
Alignment explanation
Indices: 3032981--3033028 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
3032971 TCTTGAAAAT
3032981 AAAAAT-TTTTAAAG
1 AAAAATATTTTAAAG
3032995 AAAAATATTTTAAAG
1 AAAAATATTTTAAAG
3033010 AAAAATATTTT-AAG
1 AAAAATATTTTAAAG
3033024 AAAAA
1 AAAAA
3033029 ATTGAAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 14 0.42
15 19 0.58
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (15 bp):
AAAAATATTTTAAAG
Found at i:3034068 original size:23 final size:25
Alignment explanation
Indices: 3034042--3034100 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
3034032 TCGCTCGATT
3034042 AAGCTCGATTAATATA-T-AAAAAA
1 AAGCTCGATTAATATACTCAAAAAA
* **
3034065 AAGCTTGATTTTTATACTCGAAAAAA
1 AAGCTCGATTAATATACTC-AAAAAA
3034091 AA-CTCGATTA
1 AAGCTCGATTA
3034101 TTCGAGCTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 13 0.46
24 1 0.04
25 6 0.21
26 8 0.29
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (25 bp):
AAGCTCGATTAATATACTCAAAAAA
Found at i:3034173 original size:3 final size:3
Alignment explanation
Indices: 3034165--3034196 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3034155 TTTTCAAGAT
*
3034165 AAC AAC AAC AAC AAT AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
3034197 TAATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.28, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:3034183 original size:15 final size:15
Alignment explanation
Indices: 3034163--3034193 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3034153 TATTTTCAAG
3034163 ATAACAACAACAACA
1 ATAACAACAACAACA
3034178 ATAACAACAACAACA
1 ATAACAACAACAACA
3034193 A
1 A
3034194 CAATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.06
Consensus pattern (15 bp):
ATAACAACAACAACA
Found at i:3037885 original size:25 final size:25
Alignment explanation
Indices: 3037848--3037901 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
3037838 TCCCCACAAT
* *
3037848 ATTCATAAGGGTATTTAATTTAGGC
1 ATTCATAAAGGTATTTAATTAAGGC
3037873 ATTCATAAAGGTATTTAATTAAGGC
1 ATTCATAAAGGTATTTAATTAAGGC
3037898 ATTC
1 ATTC
3037902 TTATTTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (25 bp):
ATTCATAAAGGTATTTAATTAAGGC
Found at i:3038114 original size:17 final size:17
Alignment explanation
Indices: 3038092--3038126 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3038082 TACGTTGAGG
3038092 GATCGGGTTCTGTTCAA
1 GATCGGGTTCTGTTCAA
3038109 GATCGGGTTCTGTTCAA
1 GATCGGGTTCTGTTCAA
3038126 G
1 G
3038127 CTACTACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.34
Consensus pattern (17 bp):
GATCGGGTTCTGTTCAA
Done.