Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 24
Found at i:3986044 original size:33 final size:33
Alignment explanation
Indices: 3985889--3986035 Score: 195
Period size: 33 Copynumber: 4.3 Consensus size: 33
3985879 ACTAAATTCG
* * *
3985889 CGTTGTGATTTTAATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
3985922 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
3985955 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
*
3985994 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
3986027 CGTTGCGAT
1 CGTTGCGAT
3986036 AGTAATTTCC
Statistics
Matches: 102, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
33 68 0.67
34 1 0.01
35 2 0.02
37 2 0.02
38 1 0.01
39 28 0.27
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:3986101 original size:20 final size:20
Alignment explanation
Indices: 3985976--3986101 Score: 56
Period size: 20 Copynumber: 6.6 Consensus size: 20
3985966 TCATTTCGCA
* *
3985976 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTTCGTG
** *
3985996 TTGCGATTTTCA-TTTCGTA
1 TTGCGATAGTCATTTTCGTG
*
3986015 TTGCGAT--TC--TCTC--G
1 TTGCGATAGTCATTTTCGTG
* *
3986029 TTGCGATAGTAATTTCCGTG
1 TTGCGATAGTCATTTTCGTG
**
3986049 TTGCGATAG--ATATTAAGATG
1 TTGCGATAGTCAT-TTTCG-TG
3986069 ATTGCGA-ACGTCATTTTCGTG
1 -TTGCGATA-GTCATTTTCGTG
3986090 TTGCGATAGTCA
1 TTGCGATAGTCA
3986102 AATGAATGCC
Statistics
Matches: 79, Mismatches: 14, Indels: 26
0.66 0.12 0.22
Matches are distributed among these distances:
14 7 0.09
16 4 0.05
17 2 0.03
18 4 0.05
19 14 0.18
20 33 0.42
21 10 0.13
22 3 0.04
23 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:3989500 original size:20 final size:19
Alignment explanation
Indices: 3989480--3989759 Score: 132
Period size: 20 Copynumber: 13.9 Consensus size: 19
3989470 GCGATGGACA
*
3989480 GAATCTCGTTGCGATTTAC
1 GAATCGCGTTGCGATTTAC
* *
3989499 AGATTCGCATTGCGATTTAC
1 -GAATCGCGTTGCGATTTAC
* * *
3989519 GTATTCACATTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
* * *
3989539 GTATTCACATTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
* *
3989559 GTATTCGCATTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
* * *
3989579 GGATACGCATTGTGATTTAC
1 GAAT-CGCGTTGCGATTTAC
* * * *
3989599 GTATTCTCATTACGATTTAC
1 G-AATCGCGTTGCGATTTAC
3989619 -AGATACGCGTTGCGATTTAC
1 GA-AT-CGCGTTGCGATTTAC
* *
3989639 GTATTCTCGTTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
* *
3989659 GGATACGCGTTACGATTTTAC
1 GAAT-CGCGTTGCGA-TTTAC
* * *
3989680 GTATTGTTGTTGCGATTTAC
1 GAATCG-CGTTGCGATTTAC
*
3989700 GGATACGCGTTGCGATTTTAC
1 GAAT-CGCGTTGCGA-TTTAC
* * *
3989721 GGATACTCGTTGCGATAGT-C
1 GAAT-CGCGTTGCGAT-TTAC
3989741 AGAATCGCGTTGCGATTTA
1 -GAATCGCGTTGCGATTTA
3989760 TATATTCGAG
Statistics
Matches: 210, Mismatches: 35, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.00
19 5 0.02
20 163 0.78
21 40 0.19
22 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (19 bp):
GAATCGCGTTGCGATTTAC
Found at i:3989532 original size:40 final size:40
Alignment explanation
Indices: 3989483--3989797 Score: 303
Period size: 40 Copynumber: 7.8 Consensus size: 40
3989473 ATGGACAGAA
* *
3989483 TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTAT
* * * * *
3989523 TCACATTGCGATTTAC-GTATTCACATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACAG-ATACGCGTTGCGATTTACGTAT
* * * * *
3989563 TCGCATTGCGATTTACGGATACGCATTGTGATTTACGTAT
1 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTAT
* *
3989603 TCTCATTACGATTTACAGATACGCGTTGCGATTTACGTAT
1 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTAT
* *
3989643 TCTCGTTGCGATTTACGGATACGCGTTACGATTTTACGTAT
1 TCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTAT
* * * *
3989684 TGTTGTTGCGATTTACGGATACGCGTTGCGATTTTACGGAT
1 TCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTAT
* * **
3989725 ACTCGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATAT
1 TCTCGTTGCGAT-TTACAGATA-CGCGTTGCGATTTACGTAT
** * * *
3989765 TCGAGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCTCGTTGCGATTTACAGATACGCGTTGCGATT
3989798 CTGGAAAATC
Statistics
Matches: 234, Mismatches: 34, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.01
40 162 0.69
41 69 0.29
42 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (40 bp):
TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTAT
Found at i:3989554 original size:60 final size:60
Alignment explanation
Indices: 3989488--3989659 Score: 238
Period size: 60 Copynumber: 2.9 Consensus size: 60
3989478 CAGAATCTCG
3989488 TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGTATTCACA
1 TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGTATTCACA
* * * * *
3989548 TTGCGATTTAC-GTATTCGCATTGCGATTTACGGATACGCATTGTGATTTACGTATTCTCA
1 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGTATTCACA
* * * * *
3989608 TTACGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACG
1 TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCACATTGCGATTTACG
3989660 GATACGCGTT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
59 1 0.01
60 95 0.98
61 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (60 bp):
TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGTATTCACA
Found at i:3989672 original size:60 final size:60
Alignment explanation
Indices: 3989484--3989778 Score: 231
Period size: 60 Copynumber: 4.9 Consensus size: 60
3989474 TGGACAGAAT
* * * * * *
3989484 CTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGTATT
1 CTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATA
* * * * * * * * * *
3989544 CACATTGCGATTTAC-GTATTCGCATTGCGATTTACGGATACGCATTGTGATTTACGTATT
1 CTCGTTGCGATTTACAG-ATACGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATA
* * *
3989604 CTCATTACGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
1 CTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATA
* * * * * *
3989664 CGCGTTACGATTTTAC-G-TATTGTTGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
1 CTCGTTGCGA-TTTACAGATA-CG-CGTTGCGATTTACGTATTCGCGTTGCGA-TTTACGGATA
* ** *
3989726 CTCGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATATTCGAGTTGCGATTT
1 CTCGTTGCGAT-TTACAGATA-CGCGTTGCGATTTACGTATTCGCGTTGCGATTT
3989779 TCATATTCGC
Statistics
Matches: 192, Mismatches: 34, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
59 3 0.02
60 112 0.58
61 54 0.28
62 23 0.12
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (60 bp):
CTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATA
Found at i:3989680 original size:21 final size:20
Alignment explanation
Indices: 3989486--3989736 Score: 198
Period size: 20 Copynumber: 12.4 Consensus size: 20
3989476 GACAGAATCT
* *
3989486 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTACGGATACG
* * * *
3989506 CATTGCGATTTACGTATTCA
1 CGTTGCGATTTACGGATACG
* * * *
3989526 CATTGCGATTTACGTATTCA
1 CGTTGCGATTTACGGATACG
* * *
3989546 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACG
*
3989566 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* * * * *
3989586 CATTGTGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
* * *
3989606 CATTACGATTTACAGATACG
1 CGTTGCGATTTACGGATACG
* * *
3989626 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
3989646 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* * *
3989666 CGTTACGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGGATACG
*
3989686 TTGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACGGATACG
*
3989707 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACG
3989728 CGTTGCGAT
1 CGTTGCGAT
3989737 AGTCAGAATC
Statistics
Matches: 192, Mismatches: 35, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
20 158 0.82
21 34 0.18
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:3989772 original size:20 final size:20
Alignment explanation
Indices: 3989749--3989797 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3989739 TCAGAATCGC
3989749 GTTGCGATTTAT-ATATTCGA
1 GTTGCGATTT-TCATATTCGA
*
3989769 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTTCATATTCGA
3989789 GTTGCGATT
1 GTTGCGATT
3989798 CTGGAAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.45
Consensus pattern (20 bp):
GTTGCGATTTTCATATTCGA
Found at i:3989773 original size:81 final size:81
Alignment explanation
Indices: 3989611--3989797 Score: 204
Period size: 81 Copynumber: 2.3 Consensus size: 81
3989601 ATTCTCATTA
* * * *
3989611 CGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTTACGAT
1 CGATTTACAGATACGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGCGTTACGAT
*
3989675 TTTACGTATTGTTGTTG
66 TTTAC-TATTGTAGTTG
* *
3989692 CGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAAT-CGCGTTGCG
1 CGATTTACAGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT--TCACGAATACGCGTTACG
3989755 ATTTATA-TATTCG-AGTTG
64 ATTT-TACTATT-GTAGTTG
* * *
3989773 CGATTTTCATATTCGCGTTGCGATT
1 CGATTTACAGATACGCGTTGCGATT
3989798 CTGGAAAATC
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
81 51 0.57
82 32 0.36
83 5 0.06
84 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (81 bp):
CGATTTACAGATACGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGCGTTACGAT
TTTACTATTGTAGTTG
Found at i:3989850 original size:21 final size:21
Alignment explanation
Indices: 3989770--3989862 Score: 68
Period size: 21 Copynumber: 4.5 Consensus size: 21
3989760 TATATTCGAG
* *
3989770 TTGCGATT-TTCATATTCGCG
1 TTGCGATTCTTCATAATCGCA
** *
3989790 TTGCGATTCTGGAAAATCGCA
1 TTGCGATTCTTCATAATCGCA
*
3989811 ATGCGAATT-TGT-ACT-ATCGCA
1 TTGCG-ATTCT-TCA-TAATCGCA
*
3989832 TTGCGATTCTTCATAATCGCG
1 TTGCGATTCTTCATAATCGCA
3989853 TTGCGATTCT
1 TTGCGATTCT
3989863 GGGAACTGAT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
20 13 0.23
21 40 0.71
22 3 0.05
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (21 bp):
TTGCGATTCTTCATAATCGCA
Found at i:3989896 original size:20 final size:18
Alignment explanation
Indices: 3989852--3989900 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
3989842 TCATAATCGC
3989852 GTTGCGATTCTGGGAACT
1 GTTGCGATTCTGGGAACT
*
3989870 GATTTGCGATTCTGGAGATCAT
1 G--TTGCGATTCTGG-GAAC-T
3989892 GTTGCGATT
1 GTTGCGATT
3989901 TTTATTTCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.04
20 20 0.77
21 3 0.12
22 2 0.08
ACGTcount: A:0.18, C:0.14, G:0.31, T:0.37
Consensus pattern (18 bp):
GTTGCGATTCTGGGAACT
Found at i:3991244 original size:22 final size:22
Alignment explanation
Indices: 3991216--3991260 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3991206 CAAATAATTT
3991216 GGTGTGAAGAATAAAGAGTTAA
1 GGTGTGAAGAATAAAGAGTTAA
3991238 GGTGTGAAGAATAAAGAGTTAA
1 GGTGTGAAGAATAAAGAGTTAA
3991260 G
1 G
3991261 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (22 bp):
GGTGTGAAGAATAAAGAGTTAA
Found at i:3992153 original size:20 final size:20
Alignment explanation
Indices: 3992130--3992259 Score: 179
Period size: 20 Copynumber: 6.5 Consensus size: 20
3992120 CGATAGTCAG
*
3992130 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3992150 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3992170 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3992190 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
3992210 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
3992231 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3992251 ATTCGCATT
1 ATTCGCATT
3992260 ACGAATTAGG
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 81 0.84
21 15 0.16
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3992285 original size:21 final size:21
Alignment explanation
Indices: 3992261--3992305 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
3992251 ATTCGCATTA
3992261 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* *
3992282 CGAATTTGGAAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
3992303 CGA
1 CGA
3992306 TAGTCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:3996296 original size:14 final size:13
Alignment explanation
Indices: 3996255--3996299 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
3996245 CAAAAATGAG
3996255 AATAAATAAGATA
1 AATAAATAAGATA
3996268 AA-AAATGAA-ATA
1 AATAAAT-AAGATA
3996280 AATAAATATAGATA
1 AATAAATA-AGATA
3996294 AATAAA
1 AATAAA
3996300 AGGAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 10 0.36
13 9 0.32
14 9 0.32
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (13 bp):
AATAAATAAGATA
Found at i:3996417 original size:23 final size:21
Alignment explanation
Indices: 3996368--3996419 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
3996358 TAGAAAAACC
* *
3996368 AAAAAACAATAAAATAACAAT
1 AAAAAATAATAAAATAAAAAT
3996389 ACAAAAATAATTAAAATAATAAAT
1 A-AAAAATAA-TAAAATAA-AAAT
3996413 AAAAAAT
1 AAAAAAT
3996420 TAAAAGCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (21 bp):
AAAAAATAATAAAATAAAAAT
Found at i:3997689 original size:38 final size:35
Alignment explanation
Indices: 3997615--3998005 Score: 125
Period size: 37 Copynumber: 10.9 Consensus size: 35
3997605 TATATATATA
*
3997615 TAAAAAATATTTTCCAAAACCTATATAATATATTTTT
1 TAAAAAATATTTT-CAAAA-TTATATAATATATTTTT
3997652 TAAAAAATATTTT-AAAATTATATATTATATACTTTTTT
1 TAAAAAATATTTTCAAAATTATATA--ATATA--TTTTT
* *
3997690 TAAAAAAATGTTTTC-AAA--AT-T-ATATA-GTTT
1 T-AAAAAATATTTTCAAAATTATATAATATATTTTT
* * * * * *
3997720 TCAAAAATGTTTTTAAAACTATATATTATATGTTT
1 TAAAAAATATTTTCAAAATTATATAATATATTTTT
*
3997755 TCAAAAATGA-TTTCAAAACTATAGAATATATATATATATGTTT
1 TAAAAAAT-ATTTTCAAAA-T-T---ATATA-ATATAT-T-TTT
* * *
3997798 T-CAAAATGTTTTTTAAAA--ACTAT-ATATA-TTTT
1 TAAAAAAT-ATTTTCAAAATTA-TATAATATATTTTT
*
3997830 T--AAAATGTTTT-AAAATTATATAATATATATATTT
1 TAAAAAATATTTTCAAAATTATATAATATAT-T-TTT
* * *
3997864 TAAAAAATATTTTAAAAACTATATATTATATTAATTT
1 TAAAAAATATTTTCAAAATTATATAATATATT--TTT
* * * * *
3997901 T-CAAAATGTTTTTAAAAACTATATAACATATATATTT
1 TAAAAAAT-ATTTTCAAAATTATAT-A-ATATATTTTT
* * * * *
3997938 TCAAAAATGTTTTGAAAACTATATATTATATTAATTT
1 TAAAAAATATTTTCAAAATTATATAATATATT--TTT
* * * *
3997975 T-CAAAATGTTTTTAAAAACTATATAATATAT
1 TAAAAAAT-ATTTTCAAAATTATATAATATAT
3998006 AAATGTTTTC
Statistics
Matches: 283, Mismatches: 31, Indels: 80
0.72 0.08 0.20
Matches are distributed among these distances:
29 15 0.05
30 14 0.05
31 11 0.04
32 6 0.02
33 8 0.03
34 14 0.05
35 33 0.12
36 28 0.10
37 96 0.34
38 12 0.04
39 19 0.07
40 5 0.02
41 5 0.02
42 6 0.02
43 11 0.04
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (35 bp):
TAAAAAATATTTTCAAAATTATATAATATATTTTT
Found at i:3997817 original size:44 final size:42
Alignment explanation
Indices: 3997739--3997821 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 42
3997729 TTTTTAAAAC
*
3997739 TATATATTATATGTTTTCAAAAATGATTTCAAAACTATAGAA
1 TATATATTATATGTTTTCAAAAATGATTTAAAAACTATAGAA
*
3997781 TATATATATATATGTTTTC-AAAATGTTTTTTAAAAACTATA
1 TATATAT-TATATGTTTTCAAAAATG--ATTTAAAAACTATA
3997822 TATATTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 13 0.36
43 11 0.31
44 12 0.33
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (42 bp):
TATATATTATATGTTTTCAAAAATGATTTAAAAACTATAGAA
Found at i:3997822 original size:37 final size:36
Alignment explanation
Indices: 3997781--3998087 Score: 262
Period size: 37 Copynumber: 8.4 Consensus size: 36
3997771 AACTATAGAA
*
3997781 TATATATATATATGTTTTCAAAATGTTTTTTAAAAAC
1 TATATATATATATATTTTCAAAATG-TTTTTAAAAAC
*
3997818 ----TATATATAT-TTTT-AAAATG-TTTT-AAAAT
1 TATATATATATATATTTTCAAAATGTTTTTAAAAAC
* *
3997846 TATATAATATATATATTTTAAAAAAT-ATTTTAAAAAC
1 TATAT-ATATATATATTTT-CAAAATGTTTTTAAAAAC
3997883 TATATAT-TATATTAATTTTCAAAATGTTTTTAAAAAC
1 TATATATATATA-T-ATTTTCAAAATGTTTTTAAAAAC
* *
3997920 TATATAACATATATATTTTCAAAAATG-TTTTGAAAAC
1 TATAT-ATATATATATTTTC-AAAATGTTTTTAAAAAC
3997957 TATATAT-TATATTAATTTTCAAAATGTTTTTAAAAAC
1 TATATATATATA-T-ATTTTCAAAATGTTTTTAAAAAC
*
3997994 TATATAATATATAAATGTTTTCAAACATGTTTTT-AAAAC
1 TATAT-ATATAT--ATATTTTCAAA-ATGTTTTTAAAAAC
* * ***
3998033 TATATATTATATATACATTTTAAAAATGTTTTCAAACTG
1 TATATA-TATATAT--ATTTTCAAAATGTTTTTAAAAAC
3998072 TATACTATATATATAT
1 TATA-TATATATATAT
3998088 ATATGTAAAA
Statistics
Matches: 226, Mismatches: 15, Indels: 58
0.76 0.05 0.19
Matches are distributed among these distances:
28 4 0.02
29 4 0.02
31 6 0.03
32 5 0.02
33 17 0.08
34 4 0.02
35 8 0.04
36 25 0.11
37 73 0.32
38 18 0.08
39 50 0.22
40 11 0.05
41 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.47
Consensus pattern (36 bp):
TATATATATATATATTTTCAAAATGTTTTTAAAAAC
Found at i:3998070 original size:76 final size:74
Alignment explanation
Indices: 3997780--3998085 Score: 348
Period size: 74 Copynumber: 4.2 Consensus size: 74
3997770 AAACTATAGA
*
3997780 ATATATATATATATGTTTTC-AAAATGTTTTTTAAAAAC--TATA-TATA-T--TTTT-AAAATG
1 ATATA-ATATATATATTTTCAAAAATG--TTTTAAAAACTATATATTATATTAATTTTCAAAATG
*
3997837 -TTTT-AAAATT
63 TTTTTAAAAACT
* *
3997847 ATATAATATATATATTTTAAAAAATATTTTAAAAACTATATATTATATTAATTTTCAAAATGTTT
1 ATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATTAATTTTCAAAATGTTT
3997912 TTAAAAACT
66 TTAAAAACT
* *
3997921 ATATAACATATATATTTTCAAAAATGTTTTGAAAACTATATATTATATTAATTTTCAAAATGTTT
1 ATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATTAATTTTCAAAATGTTT
3997986 TTAAAAACT
66 TTAAAAACT
* * * *
3997995 ATATAATATATAAATGTTTTCAAACATGTTTTTAAAACTATATATTATATATACATTTTAAAAAT
1 ATATAATATAT--ATATTTTCAAAAATGTTTTAAAAACTATATATTATAT-TA-ATTTTCAAAAT
*
3998060 G-TTTT-CAAACT
62 GTTTTTAAAAACT
* *
3998071 GTATACTATATATAT
1 ATATAATATATATAT
3998086 ATATATGTAA
Statistics
Matches: 208, Mismatches: 17, Indels: 21
0.85 0.07 0.09
Matches are distributed among these distances:
65 10 0.05
66 12 0.06
67 14 0.07
68 4 0.02
69 1 0.00
71 4 0.02
72 6 0.03
73 4 0.02
74 88 0.42
76 48 0.23
77 6 0.03
78 11 0.05
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (74 bp):
ATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATTAATTTTCAAAATGTTT
TTAAAAACT
Found at i:3998685 original size:84 final size:84
Alignment explanation
Indices: 3998569--3999769 Score: 1223
Period size: 84 Copynumber: 14.5 Consensus size: 84
3998559 TCGAGGGTCT
* * * * *
3998569 TTGGCATATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGTAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGT
3998634 CGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * * * *
3998653 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGTCTTGGAGATTAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGT
*
3998718 TGAACTCGAAGGTC-TTGG
66 CGAACTCGAAGGTCTTTGG
* * * * * ** * * *
3998736 -TGACATATAACCCATCTAG-CATTGAGTTATATTGTAAATGATGTGCCCTCGAAGCTGAGTGTA
1 TTGGCAGATAACCCTTCTCGAC-TTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTA
*
3998799 ATCGAACTC-AAGGGTC--T--
64 GTCGAACTCGAA-GGTCTTTGG
* * * * * *
3998816 TTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGTCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAG
* *
3998881 TCGAACTCGAGGGTC----A
65 TCGAACTCGAAGGTCTTTGG
* * * * *
3998897 TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGTTGAGTGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGT
* *
3998962 CGAACTTGAAGGTATTTGG
66 CGAACTCGAAGGTCTTTGG
* * *
3998981 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCCGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGT
*
3999046 CAAACTCGAAGGTCTTTTGG
66 CGAACTCGAAGGTC-TTTGG
* * * * ** * *
3999066 TT-ACAGATAACCCTTCTAGTCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGCGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAG
3999130 TCGAACTCGAAGGTC--T--
65 TCGAACTCGAAGGTCTTTGG
** * **
3999146 TTGGCAGATAGTCCTTCTCGACTTAAGCTATGCTGCAAATGATGCACCTTTG-AGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAAGCTGAGCGTAG
* * *
3999210 TCAAAATTGAAGGTCTTTGG
65 TCGAACTCGAAGGTCTTTGG
* * * * * *
3999230 TTGGAAGATAACCATTCTCGCCTTAAGTTATACTACAAATGATGTGCCCTCG-AGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAG
*
3999294 TCAAACTCGAAGGTCTTTGG
65 TCGAACTCGAAGGTCTTTGG
* * * *
3999314 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATAATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGT
* *
3999379 CAAACTCGAAGGTCTTTTG
66 CGAACTCGAAGGTCTTTGG
* * * * * * * * * *
3999398 TTGACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTCCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT-GCCTTGAAGCTGAGCGTAG
*
3999463 TCGAACTCGATGGTCTTTGG
65 TCGAACTCGAAGGTCTTTGG
* * * *
3999483 -T---AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTACCTTG-AGTTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGT
3999543 CGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * * * *
3999562 TTGGTAGATAACCCTTCTCGACTTAAGTTATGCTACAAATAATATGACTT-AGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGA-AGCTGAGCGTAG
*
3999626 TCGAACTCGAAGGT-TTTTG
65 TCGAACTCGAAGGTCTTTGG
* * * * *
3999645 TATGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGTAAATGTTGTGCCTTTG-AGCTGAGCGTA
1 T-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAAGCTGAGCGTA
3999709 GTCGAACTCGAAGGTCTTTGG
64 GTCGAACTCGAAGGTCTTTGG
* *
3999730 TCGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
3999770 AGTTTCTTAA
Statistics
Matches: 921, Mismatches: 164, Indels: 64
0.80 0.14 0.06
Matches are distributed among these distances:
79 28 0.03
80 58 0.06
81 174 0.19
82 41 0.04
83 73 0.08
84 472 0.51
85 75 0.08
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGG
Found at i:3999152 original size:249 final size:248
Alignment explanation
Indices: 3998569--3999769 Score: 1244
Period size: 249 Copynumber: 4.8 Consensus size: 248
3998559 TCGAGGGTCT
* * * * * * *
3998569 TTGGCATATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGTAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTCGAAGCTGAGCGTAGT
* * *
3998634 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
66 CGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
* * * * * * * * *
3998699 TCTTGGAGATTAGCGTAGTTGAACTCGAAGGTC-TTGG-TGACATATAACCCATCTAG-CATTGA
127 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAC-TTAA
* * * * * * *
3998761 GTTATATTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC-AAGGGTC--T--
191 GTTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCAAACTCGAA-GGTCTTTGG
* * * * * *
3998816 TTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGTCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTG-CCTCGAAGCTGAGCGTAG
* *
3998881 TCGAACTCGAGGGTCATTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCT
65 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCT
* * * *
3998946 TGGAGTTGAGTGTAGTCGAACTTGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
130 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
* * *
3999011 TGCTGCAAATGATATGCCTTGGAGCCGAGCGTAGTCAAACTCGAAGGTCTTTTGG
195 TACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC-TTTGG
* * * * * *
3999066 TT-ACAGATAACCCTTCTAGTCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGCGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTG-CCTCGAAGCTGAGCGTAG
* * * **
3999130 TCGAACTCGAAGGTCTTTGGCAGATAGTCCTTCTCGACTTAAGCTATGCTGCAAATGATGCACCT
65 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCT
* * * * * * *
3999195 TTGAGCTGAGCGTAGTCAAAATTGAAGGTCTTTGGTTGGAAGATAACCATTCTCGCCTTAAGTTA
130 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTA
* * *
3999260 TACTACAAATGATGTGCCCTCGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGG
195 TACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGG
** * * * *
3999314 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATAATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTCGAAGCTGAGCGTAGT
* * * * * *
3999379 CAAACTCGAAGGTCTTTTGTTGACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTC
66 CGAACTCGAAGGTC-TTTG--G-CAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGT-
* * * * * * *
3999444 CCCTCGAAGCTGAGTGTAATCGAACTCGATGGTCTTTGG-T---AGATAGCCCTTCTCGACTTAA
126 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA
* * * * *
3999505 GCTATGCTGCAAATGATGTACCTT-GAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGG
191 GTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGG
* * * * *
3999562 TTGGTAGATAACCCTTCTCGACTTAAGTTATGCTACAAATAATATGACT-TAGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTCGA-AGCTGAGCGTAG
* * * *
3999626 TCGAACTCGAAGGTTTTTGTATGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGTAAATGTTGT
65 TCGAACTCGAAGG--TCT-T-TGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
* *
3999691 GCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCGGCAGATAACCCTTCTCGACTTAA
126 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAA
3999756 GTTATACTGCAAAT
191 GTTATACTGCAAAT
3999770 AGTTTCTTAA
Statistics
Matches: 798, Mismatches: 131, Indels: 46
0.82 0.13 0.05
Matches are distributed among these distances:
244 69 0.09
245 28 0.04
246 36 0.05
247 78 0.10
248 198 0.25
249 288 0.36
250 4 0.01
251 35 0.04
252 33 0.04
253 29 0.04
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (248 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCTCGAAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTT
GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
ACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGG
Found at i:3999387 original size:333 final size:330
Alignment explanation
Indices: 3998580--3999747 Score: 1560
Period size: 333 Copynumber: 3.5 Consensus size: 330
3998570 TGGCATATAG
* * * *
3998580 CCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGTAGCTGAGCGTAGTCGAACTCGAA
1 CCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCCTAG-AGCTGAGCGTAGTCGAACTCGAA
* *
3998644 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGTCTTGGAGAT
65 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCT
* ** * * **
3998709 TAGCGTAGTTGAACTCGAAGGTC-TTGGTGACATATAACCCATCTAGCATTGAGTTATATTGTAA
130 GAGCGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGC-TTGAGTTATGCTGTAA
*
3998773 ATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC-AAGGGTCTTTGGCAGATAGCCCTTCTTGA
194 ATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAA-GGTCTTTGGCAGATAGCCCTTCTCGA
** * * * * *
3998837 CTTAAGCTATGCTGCAAATGATGTGTCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC----AT
258 CTTAAGCTATGCTGCAAATGATG-CACCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
* *
3998898 TGGCAGATAG
321 TGGAAGATAA
** * * * * *
3998908 CCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGTTGAGTGTAGTCGAACTTGAAG
1 CCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCCTAGAGCTGAGCGTAGTCGAACTCGAAG
* *
3998973 GTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCCG
66 GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTG
* *
3999038 AGCGTAGTCAAACTCGAAGGTCTTTTGGTTACAGATAACCCTTCTAGTCTTGAGTTATGCTATAA
131 AGCGTAGTCAAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAG-CTTGAGTTATGCTGTAA
* *
3999103 ATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAGTCCTTCTCGAC
194 ATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGAC
* * *
3999168 TTAAGCTATGCTGCAAATGATGCACCTTTGAGCTGAGCGTAGTCAAAATTGAAGGTCTTTGGTTG
259 TTAAGCTATGCTGCAAATGATGCACC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
3999233 GAAGATAA
323 GAAGATAA
* * * * *
3999241 CCATTCTCGCCTTAAGTTATACTACAAATGATGTGCCCTCGAGCTGAGCGTAGTCAAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCCTAGAGCTGAGCGTAGTCGAACTCGAAG
* *
3999306 GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATAATATGCCTTGGAGCTG
66 GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTG
* *
3999371 AGCGTAGTCAAACTCGAAGGTCTTTTGTTGACATATAACCCTTCTAGCCTTGAGTTATGCTGTAA
131 AGCGTAGTCAAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAG-CTTGAGTTATGCTGTAA
* * *
3999436 ATGATGTCCCCTCGAAGCTGAGTGTAATCGAACTCGATGGTCTTTGGTAGATAGCCCTTCTCGAC
194 ATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGAC
* *
3999501 TTAAGCTATGCTGCAAATGATGTACCTTGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
259 TTAAGCTATGCTGCAAATGATGCACCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
*
3999566 TAGATAA
324 AAGATAA
* * * *
3999573 CCCTTCTCGACTTAAGTTATGCTACAAATAATATGACTTAGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCCTAGAGCTGAGCGTAGTCGAACTCGAAG
* * * * * * * *
3999638 GT-TTTTGTATGGCAGATAGCCCTTCTCGATTTAAGCTATGCTGTAAATGTTGTGCCTTTGAGCT
66 GTCTTTGGT-TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCT
* *
3999702 GAGCGTAGTCGAACTCGAAGGTCTTTGGTCGGCAGATAACCCTTCT
130 GAGCGTAGTCAAACTCGAAGGTCTTTGGT-GACAGATAACCCTTCT
3999748 CGACTTAAGT
Statistics
Matches: 740, Mismatches: 88, Indels: 20
0.87 0.10 0.02
Matches are distributed among these distances:
328 133 0.18
329 26 0.04
330 116 0.16
331 13 0.02
332 183 0.25
333 269 0.36
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (330 bp):
CCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCCTAGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTG
AGCGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCTTGAGTTATGCTGTAAAT
GATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTT
AAGCTATGCTGCAAATGATGCACCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAA
GATAA
Found at i:4004603 original size:15 final size:14
Alignment explanation
Indices: 4004525--4004628 Score: 57
Period size: 15 Copynumber: 6.9 Consensus size: 14
4004515 AGAAAGTTAG
4004525 ATAAA-AAATAATAA
1 ATAAATAAATAA-AA
* *
4004539 ACAAATAAATAATA
1 ATAAATAAATAAAA
*
4004553 ATAATATTAATTAACATA
1 ATAA-A-TAAATAA-A-A
** *
4004571 ATAAATCAAAGGAGA
1 ATAAAT-AAATAAAA
4004586 ATAAATAAGATAAAA
1 ATAAATAA-ATAAAA
*
4004601 ATAAAATAAATAAAT
1 AT-AAATAAATAAAA
*
4004616 ATAGATAAATAAA
1 ATAAATAAATAAA
4004629 GGGAAAAACG
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
14 20 0.29
15 26 0.38
16 13 0.19
17 4 0.06
18 5 0.07
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (14 bp):
ATAAATAAATAAAA
Found at i:4004725 original size:25 final size:23
Alignment explanation
Indices: 4004696--4004751 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
4004686 TAGAAAAACC
*
4004696 AAAAAAACAATAAAATAACAAAAT
1 AAAAAAAAAATAAAATAA-AAAAT
* * *
4004720 ACAAAAATAATTAAAATAATAAAT
1 A-AAAAAAAAATAAAATAAAAAAT
4004744 AAAAAAAA
1 AAAAAAAA
4004752 TTAAAAAGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 6 0.23
24 6 0.23
25 14 0.54
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (23 bp):
AAAAAAAAAATAAAATAAAAAAT
Found at i:4004768 original size:24 final size:24
Alignment explanation
Indices: 4004698--4004757 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
4004688 GAAAAACCAA
* *
4004698 AAAAACAA-TAAAATAACAAAATAC
1 AAAAATAATTAAAATAA-TAAATAC
4004722 AAAAATAATTAAAATAATAAATA-
1 AAAAATAATTAAAATAATAAATAC
4004745 AAAAA-AATTAAAA
1 AAAAATAATTAAAA
4004758 AGTATATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 8 0.24
23 5 0.15
24 12 0.36
25 8 0.24
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (24 bp):
AAAAATAATTAAAATAATAAATAC
Found at i:4006014 original size:23 final size:22
Alignment explanation
Indices: 4005971--4006014 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
4005961 ATATATTATA
4005971 TATATAAAATATTTTCCTAAACC
1 TATATAAAATATTTT-CTAAACC
4005994 TATATAATATATATTTT-TAAA
1 TATATAA-A-ATATTTTCTAAA
4006015 AATATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
24 1 0.05
25 7 0.37
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (22 bp):
TATATAAAATATTTTCTAAACC
Found at i:4006015 original size:36 final size:35
Alignment explanation
Indices: 4005988--4006147 Score: 95
Period size: 34 Copynumber: 4.6 Consensus size: 35
4005978 AATATTTTCC
*
4005988 TAAACCTATATAATATATAT-TTTTAAAAATATTT
1 TAAAACTATATAATATATATATTTTAAAAATATTT
* *
4006022 TAAAATTATATAATATATATATTTTTTTAAAAATGTTT
1 TAAAACTATATAATATATATA---TTTTAAAAATATTT
* * * *
4006060 TCAAA--AT-T-ATATA-GT-TTTCAAAAATGTTTT
1 TAAAACTATATAATATATATATTTTAAAAAT-ATTT
* * *
4006090 TAAAACTATA-GAT-TATATGTTTTCAAAATGATTT
1 TAAAACTATATAATATATATATTTTAAAAAT-ATTT
*
4006124 CAAAACTATAATATATATATATAT
1 TAAAACTAT-ATA-ATATATATAT
4006148 ATATTTTCAA
Statistics
Matches: 96, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
29 9 0.09
30 7 0.07
32 4 0.04
33 4 0.04
34 43 0.45
35 2 0.02
36 2 0.02
37 2 0.02
38 23 0.24
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (35 bp):
TAAAACTATATAATATATATATTTTAAAAATATTT
Found at i:4006051 original size:38 final size:40
Alignment explanation
Indices: 4005995--4006072 Score: 124
Period size: 38 Copynumber: 2.0 Consensus size: 40
4005985 TCCTAAACCT
4005995 ATATAATATATATTTTTAAAAATATTTT-AAAATTATATA
1 ATATAATATATATTTTTAAAAATATTTTCAAAATTATATA
* *
4006034 ATAT-ATATATTTTTTTAAAAATGTTTTCAAAATTATATA
1 ATATAATATATATTTTTAAAAATATTTTCAAAATTATATA
4006073 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 21 0.58
39 15 0.42
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (40 bp):
ATATAATATATATTTTTAAAAATATTTTCAAAATTATATA
Found at i:4006129 original size:34 final size:35
Alignment explanation
Indices: 4006064--4006142 Score: 108
Period size: 34 Copynumber: 2.3 Consensus size: 35
4006054 ATGTTTTCAA
* *
4006064 AATTATATAGTTTTCAAAAATGTTTTTAAAACTAT
1 AATTATATAGTTTTCAAAAATGATTTCAAAACTAT
4006099 AGATTATAT-GTTTTC-AAAATGATTTCAAAACTAT
1 A-ATTATATAGTTTTCAAAAATGATTTCAAAACTAT
4006133 AATATATATA
1 AAT-TATATA
4006143 TATATATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
33 2 0.05
34 23 0.59
35 7 0.18
36 7 0.18
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (35 bp):
AATTATATAGTTTTCAAAAATGATTTCAAAACTAT
Found at i:4006196 original size:29 final size:30
Alignment explanation
Indices: 4006143--4006208 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
4006133 AATATATATA
* *
4006143 TATATATATTTTCAAAATGTTTTTTAAAAGC
1 TATATATATTTTCAAAA-GTCTTTTAAAAAC
*
4006174 TATATATATTTTTAAAA-TCTTTTAAAAAC
1 TATATATATTTTCAAAAGTCTTTTAAAAAC
4006203 TATATA
1 TATATA
4006209 ATATATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 16 0.50
31 16 0.50
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (30 bp):
TATATATATTTTCAAAAGTCTTTTAAAAAC
Found at i:4006205 original size:73 final size:77
Alignment explanation
Indices: 4006067--4006226 Score: 206
Period size: 75 Copynumber: 2.1 Consensus size: 77
4006057 TTTTCAAAAT
* *
4006067 TATATAGTTTTCAAAAATGTTTTTAAAACTATAGATTATATGTTTTCAAAATGATTTCAAAAC-T
1 TATATA-TTTTCAAAAATGTTTTTAAAACTATA-ATTATATGTTTTCAAAATCATTTAAAAACAT
4006131 ATAATATATATATA
64 ATAATATATATATA
*
4006145 TATATATTTTC-AAAATGTTTTTTAAAAGCTAT-A-TATAT-TTTT-AAAATCTTTTAAAAACTA
1 TATATATTTTCAAAAATG-TTTTTAAAA-CTATAATTATATGTTTTCAAAATCATTTAAAAAC-A
4006205 TATAATATATATATA
63 TATAATATATATATA
4006220 TATATAT
1 TATATAT
4006227 ATATATATTT
Statistics
Matches: 75, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
73 13 0.17
74 4 0.05
75 27 0.36
76 7 0.09
77 14 0.19
78 10 0.13
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (77 bp):
TATATATTTTCAAAAATGTTTTTAAAACTATAATTATATGTTTTCAAAATCATTTAAAAACATAT
AATATATATATA
Found at i:4006214 original size:2 final size:2
Alignment explanation
Indices: 4006203--4006234 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4006193 TTTTAAAAAC
4006203 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4006235 TTTTTCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4006214 original size:107 final size:102
Alignment explanation
Indices: 4005993--4006215 Score: 245
Period size: 107 Copynumber: 2.1 Consensus size: 102
4005983 TTTCCTAAAC
* * * *
4005993 CTATATAATATATATTTTTAAAAATATTTTAAAATTATATAATATATATATTTTTTTAAAAATGT
1 CTATATAATATATAGTTTTAAAAATATTTCAAAACTATATAATATATATATTATTTTAAAAATGT
* *
4006058 TTTCAAAATTATATAGTTTTCAAAAATGTTTTTAAAA
66 TTTCAAAATTATATAGTTTTCAAAAATCTTTTAAAAA
* * * *
4006095 CTATAGATTATAT-GTTTTCAAAATGATTTCAAAACTATAATATATATATATATATATTTTCAAA
1 CTATATAATATATAGTTTTAAAAAT-ATTTCAAAACTAT-ATA-ATATATATAT-TATTTTAAAA
* *
4006159 ATGTTTTTTAAAAGCTATATATA-TTTT-TAAAATCTTTTAAAAA
62 ATG-TTTTCAAAA--T-TATATAGTTTTCAAAAATCTTTTAAAAA
4006202 CTATATAATATATA
1 CTATATAATATATA
4006216 TATATATATA
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
101 9 0.09
102 22 0.22
103 3 0.03
104 10 0.10
105 11 0.11
106 8 0.08
107 24 0.24
108 5 0.05
109 6 0.06
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (102 bp):
CTATATAATATATAGTTTTAAAAATATTTCAAAACTATATAATATATATATTATTTTAAAAATGT
TTTCAAAATTATATAGTTTTCAAAAATCTTTTAAAAA
Found at i:4006251 original size:162 final size:168
Alignment explanation
Indices: 4006074--4006385 Score: 412
Period size: 163 Copynumber: 1.9 Consensus size: 168
4006064 AATTATATAG
* *
4006074 TTTTCAAAAATGTTTTTAAAA-CTATAGATTATA-T-GTTTTCAAAATG-ATTTCAAAACTATAA
1 TTTTCAAAAATG-TTTTAAAATCTATAGATTATATTAATTTTCAAAATGTATTTAAAAACTAT-A
* * *
4006135 TATATATATATATATATTTTC-AAAATGTTTTTTAAAAGC-TATA-TATA-T-TTTT-AAAAT-C
64 TA-ATATATATATATATATTCAAAAAT-ATTTTGAAAA-CATATATTATATTATTTTCAAAATGC
4006193 TTTTAAAAACTATATAATATATATATATATATATATATATATT
126 TTTTAAAAACTATATAATATATATATATATATATATATATATT
* *
4006236 TTTTCAAAAATGTTTTAAAATCTATATATTATATTAATTTTCAAAATGTTTTTAAAAACTATATA
1 TTTTCAAAAATGTTTTAAAATCTATAGATTATATTAATTTTCAAAATGTATTTAAAAACTATATA
*
4006301 ATATATATATATATATTCAAAAATATTTTGAAAACTATATATTATATTAATTTTCAAAATGTTTT
66 ATATATATATATATATTCAAAAATATTTTGAAAAC-ATATATTATATT-ATTTTCAAAATGCTTT
4006366 TAAAAACTATATAATATATA
129 TAAAAACTATATAATATATA
4006386 AATGTTTTCA
Statistics
Matches: 129, Mismatches: 8, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
161 8 0.06
162 24 0.19
163 26 0.20
164 23 0.18
165 15 0.12
166 1 0.01
168 4 0.03
169 5 0.04
170 23 0.18
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (168 bp):
TTTTCAAAAATGTTTTAAAATCTATAGATTATATTAATTTTCAAAATGTATTTAAAAACTATATA
ATATATATATATATATTCAAAAATATTTTGAAAACATATATTATATTATTTTCAAAATGCTTTTA
AAAACTATATAATATATATATATATATATATATATATT
Found at i:4006277 original size:37 final size:36
Alignment explanation
Indices: 4006222--4006460 Score: 227
Period size: 37 Copynumber: 6.3 Consensus size: 36
4006212 TATATATATA
4006222 TATATATATATATT--TTTTCAAAAATGTTTTAAAATC
1 TATATAT-TATATTAATTTTCAAAAATGTTTTAAAA-C
4006258 TATATATTATATTAATTTTC-AAAATGTTTTTAAAAAC
1 TATATATTATATTAATTTTCAAAAATG-TTTT-AAAAC
* *
4006295 TATATAATATATATATATATATTCAAAAATATTTTGAAAAC
1 TATAT-AT-TATAT-TA-ATTTTCAAAAATGTTTT-AAAAC
4006336 TATATATTATATTAATTTTC-AAAATGTTTTTAAAAAC
1 TATATATTATATTAATTTTCAAAAATG-TTTT-AAAAC
* * *
4006373 TATATAATATATAAATGTTTTCAAACATGTTTTCAAAAC
1 TATATATTATATTAA--TTTTCAAAAATGTTTT-AAAAC
*
4006412 TATATATTATATATACATTTT-AAAAATGTTTTCAAAC
1 TATATATTATAT-TA-ATTTTCAAAAATGTTTTAAAAC
* *
4006449 TGTATACTATAT
1 TATATATTATAT
4006461 ATATATATGT
Statistics
Matches: 172, Mismatches: 16, Indels: 29
0.79 0.07 0.13
Matches are distributed among these distances:
35 6 0.03
36 18 0.10
37 56 0.33
38 18 0.10
39 39 0.23
40 10 0.06
41 20 0.12
42 5 0.03
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (36 bp):
TATATATTATATTAATTTTCAAAAATGTTTTAAAAC
Found at i:4006339 original size:78 final size:78
Alignment explanation
Indices: 4006067--4006468 Score: 356
Period size: 78 Copynumber: 5.1 Consensus size: 78
4006057 TTTTCAAAAT
* * * * *
4006067 TATATAGTTTTCAAAAATGTTTTTAAAACTATAGATTATA-T-GTTTTCAAAATG-ATTTCAAAA
1 TATATA-TTTTCAAAAATATTTTTAAAACTATATATTATATTAATTTTCAAAATGTTTTTAAAAA
4006129 CTATAATATATATATA
65 CTAT-ATA-ATATATA
* * * ** * *
4006145 TATATATTTTC-AAAATGTTTTTTAAAAGCTATATA-TATTTTTAAAATCTTTTAAAAACTATAT
1 TATATATTTTCAAAAAT-ATTTTTAAAA-CTATATATTA-TATT--AAT-TTTCAAAATGTTTTT
*
4006208 AATATA-TATATATATATATA
60 AA-AAACTATATA-ATATATA
*** *
4006228 TATATATTTTTTCAAAAATGTTTTAAAATCTATATATTATATTAATTTTCAAAATGTTTTTAAAA
1 TATATATTTTCAAAAATAT-TTTTAAAA-CTATATATTATATTAATTTTCAAAATGTTTTTAAAA
4006293 ACTATATAATATATA
64 ACTATATAATATATA
* *
4006308 TATATATATTCAAAAATATTTTGAAAACTATATATTATATTAATTTTCAAAATGTTTTTAAAAAC
1 TATATATTTTCAAAAATATTTTTAAAACTATATATTATATTAATTTTCAAAATGTTTTTAAAAAC
4006373 TATATAATATATA
66 TATATAATATATA
* * * * * *
4006386 -A-ATGTTTTCAAACATGTTTTCAAAACTATATATTATATATACATTTTAAAAATG-TTTT-CAA
1 TATATATTTTCAAAAATATTTTTAAAACTATATATTATAT-TA-ATTTTCAAAATGTTTTTAAAA
* *
4006447 ACTGTATACTATATA
64 ACTATATAATATATA
4006462 TATATAT
1 TATATAT
4006469 GTAAAAAAAA
Statistics
Matches: 268, Mismatches: 38, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
76 52 0.19
77 24 0.09
78 78 0.29
79 8 0.03
80 23 0.09
81 18 0.07
82 4 0.01
83 29 0.11
84 28 0.10
85 4 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (78 bp):
TATATATTTTCAAAAATATTTTTAAAACTATATATTATATTAATTTTCAAAATGTTTTTAAAAAC
TATATAATATATA
Found at i:4006461 original size:37 final size:39
Alignment explanation
Indices: 4006246--4006466 Score: 233
Period size: 37 Copynumber: 5.8 Consensus size: 39
4006236 TTTTCAAAAA
*
4006246 TGTTTTAAAATCTATATATTATAT-TA-ATTTTC-AAAA
1 TGTTTTAAAAACTATATATTATATATATATTTTCAAAAA
*
4006282 TGTTTTTAAAAACTATATAATATATATATATATATTCAAAAA
1 TG-TTTTAAAAACTATAT-AT-TATATATATATTTTCAAAAA
* *
4006324 TATTTTGAAAACTATATATTATAT-TA-ATTTTC-AAAA
1 TGTTTTAAAAACTATATATTATATATATATTTTCAAAAA
* * * *
4006360 TGTTTTTAAAAACTATATAATATATAAATGTTTTCAAACA
1 TG-TTTTAAAAACTATATATTATATATATATTTTCAAAAA
* *
4006400 TGTTTTCAAAACTATATATTATATATACATTTT-AAAAA
1 TGTTTTAAAAACTATATATTATATATATATTTTCAAAAA
* * *
4006438 TGTTTT-CAAACTGTATACTATATATATAT
1 TGTTTTAAAAACTATATATTATATATATAT
4006467 ATGTAAAAAA
Statistics
Matches: 154, Mismatches: 21, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
36 7 0.05
37 58 0.38
38 15 0.10
39 41 0.27
40 9 0.06
41 19 0.12
42 5 0.03
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (39 bp):
TGTTTTAAAAACTATATATTATATATATATTTTCAAAAA
Found at i:4006476 original size:39 final size:38
Alignment explanation
Indices: 4006241--4006476 Score: 137
Period size: 39 Copynumber: 6.1 Consensus size: 38
4006231 ATATTTTTTC
* *
4006241 AAAAATGTTTT-AAAATCTATATATTATAT-TA-ATTTT
1 AAAAATGTTTTCAAAA-CTATATATTATATATACATGTA
* * * * *
4006277 CAAAATGTTTTTAAAAACTATATAATATATATATATATATTC
1 AAAAATG-TTTTCAAAACTATAT-AT-TATATATACAT-GTA
* * * *
4006319 AAAAATATTTTGAAAACTATATATTATAT-TA-ATTTT
1 AAAAATGTTTTCAAAACTATATATTATATATACATGTA
* * * *
4006355 CAAAATGTTTTTAAAAACTATATA--ATATATAAATGTTTTC
1 AAAAATG-TTTTCAAAACTATATATTATATATACATG---TA
* * *
4006395 AAACATGTTTTCAAAACTATATATTATATATACATTTT
1 AAAAATGTTTTCAAAACTATATATTATATATACATGTA
* *
4006433 AAAAATGTTTTC-AAACTGTATACTATATATATATATGTA
1 AAAAATGTTTTCAAAACTATATA-T-TATATATACATGTA
4006472 AAAAA
1 AAAAA
4006477 AAGGGACAAA
Statistics
Matches: 161, Mismatches: 22, Indels: 31
0.75 0.10 0.14
Matches are distributed among these distances:
35 4 0.02
36 15 0.09
37 38 0.24
38 21 0.13
39 41 0.25
40 10 0.06
41 25 0.16
42 7 0.04
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (38 bp):
AAAAATGTTTTCAAAACTATATATTATATATACATGTA
Found at i:4008999 original size:3 final size:3
Alignment explanation
Indices: 4008987--4009035 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
4008977 CGAAAAAATG
4008987 TTA TTA -TA TTA TTA TT- TTA TTA TCTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
4009030 TTA TTA
1 TTA TTA
4009036 ATCTTATTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.14
3 34 0.81
4 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4009042 original size:12 final size:12
Alignment explanation
Indices: 4008993--4009049 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
4008983 AATGTTATTA
*
4008993 TATTATT-ATTT
1 TATTATTAATAT
4009004 TATTATCT-ATAT
1 TATTAT-TAATAT
*
4009016 TATTATTATTAT
1 TATTATTAATAT
*
4009028 TATTATTAATCT
1 TATTATTAATAT
*
4009040 TATTACTAAT
1 TATTATTAAT
4009050 TAATTACATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 7 0.18
12 32 0.82
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:4009138 original size:17 final size:17
Alignment explanation
Indices: 4009126--4009162 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4009116 CCCAACAGAC
4009126 CCAGATCAGCAACAGTA
1 CCAGATCAGCAACAGTA
* *
4009143 TCAGATCAGCAATAGTA
1 CCAGATCAGCAACAGTA
4009160 CCA
1 CCA
4009163 AGTCTCTCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (17 bp):
CCAGATCAGCAACAGTA
Found at i:4014082 original size:2 final size:2
Alignment explanation
Indices: 4014077--4014142 Score: 116
Period size: 2 Copynumber: 33.0 Consensus size: 2
4014067 TTAAACAATA
4014077 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4014118 AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT
4014143 TATTAAGTGA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 59 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4019998 original size:18 final size:18
Alignment explanation
Indices: 4019975--4020030 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
4019965 GAAAGTTTCA
4019975 TGGGTATTAGACTCGTTT
1 TGGGTATTAGACTCGTTT
* *
4019993 TGGGTATTACACTTGTTT
1 TGGGTATTAGACTCGTTT
* *
4020011 TGGGTATCAGACTCATTT
1 TGGGTATTAGACTCGTTT
4020029 TG
1 TG
4020031 TATAGCAGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.45
Consensus pattern (18 bp):
TGGGTATTAGACTCGTTT
Found at i:4020376 original size:2 final size:2
Alignment explanation
Indices: 4020296--4020356 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
4020286 TCACCCCGAT
4020296 TA TA T- TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4020336 TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
4020357 TTTTTATATT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4020911 original size:56 final size:56
Alignment explanation
Indices: 4020847--4020958 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
4020837 CCCTATGCTG
4020847 GGGTTATTGTACATTTACTTGGTTTTTTGAGTATTTATTTGTAGCAAGATGAAAGT
1 GGGTTATTGTACATTTACTTGGTTTTTTGAGTATTTATTTGTAGCAAGATGAAAGT
4020903 GGGTTATTGTACATTTACTTGGTTTTTTGAGTATTTATTTGTAGCAAGATGAAAGT
1 GGGTTATTGTACATTTACTTGGTTTTTTGAGTATTTATTTGTAGCAAGATGAAAGT
4020959 CTGGCTTGCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.46
Consensus pattern (56 bp):
GGGTTATTGTACATTTACTTGGTTTTTTGAGTATTTATTTGTAGCAAGATGAAAGT
Found at i:4021441 original size:18 final size:18
Alignment explanation
Indices: 4021420--4021456 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4021410 TATGATACCT
*
4021420 AAAACGAGTGTAAAACCC
1 AAAACGAGTCTAAAACCC
*
4021438 AAAACGAGTCTAATACCC
1 AAAACGAGTCTAAAACCC
4021456 A
1 A
4021457 TGAAACTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.24, G:0.14, T:0.14
Consensus pattern (18 bp):
AAAACGAGTCTAAAACCC
Found at i:4026221 original size:22 final size:21
Alignment explanation
Indices: 4026153--4026230 Score: 59
Period size: 22 Copynumber: 3.6 Consensus size: 21
4026143 CAATTCACGG
*
4026153 AAGTGCCTTAGCAGTGATACTA
1 AAGTG-CTTAGCACTGATACTA
* * **
4026175 AAGTG-TCTCGCACCGATACGG
1 AAGTGCT-TAGCACTGATACTA
*
4026196 AAGTGCATTTGCACTGATACTA
1 AAGTGC-TTAGCACTGATACTA
4026218 AAGTGTCTTAGCA
1 AAGTG-CTTAGCA
4026231 TTTCTGGTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 1 0.02
21 14 0.33
22 25 0.60
23 2 0.05
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (21 bp):
AAGTGCTTAGCACTGATACTA
Found at i:4034385 original size:21 final size:21
Alignment explanation
Indices: 4034361--4034403 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4034351 AATAAATATT
*
4034361 AAATTGTAT-TATATTAATAAA
1 AAATTGAATATATA-TAATAAA
4034382 AAATTGAATATATATAATAAA
1 AAATTGAATATATATAATAAA
4034403 A
1 A
4034404 CACTTAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
AAATTGAATATATATAATAAA
Found at i:4041823 original size:21 final size:20
Alignment explanation
Indices: 4041737--4041893 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
4041727 AAATGACCAA
**
4041737 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
4041756 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
4041776 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
4041796 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
4041817 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
4041837 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
4041857 ACAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
4041878 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
4041894 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:4041846 original size:41 final size:41
Alignment explanation
Indices: 4041796--4041893 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
4041786 AATCAGTTTC
* *
4041796 CAAAATCGCAACGCGATTCTT-GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGATT-TTACAAAATCGCAACGCGAATA-T
* **
4041837 CAAATTCGCATTGCGATTTTACAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTTACAAAATCGCAACGCGAATAT
*
4041878 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
4041894 ACACATAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 41 0.89
42 3 0.07
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (41 bp):
CAAAATCGCAACGCGATTTTACAAAATCGCAACGCGAATAT
Found at i:4041903 original size:20 final size:20
Alignment explanation
Indices: 4041880--4042053 Score: 118
Period size: 20 Copynumber: 8.7 Consensus size: 20
4041870 GCGAATATGA
4041880 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
4041900 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
4041920 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
4041940 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
4041960 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
4041980 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
4042000 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
4042020 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
4042041 AAATCGCAACGCG
1 AAATCGCAACGCG
4042054 ATATTTAAAG
Statistics
Matches: 126, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
19 2 0.02
20 107 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:4041907 original size:61 final size:61
Alignment explanation
Indices: 4041736--4041912 Score: 182
Period size: 61 Copynumber: 2.9 Consensus size: 61
4041726 AAAATGACCA
* * * *
4041736 ACAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCAGAATCGCAAAT-C-AGTTT
1 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGC-AATGCGAGTTT
* * * * ** * * *
4041795 CCAAAATCGCAACGCGATTCTTGAAAATCGCAATGCGATAGTCAAATTCGCATTGCGATTTT
1 ACAAAATCGCAACGCGAAT-ATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTTT
4041857 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAATGCG
1 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACA-AAATCGCAATGCG
4041913 TATCCGTAAA
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
59 16 0.17
60 5 0.05
61 51 0.55
62 21 0.23
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (61 bp):
ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTTT
Found at i:4041924 original size:40 final size:39
Alignment explanation
Indices: 4041860--4042054 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 39
4041850 CGATTTTACA
* ** *
4041860 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * * *
4041900 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
4041940 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* * ** *
4041980 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
4042020 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
4042055 TATTTAAAGC
Statistics
Matches: 127, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.74
41 32 0.25
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:4041945 original size:60 final size:60
Alignment explanation
Indices: 4041860--4042053 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
4041850 CGATTTTACA
* ** * *
4041860 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
4041920 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
4041980 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
4042041 AAATCGCAACGCG
1 AAATCGCAACGCG
4042054 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:4042475 original size:33 final size:33
Alignment explanation
Indices: 4042436--4042506 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
4042426 TTCACTTAGA
4042436 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
4042469 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
4042502 TTTCA
1 TTTCA
4042507 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:4042650 original size:21 final size:21
Alignment explanation
Indices: 4042586--4042660 Score: 100
Period size: 20 Copynumber: 3.7 Consensus size: 21
4042576 TGCAGAAGAG
*
4042586 TCGCAACGAGA-TAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
4042606 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
4042626 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
4042647 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
4042661 TCGCAAAGCG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 28 0.60
21 19 0.40
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:4042650 original size:41 final size:40
Alignment explanation
Indices: 4042585--4042661 Score: 136
Period size: 41 Copynumber: 1.9 Consensus size: 40
4042575 TTGCAGAAGA
*
4042585 GTCGCAACGAGATAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAAAATGAAAATCGCAACGAGAGAATGACT
4042625 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGA-AAATGAAAATCGCAACGAGAGAAT
4042662 CGCAAAGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 12 0.34
41 23 0.66
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.13
Consensus pattern (40 bp):
GTCGCAACGAGAAAATGAAAATCGCAACGAGAGAATGACT
Found at i:4042664 original size:14 final size:14
Alignment explanation
Indices: 4042645--4042701 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4042635 GAGAAATGAA
4042645 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4042659 AATCGCAAAGCGATATGAA
1 AATCGC-AA-CG--A-GAG
4042678 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4042692 AATCGCAACG
1 AATCGCAACG
4042702 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 8 0.22
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4042678 original size:33 final size:33
Alignment explanation
Indices: 4042640--4042704 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
4042630 AACGAGAGAA
4042640 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
*
4042673 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGA
4042705 AACCAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
Found at i:4042713 original size:33 final size:33
Alignment explanation
Indices: 4042643--4042717 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
4042633 GAGAGAAATG
* **
4042643 AAAATCGCAACGAGAGAATCGCAAAGCGATATG
1 AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
*
4042676 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
4042709 AAAATCGCA
1 AAAATCGCA
4042718 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
Found at i:4042735 original size:19 final size:19
Alignment explanation
Indices: 4042713--4042810 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
4042703 GAAACCAAAA
*
4042713 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4042732 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
4042746 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4042765 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
4042779 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4042798 TCGCGTTGCGATT
1 TCGCGTTGCGATT
4042811 CTCTCGTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
16 6 0.09
17 6 0.09
19 32 0.50
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4042754 original size:14 final size:14
Alignment explanation
Indices: 4042735--4042824 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
4042725 TTTCATTTCG
4042735 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4042749 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4042768 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4042782 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4042801 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4042815 CGTTGCGATT
1 CGTTGCGATT
4042825 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
16 6 0.10
17 6 0.10
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4042760 original size:33 final size:33
Alignment explanation
Indices: 4042718--4042832 Score: 230
Period size: 33 Copynumber: 3.5 Consensus size: 33
4042708 CAAAATCGCA
4042718 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
4042751 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
4042784 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
4042817 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
4042833 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:4044811 original size:93 final size:93
Alignment explanation
Indices: 4044518--4044891 Score: 718
Period size: 93 Copynumber: 4.1 Consensus size: 93
4044508 TAGATTGCTT
*
4044518 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4044583 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4044610 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4044674 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4044702 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4044767 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4044795 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4044860 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4044887 AGTAA
1 AGTAA
4044892 TGCAATCCAT
Statistics
Matches: 279, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 29 0.10
92 112 0.40
93 138 0.49
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:4044979 original size:19 final size:19
Alignment explanation
Indices: 4044939--4045067 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
4044929 TAGTTTACTT
* *
4044939 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
4044959 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
4044978 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
4044997 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
4045011 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
4045030 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
4045044 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
4045063 TCGCA
1 TCGCA
4045068 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:4045018 original size:33 final size:32
Alignment explanation
Indices: 4044975--4045067 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
4044965 CGCGAAACCA
**
4044975 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
4045007 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
4045040 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
4045068 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:4045065 original size:52 final size:52
Alignment explanation
Indices: 4044939--4045067 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
4044929 TAGTTTACTT
**
4044939 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
4044991 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
4045044 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
4045068 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:4047019 original size:14 final size:14
Alignment explanation
Indices: 4047000--4047036 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4046990 TGATTGTTTA
4047000 ATGATTTGTAAAAG
1 ATGATTTGTAAAAG
4047014 ATGATTTGTAAAAG
1 ATGATTTGTAAAAG
*
4047028 TTGATTTGT
1 ATGATTTGT
4047037 GTAATGATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (14 bp):
ATGATTTGTAAAAG
Found at i:4047151 original size:19 final size:17
Alignment explanation
Indices: 4047135--4047193 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 17
4047125 AAAAATGACT
4047135 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
4047154 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
4047168 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
4047185 A-CGCAATGC
1 ATCGCAATGC
4047194 TTCGCATTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 8 0.23
16 13 0.37
17 7 0.20
19 7 0.20
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:4047218 original size:19 final size:19
Alignment explanation
Indices: 4047194--4047369 Score: 211
Period size: 19 Copynumber: 10.0 Consensus size: 19
4047184 AACGCAATGC
4047194 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
4047213 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
4047229 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
4047246 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
4047265 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
4047281 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
4047298 TTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
4047317 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
4047333 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
4047350 TTCCGCATTGCGATTTTCAT
1 TT-CGCATTGCGATTTTCAT
4047370 GTTGGCTCAT
Statistics
Matches: 135, Mismatches: 6, Indels: 31
0.78 0.03 0.18
Matches are distributed among these distances:
14 18 0.13
16 21 0.16
17 19 0.14
18 2 0.01
19 62 0.46
20 13 0.10
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:4047237 original size:33 final size:33
Alignment explanation
Indices: 4047200--4047364 Score: 174
Period size: 33 Copynumber: 4.8 Consensus size: 33
4047190 ATGCTTCGCA
4047200 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
4047233 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
4047269 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
4047304 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
4047337 TTGCGATTTTCATTTCCGCATTGCGATT
1 TTGCGATTTTCATTT-CGCATTGCGATT
4047365 TTCATGTTGG
Statistics
Matches: 108, Mismatches: 12, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
31 9 0.08
32 5 0.05
33 51 0.47
34 12 0.11
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.07
39 3 0.03
40 9 0.08
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:4047272 original size:52 final size:52
Alignment explanation
Indices: 4047194--4047369 Score: 343
Period size: 52 Copynumber: 3.4 Consensus size: 52
4047184 AACGCAATGC
4047194 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
4047246 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
4047298 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
4047350 TTCCGCATTGCGATTTTCAT
1 TT-CGCATTGCGATTTTCAT
4047370 GTTGGCTCAT
Statistics
Matches: 123, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 106 0.86
53 17 0.14
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
Found at i:4048036 original size:20 final size:20
Alignment explanation
Indices: 4048008--4048217 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
4047998 AAATTTCAGT
* * *
4048008 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
4048028 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
4048048 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
4048068 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
4048088 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
4048108 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
** *
4048128 GTTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
4048148 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
4048168 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
4048188 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
4048208 GTTGCGATTT
1 GTTGCGATTT
4048218 TGGAAAATCG
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 161 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:4048234 original size:21 final size:20
Alignment explanation
Indices: 4048184--4048281 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
4048174 ATTTATGTGT
* * * *
4048184 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
4048204 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
4048225 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
4048245 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
4048266 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
4048282 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:4048276 original size:41 final size:41
Alignment explanation
Indices: 4048184--4048281 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
4048174 ATTTATGTGT
* * *
4048184 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
4048225 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
4048266 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
4048282 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 42 0.91
42 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:4049466 original size:29 final size:30
Alignment explanation
Indices: 4049432--4049495 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 30
4049422 TTGTTTTTTT
4049432 CTTAAAATTTTATAAGTTTAAATTTACC-C
1 CTTAAAATTTTATAAGTTTAAATTTACCTC
*
4049461 CTTAAAATTTTATAAGTTTAAGTTTACCTC
1 CTTAAAATTTTATAAGTTTAAATTTACCTC
4049491 CTTAA
1 CTTAA
4049496 CATAAAATCC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (30 bp):
CTTAAAATTTTATAAGTTTAAATTTACCTC
Found at i:4050395 original size:117 final size:117
Alignment explanation
Indices: 4050189--4050423 Score: 452
Period size: 117 Copynumber: 2.0 Consensus size: 117
4050179 TCGTGGGATC
4050189 GAGTCCCACGGAGGGCATTTCATAATTCGGAGGTCTTCTACGAAAGCTGCTCTCAACCTGGTGTT
1 GAGTCCCACGGAGGGCATTTCATAATTCGGAGGTCTTCTACGAAAGCTGCTCTCAACCTGGTGTT
*
4050254 GGGGGCAACCTACTATCTTACCTCCCCCTTATCCCATTACATATGGGAACAA
66 GGGGGCAACCTACTATCTTACCTCCCCCTTACCCCATTACATATGGGAACAA
*
4050306 GAGTCCCACGGAGGGCATTTCATAATTCGGAGGTCTTCTACGGAAGCTGCTCTCAACCTGGTGTT
1 GAGTCCCACGGAGGGCATTTCATAATTCGGAGGTCTTCTACGAAAGCTGCTCTCAACCTGGTGTT
4050371 GGGGGCAACCTACTATCTTACCTCCCCCTTACCCCATTACATATGGGAACAA
66 GGGGGCAACCTACTATCTTACCTCCCCCTTACCCCATTACATATGGGAACAA
4050423 G
1 G
4050424 GGACAGTAAT
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 116 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (117 bp):
GAGTCCCACGGAGGGCATTTCATAATTCGGAGGTCTTCTACGAAAGCTGCTCTCAACCTGGTGTT
GGGGGCAACCTACTATCTTACCTCCCCCTTACCCCATTACATATGGGAACAA
Found at i:4050596 original size:17 final size:18
Alignment explanation
Indices: 4050574--4050612 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
4050564 TTATCACTTT
4050574 TATTTATCTAT-TTTATA
1 TATTTATCTATATTTATA
* *
4050591 TATTTATTTATATTTTTA
1 TATTTATCTATATTTATA
4050609 TATT
1 TATT
4050613 ATTAATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTATCTATATTTATA
Found at i:4050596 original size:21 final size:21
Alignment explanation
Indices: 4050572--4050620 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
4050562 TCTTATCACT
*
4050572 TTTATTTATCTATTTTATA-TA
1 TTTATTTATAT-TTTTATATTA
4050593 TTTATTTATATTTTTATATTA
1 TTTATTTATATTTTTATATTA
*
4050614 TTAATTT
1 TTTATTT
4050621 GAAAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTATTTATATTTTTATATTA
Found at i:4050648 original size:2 final size:2
Alignment explanation
Indices: 4050643--4050702 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
4050633 TTTTTAGTTA
4050643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4050685 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
4050703 GATCTCATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4050811 original size:16 final size:15
Alignment explanation
Indices: 4050762--4050812 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
4050752 TCTAGATATA
*
4050762 TTTATATTTTTCT-T
1 TTTATATTTTACTAT
* *
4050776 TTTATTATTTTCCTAA
1 TTTA-TATTTTACTAT
4050792 TTTATATGTTTACTAT
1 TTTATAT-TTTACTAT
4050808 TTTAT
1 TTTAT
4050813 TTTATTATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 4 0.13
15 11 0.37
16 15 0.50
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTATATTTTACTAT
Found at i:4050846 original size:37 final size:37
Alignment explanation
Indices: 4050775--4050856 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 37
4050765 ATATTTTTCT
*
4050775 TTTTATTATTTTCCTAATTTATATGTTTACTATTTTA
1 TTTTATTATTTTCCTAATTTATATGTCTACTATTTTA
** *
4050812 TTTTATTATTCTTGGTAATTT-TAGTGTCTA-TATTTTC
1 TTTTATTATT-TTCCTAATTTATA-TGTCTACTATTTTA
4050849 TTTGTATT
1 TTT-TATT
4050857 TAATTTGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
37 21 0.55
38 17 0.45
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65
Consensus pattern (37 bp):
TTTTATTATTTTCCTAATTTATATGTCTACTATTTTA
Found at i:4055766 original size:21 final size:21
Alignment explanation
Indices: 4055705--4055760 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
4055695 CTTAGAGCAA
4055705 GATGACTCATCACACATATGT
1 GATGACTCATCACACATATGT
4055726 GATGACTCATCACACATATGT
1 GATGACTCATCACACATATGT
4055747 GATGACTCATCACA
1 GATGACTCATCACA
4055761 TGTATGGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (21 bp):
GATGACTCATCACACATATGT
Found at i:4058861 original size:23 final size:22
Alignment explanation
Indices: 4058826--4058881 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 22
4058816 ATGTTTTAGT
*
4058826 TATATGAATTGTATTACATG-AAG
1 TATATG-ATTGTA-TAAATGAAAG
4058849 TATATGATGTGTATAAATGACAAG
1 TATATGAT-TGTATAAATGA-AAG
4058873 TATATGATT
1 TATATGATT
4058882 ATAAGATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 7 0.24
23 11 0.38
24 11 0.38
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (22 bp):
TATATGATTGTATAAATGAAAG
Found at i:4059305 original size:21 final size:21
Alignment explanation
Indices: 4059283--4059323 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4059273 AAAGATGGGG
*
4059283 AACCGATTCCCCTGCTACAGGA
1 AACCGA-TACCCTGCTACAGGA
*
4059305 AATCGATACCCTGCTACAG
1 AACCGATACCCTGCTACAG
4059324 TACTGCTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (21 bp):
AACCGATACCCTGCTACAGGA
Found at i:4060395 original size:2 final size:2
Alignment explanation
Indices: 4060382--4060411 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
4060372 GTCTTATTCT
4060382 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
4060412 CATCTATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4061715 original size:17 final size:17
Alignment explanation
Indices: 4061685--4061719 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4061675 TTTTAAATGG
4061685 ATTTGATGAGTATTGAA
1 ATTTGATGAGTATTGAA
* *
4061702 ATTTGGTGATTATTGAA
1 ATTTGATGAGTATTGAA
4061719 A
1 A
4061720 CAAATGGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (17 bp):
ATTTGATGAGTATTGAA
Found at i:4064264 original size:21 final size:21
Alignment explanation
Indices: 4064216--4064275 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
4064206 GTCGAGGGAT
*
4064216 TATCAGTGGTCCTTCGAGAC-
1 TATCAGTGGTCCTTCGGGACA
*
4064236 -AT-AGTGGTCATTCGGGACA
1 TATCAGTGGTCCTTCGGGACA
4064255 TATCAGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGGGACA
4064276 AATATTCAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 14 0.41
19 2 0.06
20 2 0.06
21 16 0.47
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (21 bp):
TATCAGTGGTCCTTCGGGACA
Found at i:4067586 original size:14 final size:14
Alignment explanation
Indices: 4067563--4067597 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
4067553 TACAAATTAG
*
4067563 TTTAAGTATGTATA
1 TTTAAATATGTATA
4067577 TTTAAATATGTATA
1 TTTAAATATGTATA
4067591 TTTAAAT
1 TTTAAAT
4067598 GGAAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (14 bp):
TTTAAATATGTATA
Found at i:4068742 original size:24 final size:25
Alignment explanation
Indices: 4068702--4068751 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
4068692 ATCGAAGTGT
4068702 CGCGTAGAAATTTGTCCCGAAGGAC
1 CGCGTAGAAATTTGTCCCGAAGGAC
*
4068727 CGCGTAG-AATTTGTCCCTAAGGAC
1 CGCGTAGAAATTTGTCCCGAAGGAC
4068751 C
1 C
4068752 ACATATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (25 bp):
CGCGTAGAAATTTGTCCCGAAGGAC
Found at i:4068989 original size:30 final size:31
Alignment explanation
Indices: 4068940--4069010 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
4068930 ACATAATTTA
* *
4068940 TATCGCATAGACATATCA-TTTACATACCTT
1 TATCACATAAACATATCATTTTACATACCTT
* *
4068970 TATCACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATATCATTTTACATACCTT
*
4069001 TATCCCATAA
1 TATCACATAA
4069011 TTCACATAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 15 0.43
31 20 0.57
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (31 bp):
TATCACATAAACATATCATTTTACATACCTT
Found at i:4069163 original size:21 final size:21
Alignment explanation
Indices: 4069139--4069181 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4069129 TCATATTCGT
* *
4069139 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
4069160 TTGAATGGGTACCGATTTCCC
1 TTGAAGGGGTACCGATTCCCC
4069181 T
1 T
4069182 AGCCCATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:4070846 original size:12 final size:12
Alignment explanation
Indices: 4070829--4070871 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
4070819 CGAAATATTT
4070829 TACTGTTCACGG
1 TACTGTTCACGG
*
4070841 TACTGTTCA--T
1 TACTGTTCACGG
4070851 TACTGTTCACGG
1 TACTGTTCACGG
4070863 TACTGTTCA
1 TACTGTTCA
4070872 TTATTGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (12 bp):
TACTGTTCACGG
Found at i:4070856 original size:22 final size:22
Alignment explanation
Indices: 4070828--4070894 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
4070818 TCGAAATATT
4070828 TTACTGTTCACGGTACTGTTCA
1 TTACTGTTCACGGTACTGTTCA
4070850 TTACTGTTCACGGTACTGTTCA
1 TTACTGTTCACGGTACTGTTCA
* * *
4070872 TTATTGTTCACGATACTATTCA
1 TTACTGTTCACGGTACTGTTCA
4070894 T
1 T
4070895 ACCGTATAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (22 bp):
TTACTGTTCACGGTACTGTTCA
Found at i:4074271 original size:27 final size:27
Alignment explanation
Indices: 4074233--4074286 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
4074223 CTTAAGGAGT
4074233 GGTCATTCGGGACAAATACAGTACATA
1 GGTCATTCGGGACAAATACAGTACATA
*
4074260 GGTCCTTCGGGACAAATACAGTACATA
1 GGTCATTCGGGACAAATACAGTACATA
4074287 TGTATATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
GGTCATTCGGGACAAATACAGTACATA
Found at i:4077495 original size:21 final size:21
Alignment explanation
Indices: 4077469--4077510 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4077459 AACTTAAAAT
*
4077469 GTGCATCGATACACTGTTACA
1 GTGCATCGATACACTGCTACA
*
4077490 GTGCATCGATGCACTGCTACA
1 GTGCATCGATACACTGCTACA
4077511 ATAATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GTGCATCGATACACTGCTACA
Found at i:4078034 original size:44 final size:44
Alignment explanation
Indices: 4077903--4078180 Score: 405
Period size: 44 Copynumber: 6.3 Consensus size: 44
4077893 AATTTCTTAT
* * *
4077903 CAATATACATACCATTTAATCCATAATCTCGTAAGCTTATTTTAC
1 CAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTAC
* * ** *
4077948 CAATATACTTACAATTAAATCTTTAAGCTTGTAAGCTTATTTTAC
1 CAATATACTTACCATT-ATTCCATAAGCTCGTAAGCTTATTTTAC
4077993 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
4078037 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
4078081 CAATATACTTACTA-TAGTTTCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTA-TTCCATAAGCTCGTAAGCTTATTTTAC
* * *
4078125 CAATATACTTACTATAATTTCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
4078169 CAATATACTTAC
1 CAATATACTTAC
4078181 TATAATTTAC
Statistics
Matches: 216, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
43 2 0.01
44 162 0.75
45 52 0.24
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (44 bp):
CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:4078389 original size:59 final size:58
Alignment explanation
Indices: 4078317--4078763 Score: 253
Period size: 59 Copynumber: 7.6 Consensus size: 58
4078307 AGAATATCAT
* *
4078317 ATAC-TTAATATGATTTCCTTCTCATTTTAGCAAACTAAGTGCCCTATGCAAGAATCC
1 ATACATTAGTATGATTTCCTTATCATTTTAGCAAACTAAGTGCCCTATGCAAGAATCC
* * * * *
4078374 ATAACATTAGTATGA-TTCATTTACCATTTTTAGCATA-TGAAGTGCCCTATTCGAGAATCC
1 AT-ACATTAGTATGATTTC-CTTATCA-TTTTAGCAAACT-AAGTGCCCTATGCAAGAATCC
** * *
4078434 ATACCATTAGTATGA-CCCCTTTACCATTTTTAGCACA-TGAAGTGCCCTATATG-AA-AATCC
1 ATA-CATTAGTATGATTTCC-TTATCA-TTTTAGCAAACT-AAGTGCCC--TATGCAAGAATCC
* * ** * * * * **
4078494 ATACTATTAGTATGATTTCCTTATCCTTGTAGCACCCTTAGTG-CTTTTTCTGGAAATCC
1 ATAC-ATTAGTATGATTTCCTTATCATTTTAGCAAACTAAGTGCCCTATGCAAG-AATCC
* **
4078553 ATACACTTAGTATG-TTTCCCTTACCATTTTAGCACATA-TAA-TGCCCTAT-CTGGAAATCC
1 ATACA-TTAGTATGATTT-CCTTATCATTTTAGCA-A-ACTAAGTGCCCTATGCAAG-AATCC
* * * * *
4078612 ATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATG-GA-AATCC
1 ATACATT-AGTATGATTTCCTTATCATTTTAGCAAACTAAGTGC-CC-TATGCAAGAATCC
* * *
4078671 ATACACTGAGTATGATTTCCTTATCATTTTAG-AACACTTAGTGCACCATATG-AA-AATTC
1 ATACA-TTAGTATGATTTCCTTATCATTTTAGCAA-ACTAAGTGC-CC-TATGCAAGAATCC
*
4078730 ATACACTCAGTATGATTTCCTTATCATTTTAGCA
1 ATACA-TTAGTATGATTTCCTTATCATTTTAGCA
4078764 CATATAGTGC
Statistics
Matches: 311, Mismatches: 49, Indels: 57
0.75 0.12 0.14
Matches are distributed among these distances:
56 2 0.01
57 3 0.01
58 15 0.05
59 179 0.58
60 103 0.33
61 6 0.02
62 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (58 bp):
ATACATTAGTATGATTTCCTTATCATTTTAGCAAACTAAGTGCCCTATGCAAGAATCC
Found at i:4078408 original size:60 final size:60
Alignment explanation
Indices: 4078341--4078510 Score: 204
Period size: 60 Copynumber: 2.8 Consensus size: 60
4078331 TTCCTTCTCA
4078341 TTTTAGCAAACT-AAGTGCCCTATGCAAGAATCCATAACATTAGTATGATTCATTTACCAT
1 TTTTAGCAAA-TGAAGTGCCCTATGCAAGAATCCATAACATTAGTATGATTCATTTACCAT
* * * * ** *
4078401 TTTTAGCATATGAAGTGCCCTATTCGAGAATCCATACCATTAGTATGACCCCTTTACCAT
1 TTTTAGCAAATGAAGTGCCCTATGCAAGAATCCATAACATTAGTATGATTCATTTACCAT
*
4078461 TTTTAGCACATGAAGTGCCCTATATG-AA-AATCCAT-ACTATTAGTATGATT
1 TTTTAGCAAATGAAGTGCCC--TATGCAAGAATCCATAAC-ATTAGTATGATT
4078511 TCCTTATCCT
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 2 0.02
60 87 0.94
61 1 0.01
62 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (60 bp):
TTTTAGCAAATGAAGTGCCCTATGCAAGAATCCATAACATTAGTATGATTCATTTACCAT
Found at i:4078630 original size:118 final size:118
Alignment explanation
Indices: 4078429--4078765 Score: 373
Period size: 118 Copynumber: 2.8 Consensus size: 118
4078419 CCTATTCGAG
**
4078429 AATCCATAC-CATTAGTATG-ACCCCTTTACCATTTTTAGCACATGA-AGTGCCCTATATGAAAA
1 AATCCATACAC-TTAGTATGTTTCCC-TTACCA-TTTTAGCACAT-ATAGTGCCCTATATGAAAA
* * * * *** *
4078491 TCCATACTATT-AGTATGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTTTCTGGA
62 TCCATA-TATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGA
* * *
4078548 AATCCATACACTTAGTATGTTTCCCTTACCATTTTAGCACATATAATGCCCTATCTGGAAATCCA
1 AATCCATACACTTAGTATGTTTCCCTTACCATTTTAGCACATATAGTGCCCTATATGAAAATCCA
*
4078613 TATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGA
66 TATATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGA
* * *
4078666 AATCCATACACTGAGTATGATTT-CCTTATCATTTTAGAACACT-TAGTGCACC-ATATGAAAAT
1 AATCCATACACTTAGTATG-TTTCCCTTACCATTTTAGCACA-TATAGTGC-CCTATATGAAAAT
* * *
4078728 TCATACACTCAGTATGATTTCCTTATCATTTTAGCACA
63 CCATATATTCAGTATGATTTCCTTATCATTTTAGCACA
4078766 TATAGTGCCA
Statistics
Matches: 187, Mismatches: 24, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
117 5 0.03
118 149 0.80
119 29 0.16
120 4 0.02
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (118 bp):
AATCCATACACTTAGTATGTTTCCCTTACCATTTTAGCACATATAGTGCCCTATATGAAAATCCA
TATATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGA
Found at i:4078793 original size:59 final size:57
Alignment explanation
Indices: 4078461--4078774 Score: 299
Period size: 59 Copynumber: 5.3 Consensus size: 57
4078451 CCTTTACCAT
* * * *
4078461 TTTTAGCACATGAAGTGCCCTATATGAAAATCCATACTA-TTAGTATGATTTCCTTATCC
1 TTTTAGCACAT-TAGTGCCC-ATATGGAAATCCATAC-ACTCAGTATGATTTCCTTATCA
* * *** * * *
4078520 TTGTAGCACCCTTAGTGCTTTTTCTGGAAATCCATACACTTAGTATG-TTTCCCTTACCA
1 TTTTAGCA-CATTAGTGC-CCATATGGAAATCCATACACTCAGTATGATTT-CCTTATCA
* * * * *
4078579 TTTTAGCACATATAATGCCCTATCTGGAAATCCATATATTCAATATGATTTCCTTATCA
1 TTTTAGCACAT-TAGTGCCC-ATATGGAAATCCATACACTCAGTATGATTTCCTTATCA
* *
4078638 TTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTGAGTATGATTTCCTTATCA
1 TTTTAGCACA-TTAGTGC-CCATATGGAAATCCATACACTCAGTATGATTTCCTTATCA
* * *
4078697 TTTTAGAACACTTAGTGCACCATATGAAAATTCATACACTCAGTATGATTTCCTTATCA
1 TTTTAGCACA-TTAGTGC-CCATATGGAAATCCATACACTCAGTATGATTTCCTTATCA
4078756 TTTTAGCACATATAGTGCC
1 TTTTAGCACAT-TAGTGCC
4078775 ATTTGGTAAT
Statistics
Matches: 210, Mismatches: 35, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
58 8 0.04
59 194 0.92
60 8 0.04
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (57 bp):
TTTTAGCACATTAGTGCCCATATGGAAATCCATACACTCAGTATGATTTCCTTATCA
Found at i:4080287 original size:38 final size:37
Alignment explanation
Indices: 4080135--4080333 Score: 168
Period size: 37 Copynumber: 5.4 Consensus size: 37
4080125 CGTTCATATT
* * * * *
4080135 GTTTTTCTTGAAACAAAATTATGTCTCACTCAAGACA
1 GTTTCTCTTGAAACAAAATTTTATCTCACTCGAGATA
* * * ** *
4080172 ATTTCCCTTGAAATAATTTTTTTATCTCACTTGAGATA
1 GTTTCTCTTGAAACAA-AATTTTATCTCACTCGAGATA
* * * *
4080210 GTTT-TCTTTAAA-ACAAGTATCATCTCACTCGAGATA
1 GTTTCTCTTGAAACA-AAATTTTATCTCACTCGAGATA
* *
4080246 GTTTCTCCTGAAACAAAAGTTTTATCTCACTCGAGACA
1 GTTTCTCTTGAAACAAAA-TTTTATCTCACTCGAGATA
* * *
4080284 GTTTCTCTTGAAACAAAAATTTATCTCTCTTGAGATA
1 GTTTCTCTTGAAACAAAATTTTATCTCACTCGAGATA
*
4080321 TTTTCTCTTGAAA
1 GTTTCTCTTGAAA
4080334 ATACAGTTTC
Statistics
Matches: 126, Mismatches: 31, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
36 21 0.17
37 54 0.43
38 51 0.40
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (37 bp):
GTTTCTCTTGAAACAAAATTTTATCTCACTCGAGATA
Found at i:4080326 original size:37 final size:37
Alignment explanation
Indices: 4080192--4080333 Score: 153
Period size: 38 Copynumber: 3.8 Consensus size: 37
4080182 AAATAATTTT
* * * *
4080192 TTTATCTCACTTGAGATAGTTT-TCTTTAAA-ACAAG
1 TTTATCTCACTCGAGATAGTTTCTCTTGAAACAAAAA
* * *
4080227 TATCATCTCACTCGAGATAGTTTCTCCTGAAACAAAAGT
1 T-TTATCTCACTCGAGATAGTTTCTCTTGAAACAAAA-A
*
4080266 TTTATCTCACTCGAGACAGTTTCTCTTGAAACAAAAA
1 TTTATCTCACTCGAGATAGTTTCTCTTGAAACAAAAA
* * *
4080303 TTTATCTCTCTTGAGATATTTTCTCTTGAAA
1 TTTATCTCACTCGAGATAGTTTCTCTTGAAA
4080334 ATACAGTTTC
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
35 1 0.01
36 19 0.21
37 33 0.37
38 35 0.39
39 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (37 bp):
TTTATCTCACTCGAGATAGTTTCTCTTGAAACAAAAA
Found at i:4080342 original size:75 final size:74
Alignment explanation
Indices: 4080191--4080333 Score: 171
Period size: 75 Copynumber: 1.9 Consensus size: 74
4080181 GAAATAATTT
* * * * *
4080191 TTTTATCTCACTTGAGATAGTTTTCTTTAAAACAAGTATCATCTCACTCGAGATAGTTTCTCCTG
1 TTTTATCTCACTCGAGACAGTTTTCTTGAAAAAAAATATCATCTCACTCGAGATAGTTTCTCCTG
4080256 AAACAAAAG
66 AAACAAAAG
* * * * *
4080265 TTTTATCTCACTCGAGACAGTTTCTCTTGAAACAAAAAT-TTATCTCTCTTGAGATATTTTCTCT
1 TTTTATCTCACTCGAGACAGTTT-TCTTGAAA-AAAAATATCATCTCACTCGAGATAGTTTCTCC
4080329 TGAAA
64 TGAAA
4080334 ATACAGTTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
74 21 0.37
75 32 0.56
76 4 0.07
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (74 bp):
TTTTATCTCACTCGAGACAGTTTTCTTGAAAAAAAATATCATCTCACTCGAGATAGTTTCTCCTG
AAACAAAAG
Found at i:4087425 original size:21 final size:21
Alignment explanation
Indices: 4087387--4087426 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4087377 GGATCTTTGC
*
4087387 ATTATTTTAATATTATTTTTA
1 ATTATTTTAATATAATTTTTA
* *
4087408 ATTATTTTTATCTAATTTT
1 ATTATTTTAATATAATTTT
4087427 AATGAAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTATTTTAATATAATTTTTA
Found at i:4089434 original size:24 final size:21
Alignment explanation
Indices: 4089384--4089442 Score: 57
Period size: 24 Copynumber: 2.7 Consensus size: 21
4089374 TCCCCTTTGA
4089384 AGTGTATCGATACA-CACTAT
1 AGTGTATCGATACATCACTAT
* *
4089404 AGGGTATCGATACATCCCTTTACT
1 AGTGTATCGATACATCAC--TA-T
*
4089428 AGTGTATCGGTACAT
1 AGTGTATCGATACAT
4089443 TACCTATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 13 0.42
21 2 0.06
23 2 0.06
24 14 0.45
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (21 bp):
AGTGTATCGATACATCACTAT
Found at i:4092732 original size:18 final size:18
Alignment explanation
Indices: 4092705--4092775 Score: 108
Period size: 18 Copynumber: 3.9 Consensus size: 18
4092695 CCACTATGAA
*
4092705 ATGTCCCGAAGGACCACT
1 ATGTCTCGAAGGACCACT
*
4092723 ATGTCTCGAATGACCACT
1 ATGTCTCGAAGGACCACT
4092741 ATGT-TCCGAAGGACCACT
1 ATGTCT-CGAAGGACCACT
4092759 ATGTCTCGAAGGACCAC
1 ATGTCTCGAAGGACCAC
4092776 GTATAACCCT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
17 1 0.02
18 46 0.96
19 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (18 bp):
ATGTCTCGAAGGACCACT
Found at i:4092757 original size:36 final size:36
Alignment explanation
Indices: 4092705--4092775 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
4092695 CCACTATGAA
*
4092705 ATGTCCCGAAGGACCACTATGTCTCGAATGACCACT
1 ATGTCCCGAAGGACCACTATGTCTCGAAGGACCACT
*
4092741 ATGTTCCGAAGGACCACTATGTCTCGAAGGACCAC
1 ATGTCCCGAAGGACCACTATGTCTCGAAGGACCAC
4092776 GTATAACCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (36 bp):
ATGTCCCGAAGGACCACTATGTCTCGAAGGACCACT
Found at i:4095595 original size:13 final size:13
Alignment explanation
Indices: 4095577--4095602 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4095567 ATATTTTTGA
4095577 ACAGTCTTCATAT
1 ACAGTCTTCATAT
4095590 ACAGTCTTCATAT
1 ACAGTCTTCATAT
4095603 GTGCTTCTGT
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAGTCTTCATAT
Found at i:4100714 original size:12 final size:13
Alignment explanation
Indices: 4100697--4100763 Score: 73
Period size: 15 Copynumber: 4.9 Consensus size: 13
4100687 TGCAAACATG
*
4100697 TAATAACAA-AAT
1 TAATAATAATAAT
4100709 TAATAATAATAAT
1 TAATAATAATAAT
4100722 AATAATAATAATAAT
1 --TAATAATAATAAT
*
4100737 TAATAATAATTAT
1 TAATAATAATAAT
4100750 TATTATAATAATAA
1 TA--ATAATAATAA
4100764 AAAATTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
12 8 0.17
13 17 0.36
15 22 0.47
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:4100717 original size:3 final size:3
Alignment explanation
Indices: 4100709--4100763 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
4100699 ATAACAAAAT
* * *
4100709 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TAA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
4100755 TAA TAA TAA
1 TAA TAA TAA
4100764 AAAATTAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:4100739 original size:28 final size:28
Alignment explanation
Indices: 4100697--4100763 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
4100687 TGCAAACATG
*
4100697 TAATAACAA-AATTAATAATAATAATAA
1 TAATAATAATAATTAATAATAATAATAA
* *
4100724 TAATAATAATAATTAATAATAATTATTA
1 TAATAATAATAATTAATAATAATAATAA
*
4100752 TTATAATAATAA
1 TAATAATAATAA
4100764 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
27 8 0.23
28 27 0.77
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (28 bp):
TAATAATAATAATTAATAATAATAATAA
Found at i:4100746 original size:25 final size:25
Alignment explanation
Indices: 4100712--4100761 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4100702 ACAAAATTAA
4100712 TAATAATAATAATAATAATAATAAT
1 TAATAATAATAATAATAATAATAAT
* * *
4100737 TAATAATAATTATTATTATAATAAT
1 TAATAATAATAATAATAATAATAAT
4100762 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAATAATAATAATAATAATAATAAT
Found at i:4101237 original size:135 final size:135
Alignment explanation
Indices: 4100958--4101283 Score: 415
Period size: 135 Copynumber: 2.4 Consensus size: 135
4100948 GTTCGGGTCG
* ** * * * * ** * *
4100958 TCTAAGGGTGACACGAATCCTACTTGATGAGGATATTTGGTCGGGGGATGACACTACTTATACGT
1 TCTATGGGTGACACGGCTCCTACGTGATGAGGATGTCTGGTCAGGGGATGACACGGCTCATACGC
* ** * *
4101023 GATGAAGAGTTCTTGGCCATCTTTAGAAATGGTGATAATTGAGTTCCTACGCGATGAGGATTATT
66 GATGAAGAGTTCTTGGCCATCTTTAGAAATGATGATAAACGAGTTCCTACGCGATGAGGATAACT
4101088 GGTTA
131 GGTTA
*
4101093 TCTATGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACGGCTCATACGC
1 TCTATGGGTGACACGGCTCCTACGTGATGAGGATGTCTGGTCAGGGGATGACACGGCTCATACGC
* *
4101158 GATGAAGAGTTC-TGGCCATCTTTAGGAGA-GATGATAACACG-GTTCCTACGTGATGAGGATAA
66 GATGAAGAGTTCTTGGCCATCTTTA-GAAATGATGATAA-ACGAGTTCCTACGCGATGAGGATAA
4101220 CTGGTTA
129 CTGGTTA
* *
4101227 TCTATGGGGTGACACGGCTCCTACGTGATGAGGATGTCTAGTTAGGGGATGACACGG
1 TCTAT-GGGTGACACGGCTCCTACGTGATGAGGATGTCTGGTCAGGGGATGACACGG
4101284 TTCCTACATG
Statistics
Matches: 166, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
134 49 0.30
135 117 0.70
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (135 bp):
TCTATGGGTGACACGGCTCCTACGTGATGAGGATGTCTGGTCAGGGGATGACACGGCTCATACGC
GATGAAGAGTTCTTGGCCATCTTTAGAAATGATGATAAACGAGTTCCTACGCGATGAGGATAACT
GGTTA
Found at i:4101366 original size:28 final size:28
Alignment explanation
Indices: 4101326--4101388 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
4101316 AGTTATTATG
** * *
4101326 GTTTCAAGGGAAACCGACTCAAATATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
4101354 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
4101382 GTTTCAA
1 GTTTCAA
4101389 GAAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:4101401 original size:26 final size:28
Alignment explanation
Indices: 4101326--4101403 Score: 72
Period size: 28 Copynumber: 2.9 Consensus size: 28
4101316 AGTTATTATG
** * * *
4101326 GTTTCAAGGGAAACCGACTCAAATATTT
1 GTTTCAAAAGAAACAGAATCAAAGATTT
*
4101354 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGAATCAAAGATTT
4101382 GTTTCAAGAA-AAA-A-AATCAAAG
1 GTTTCAA-AAGAAACAGAATCAAAG
4101404 GTGATGTGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
26 7 0.16
27 1 0.02
28 34 0.77
29 2 0.05
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.24
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGAATCAAAGATTT
Found at i:4101585 original size:32 final size:33
Alignment explanation
Indices: 4101538--4101635 Score: 90
Period size: 38 Copynumber: 2.8 Consensus size: 33
4101528 CAAAGATCGG
* * *
4101538 TGTTTCGAGAGAAACAAATTCAAAGATGTT-TT
1 TGTTTCAAGAAAAACAAACTCAAAGATGTTGTT
*
4101570 TGTTTCAAGAAAAACATACTCAAAGATTTTGTTTGTTT
1 TGTTTCAAGAAAAACAAACTCAAAGA---TG-TTG-TT
**
4101608 TGTTTCAAGGGAAACAAACTCAAAGATG
1 TGTTTCAAGAAAAACAAACTCAAAGATG
4101636 GTAAATTTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
32 22 0.42
35 4 0.08
36 2 0.04
38 25 0.47
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTTTCAAGAAAAACAAACTCAAAGATGTTGTT
Found at i:4101673 original size:74 final size:70
Alignment explanation
Indices: 4101538--4101673 Score: 166
Period size: 74 Copynumber: 1.9 Consensus size: 70
4101528 CAAAGATCGG
* * *
4101538 TGTTTCGAGAGAAACAAATTCAAAGATGTTTTTGTTTCAAGAAAAACATACTCAAAGATTTTGTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTTTTTGTTTCAAGAAAAACAAACTCAAAGATTTTGTT
4101603 TGTTT
66 TGTTT
* * *
4101608 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTTTGTTTCCAA-AGAAACAAACTCAAATATT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT---TTTTGTTT-CAAGAAAAACAAACTCAAAGATT
4101672 TT
61 TT
4101674 TCTCAAAGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
70 24 0.44
71 2 0.04
74 26 0.47
75 3 0.05
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (70 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTTTTTGTTTCAAGAAAAACAAACTCAAAGATTTTGTT
TGTTT
Found at i:4102003 original size:31 final size:31
Alignment explanation
Indices: 4101953--4102012 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
4101943 AAGGGAAACG
4101953 ACTCAAAGATAGTTTTATTTCAAGAGAAATAA
1 ACTCAAAGATA-TTTTATTTCAAGAGAAATAA
*
4101985 ACTCAAAGAT-TTTGTATTTCTAGAGAAA
1 ACTCAAAGATATTT-TATTTCAAGAGAAA
4102013 CTGCCTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.12
31 13 0.50
32 10 0.38
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (31 bp):
ACTCAAAGATATTTTATTTCAAGAGAAATAA
Done.