Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002126.1 Hibiscus syriacus cultivar Beakdansim tig00004355_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: 1482737
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:993634 original size:24 final size:25
Alignment explanation
Indices: 993595--993644 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
993585 TAGTATATTC
993595 ATAATAAAAAAATATTAAAAAAATT
1 ATAATAAAAAAATATTAAAAAAATT
* *
993620 ATAAT-AAAAAGTATTGAAAAAATT
1 ATAATAAAAAAATATTAAAAAAATT
993644 A
1 A
993645 GACTCATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (25 bp):
ATAATAAAAAAATATTAAAAAAATT
Found at i:993765 original size:29 final size:30
Alignment explanation
Indices: 993699--993780 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
993689 AGCATTCCTC
*
993699 TAATAACAAATATTGAAAAAAAAATGGACCTT
1 TAATAACAAATATTG--AAAAAAATGGACATT
* * *
993731 TGATAACAAGTATTG-AAAAATTGGACATT
1 TAATAACAAATATTGAAAAAAATGGACATT
*
993760 TAATAACAAATGTTAGAAAAA
1 TAATAACAAATATT-GAAAAA
993781 GATATTGATA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
29 23 0.56
30 1 0.02
31 4 0.10
32 13 0.32
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (30 bp):
TAATAACAAATATTGAAAAAAATGGACATT
Found at i:1008799 original size:15 final size:15
Alignment explanation
Indices: 1008775--1008808 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1008765 CCGTAGGACC
1008775 ACTACATCCCGAATG
1 ACTACATCCCGAATG
*
1008790 ACTACGTCCCGAATG
1 ACTACATCCCGAATG
1008805 ACTA
1 ACTA
1008809 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (15 bp):
ACTACATCCCGAATG
Found at i:1009393 original size:64 final size:64
Alignment explanation
Indices: 1009324--1009479 Score: 192
Period size: 64 Copynumber: 2.4 Consensus size: 64
1009314 AATGAAGGTA
* **
1009324 TGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGGA
1 TGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATAGTTTTATT-TTAAAAGA
1009387 G
64 G
* * * *
1009388 TGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATATTTTTATTTTAAAAGAG
1 TGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATAGTTTTATTTTAAAAGAG
*
1009452 TGCATCGATGCACTACCTGTGCATCGAT
1 TGCATCGATGCACTACTTGTGCATCGAT
1009480 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 68 0.87
65 9 0.12
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (64 bp):
TGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATAGTTTTATTTTAAAAGAG
Found at i:1013162 original size:17 final size:17
Alignment explanation
Indices: 1013140--1013172 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1013130 TAATCACCCG
1013140 TTAAAATAATAAAAATA
1 TTAAAATAATAAAAATA
*
1013157 TTAAAATATTAAAAAT
1 TTAAAATAATAAAAAT
1013173 TTATTCCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATAATAAAAATA
Found at i:1019904 original size:2 final size:2
Alignment explanation
Indices: 1019899--1019928 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1019889 TAATTTTTTA
1019899 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
1019929 GTTTTAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1021080 original size:16 final size:16
Alignment explanation
Indices: 1021059--1021091 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1021049 TAATAAAATC
*
1021059 ATTAATTTACTTTTTA
1 ATTAATTAACTTTTTA
1021075 ATTAATTAACTTTTTA
1 ATTAATTAACTTTTTA
1021091 A
1 A
1021092 AATTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTAATTAACTTTTTA
Found at i:1021278 original size:18 final size:17
Alignment explanation
Indices: 1021257--1021298 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
1021247 AATTTTAAAG
1021257 TTTTAAAATTTAATTTAT
1 TTTTAAAATTTAATTT-T
*
1021275 TTTTATAATTTAATTTT
1 TTTTAAAATTTAATTTT
1021292 TTTTAAA
1 TTTTAAA
1021299 TGGACTTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTAAAATTTAATTTT
Found at i:1025197 original size:13 final size:13
Alignment explanation
Indices: 1025179--1025204 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1025169 TTACAGATAC
1025179 GCATATGAAGACT
1 GCATATGAAGACT
1025192 GCATATGAAGACT
1 GCATATGAAGACT
1025205 ATTCAACCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:1025660 original size:15 final size:15
Alignment explanation
Indices: 1025632--1025665 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1025622 GGTCGGTGAG
*
1025632 AATT-AAATATATTA
1 AATTAAAATAAATTA
1025646 AATTAAAATAAATTA
1 AATTAAAATAAATTA
1025661 AATTA
1 AATTA
1025666 TTCAATCGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTAAAATAAATTA
Found at i:1032373 original size:20 final size:18
Alignment explanation
Indices: 1032306--1032382 Score: 118
Period size: 18 Copynumber: 4.2 Consensus size: 18
1032296 TTATAATGTT
1032306 TTTTTGGATTAGAAATAC
1 TTTTTGGATTAGAAATAC
* *
1032324 TCTTTGGACTAGAAATAC
1 TTTTTGGATTAGAAATAC
1032342 TTTTTGGATTAGAAATAC
1 TTTTTGGATTAGAAATAC
1032360 TTTTTGATGATTAGAAATAC
1 TTTTTG--GATTAGAAATAC
1032380 TTT
1 TTT
1032383 GTTATGTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
18 38 0.72
20 15 0.28
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (18 bp):
TTTTTGGATTAGAAATAC
Found at i:1034964 original size:34 final size:33
Alignment explanation
Indices: 1034914--1034977 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
1034904 TATCATTTAA
1034914 TTTTTATTTACCACTTTAATTTATTTTACTTCAT
1 TTTTTATTTACCACTTTAATTTA-TTTACTTCAT
* * **
1034948 TTTTTATTTTCTACTTTTGTTTATTTACTT
1 TTTTTATTTACCACTTTAATTTATTTACTT
1034978 TTATCTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 7 0.27
34 19 0.73
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (33 bp):
TTTTTATTTACCACTTTAATTTATTTACTTCAT
Found at i:1038351 original size:15 final size:16
Alignment explanation
Indices: 1038325--1038358 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1038315 CTTTCAAAAA
1038325 TGAAAAATGAAAATTT
1 TGAAAAATGAAAATTT
*
1038341 TGAAAAA-GAAAGTTT
1 TGAAAAATGAAAATTT
1038356 TGA
1 TGA
1038359 TTTAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (16 bp):
TGAAAAATGAAAATTT
Found at i:1042996 original size:22 final size:22
Alignment explanation
Indices: 1042963--1043083 Score: 160
Period size: 22 Copynumber: 5.7 Consensus size: 22
1042953 GACCATTACA
*
1042963 TCCCTAAGGACCACTGGATATG
1 TCCCGAAGGACCACTGGATATG
* *
1042985 TCCTGAAGGACCACT--ACA--
1 TCCCGAAGGACCACTGGATATG
* *
1043003 TCCCGAATGACCACTGGATCTG
1 TCCCGAAGGACCACTGGATATG
*
1043025 TCCCGAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATATG
1043047 TCCCGAAGGACCACTGGATATG
1 TCCCGAAGGACCACTGGATATG
1043069 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
1043084 ATAAGCCCTC
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
18 13 0.15
20 3 0.04
22 68 0.81
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.18
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATATG
Found at i:1043003 original size:40 final size:40
Alignment explanation
Indices: 1042943--1043084 Score: 194
Period size: 40 Copynumber: 3.5 Consensus size: 40
1042933 AGTGAATATT
* *
1042943 TGTCCCGAAGGACCATTACATCCCTAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
* * *
1042983 TGTCCTGAAGGACCACTACATCCCGAATGACCACTGGATC
1 TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
*
1043023 TGTCCCGAAGGACCACTGGATACGTCCCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCAC----TACATCCCGAAGGACCACTGGATA
1043067 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1043085 TAAGCCCTCG
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
40 52 0.58
44 37 0.42
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTACATCCCGAAGGACCACTGGATA
Found at i:1049887 original size:18 final size:18
Alignment explanation
Indices: 1049861--1049911 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
1049851 TGAATATTTG
*
1049861 TCCCAAAGGACCATTACA
1 TCCCAAAGGACCACTACA
*
1049879 TCCCTAAGGACCACTACA
1 TCCCAAAGGACCACTACA
* *
1049897 TCCCGAATGACCACT
1 TCCCAAAGGACCACT
1049912 GGATCTGTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.33, C:0.37, G:0.12, T:0.18
Consensus pattern (18 bp):
TCCCAAAGGACCACTACA
Found at i:1049937 original size:22 final size:22
Alignment explanation
Indices: 1049905--1049977 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
1049895 CATCCCGAAT
*
1049905 GACCACTGGAT-CTGTCTCAAAG
1 GACCACTGGATAC-GTCCCAAAG
* *
1049927 GACTACTGGATACGTCCCGAAG
1 GACCACTGGATACGTCCCAAAG
* *
1049949 GACCACTGGATACGTCCCGAAT
1 GACCACTGGATACGTCCCAAAG
1049971 GACCACT
1 GACCACT
1049978 ATAAACCCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.19
Consensus pattern (22 bp):
GACCACTGGATACGTCCCAAAG
Found at i:1051925 original size:117 final size:116
Alignment explanation
Indices: 1051719--1051953 Score: 461
Period size: 117 Copynumber: 2.0 Consensus size: 116
1051709 ATACCAATTG
1051719 TTGGGATTGCGATGAAACTCAAATTGATCAACCGAATAATTTACCAAGAGGGGGTGAATTGGATT
1 TTGGGATTGCGATGAAACTCAAATTGATCAACCGAATAATTTACCAAGAGGGGGTGAATTGGATT
1051784 TTTAAGTTTAGGGAGTAATGAGTATAAAGATGAAACAATTTGCACAAGGGAT
66 TTTAAGTTTAGGGAGTAATGAGTATAAAGATGAAACAATTTGCACAA-GGAT
1051836 TTGGGATTGCGATGAAACTCAAATTGATCAACCGAATAATTTACCAAGAGGGGGTGAATTGGATT
1 TTGGGATTGCGATGAAACTCAAATTGATCAACCGAATAATTTACCAAGAGGGGGTGAATTGGATT
1051901 TTTAAGTTTAGGGAGTAATGAGTATAAAGATGAAACAATTTGCACAAGGAT
66 TTTAAGTTTAGGGAGTAATGAGTATAAAGATGAAACAATTTGCACAAGGAT
1051952 TT
1 TT
1051954 ATAGTGGTTC
Statistics
Matches: 118, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 6 0.05
117 112 0.95
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (116 bp):
TTGGGATTGCGATGAAACTCAAATTGATCAACCGAATAATTTACCAAGAGGGGGTGAATTGGATT
TTTAAGTTTAGGGAGTAATGAGTATAAAGATGAAACAATTTGCACAAGGAT
Found at i:1053831 original size:12 final size:11
Alignment explanation
Indices: 1053812--1053850 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1053802 CTTTGTTTCA
1053812 CGAAAAAAATT
1 CGAAAAAAATT
1053823 CGAAAAAAATT
1 CGAAAAAAATT
*
1053834 TG--AAAAATT
1 CGAAAAAAATT
1053843 CGAAAAAA
1 CGAAAAAA
1053851 GTTTGAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 8 0.33
11 16 0.67
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (11 bp):
CGAAAAAAATT
Found at i:1053841 original size:20 final size:20
Alignment explanation
Indices: 1053816--1053861 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
1053806 GTTTCACGAA
1053816 AAAAATTCGAAAAAAATTTG
1 AAAAATTCGAAAAAAATTTG
*
1053836 AAAAATTCGAAAAAAGTTTG
1 AAAAATTCGAAAAAAATTTG
1053856 AGAAAA
1 A-AAAA
1053862 GAAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.61, C:0.04, G:0.13, T:0.22
Consensus pattern (20 bp):
AAAAATTCGAAAAAAATTTG
Found at i:1054799 original size:36 final size:37
Alignment explanation
Indices: 1054752--1054830 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
1054742 GGAGTCTAAA
1054752 TTTAAGTTTGAATTC-AAAAACACTTGGGATTATCTT
1 TTTAAGTTTGAATTCAAAAAACACTTGGGATTATCTT
1054788 TTTAAGTTTGAATTCAAAAAACACTTGGGATTATCTT
1 TTTAAGTTTGAATTCAAAAAACACTTGGGATTATCTT
1054825 TTTAAG
1 TTTAAG
1054831 ATTATCTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 15 0.36
37 27 0.64
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTAAGTTTGAATTCAAAAAACACTTGGGATTATCTT
Found at i:1059188 original size:27 final size:27
Alignment explanation
Indices: 1059153--1059207 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1059143 ATTTCAAAAT
1059153 TATAATTATGAAA-AAAATATTAATTTA
1 TATAATTAT-AAATAAAATATTAATTTA
* *
1059180 TATATTTATAAATAAAATATTTATTTA
1 TATAATTATAAATAAAATATTAATTTA
1059207 T
1 T
1059208 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TATAATTATAAATAAAATATTAATTTA
Found at i:1059302 original size:20 final size:19
Alignment explanation
Indices: 1059263--1059304 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1059253 TTTCTTCGAT
1059263 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1059282 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
1059302 ATT
1 ATT
1059305 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1059377 original size:120 final size:119
Alignment explanation
Indices: 1059171--1059396 Score: 267
Period size: 120 Copynumber: 1.9 Consensus size: 119
1059161 TGAAAAAAAT
* * * * *
1059171 ATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGG
1 ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGG
* * * *
1059236 TGCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACA
66 TACCTTAAGACAGCACATTTCTT-AATATTAAAAAATAAATAAATAATTAAAACA
**
1059291 ATTAATATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATAGACATCCA
1 ATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-AGACATCCA
* ** * *
1059355 GTTATTTTAAGACTG-ACATTTCTTAATATTGAAAAATAAATA
64 GGTACCTTAAGACAGCACATTTCTTAATATTAAAAAATAAATA
1059397 TTAAAACATG
Statistics
Matches: 88, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
119 22 0.25
120 50 0.57
121 16 0.18
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (119 bp):
ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACATCCAGG
TACCTTAAGACAGCACATTTCTTAATATTAAAAAATAAATAAATAATTAAAACA
Found at i:1059432 original size:20 final size:20
Alignment explanation
Indices: 1059397--1059436 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1059387 AAAATAAATA
*
1059397 TTAAAACATGATTAAAATAAG
1 TTAAAACATAATT-AAATAAG
1059418 TTAAAA-ATAATTAAATAAG
1 TTAAAACATAATTAAATAAG
1059437 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAAAACATAATTAAATAAG
Found at i:1059501 original size:3 final size:3
Alignment explanation
Indices: 1059493--1059522 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1059483 TTTATGGCTA
*
1059493 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1059523 TAAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1060886 original size:3 final size:3
Alignment explanation
Indices: 1060869--1060933 Score: 78
Period size: 3 Copynumber: 21.0 Consensus size: 3
1060859 TTTGGACCTG
*
1060869 TAA TAA -AA TTAA TAA TAAA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1060915 TAAA TAA TAT TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA
1060934 AAAAAACCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 2 0.04
3 44 0.81
4 8 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1060893 original size:19 final size:19
Alignment explanation
Indices: 1060869--1060935 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 19
1060859 TTTGGACCTG
1060869 TAATAAAATTAATAATAAA
1 TAATAAAATTAATAATAAA
*
1060888 TAATAATATTAATAAT-AA
1 TAATAAAATTAATAATAAA
*
1060906 TAATAATAATAAATAATATTAA
1 TAATAA-AATTAATAATA--AA
1060928 TAATAAAA
1 TAATAAAA
1060936 AAAACCAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.20
19 23 0.56
21 2 0.05
22 8 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAATAAAATTAATAATAAA
Found at i:1060909 original size:28 final size:29
Alignment explanation
Indices: 1060879--1060933 Score: 87
Period size: 28 Copynumber: 1.9 Consensus size: 29
1060869 TAATAAAATT
1060879 AATAATAA-ATAATAATATTAATAATAA-T
1 AATAATAATA-AATAATATTAATAATAATT
1060907 AATAATAATAAATAATATTAATAATAA
1 AATAATAATAAATAATATTAATAATAA
1060934 AAAAAACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
AATAATAATAAATAATATTAATAATAATT
Found at i:1061399 original size:112 final size:112
Alignment explanation
Indices: 1061266--1061819 Score: 730
Period size: 112 Copynumber: 4.9 Consensus size: 112
1061256 TAGAGTTATG
*
1061266 CAAAAAGTTGAACAAGCTCTTCTCAATATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
1 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
1061331 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
66 TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
**
1061378 CAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATGACGAGTTCTTCT
1 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT-A--AGTTCTTCT
* * * * * * *
1061440 CATTATGAACTCTAC-CTAGCAATGTTGATCCATCAAATGATGAATTTAAA
63 CATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
* *
1061490 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCA
* *
1061555 TTATGAATTTTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAAA
65 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
**
1061603 CAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATGACGAGTTCTTCT
1 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT-A--AGTTCTTCT
* * * * * *
1061665 CATTATGAACTCTAC-CTGGTAATGTTGATCCATCAAATGATGAATTTAAA
63 CATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
* *
1061715 CAAAATGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCA
1061780 TTATGAACTTTCTCTGGAAAA-TCTGATCCATCGAGTGATG
65 TTATGAACTTTCTCTGGAAAAGT-TGATCCATCGAGTGATG
1061820 GATTTGAATC
Statistics
Matches: 379, Mismatches: 44, Indels: 37
0.82 0.10 0.08
Matches are distributed among these distances:
109 27 0.07
110 7 0.02
111 1 0.00
112 189 0.50
113 121 0.32
114 2 0.01
115 10 0.03
116 22 0.06
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (112 bp):
CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAA
Found at i:1061569 original size:225 final size:225
Alignment explanation
Indices: 1061266--1061819 Score: 1013
Period size: 225 Copynumber: 2.5 Consensus size: 225
1061256 TAGAGTTATG
* *
1061266 CAAAAAGTTGAACAAGCTCTTCTCAATATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCA
1 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCA
1061330 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAAT
1061395 TCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTAGC
131 TCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTAGC
1061460 AATGTTGATCCATCAAATGATGAATTTAAA
196 AATGTTGATCCATCAAATGATGAATTTAAA
*
1061490 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCA
* *
1061555 TTATGAATTTTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAAT
* *
1061620 TCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGT
131 TCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTAGC
1061685 AATGTTGATCCATCAAATGATGAATTTAAA
196 AATGTTGATCCATCAAATGATGAATTTAAA
*
1061715 CAAAATGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCA
1061780 TTATGAACTTTCTCTGGAAAA-TCTGATCCATCGAGTGATG
66 TTATGAACTTTCTCTGGAAAAGT-TGATCCATCGAGTGATG
1061820 GATTTGAATC
Statistics
Matches: 318, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
224 38 0.12
225 280 0.88
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (225 bp):
CAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAAT
TCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTAGC
AATGTTGATCCATCAAATGATGAATTTAAA
Found at i:1063371 original size:23 final size:23
Alignment explanation
Indices: 1063344--1063390 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1063334 ATCTGACCCC
1063344 CTCTT-TTTTTCTTTTTTCTTCTT
1 CTCTTCTTTTT-TTTTTTCTTCTT
*
1063367 CTCTTCTTTTTTTTTTTTTTCTT
1 CTCTTCTTTTTTTTTTTCTTCTT
1063390 C
1 C
1063391 AAGTATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (23 bp):
CTCTTCTTTTTTTTTTTCTTCTT
Found at i:1066061 original size:17 final size:18
Alignment explanation
Indices: 1066028--1066061 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1066018 TGATTATATC
1066028 ATGAAAAGCCATCCATGA
1 ATGAAAAGCCATCCATGA
*
1066046 ATGAAAA-CCATGCATG
1 ATGAAAAGCCATCCATG
1066062 TCCTGCAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (18 bp):
ATGAAAAGCCATCCATGA
Found at i:1073783 original size:17 final size:17
Alignment explanation
Indices: 1073766--1073799 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1073756 AAATATTAAT
1073766 ATAAATACTATAAAAATA
1 ATAAATA-TATAAAAATA
*
1073784 ATAAGTATATAAAAAT
1 ATAAATATATAAAAAT
1073800 TTGAAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
ATAAATATATAAAAATA
Found at i:1074318 original size:26 final size:24
Alignment explanation
Indices: 1074276--1074329 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
1074266 TATTTCAAAA
*
1074276 TTATAATTATGAAAAAATATTAAT
1 TTATAATTATAAAAAAATATTAAT
*
1074300 TTATATATTATAAATAAAATATTTAT
1 TTATA-ATTATAAA-AAAATATTAAT
1074326 TTAT
1 TTAT
1074330 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 5 0.19
25 7 0.27
26 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TTATAATTATAAAAAAATATTAAT
Found at i:1074402 original size:17 final size:17
Alignment explanation
Indices: 1074380--1074427 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1074370 GCTTTCTTCG
1074380 ATATTAAAAAATAAATA
1 ATATTAAAAAATAAATA
*
1074397 ATATTAAAACAATTATATA
1 ATATTAAAA-AA-TAAATA
*
1074416 AT-TTATAAAATA
1 ATATTAAAAAATA
1074428 GGATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 2 0.07
17 11 0.41
18 7 0.26
19 7 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
ATATTAAAAAATAAATA
Found at i:1074671 original size:25 final size:27
Alignment explanation
Indices: 1074631--1074680 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
1074621 AACATTTACA
*
1074631 TATAACTAACAATAAAAAAATTAAAAC
1 TATAACTAACAATAAAAAAAATAAAAC
1074658 TATAA-TAAC-ATAAAAAAAATAAA
1 TATAACTAACAATAAAAAAAATAAA
1074681 TAAAAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 4 0.18
27 5 0.23
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (27 bp):
TATAACTAACAATAAAAAAAATAAAAC
Found at i:1076148 original size:3 final size:3
Alignment explanation
Indices: 1076131--1076202 Score: 83
Period size: 3 Copynumber: 23.0 Consensus size: 3
1076121 TTTAGGCCTG
* *
1076131 TAA TAA -AA TTAA TAA TAAA TAA TAA TAT TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1076177 TAA TAAA TAA TAA TAA TAAA TAA TAA
1 TAA T-AA TAA TAA TAA T-AA TAA TAA
1076203 AAAACCAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.03
3 47 0.78
4 11 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1076163 original size:28 final size:26
Alignment explanation
Indices: 1076131--1076203 Score: 94
Period size: 28 Copynumber: 2.7 Consensus size: 26
1076121 TTTAGGCCTG
1076131 TAATAAAATTAATAATAAATAATAATA
1 TAATAAAATTAATAATAAATAATAA-A
*
1076158 TTAATAATATTAATAAT-AATAATAAA
1 -TAATAAAATTAATAATAAATAATAAA
*
1076184 TAATAATAATAAATAATAAA
1 TAATAA-AATTAATAATAAA
1076204 AAACCAAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 6 0.15
26 9 0.22
27 10 0.25
28 15 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
TAATAAAATTAATAATAAATAATAAA
Found at i:1079101 original size:19 final size:19
Alignment explanation
Indices: 1079073--1079208 Score: 130
Period size: 19 Copynumber: 7.2 Consensus size: 19
1079063 GGAATTAAGT
1079073 GTTGGAAACCAGATTTTAG
1 GTTGGAAACCAGATTTTAG
*
1079092 GTTGGCAACCAGATTTTAG
1 GTTGGAAACCAGATTTTAG
1079111 GTTGGAAACCAGATTTTAG
1 GTTGGAAACCAGATTTTAG
* * *
1079130 GTTGGAAGCGAGATTATAG
1 GTTGGAAACCAGATTTTAG
** * *
1079149 GTAAGCAACCATATTTTAG
1 GTTGGAAACCAGATTTTAG
* **
1079168 GTTAGAGGCCAGATTTTAG
1 GTTGGAAACCAGATTTTAG
* * *
1079187 ATTGAAAATC-GAATTTTAG
1 GTTGGAAACCAG-ATTTTAG
1079206 GTT
1 GTT
1079209 AACAACTAGA
Statistics
Matches: 92, Mismatches: 24, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
18 1 0.01
19 91 0.99
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (19 bp):
GTTGGAAACCAGATTTTAG
Found at i:1079165 original size:57 final size:57
Alignment explanation
Indices: 1079073--1079186 Score: 147
Period size: 57 Copynumber: 2.0 Consensus size: 57
1079063 GGAATTAAGT
* ** *
1079073 GTTGGAAACCAGATTTTAGGTTGGCAACCAGATTTTAGGTTGGAAACCAGATTTTAG
1 GTTGGAAACCAGATTATAGGTAAGCAACCAGATTTTAGGTTAGAAACCAGATTTTAG
* * * **
1079130 GTTGGAAGCGAGATTATAGGTAAGCAACCATATTTTAGGTTAGAGGCCAGATTTTAG
1 GTTGGAAACCAGATTATAGGTAAGCAACCAGATTTTAGGTTAGAAACCAGATTTTAG
1079187 ATTGAAAATC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (57 bp):
GTTGGAAACCAGATTATAGGTAAGCAACCAGATTTTAGGTTAGAAACCAGATTTTAG
Found at i:1079207 original size:57 final size:57
Alignment explanation
Indices: 1079083--1079220 Score: 145
Period size: 57 Copynumber: 2.4 Consensus size: 57
1079073 GTTGGAAACC
** * * *
1079083 AGATTTTAGGTTGGCAACCAGATTTTAGGTTGGAAACCAGATTTTAGGTTGGAAGCG
1 AGATTTTAGGTAAGCAACCAGATTTTAGGTTAGAAACCAGATTTTAGATTGAAAGCG
* * ** *
1079140 AGATTATAGGTAAGCAACCATATTTTAGGTTAGAGGCCAGATTTTAGATTGAAAATCG
1 AGATTTTAGGTAAGCAACCAGATTTTAGGTTAGAAACCAGATTTTAGATTG-AAAGCG
*
1079198 A-ATTTTAGGTTAA-CAACTAGATT
1 AGATTTTAGG-TAAGCAACCAGATT
1079221 GATGGTTGAT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
57 58 0.88
58 8 0.12
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (57 bp):
AGATTTTAGGTAAGCAACCAGATTTTAGGTTAGAAACCAGATTTTAGATTGAAAGCG
Found at i:1079619 original size:36 final size:36
Alignment explanation
Indices: 1079579--1079812 Score: 243
Period size: 36 Copynumber: 6.5 Consensus size: 36
1079569 TTGATGTTCC
* * *
1079579 TATGCATGATATGCATGCACCTGCTACTGATGATTA
1 TATGCATGATATACATGCGCTTGCTACTGATGATTA
* *
1079615 TATGCATGATATACATGTGTTTGCTACTGATGATTA
1 TATGCATGATATACATGCGCTTGCTACTGATGATTA
* **
1079651 TTTGCATGATATACACACGCTTGCTACTGATGATTA
1 TATGCATGATATACATGCGCTTGCTACTGATGATTA
* * * * ***
1079687 CATGCATAATATACATACGCTTGCTACGGATGAACG
1 TATGCATGATATACATGCGCTTGCTACTGATGATTA
** * * *
1079723 TATGCATGATATACATATGCTTGCTATTCATGATAA
1 TATGCATGATATACATGCGCTTGCTACTGATGATTA
* **
1079759 TATGCATGATATACATGTGCTTGCTACTGATGAACA
1 TATGCATGATATACATGCGCTTGCTACTGATGATTA
**
1079795 TATTTATGATATACATGC
1 TATGCATGATATACATGC
1079813 ATTTGTTATT
Statistics
Matches: 163, Mismatches: 35, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 163 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (36 bp):
TATGCATGATATACATGCGCTTGCTACTGATGATTA
Found at i:1079692 original size:72 final size:72
Alignment explanation
Indices: 1079579--1079809 Score: 268
Period size: 72 Copynumber: 3.2 Consensus size: 72
1079569 TTGATGTTCC
* *
1079579 TATGCATGATATGCATGCAC-C-TGCTACTGATGATTATATGCATGATATACATGTGTTTGCTAC
1 TATGCATGATATACA--CACGCTTGCTACTGATGATTATATGCATGATATACATGTGCTTGCTAC
**
1079642 TGATGATTA
64 TGATGAACA
* * * ** *
1079651 TTTGCATGATATACACACGCTTGCTACTGATGATTACATGCATAATATACATACGCTTGCTACGG
1 TATGCATGATATACACACGCTTGCTACTGATGATTATATGCATGATATACATGTGCTTGCTACTG
*
1079716 ATGAACG
66 ATGAACA
* * * * *
1079723 TATGCATGATATACATATGCTTGCTATTCATGATAATATGCATGATATACATGTGCTTGCTACTG
1 TATGCATGATATACACACGCTTGCTACTGATGATTATATGCATGATATACATGTGCTTGCTACTG
1079788 ATGAACA
66 ATGAACA
**
1079795 TATTTATGATATACA
1 TATGCATGATATACA
1079810 TGCATTTGTT
Statistics
Matches: 132, Mismatches: 25, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
70 3 0.02
71 1 0.01
72 128 0.97
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (72 bp):
TATGCATGATATACACACGCTTGCTACTGATGATTATATGCATGATATACATGTGCTTGCTACTG
ATGAACA
Found at i:1084896 original size:20 final size:20
Alignment explanation
Indices: 1084868--1084911 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1084858 AGATTTTATC
1084868 AAGCGAGAAGGTACTCCATT
1 AAGCGAGAAGGTACTCCATT
*
1084888 AAGCTAGAAGGTACTCCATT
1 AAGCGAGAAGGTACTCCATT
1084908 AAGC
1 AAGC
1084912 CATGCTCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (20 bp):
AAGCGAGAAGGTACTCCATT
Found at i:1089568 original size:15 final size:14
Alignment explanation
Indices: 1089548--1089577 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1089538 GACTCGAGTT
1089548 AAAGAAAAAAATGAA
1 AAAGAAAAAAA-GAA
1089563 AAAGAAAAAAAGAA
1 AAAGAAAAAAAGAA
1089577 A
1 A
1089578 GAGTTTGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:1090690 original size:36 final size:36
Alignment explanation
Indices: 1090559--1090698 Score: 183
Period size: 36 Copynumber: 3.9 Consensus size: 36
1090549 ATGTGTGTCA
1090559 ATGTGCTTGCTATTAATGATTATATGCATGATATAC
1 ATGTGCTTGCTATTAATGATTATATGCATGATATAC
* ** *
1090595 ATGCG-TTCGCTACCAATGATTATATACATGATATAC
1 ATGTGCTT-GCTATTAATGATTATATGCATGATATAC
*
1090631 ATGTGCTTGATATTAATGATTATATGCATGATATAC
1 ATGTGCTTGCTATTAATGATTATATGCATGATATAC
* ** *
1090667 GTGTGCTTGCTATTGGTGGTTATATGCATGAT
1 ATGTGCTTGCTATTAATGATTATATGCATGAT
1090699 CTTTTACTCT
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
35 2 0.02
36 84 0.95
37 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (36 bp):
ATGTGCTTGCTATTAATGATTATATGCATGATATAC
Found at i:1091498 original size:15 final size:16
Alignment explanation
Indices: 1091457--1091499 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
1091447 TGCAAAGGTG
1091457 AATTCTCTTGTTAGTC
1 AATTCTCTTGTTAGTC
1091473 AATTCTCTTGTTAGTC
1 AATTCTCTTGTTAGTC
1091489 AATT-TCTTGTT
1 AATTCTCTTGTT
1091500 GAATTCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (16 bp):
AATTCTCTTGTTAGTC
Found at i:1098592 original size:20 final size:20
Alignment explanation
Indices: 1098567--1098627 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
1098557 TTTTGGTGCA
*
1098567 GAGGGAATCGATCCCCCCAT
1 GAGGGAACCGATCCCCCCAT
**
1098587 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCCCAT
1098608 GAAGGGGAACCGATCCCCCC
1 G-A-GGGAACCGATCCCCCC
1098628 CCACAGGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 7 0.21
23 9 0.26
ACGTcount: A:0.23, C:0.36, G:0.26, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCAT
Found at i:1099040 original size:24 final size:24
Alignment explanation
Indices: 1099013--1099060 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1099003 GAATTTTCCA
1099013 AAAAAAAAAT-TAAATTTTCGAAAT
1 AAAAAAAAATGTAAATTTTC-AAAT
*
1099037 AAAAAAAAATGTTAATTTTCAAAT
1 AAAAAAAAATGTAAATTTTCAAAT
1099061 TATTGTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAAAAAAATGTAAATTTTCAAAT
Found at i:1100886 original size:11 final size:11
Alignment explanation
Indices: 1100870--1100902 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
1100860 AAAGGGGGAG
1100870 AAGTGTGTTTT
1 AAGTGTGTTTT
1100881 AAGTGTGTTTT
1 AAGTGTGTTTT
1100892 AAGTGTGTTTT
1 AAGTGTGTTTT
1100903 TAAAATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (11 bp):
AAGTGTGTTTT
Found at i:1102481 original size:19 final size:19
Alignment explanation
Indices: 1102453--1102496 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1102443 CACAATCACA
*
1102453 AGATAAGATATATAACATG
1 AGATATGATATATAACATG
*
1102472 AGATATGATATATGACATG
1 AGATATGATATATAACATG
1102491 AGATAT
1 AGATAT
1102497 AAGAAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.30
Consensus pattern (19 bp):
AGATATGATATATAACATG
Found at i:1102670 original size:31 final size:30
Alignment explanation
Indices: 1102631--1102751 Score: 143
Period size: 31 Copynumber: 3.9 Consensus size: 30
1102621 AGAGTCGAGG
* * *
1102631 GTTACCTATGTCTTTCGAGACATATGGATA
1 GTTACCTATGTCCTTCGGGACATATGGACA
1102661 GTTTACCTATGTCCTTCGGGACATATGGACA
1 G-TTACCTATGTCCTTCGGGACATATGGACA
** *
1102692 GGATTATATATGCCCTTCGGGACATATGGACA
1 -G-TTACCTATGTCCTTCGGGACATATGGACA
* *
1102724 GTTACCTATGTTCTTCGGAACATATGGA
1 GTTACCTATGTCCTTCGGGACATATGGA
1102752 TAGGTCCTTC
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
30 23 0.30
31 27 0.35
32 27 0.35
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (30 bp):
GTTACCTATGTCCTTCGGGACATATGGACA
Found at i:1105735 original size:3 final size:3
Alignment explanation
Indices: 1105727--1105752 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1105717 AAATAAAAAC
1105727 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1105753 GTTTAGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1106566 original size:16 final size:15
Alignment explanation
Indices: 1106540--1106570 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1106530 AATATCGGAT
1106540 CGAATAGAATCGATA
1 CGAATAGAATCGATA
1106555 CGAATAAGAATCGATA
1 CGAAT-AGAATCGATA
1106571 AAAAATCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.19
Consensus pattern (15 bp):
CGAATAGAATCGATA
Found at i:1107694 original size:15 final size:15
Alignment explanation
Indices: 1107674--1107704 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1107664 GTCATGTAAA
1107674 TAGAAAATAATTTTG
1 TAGAAAATAATTTTG
1107689 TAGAAAATAATTTTG
1 TAGAAAATAATTTTG
1107704 T
1 T
1107705 TTTACGTGAC
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:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (15 bp):
TAGAAAATAATTTTG
Found at i:1109320 original size:16 final size:16
Alignment explanation
Indices: 1109279--1109321 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1109269 TTTTAAAGAA
*
1109279 AAATATAAATATTTTAC
1 AAATAT-AATATTATAC
* *
1109296 AATTGTAATATTATAC
1 AAATATAATATTATAC
1109312 AAATATAATA
1 AAATATAATA
1109322 AGGACAATTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (16 bp):
AAATATAATATTATAC
Found at i:1110663 original size:183 final size:184
Alignment explanation
Indices: 1110327--1110708 Score: 599
Period size: 183 Copynumber: 2.1 Consensus size: 184
1110317 ATTAATTAAA
* * * *
1110327 TTAATTAAAATTAAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACTATTTAAAA
1 TTAATTAAAA--AAATATTAAATATATTATATATAACATATGGGCTAAACCCAAACCATTTAAAA
*
1110392 TTCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAAAAT
64 TTCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAAT
*
1110457 TATATAAATTTTTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTTTTT
129 TATATAAATTTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTT
* *
1110513 TTAATTAAAAAAATATTATATATATTATATATAACATATGGAG-TAAATCCAAACCATTTAAAAT
1 TTAATTAAAAAAATATTAAATATATTATATATAACATATGG-GCTAAACCCAAACCATTTAAAAT
*
1110577 TCAATTAATAATTTAAGA-CCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTT
65 TCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATT
*
1110641 ATCTGAAA-TTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTT
130 ATAT-AAATTTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTT
*
1110696 TAGAATTAAAAAA
1 T-TAATTAAAAAA
1110709 CATTTAATTT
Statistics
Matches: 182, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
183 94 0.52
184 77 0.42
185 1 0.01
186 10 0.05
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (184 bp):
TTAATTAAAAAAATATTAAATATATTATATATAACATATGGGCTAAACCCAAACCATTTAAAATT
CAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTA
TATAAATTTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTT
Found at i:1110827 original size:35 final size:34
Alignment explanation
Indices: 1110787--1110859 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
1110777 ATCGAAATTT
1110787 ATTCGATT-CGATTAATATTTTTTTTAAAAAATTCA
1 ATTCGATTACGATT-A-ATTTTTTTTAAAAAATTCA
* **
1110822 ATTCGATTAACGGTTAATTTTTTTTAATTAATTCA
1 ATTCGATT-ACGATTAATTTTTTTTAAAAAATTCA
1110857 ATT
1 ATT
1110860 ATAGTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 28 0.85
36 1 0.03
37 4 0.12
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (34 bp):
ATTCGATTACGATTAATTTTTTTTAAAAAATTCA
Found at i:1116488 original size:51 final size:51
Alignment explanation
Indices: 1116422--1116521 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
1116412 GTATATGTAG
* *
1116422 AAATGTCTTGTTAGCAACATGTGTTGATTTTTAGTTAACTAACAATTTTTA
1 AAATGTCATGATAGCAACATGTGTTGATTTTTAGTTAACTAACAATTTTTA
1116473 AAATGTCATGATAGCAACATGTGTTGATTTTTAGTTAACTAACAATTTT
1 AAATGTCATGATAGCAACATGTGTTGATTTTTAGTTAACTAACAATTTT
1116522 CATCTAACAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (51 bp):
AAATGTCATGATAGCAACATGTGTTGATTTTTAGTTAACTAACAATTTTTA
Found at i:1122081 original size:330 final size:332
Alignment explanation
Indices: 1121450--1122427 Score: 1550
Period size: 330 Copynumber: 2.9 Consensus size: 332
1121440 TATTAAATTT
* *
1121450 TAATTTTATTAAAAAATAAATAAACATTATTAATTGTTCTTAAAAAATAATAATTAATGAATAAT
1 TAATTTTATT-AAAAATGAATAAACATTATTAAATGTTCTT-AAAAATAATAATTAATGAATAAT
*
1121515 AATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
64 AATTCATTTGATCCCTCAATTGTAATTAAAAATTTATTTTAATATTTTTTATATTTTTAAAC---
*
1121580 TAATTTTAAAAGTCAATAAATATTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
126 -AA-TTTAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
* * *
1121645 ATTTATTATAGTCATCATCATCATTTTGTAAAAGAAATATTGGTTATAAAAGTTTTATAAAATTA
189 ATTTATTATA-TCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTA
* *
1121710 TTCATATTTTAAAATACTTACCCTCAAATTTTTCCTATACTAGATTATACGTATTGTGTAATTTC
253 TTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTATGTAATTTC
*
1121775 ATGCAAAAGTCAAAA
318 ATGCAAAAATCAAAA
*
1121790 TAATTTTATTAAAAATGAATAAACATTATTAAATGTTGTTAAAAATAATAATTAATGAATAATAA
1 TAATTTTATTAAAAATGAATAAACATTATTAAATGTTCTTAAAAATAATAATTAATGAATAATAA
*
1121855 TTCATTTGATCCCTCAATTGTAATTAAAATTTTATTTTAATATTTTTTTATATTTTTAAACAA-T
66 TTCATTTGATCCCTCAATTGTAATTAAAAATTTATTTTAATA-TTTTTTATATTTTTAAACAATT
* **
1121919 TAAAAGTAAATATTTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTAT
130 TAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTAT
*
1121984 TAT-T-ATCATCATCATTTTGTAAAAGAAATACTAGTAATAAAACTTTTATAAAATTATTCATAT
195 TATATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATTCATAT
* *
1122047 TTTAAAATACTTATCTTCAAAGTTTTCCTATACTAGATTATACGTATTATGTAATTTCATGCAAA
260 TTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTATGTAATTTCATGCAAA
1122112 AATCAAAA
325 AATCAAAA
* *
1122120 TAGTTTTATTAAAAATGAATAAACATTATTAACA-GTTCTTAAAAATAATAATTAATTAATAATA
1 TAATTTTATTAAAAATGAATAAACATTATTAA-ATGTTCTTAAAAATAATAATTAATGAATAATA
* *
1122184 ATTCATTTGATCCCTCAATTTTAATTAAAAATTTATTTTAATATTTTTTATATTTTTAAATAATT
65 ATTCATTTGATCCCTCAATTGTAATTAAAAATTTATTTTAATATTTTTTATATTTTT--A-AA-C
*
1122249 AATTTTAAAAGTCAATAAATTTTTCAAAAAAAATATGAAATTTATAATTTTTTAAATTATAAAAT
126 AA-TTTAAAAGTCAATAAATTTTTC-AAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
1122314 ATTTATTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTA
189 ATTTATTAT-ATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTA
* *
1122379 TTCATATTTTAAAATACTTACCCTCAAAGTTTTCATATATTAGATTATA
253 TTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATA
1122428 TATAGAGAAA
Statistics
Matches: 594, Mismatches: 32, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
329 14 0.02
330 223 0.38
331 3 0.01
332 2 0.00
333 67 0.11
335 20 0.03
336 47 0.08
338 67 0.11
339 141 0.24
340 10 0.02
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (332 bp):
TAATTTTATTAAAAATGAATAAACATTATTAAATGTTCTTAAAAATAATAATTAATGAATAATAA
TTCATTTGATCCCTCAATTGTAATTAAAAATTTATTTTAATATTTTTTATATTTTTAAACAATTT
AAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAATATTTATT
ATATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATTCATATT
TTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTATGTAATTTCATGCAAAA
ATCAAAA
Found at i:1122665 original size:20 final size:21
Alignment explanation
Indices: 1122640--1122691 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1122630 TTTTCCCAAT
*
1122640 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1122660 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1122681 TCGCAATGCGA
1 TCGCAATGCGA
1122692 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1122705 original size:20 final size:20
Alignment explanation
Indices: 1122680--1122774 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
1122670 AATTGGGAAA
*
1122680 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1122700 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
1122721 ATCGCAACGAGTTACTGACT
1 ATCGCAACGCGATACTGACT
* *
1122741 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1122761 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1122775 ATACATAATC
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.03
20 44 0.73
21 12 0.20
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1122990 original size:22 final size:22
Alignment explanation
Indices: 1122962--1123005 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1122952 CACTCTCTCA
*
1122962 CCCATCTCAGACGAAATTCGTC
1 CCCATCTCAGACGAAATCCGTC
* *
1122984 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCAGACGAAATCCGTC
1123006 TATCTCCATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.41, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCAGACGAAATCCGTC
Found at i:1123323 original size:19 final size:20
Alignment explanation
Indices: 1123268--1123325 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1123258 GCGATTCTCT
**
1123268 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1123288 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
1123308 TGTTGCGAT-TTCATTTTC
1 CGTTGCGATAGTCATTTTC
1123326 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.24
20 26 0.76
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1123516 original size:25 final size:24
Alignment explanation
Indices: 1123462--1123516 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1123452 TGTTTATTAT
* *
1123462 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1123486 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1123512 TGTTT
1 TGTTT
1123517 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1124666 original size:18 final size:18
Alignment explanation
Indices: 1124645--1124689 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1124635 TCCACTTCGG
*
1124645 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1124663 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1124681 GAGCCATCA
1 GAGCCATCA
1124690 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1125244 original size:14 final size:14
Alignment explanation
Indices: 1125225--1125282 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1125215 ATGTGAAATG
1125225 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1125239 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1125255 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1125271 AAAATCGCAACG
1 AAAATCGCAACG
1125283 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1125267 original size:32 final size:33
Alignment explanation
Indices: 1125209--1125299 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1125199 GGAAATGGCT
*
1125209 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1125242 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1125274 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1125300 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1125293 original size:19 final size:19
Alignment explanation
Indices: 1125209--1125304 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
1125199 GGAAATGGCT
*
1125209 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1125228 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1125242 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1125260 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1125274 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1125293 ATCGCAATGCGA
1 ATCGCAATGCGA
1125305 TTTGTGTTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 22
0.68 0.07 0.25
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 6 0.10
17 1 0.02
18 11 0.18
19 21 0.35
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1125335 original size:14 final size:14
Alignment explanation
Indices: 1125316--1125373 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1125306 TTGTGTTTCG
1125316 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1125330 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
1125346 CGCATTTCGATTTTGT
1 CG--TTGCGATTTTGT
1125362 CGTTGCGATTTT
1 CGTTGCGATTTT
1125374 CATTTCGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.10, C:0.17, G:0.22, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1125380 original size:33 final size:33
Alignment explanation
Indices: 1125311--1125422 Score: 172
Period size: 33 Copynumber: 3.4 Consensus size: 33
1125301 GCGATTTGTG
*
1125311 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
1125343 TTTCGCATTTCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* * *
1125376 TTTCGTATTGCGATTTTGTCGATACGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1125409 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1125423 AGCCATTTCC
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 25 0.35
33 47 0.65
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1125458 original size:21 final size:20
Alignment explanation
Indices: 1125409--1125463 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1125399 ACGATTTTCA
*
1125409 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
* *
1125429 TTCCGCGTTGCGATAGTCATT
1 TTTCGCGTTGCGATAGCCA-T
1125450 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1125464 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:1127352 original size:14 final size:14
Alignment explanation
Indices: 1127333--1127368 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1127323 ATTGTTTAAT
1127333 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1127347 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1127361 TGATTTGT
1 TGATTTGT
1127369 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1127515 original size:14 final size:17
Alignment explanation
Indices: 1127505--1127565 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
1127495 GTCGCAACGA
1127505 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAA-GCG-AAT
1127524 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAA-GCG-AAT
*
1127543 GAAAATTGCAA-CG-A-
1 GAAAATCGCAAGCGAAT
1127557 GAAAATCGC
1 GAAAATCGC
1127566 TATGCAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
14 8 0.20
15 1 0.03
17 2 0.05
19 29 0.73
ACGTcount: A:0.48, C:0.16, G:0.21, T:0.15
Consensus pattern (17 bp):
GAAAATCGCAAGCGAAT
Found at i:1127560 original size:19 final size:19
Alignment explanation
Indices: 1127505--1127553 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1127495 GTCGCAACGA
1127505 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1127524 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
1127543 GAAAATTGCAA
1 GAAAATCGCAA
1127554 CGAGAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1127616 original size:20 final size:20
Alignment explanation
Indices: 1127591--1127686 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
1127581 TCGCATTGCG
*
1127591 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
1127611 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
* *
1127632 A-TTTCGAATTGCGATAGCT
1 ATTTTCGAGTTGCGATAGCC
1127651 ATTTTC-ACGTTGCGATAGCC
1 ATTTTCGA-GTTGCGATAGCC
*
1127671 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
1127687 TTCCCCGTTG
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
19 3 0.05
20 52 0.90
21 3 0.05
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:1127677 original size:40 final size:41
Alignment explanation
Indices: 1127591--1127686 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 41
1127581 TCGCATTGCG
* * ***
1127591 ATTTTCTAGTTGCGATAGCCATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGATAGCCATTTTCACGTTGCGATTAGCC
* *
1127632 A-TTTCGAATTGCGATAGCTATTTTCACGTTGCGA-TAGCC
1 ATTTTCGAGTTGCGATAGCCATTTTCACGTTGCGATTAGCC
*
1127671 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
1127687 TTCCCCGTTG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
39 3 0.07
40 41 0.91
41 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.42
Consensus pattern (41 bp):
ATTTTCGAGTTGCGATAGCCATTTTCACGTTGCGATTAGCC
Found at i:1127926 original size:20 final size:20
Alignment explanation
Indices: 1127901--1127992 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
1127891 TTGAAGATGA
1127901 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
*** *
1127921 TTGCGAAAGTCATAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
1127941 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
1127962 TTGCGATAGTCAGTATCACA
1 TTGCGATTTTCAGAATCTCG
1127982 TTGCGATTTTC
1 TTGCGATTTTC
1127993 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 38 0.70
21 16 0.30
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1128006 original size:21 final size:21
Alignment explanation
Indices: 1127980--1128029 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1127970 GTCAGTATCA
*
1127980 CATTGCGATTTTCCAAATTCG
1 CATTGCGATTTTACAAATTCG
**
1128001 CATTGCGATTTTACTTATTCG
1 CATTGCGATTTTACAAATTCG
1128022 CATTGCGA
1 CATTGCGA
1128030 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (21 bp):
CATTGCGATTTTACAAATTCG
Found at i:1128245 original size:12 final size:12
Alignment explanation
Indices: 1128226--1128259 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1128216 CTCTCCGGCG
1128226 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1128238 ATATCCGTTCCT
1 ACATCCGTTCCT
1128250 ACATCC-TTCC
1 ACATCCGTTCC
1128260 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1128867 original size:24 final size:24
Alignment explanation
Indices: 1128809--1128855 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1128799 AGTCAGTATT
* *
1128809 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATATTGGTCAATACC
1128833 CGAACTTTGATATTGGTCAATAC
1 CGAACTTTGATATTGGTCAATAC
1128856 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATATTGGTCAATACC
Found at i:1129060 original size:12 final size:12
Alignment explanation
Indices: 1129043--1129078 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
1129033 TATAATCCTA
1129043 AAGAAGAAAAAG
1 AAGAAGAAAAAG
1129055 AAGAAGAAAAAG
1 AAGAAGAAAAAG
1129067 AAGAAGAAAAAG
1 AAGAAGAAAAAG
1129079 TCCCCGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:1131391 original size:19 final size:19
Alignment explanation
Indices: 1131369--1131598 Score: 88
Period size: 19 Copynumber: 13.7 Consensus size: 19
1131359 GGAAATTACT
*
1131369 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
1131388 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1131402 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1131421 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1131435 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1131454 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1131468 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1131487 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1131501 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1131520 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
1131534 TTCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1131553 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
1131567 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1131586 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1131599 TTTAATTTCG
Statistics
Matches: 148, Mismatches: 33, Indels: 60
0.61 0.14 0.25
Matches are distributed among these distances:
14 50 0.34
15 6 0.04
16 12 0.08
17 12 0.08
18 6 0.04
19 62 0.42
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1131411 original size:33 final size:33
Alignment explanation
Indices: 1131368--1131599 Score: 281
Period size: 33 Copynumber: 7.0 Consensus size: 33
1131358 CGGAAATTAC
*
1131368 TATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGA-A
**
1131402 -ATCGCAATGCGAAATGAAAATCGCAACGCTAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
1131434 TTTCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGA-A
* **
1131468 -ATCGTAATGCGAAATGAAAATCGCAACGCTAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
* **
1131500 TTTCGCAATGCGAAATGAAAATCGCAACGCTAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
* * *
1131533 TTTCGTAATGCGAAATGAAAATCGCAACGAGGGA
1 TATCGCAATGCGAAATGAAAATCGCAACGA-GAA
* *
1131567 -ATCGCAATACGAAATGAAAATCGCAACGCGAA
1 TATCGCAATGCGAAATGAAAATCGCAACGAGAA
1131599 T
1 T
1131600 TTAATTTCGC
Statistics
Matches: 172, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
32 4 0.02
33 166 0.97
34 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.18
Consensus pattern (33 bp):
TATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:1131477 original size:66 final size:66
Alignment explanation
Indices: 1131370--1131594 Score: 330
Period size: 66 Copynumber: 3.4 Consensus size: 66
1131360 GAAATTACTA
* *
1131370 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCTAAT
1131435 T
66 T
1131436 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCTAAT
1131501 T
66 T
** * **
1131502 TCGCAATGCGAAATGAAAATCGCAACGCTA-ATTTCGTAATGCGAAATGAAAATCGCAACGAGGG
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGA-ATCGTAATGCGAAATGAAAATCGCAAC--GCT
1131566 AA--
63 AATT
*
1131568 TCGCAATACGAAATGAAAATCGCAACG
1 TCGCAATGCGAAATGAAAATCGCAACG
1131595 CGAATTTAAT
Statistics
Matches: 148, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
65 1 0.01
66 144 0.97
68 3 0.02
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAACGCTAAT
T
Found at i:1131545 original size:99 final size:99
Alignment explanation
Indices: 1131369--1131601 Score: 378
Period size: 99 Copynumber: 2.4 Consensus size: 99
1131359 GGAAATTACT
* * *
1131369 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA-ATCGCAATGCGAAATGAAAATCGCAACGCTA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGA-ATTTCGCAATGCGAAATGAAAATCGCAACGCTA
1131433 ATTTCGCAATGCGAAATGAAAATCGCAACGAGAGA
65 ATTTCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1131468 ATCGTAATGCGAAATGAAAATCGCAACGCTAATTTCGCAATGCGAAATGAAAATCGCAACGCTAA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCGCAATGCGAAATGAAAATCGCAACGCTAA
* *
1131533 TTTCGTAATGCGAAATGAAAATCGCAACGAGGGA
66 TTTCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1131567 ATCGCAATACGAAATGAAAATCGCAACGCGAATTT
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1131602 AATTTCGCGT
Statistics
Matches: 123, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
98 1 0.01
99 122 0.99
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (99 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCGCAATGCGAAATGAAAATCGCAACGCTAA
TTTCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1131616 original size:19 final size:19
Alignment explanation
Indices: 1131603--1131674 Score: 135
Period size: 19 Copynumber: 3.8 Consensus size: 19
1131593 CGCGAATTTA
1131603 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1131622 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1131641 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
1131660 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
1131675 AGTACTTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:1131654 original size:38 final size:38
Alignment explanation
Indices: 1131594--1131674 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
1131584 AAATCGCAAC
* *
1131594 GCGAATTTAATTTCGCGTTGCGATTTTCATTTCGCGTT
1 GCGATTTTAATTTCGCGTTGCGATTTTCATTTCGCATT
*
1131632 GCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATT
1 GCGATTTTAATTTCGCGTTGCGATTTTCATTTCGCATT
1131670 GCGAT
1 GCGAT
1131675 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.44
Consensus pattern (38 bp):
GCGATTTTAATTTCGCGTTGCGATTTTCATTTCGCATT
Found at i:1131800 original size:14 final size:14
Alignment explanation
Indices: 1131781--1131817 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1131771 CATAAATTAA
1131781 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1131795 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1131809 ACAAATCAA
1 ACAAATCAA
1131818 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1132083 original size:19 final size:19
Alignment explanation
Indices: 1132055--1132119 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
1132045 AATTATTAAA
*
1132055 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1132074 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
* *
1132090 CTCG--TTGCGATTTTTAT
1 TTCGCATTGCGATTTTCAT
1132107 TTCGCATTGCGAT
1 TTCGCATTGCGAT
1132120 AGTAATTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 6 0.16
16 6 0.16
17 7 0.19
19 18 0.49
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1134425 original size:12 final size:12
Alignment explanation
Indices: 1134408--1134432 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1134398 TTCTTCGGGA
1134408 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1134420 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1134432 C
1 C
1134433 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:1135462 original size:20 final size:21
Alignment explanation
Indices: 1135437--1135488 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1135427 TTTTCCTAAT
*
1135437 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1135457 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1135478 TCGCAATGCGA
1 TCGCAATGCGA
1135489 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1135510 original size:20 final size:20
Alignment explanation
Indices: 1135477--1135550 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
1135467 AATTTGGAAA
* *
1135477 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
1135497 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
1135518 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
*
1135538 TTCGCAACGAGAT
1 ATCGCAACGAGAT
1135551 TCTAAAAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 25 0.58
21 14 0.33
22 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:1135519 original size:41 final size:40
Alignment explanation
Indices: 1135474--1135565 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
1135464 GCGAATTTGG
*
1135474 AAAATCGCAATGCGATACTGACTATCGCAACGAGATAATA
1 AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
* * * **
1135514 CAAAATCGCAACGAGATTCTGACTTTCGCAACGAGATTCTA
1 -AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
1135555 AAAATCGCAAT
1 AAAATCGCAAT
1135566 TATCTTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (40 bp):
AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
Found at i:1135562 original size:20 final size:20
Alignment explanation
Indices: 1135497--1135564 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1135487 GATACTGACT
**
1135497 ATCGCAACGAGATAATACAAA
1 ATCGCAACGAGATTCTA-AAA
* **
1135518 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTAAAA
*
1135538 TTCGCAACGAGATTCTAAAA
1 ATCGCAACGAGATTCTAAAA
1135558 ATCGCAA
1 ATCGCAA
1135565 TTATCTTCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGATTCTAAAA
Found at i:1135783 original size:14 final size:14
Alignment explanation
Indices: 1135764--1135793 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1135754 TCATTTGACT
*
1135764 ATCGCAACGGGAAA
1 ATCGCAACGCGAAA
1135778 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1135792 AT
1 AT
1135794 GGCTATCGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGCGAAA
Found at i:1135803 original size:20 final size:20
Alignment explanation
Indices: 1135778--1135845 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1135768 CAACGGGAAA
1135778 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
1135798 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
1135818 ATCGCAATGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1135838 ATCGCAAC
1 ATCGCAAC
1135846 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1135857 original size:34 final size:34
Alignment explanation
Indices: 1135762--1135865 Score: 118
Period size: 40 Copynumber: 2.9 Consensus size: 34
1135752 ATTCATTTGA
** *
1135762 CTATCGCAACGGGAAAATCGCAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAATGCGAAAATGG
1135796 CTATCGCAATTCGAAATGAAAAATCGCAATGCGAAAATGG
1 CTATCGCAA--C--AA-G-AAAATCGCAATGCGAAAATGG
*
1135836 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACAAGAAAATCGCAATGCGAAA
1135866 TGAAAATCGC
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
34 26 0.43
35 1 0.02
36 2 0.03
38 1 0.02
39 1 0.02
40 29 0.48
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAATGCGAAAATGG
Found at i:1135927 original size:19 final size:19
Alignment explanation
Indices: 1135905--1135953 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1135895 GATTTTCTCG
1135905 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1135924 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1135943 TTGCGATTTTC
1 TTGCGATTTTC
1135954 TGGTTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1135934 original size:14 final size:14
Alignment explanation
Indices: 1135877--1135915 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
1135867 GAAAATCGCA
1135877 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1135891 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1135905 TTGCGATTTTC
1 TTGCGATTTTC
1135916 ATTTCGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.08, C:0.21, G:0.21, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1136624 original size:22 final size:21
Alignment explanation
Indices: 1136596--1136651 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 21
1136586 AACCTGCATT
*
1136596 TATAATAAAAGTTATCATTTTA
1 TATAATAAAA-CTATCATTTTA
1136618 TATAATAACTATACTATCATTTTA
1 TATAATAA--A-ACTATCATTTTA
*
1136642 TATAAAAAAA
1 TATAATAAAA
1136652 ATTAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
24 18 0.62
25 1 0.03
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (21 bp):
TATAATAAAACTATCATTTTA
Found at i:1137635 original size:18 final size:18
Alignment explanation
Indices: 1137612--1137650 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1137602 TACTGTCAAC
1137612 ATTTAAAATTTGTAAT-CA
1 ATTTAAAATTT-TAATCCA
*
1137630 ATTTAAAGTTTTAATCCA
1 ATTTAAAATTTTAATCCA
1137648 ATT
1 ATT
1137651 ACCATTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTTAAAATTTTAATCCA
Found at i:1137948 original size:19 final size:20
Alignment explanation
Indices: 1137901--1137949 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1137891 CATTTATACA
1137901 ACCTA-AAATATCATTTTCT
1 ACCTATAAATATCATTTTCT
1137920 ACCTAT-AATATCATTTT-T
1 ACCTATAAATATCATTTTCT
1137938 ACCTATAAATAT
1 ACCTATAAATAT
1137950 TAACTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (20 bp):
ACCTATAAATATCATTTTCT
Found at i:1138711 original size:182 final size:182
Alignment explanation
Indices: 1138331--1139537 Score: 1653
Period size: 182 Copynumber: 6.6 Consensus size: 182
1138321 TACGCGTACT
* * * * *
1138331 TATTAAAATATCCACACTTTCAACATATCCGGTATCTATTTACCGGTTTTGTCA-TTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACT-TTTTCCGGTTTTGTCATTTTTGAGACA
* * *
1138395 GGTTTTATCATATTTTTACCTGTTATATTGTTCTGGATTGATACATTTTCATAAAGTG-CGACAC
65 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* *
1138459 TTTTTAAGCGCTATAACTTCTTCTTTTTTAAATTCAGAAAGTGTCGATACTTA
130 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * *
1138512 TATTAAATTAACGACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTTAGACAT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACAT
* * * * *
1138577 GTTTTATCATATTTTTACCTATTATATTGGTAAGGATCAATACATTTTCATAAAATGTCGACACT
66 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
* * *
1138642 TTTTAGGCGTTATAACTTCTTATCTTTTAAATTTAGAAAGTGTCGATA-TTAA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTT-A
* * * *
1138694 TATTAAATTATCGACACTTTCAATATATCCGGTAGCGTTTTAT-TGGTTTTGTCAATTTTGAGAC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAAC-TTTT-TCCGGTTTTGTCATTTTTGAGAC
* *
1138758 TTGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGATA
64 ATGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACA
* * * *
1138823 ATTTTTAGGCGTTATAACTTCTTCTATTTTAAATTAAGAAAGTGTCGATACTTA
129 CTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* *
1138877 TATTAAATTATCGACACTTTTAACATATCCGATAACTTTTTCCGGTTTTGTCATTTTTGAGACAT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACAT
* ** *
1138942 GTTTTATCATATTTTTACCTGTTATATTGTTGTGGATCGAT--ATTTTTTTAAAGTATCGACACT
66 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
* *
1139005 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * * ** * *
1139057 TATTAAATTATCGACACTTTCAATATATCTGGTAGCGTTTTACTAGTTTTGTCAATTTTGAGACT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAAC-TTTTTCCGGTTTTGTCATTTTTGAGACA
1139122 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
65 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* * *
1139187 TTTTTAAGCGCAATAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
130 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* *
1139240 TATTAAATTATCGATACTTTTAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACAT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACAT
* *
1139305 GTTTTATCATATTTTTACCTGTTATATTGGTAAGGATCGATACATTTTCATAAAGTGTCGACACT
66 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
* *
1139370 TTTTAGGTGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * *
1139422 TATTAAATTATCGACAC--TCGACACATATCCGGTAGCGTTTTACCGGTTTTGTCA-TTTTGGGA
1 TATTAAATTATCGACACTTTC-A-ACATATCCGGTAAC-TTTTTCCGGTTTTGTCATTTTTGAGA
* * * * * * *
1139484 C-CGATTTTGTCATATTTGTACATGTAATATTGCTATGGGTCGAT-CAATTTTCAT
63 CATG-TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC-ATTTTCAT
1139538 TTGTATTGAC
Statistics
Matches: 907, Mismatches: 104, Indels: 29
0.87 0.10 0.03
Matches are distributed among these distances:
180 111 0.12
181 160 0.18
182 361 0.40
183 272 0.30
184 3 0.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACAT
GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
Found at i:1139146 original size:363 final size:363
Alignment explanation
Indices: 1138331--1139537 Score: 1800
Period size: 363 Copynumber: 3.3 Consensus size: 363
1138321 TACGCGTACT
* * * *
1138331 TATTAAAATATCCACACTTTCAACATATCCGGTATC-TATTTACCGGTTTTGTCATTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGT-TTTACCGGTTTTGTCATTTTGAGACT
* * *
1138395 GGTTTTATCATATTTTTACCTGTTATATTGTTCTGGATTGATACATTTTCATAAAGTG-CGACAC
65 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* *
1138459 TTTTTAAGCGCTATAACTTCTTCTTTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTAAC
130 TTTTTAAGCGCTATAACTTCTTCTATTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
* * *
1138524 GACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTTAGACATGTTTTATCATAT
195 GACACTTTTAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACATGTTTTATCATAT
* * * *
1138589 TTTTACCTATTATATTGGTAAGGATCAATACATTTTCATAAAATGTCGACACTTTTTAGGCGTTA
260 TTTTACCTGTTATATTGGTAAGGATCGATA-ATTTTCATAAAGTGTCGACACTTTTTAGGCGCTA
* * *
1138654 TAACTTCTTATCTTTTAAATTTAGAAAGTGTCGATA-TTAA
324 TAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTT-A
* **
1138694 TATTAAATTATCGACACTTTCAATATATCCGGTAGCGTTTTATTGGTTTTGTCAATTTTGAGACT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTC-ATTTTGAGACT
* *
1138759 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGATAA
65 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* * *
1138824 TTTTTAGGCGTTATAACTTCTTCTATTTTAAATTAAGAAAGTGTCGATACTTATATTAAATTATC
130 TTTTTAAGCGCTATAACTTCTTCTATTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
*
1138889 GACACTTTTAACATATCCGATAACTTTTTCCGGTTTTGTCATTTTTGAGACATGTTTTATCATAT
195 GACACTTTTAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACATGTTTTATCATAT
* ** ** * *
1138954 TTTTACCTGTTATATTGTTGTGGATCGAT-ATTTTTTTAAAGTATCGACACTTTATAGGCGCTAT
260 TTTTACCTGTTATATTGGTAAGGATCGATAATTTTCATAAAGTGTCGACACTTTTTAGGCGCTAT
1139018 AACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
325 AACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
* * **
1139057 TATTAAATTATCGACACTTTCAATATATCTGGTAGCGTTTTACTAGTTTTGTCAATTTTGAGACT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTC-ATTTTGAGACT
1139122 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
65 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* * *
1139187 TTTTTAAGCGCAATAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
130 TTTTTAAGCGCTATAACTTCTTCTATTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
*
1139252 GATACTTTTAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACATGTTTTATCATAT
195 GACACTTTTAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACATGTTTTATCATAT
*
1139317 TTTTACCTGTTATATTGGTAAGGATCGATACATTTTCATAAAGTGTCGACACTTTTTAGGTGCTA
260 TTTTACCTGTTATATTGGTAAGGATCGATA-ATTTTCATAAAGTGTCGACACTTTTTAGGCGCTA
1139382 TAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
324 TAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
*
1139422 TATTAAATTATCGACAC--TCGACACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGGGAC
1 TATTAAATTATCGACACTTTC-A-ACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGAC
* * * * * * *
1139485 -CGATTTTGTCATATTTGTACATGTAATATTGCTATGGGTCGAT-CAATTTTCAT
64 TTG-TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC-ATTTTCAT
1139538 TTGTATTGAC
Statistics
Matches: 766, Mismatches: 68, Indels: 19
0.90 0.08 0.02
Matches are distributed among these distances:
363 384 0.50
364 120 0.16
365 262 0.34
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (363 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACTT
GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
TTTTAAGCGCTATAACTTCTTCTATTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
ACACTTTTAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACATGTTTTATCATATT
TTTACCTGTTATATTGGTAAGGATCGATAATTTTCATAAAGTGTCGACACTTTTTAGGCGCTATA
ACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
Found at i:1139386 original size:545 final size:545
Alignment explanation
Indices: 1138331--1139537 Score: 1692
Period size: 545 Copynumber: 2.2 Consensus size: 545
1138321 TACGCGTACT
* * * *
1138331 TATTAAAATATCCACACTTTCAACATATCCGGTATCTATTTACCGGTTTTGTCA-TTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACT-TTTACCGGTTTTGTCATTTTTGAGACA
*
1138395 GGTTTTATCATATTTTTACCTGTTATATTGTTCTGGATTGATACATTTTCATAAAGTGCGACACT
65 GGTTTTATCATATTTTTACCTGTTATATTGTTCTGGATCGATA-ATTTTCATAAAGTGCGACACT
* *
1138460 TTTTAAGCGCTATAACTTCTTCTTTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTAACG
129 TTATAAGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTAACG
* * * *
1138525 ACACTTTCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTTAGACATGTTTTATCATATT
194 ACACTTTCAATATATCCGGTAACTTTTACCAGTTTTGTCAATTTTGAGACATGTTTTATCATATT
* **
1138590 TTTACCTATTATATTGGTAAGGATCAATACATTTTCATAAAATGTCGACACTTTTTAGGCGTTAT
259 TTTACCTATTATATTGGTAAGGATCAATACATTTTCATAAAATGTCGACACTTTTTAAGCGCAAT
* *
1138655 AACTTCTTATCTTTTAAATTTAGAAAGTGTCGATATTAATATTAAATTATCGACACTTTCAATAT
324 AACTTCTTATCTTTTAAATTCAGAAAGTGTCGATATTAATATTAAATTATCGACACTTTCAACAT
* * *
1138720 ATCCGGTAGCGTTTTATTGGTTTTGTCAATTTTGAGACTTGTTTTATCATATTTTTACCTGTTAT
389 ATCCGGTAACGTTTTATCGGTTTTGTCAATTTTGAGACATGTTTTATCATATTTTTACCTGTTAT
* * * *
1138785 ATTGTTATGGATCGATACATTTTCATAAAGTGTCGATAATTTTTAGGCGTTATAACTTCTTCTAT
454 ATTGGTAAGGATCGATACATTTTCATAAAGTGTCGACAATTTTTAGGCGCTATAACTTCTTCTAT
1138850 TTTAAATTAAGAAAGTGTCGATACTTA
519 TTTAAATTAAGAAAGTGTCGATACTTA
* * * *
1138877 TATTAAATTATCGACACTTTTAACATATCCGATAACTTTTTCCGGTTTTGTCATTTTTGAGACAT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTACCGGTTTTGTCATTTTTGAGACAG
* ** *
1138942 GTTTTATCATATTTTTACCTGTTATATTGTTGTGGATCGAT-ATTTTTTTAAAGTATCGACACTT
66 GTTTTATCATATTTTTACCTGTTATATTGTTCTGGATCGATAATTTTCATAAAGT-GCGACACTT
* * *
1139006 TATAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGA
130 TATAAGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTAACGA
* * * *
1139071 CACTTTCAATATATCTGGTAGCGTTTTACTAGTTTTGTCAATTTTGAGACTTGTTTTATCATATT
195 CACTTTCAATATATCCGGTAAC-TTTTACCAGTTTTGTCAATTTTGAGACATGTTTTATCATATT
* * * * *
1139136 TTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTTTTTAAGCGCAAT
259 TTTACCTATTATATTGGTAAGGATCAATACATTTTCATAAAATGTCGACACTTTTTAAGCGCAAT
* * * *
1139201 AACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTT-ATATTAAATTATCGATACTTTTAACA
324 AACTTCTTATCTTTTAAATTCAGAAAGTGTCGATA-TTAATATTAAATTATCGACACTTTCAACA
*
1139265 TATCCGGTAAC-TTTT-TCCGGTTTTGTCATTTTTGAGACATGTTTTATCATATTTTTACCTGTT
388 TATCCGGTAACGTTTTAT-CGGTTTTGTCAATTTTGAGACATGTTTTATCATATTTTTACCTGTT
* *
1139328 ATATTGGTAAGGATCGATACATTTTCATAAAGTGTCGACACTTTTTAGGTGCTATAACTTCTTCT
452 ATATTGGTAAGGATCGATACATTTTCATAAAGTGTCGACAATTTTTAGGCGCTATAACTTCTTCT
* * *
1139393 CTTTTAAATTCAGAAAGTTTCGATACTTA
517 ATTTTAAATTAAGAAAGTGTCGATACTTA
* *
1139422 TATTAAATTATCGACAC--TCGACACATATCCGGTAGCGTTTTACCGGTTTTGTCA-TTTTGGGA
1 TATTAAATTATCGACACTTTC-A-ACATATCCGGTAAC-TTTTACCGGTTTTGTCATTTTTGAGA
* * * * * * * * *
1139484 CCGATTTTGTCATATTTGTACATGTAATATTGCTATGGGTCGATCAATTTTCAT
63 CAGGTTTTATCATATTTTTACCTGTTATATTGTTCTGGATCGAT-AATTTTCAT
1139538 TTGTATTGAC
Statistics
Matches: 581, Mismatches: 70, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
543 1 0.00
544 13 0.02
545 305 0.52
546 254 0.44
547 8 0.01
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (545 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTACCGGTTTTGTCATTTTTGAGACAG
GTTTTATCATATTTTTACCTGTTATATTGTTCTGGATCGATAATTTTCATAAAGTGCGACACTTT
ATAAGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTAACGAC
ACTTTCAATATATCCGGTAACTTTTACCAGTTTTGTCAATTTTGAGACATGTTTTATCATATTTT
TACCTATTATATTGGTAAGGATCAATACATTTTCATAAAATGTCGACACTTTTTAAGCGCAATAA
CTTCTTATCTTTTAAATTCAGAAAGTGTCGATATTAATATTAAATTATCGACACTTTCAACATAT
CCGGTAACGTTTTATCGGTTTTGTCAATTTTGAGACATGTTTTATCATATTTTTACCTGTTATAT
TGGTAAGGATCGATACATTTTCATAAAGTGTCGACAATTTTTAGGCGCTATAACTTCTTCTATTT
TAAATTAAGAAAGTGTCGATACTTA
Found at i:1139491 original size:20 final size:21
Alignment explanation
Indices: 1139463--1139501 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1139453 GTAGCGTTTT
*
1139463 ACCGGTTTTGTCAT-TTTGGG
1 ACCGATTTTGTCATATTTGGG
1139483 ACCGATTTTGTCATATTTG
1 ACCGATTTTGTCATATTTG
1139502 TACATGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (21 bp):
ACCGATTTTGTCATATTTGGG
Found at i:1142412 original size:13 final size:14
Alignment explanation
Indices: 1142389--1142418 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1142379 TTCCCATTAC
1142389 AGACGTGCATATGA
1 AGACGTGCATATGA
1142403 AGAC-TGCATATGA
1 AGACGTGCATATGA
1142416 AGA
1 AGA
1142419 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:1145393 original size:12 final size:11
Alignment explanation
Indices: 1145376--1145439 Score: 64
Period size: 12 Copynumber: 5.9 Consensus size: 11
1145366 TTTGGGCTTG
1145376 TAATAATATATT
1 TAATAATA-ATT
1145388 TAATAATAA--
1 TAATAATAATT
1145397 TAATAATAA--
1 TAATAATAATT
*
1145406 TAATAATTATT
1 TAATAATAATT
1145417 ATAATAATAATTT
1 -TAATAATAA-TT
1145430 TAATAATAAT
1 TAATAATAAT
1145440 AATAAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
9 17 0.37
11 2 0.04
12 25 0.54
13 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAATAATAATT
Found at i:1145394 original size:3 final size:3
Alignment explanation
Indices: 1145388--1145444 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
1145378 ATAATATATT
* * **
1145388 TAA TAA TAA TAA TAA TAA TAA TAA TTA TTA TAA TAA TAA TTT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1145436 TAA TAA TAA
1 TAA TAA TAA
1145445 AAAAACAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1145396 original size:15 final size:14
Alignment explanation
Indices: 1145376--1145442 Score: 84
Period size: 15 Copynumber: 4.7 Consensus size: 14
1145366 TTTGGGCTTG
1145376 TAATAATATATTTAA
1 TAATAATA-ATTTAA
1145391 TAATAATAA--TAA
1 TAATAATAATTTAA
*
1145403 TAATAATAATTATTA
1 TAATAATAATT-TAA
1145418 TAATAATAATTTTAA
1 TAATAATAA-TTTAA
1145433 TAATAATAAT
1 TAATAATAAT
1145443 AAAAAAACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
12 12 0.26
14 2 0.04
15 30 0.65
16 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATAATAATTTAA
Found at i:1145730 original size:76 final size:76
Alignment explanation
Indices: 1145604--1146131 Score: 984
Period size: 76 Copynumber: 6.9 Consensus size: 76
1145594 AGAGGTCTTA
* *
1145604 GAAACATCATGCACTGCAGGACTTACATATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
*
1145669 AAGGATTTTTG
66 AAGGCTTTTTG
*
1145680 GAAACATCATGCACTGCAGGACTTACAGACGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1145745 AAGGCTTTTTG
66 AAGGCTTTTTG
1145756 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1145821 AAGGCTTTTTG
66 AAGGCTTTTTG
* *
1145832 GAAACATCATGCACTACAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1145897 AAGGCTTTTTG
66 AAGGCTTTTTG
1145908 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1145973 AAGGCTTTTTG
66 AAGGCTTTTTG
*
1145984 GAAACATCATGCATTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1146049 AAGGCTTTTTG
66 AAGGCTTTTTG
*
1146060 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
1 GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1146125 AAGGCTT
66 AAGGCTT
1146132 GAAAACATCA
Statistics
Matches: 440, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 440 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
AAGGCTTTTTG
Found at i:1146145 original size:29 final size:28
Alignment explanation
Indices: 1146096--1146159 Score: 110
Period size: 28 Copynumber: 2.2 Consensus size: 28
1146086 AGATGACCCT
1146096 AAGGCTTTGAAAACATCAAAAAGCTCCCG
1 AAGGC-TTGAAAACATCAAAAAGCTCCCG
*
1146125 AAGGCTTGAAAACATCAAAAAGCTCCTG
1 AAGGCTTGAAAACATCAAAAAGCTCCCG
1146153 AAGGCTT
1 AAGGCTT
1146160 TTTGGAAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (28 bp):
AAGGCTTGAAAACATCAAAAAGCTCCCG
Found at i:1146834 original size:22 final size:22
Alignment explanation
Indices: 1146809--1146863 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1146799 CATAAAGCTT
1146809 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1146831 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1146853 TCATCTTTGAA
1 TCATCTTTGAA
1146864 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1149291 original size:114 final size:114
Alignment explanation
Indices: 1149091--1149314 Score: 367
Period size: 114 Copynumber: 2.0 Consensus size: 114
1149081 GATCATGCAG
* * * *
1149091 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1149156 TCACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTAATATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTAATATGAGCAAA
* * *
1149205 TTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1149270 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTAATATGAG
1149315 AACATGGCAC
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTAATATGAGCAAA
Found at i:1151493 original size:10 final size:9
Alignment explanation
Indices: 1151462--1151516 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
1151452 CCTTTTTCCT
1151462 TTTTTTTTC
1 TTTTTTTTC
1151471 TTTTTTTTC
1 TTTTTTTTC
*
1151480 TTTTTTCTC
1 TTTTTTTTC
* *
1151489 -ATTTTTCC
1 TTTTTTTTC
**
1151497 TTTTTCATC
1 TTTTTTTTC
1151506 -TTTTTTTC
1 TTTTTTTTC
1151514 TTT
1 TTT
1151517 CTTTGCTGGA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
8 11 0.32
9 23 0.68
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1151510 original size:17 final size:16
Alignment explanation
Indices: 1151465--1151516 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1151455 TTTTCCTTTT
* *
1151465 TTTTTCTTTTTTTTCT
1 TTTTTCTCTTTTTTCC
*
1151481 TTTTTCTCATTTTTCC
1 TTTTTCTCTTTTTTCC
*
1151497 TTTTTCATCTTTTTTTC
1 TTTTTC-TCTTTTTTCC
1151514 TTT
1 TTT
1151517 CTTTGCTGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 19 0.63
17 11 0.37
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCTCTTTTTTCC
Found at i:1154449 original size:7 final size:7
Alignment explanation
Indices: 1154439--1154479 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
1154429 TAAAAGTATG
1154439 AATGCAA
1 AATGCAA
*
1154446 AATGAAA
1 AATGCAA
1154453 AATGCAA
1 AATGCAA
1154460 AGATGCAA
1 A-ATGCAA
1154468 AATG-AA
1 AATGCAA
1154474 AATGCA
1 AATGCA
1154480 TATATGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:1158768 original size:3 final size:3
Alignment explanation
Indices: 1158762--1158815 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
1158752 ATAATATATT
* **
1158762 TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TTT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1158810 TAA TAA
1 TAA TAA
1158816 AAACAAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Done.