Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 26
Found at i:2431280 original size:38 final size:37
Alignment explanation
Indices: 2431237--2431573 Score: 202
Period size: 38 Copynumber: 8.8 Consensus size: 37
2431227 TATTTTTTTT
* *
2431237 AAAACTATATATTATACGTATTTTCAAAAACGTTTCAA
1 AAAACTATATATTATATGTATTTTCAAAAATGTTT-AA
* ** *
2431275 AAAACTATATAATATATGTATTTTTTAAAATGTTTTA
1 AAAACTATATATTATATGTATTTTCAAAAATGTTTAA
** *
2431312 AAAGTTATATATTATATATATTTTCAAAAATGTTTTTTTTTAA
1 AAAACTATATATTATATGTATTTTCAAAAATG------TTTAA
* * **
2431355 AAAATCATATAACATATAAATG--TTTTC-AAAATGTTTTC
1 AAAA-C-TAT-ATAT-TATATGTATTTTCAAAAATGTTTAA
** **
2431393 AAAACTATATATTATATAAATTTTCAAAAATGTTTTC
1 AAAACTATATATTATATGTATTTTCAAAAATGTTTAA
* *
2431430 AAAATTATATATTATATAAG-A-TTTCAAAAATGATTTTA
1 AAAACTATATATTATAT--GTATTTTCAAAAATG-TTTAA
* * * * * *
2431468 AAAATTATATATTATCTATATTTTCTAAAACGTTTTTTTA
1 AAAACTATATATTATATGTATTTTC-AAAA--ATGTTTAA
* *
2431508 AAAACTGTATATTATA--TAGTTTTCAAAAATGTTTTA
1 AAAACTATATATTATATGTA-TTTTCAAAAATGTTTAA
2431544 AAAACTATATATTATATACGTATTTTCAAA
1 AAAACTATATATTATAT--GTATTTTCAAA
2431574 GATCGGTTGC
Statistics
Matches: 237, Mismatches: 36, Indels: 51
0.73 0.11 0.16
Matches are distributed among these distances:
34 4 0.02
35 3 0.01
36 29 0.12
37 67 0.28
38 68 0.29
39 17 0.07
40 20 0.08
41 1 0.00
43 7 0.03
44 6 0.03
45 8 0.03
46 3 0.01
47 4 0.02
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (37 bp):
AAAACTATATATTATATGTATTTTCAAAAATGTTTAA
Found at i:2431328 original size:37 final size:37
Alignment explanation
Indices: 2431232--2431573 Score: 285
Period size: 37 Copynumber: 8.9 Consensus size: 37
2431222 AAATATATTT
* ** *
2431232 TTTTTAAAACTATATATTATACGTATTTTCAAAAACG
1 TTTTAAAAACTATATATTATATATATTTTCAAAAATG
* * * **
2431269 TTTCAAAAAACTATATAATATATGTATTTTTTAAAATG
1 TTT-TAAAAACTATATATTATATATATTTTCAAAAATG
**
2431307 TTTTAAAAGTTATATATTATATATATTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAAATG
* * * *
2431344 TTTTTTTTTAAAAAATCATATAACATATAAATGTTTTC-AAAATG
1 -----TTTTAAAAACT-ATAT-A-TTATATATATTTTCAAAAATG
* *
2431388 TTTTCAAAACTATATATTATATAAATTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAAATG
* * *
2431425 TTTTCAAAATTATATATTATATA-AGATTTCAAAAATG
1 TTTTAAAAACTATATATTATATATA-TTTTCAAAAATG
* * * *
2431462 ATTTTAAAAATTATATATTATCTATATTTTCTAAAACGTTT
1 -TTTTAAAAACTATATATTATATATATTTTC-AAAA--ATG
* *
2431503 TTTTAAAAACTGTATATTATATA-GTTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAAATG
2431539 TTTTAAAAACTATATATTATATACGTATTTTCAAA
1 TTTTAAAAACTATATATTATATA--TATTTTCAAA
2431574 GATCGGTTGC
Statistics
Matches: 246, Mismatches: 40, Indels: 36
0.76 0.12 0.11
Matches are distributed among these distances:
36 34 0.14
37 70 0.28
38 63 0.26
39 27 0.11
40 20 0.08
41 1 0.00
42 9 0.04
43 4 0.02
44 7 0.03
45 11 0.04
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.46
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAAATG
Found at i:2431388 original size:11 final size:11
Alignment explanation
Indices: 2431372--2431396 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2431362 TATAACATAT
2431372 AAATGTTTTCA
1 AAATGTTTTCA
2431383 AAATGTTTTCA
1 AAATGTTTTCA
2431394 AAA
1 AAA
2431397 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:2435136 original size:13 final size:11
Alignment explanation
Indices: 2435095--2435179 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
2435085 ACAATCTTTC
2435095 CATCACCATTAT
1 CATCACCA-TAT
*
2435107 CA-CGCCTATAT
1 CATCACC-ATAT
2435118 CATCACCATAGT
1 CATCACCATA-T
2435130 CCATCACCATTAT
1 -CATCACCA-TAT
*
2435143 CA-CGCCTATAT
1 CATCACC-ATAT
2435154 CATCACCATATT
1 CATCACCATA-T
2435166 CCATCACCATAT
1 -CATCACCATAT
2435178 CA
1 CA
2435180 CTCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:2435140 original size:36 final size:36
Alignment explanation
Indices: 2435093--2435196 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
2435083 ATACAATCTT
2435093 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
2435129 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
2435165 TCCATCACCA-TATCACTCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
2435197 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:2440842 original size:13 final size:11
Alignment explanation
Indices: 2440801--2440885 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
2440791 ACAATCTGTC
2440801 CATCACCATTAT
1 CATCACCA-TAT
*
2440813 CA-CGCCTATAT
1 CATCACC-ATAT
2440824 CATCACCATAGT
1 CATCACCATA-T
2440836 CCATCACCATTAT
1 -CATCACCA-TAT
*
2440849 CA-CGCCTATAT
1 CATCACC-ATAT
2440860 CATCACCATATT
1 CATCACCATA-T
2440872 CCATCACCATAT
1 -CATCACCATAT
2440884 CA
1 CA
2440886 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:2440845 original size:36 final size:36
Alignment explanation
Indices: 2440798--2440902 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
2440788 GATACAATCT
2440798 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
2440834 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
2440870 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
2440903 ACATATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:2455756 original size:24 final size:23
Alignment explanation
Indices: 2455720--2455765 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
2455710 GACAGGTTTA
2455720 ATTTTTTTTTTTTGCTAAATATC
1 ATTTTTTTTTTTTGCTAAATATC
*
2455743 ATTTTTTTTATTTTGGTAAATAT
1 ATTTTTTTT-TTTTGCTAAATAT
2455766 TTTTCTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (23 bp):
ATTTTTTTTTTTTGCTAAATATC
Found at i:2458706 original size:12 final size:12
Alignment explanation
Indices: 2458689--2458713 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2458679 TAGCATTAGC
2458689 AATATTCGCAGG
1 AATATTCGCAGG
2458701 AATATTCGCAGG
1 AATATTCGCAGG
2458713 A
1 A
2458714 TGGTGCAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (12 bp):
AATATTCGCAGG
Found at i:2459904 original size:13 final size:13
Alignment explanation
Indices: 2459888--2459935 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
2459878 CACAATGAGT
*
2459888 GTCATAAATGTGC
1 GTCATAAATGCGC
* *
2459901 GTCATAAATACGT
1 GTCATAAATGCGC
2459914 GTCATAAATGCGC
1 GTCATAAATGCGC
2459927 GTCATAAAT
1 GTCATAAAT
2459936 TCATGACGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:2459915 original size:26 final size:26
Alignment explanation
Indices: 2459886--2459935 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
2459876 CGCACAATGA
*
2459886 GTGTCATAAATGTGCGTCATAAATAC
1 GTGTCATAAATGCGCGTCATAAATAC
2459912 GTGTCATAAATGCGCGTCATAAAT
1 GTGTCATAAATGCGCGTCATAAAT
2459936 TCATGACGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (26 bp):
GTGTCATAAATGCGCGTCATAAATAC
Found at i:2465002 original size:16 final size:16
Alignment explanation
Indices: 2464981--2465014 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2464971 AACCCCTAAC
2464981 TTTATTTTAATGTAAT
1 TTTATTTTAATGTAAT
* *
2464997 TTTATTTTTATGTTAT
1 TTTATTTTAATGTAAT
2465013 TT
1 TT
2465015 AAATTTTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTATTTTAATGTAAT
Found at i:2465042 original size:15 final size:14
Alignment explanation
Indices: 2465024--2465080 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 14
2465014 TAAATTTTAT
2465024 CACTTTAATTTCCAA
1 CACTTTAATTT-CAA
2465039 CACTTTTTAATTTCAA
1 CAC--TTTAATTTCAA
*
2465055 CACTTTAATTTTCAG
1 CACTTTAA-TTTCAA
*
2465070 CAATTTAATTT
1 CACTTTAATTT
2465081 TAGTCATGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 8 0.22
15 15 0.41
16 6 0.16
17 8 0.22
ACGTcount: A:0.32, C:0.19, G:0.02, T:0.47
Consensus pattern (14 bp):
CACTTTAATTTCAA
Found at i:2465057 original size:16 final size:17
Alignment explanation
Indices: 2465027--2465060 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
2465017 ATTTTATCAC
2465027 TTTAATTTCCAACACTT
1 TTTAATTTCCAACACTT
2465044 TTTAATTT-CAACACTT
1 TTTAATTTCCAACACTT
2465060 T
1 T
2465061 AATTTTCAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAATTTCCAACACTT
Found at i:2465441 original size:2 final size:2
Alignment explanation
Indices: 2465434--2465469 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2465424 TGTGTACGTA
2465434 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
2465470 GAGCTAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2489963 original size:17 final size:17
Alignment explanation
Indices: 2489941--2489982 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
2489931 ATAGGAAAGC
2489941 AACAAGAATCCTGCACA
1 AACAAGAATCCTGCACA
2489958 AACAAGAATCCTGCACA
1 AACAAGAATCCTGCACA
2489975 AACAAGAA
1 AACAAGAA
2489983 AGCTCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.52, C:0.26, G:0.12, T:0.10
Consensus pattern (17 bp):
AACAAGAATCCTGCACA
Found at i:2491847 original size:28 final size:28
Alignment explanation
Indices: 2491815--2491871 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2491805 CAATAGACAA
*
2491815 ATGTGATTCATCAATTTGCAATGGTATG
1 ATGTGATTCATCAATTTGAAATGGTATG
2491843 ATGTGATTCATCAATTTGAAATGGTATG
1 ATGTGATTCATCAATTTGAAATGGTATG
2491871 A
1 A
2491872 CCTTTGGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.39
Consensus pattern (28 bp):
ATGTGATTCATCAATTTGAAATGGTATG
Found at i:2494733 original size:48 final size:49
Alignment explanation
Indices: 2494555--2494996 Score: 464
Period size: 49 Copynumber: 9.0 Consensus size: 49
2494545 AACTGCTCTA
* * *
2494555 TAATGCAAGTTAAATGTATAATAGTGCATTTTTGGCAGAAAGGTTCCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* * * * ** *
2494604 TAATGCGAGTTAAATGCATAACGATACATTTTTTTACAGAAAGGTGCCAT
1 TAATGCAAGTTAAATGCATAATGGTGCA-TTTTTGGCAGAAAGGTGCCAC
* * * *
2494654 TAATGCAAGTTAAAAGCATATTGGTGTATTTTTGGCAGAAAGGTGCTAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* ** * *
2494703 TAATGCAAATTAAATGCATAAT-GTTAATTTTTGGCAGAATGGTGCCTC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
*
2494751 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTG-CAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* *
2494799 TAATGTC-AGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTTCAAC
1 TAATG-CAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* * *
2494848 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGTAGAAAAGGTGTCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAG-AAAGGTGCCAC
* * * * * * *
2494898 TAAAT-CGAGTTAAATGCATAAAGGTGCCTTTTTGGAATAAATGTGTCAC
1 T-AATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
* * * *
2494947 TAATG-ATTGTTAAATGTATAATGGTGCA-TTTCGGCATAAAAGGTGCCAC
1 TAATGCA-AGTTAAATGCATAATGGTGCATTTTTGGCA-GAAAGGTGCCAC
2494996 T
1 T
2494997 CATGGTGTAA
Statistics
Matches: 325, Mismatches: 58, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
48 94 0.29
49 152 0.47
50 76 0.23
51 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (49 bp):
TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCAC
Found at i:2494782 original size:97 final size:97
Alignment explanation
Indices: 2494555--2494918 Score: 425
Period size: 97 Copynumber: 3.7 Consensus size: 97
2494545 AACTGCTCTA
* * *
2494555 TAATGCAAGTTAAATGTATAATA-GTGCATTTTTGGCAGAAAGGTTCCACTAATGCGAGTTAAAT
1 TAATGCAAGTTAAATGCATAA-AGGTGCATTTTTGGCAGAAAGGTGCTACTAATGCGAGTTAAAT
* * **
2494619 GCATAACGATACATTTTTTTACAGAAAGGTGCCAT-
65 GCATAATGTTA-A-TTTTTGGCAGAAAGGTGCC-TC
* ** * * *
2494654 TAATGCAAGTTAAAAGCATATTGGTGTATTTTTGGCAGAAAGGTGCTACTAATGCAAATTAAATG
1 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGCTACTAATGCGAGTTAAATG
*
2494719 CATAATGTTAATTTTTGGCAGAATGGTGCCTC
66 CATAATGTTAATTTTTGGCAGAAAGGTGCCTC
2494751 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGC-ACTAATGTC-AGTTAAAT
1 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGCTACTAATG-CGAGTTAAAT
** * **
2494814 GCATAATGGTGCATTTTTGGCAGAAAGGTTCAAC
65 GCATAAT-GTTAATTTTTGGCAGAAAGGTGCCTC
*
2494848 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGTAGAAAAGGTG-TCACTAAAT-CGAGTTAA
1 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAG-AAAGGTGCT-ACT-AATGCGAGTTAA
2494911 ATGCATAA
63 ATGCATAA
2494919 AGGTGCCTTT
Statistics
Matches: 230, Mismatches: 26, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
96 22 0.10
97 116 0.50
98 9 0.04
99 80 0.35
100 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (97 bp):
TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGCTACTAATGCGAGTTAAATG
CATAATGTTAATTTTTGGCAGAAAGGTGCCTC
Found at i:2494959 original size:99 final size:97
Alignment explanation
Indices: 2494555--2494977 Score: 383
Period size: 99 Copynumber: 4.3 Consensus size: 97
2494545 AACTGCTCTA
* * *
2494555 TAATGCAAGTTAAATGTATAATA-GTGCATTTTTGGCAGAAAGGTTCCACTAAT-GCGAGTTAAA
1 TAATGCAAGTTAAATGCATAA-AGGTGCATTTTTGGCAGAAAGG-TGCACTAATATC-AGTTAAA
* * * ** * * *
2494618 TGCATAACGATACATTTTTTTACAGAAAGGTGCCAT
63 TGCATAAAGGTGCATTTTTGGA-AGAAAGGTTCAAC
* ** * * *
2494654 TAATGCAAGTTAAAAGCATATTGGTGTATTTTTGGCAGAAAGGTGCTACTAAT-GCAAATTAAAT
1 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGC-ACTAATATC-AGTTAAAT
* ** * * * **
2494718 GCAT-AATGTTAATTTTTGGCAGAATGGTGCCTC
64 GCATAAAGGTGCATTTTTGGAAGAAAGGTTCAAC
*
2494751 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGCACTAATGTCAGTTAAATGC
1 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGCACTAATATCAGTTAAATGC
* *
2494816 ATAATGGTGCATTTTTGGCAGAAAGGTTCAAC
66 ATAAAGGTGCATTTTTGGAAGAAAGGTTCAAC
*
2494848 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGTAGAAAAGGTGTCACTAA-ATCGAGTTAAA
1 TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAG-AAAGGTG-CACTAATATC-AGTTAAA
* * *
2494912 TGCATAAAGGTGCCTTTTTGGAATAAATGTGTC-AC
63 TGCATAAAGGTGCATTTTTGGAAGAAAGGT-TCAAC
* * *
2494947 TAATG-ATTGTTAAATGTATAATGGTGCATTT
1 TAATGCA-AGTTAAATGCATAAAGGTGCATTT
2494978 CGGCATAAAA
Statistics
Matches: 272, Mismatches: 43, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
96 17 0.06
97 111 0.41
98 20 0.07
99 122 0.45
100 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (97 bp):
TAATGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAGGTGCACTAATATCAGTTAAATGC
ATAAAGGTGCATTTTTGGAAGAAAGGTTCAAC
Found at i:2503133 original size:195 final size:195
Alignment explanation
Indices: 2502839--2503258 Score: 520
Period size: 195 Copynumber: 2.1 Consensus size: 195
2502829 TGCTCTATAG
* * * *
2502839 TGCAAGTTAAATGTATAATA-GTGCATTTTTTGTAGAAAGGTACCACTAATGCGAGTTAAATGCA
1 TGCAAGTTAAATGAATAA-AGGTGCA-TTTTGGCAGAAAGGTACCACTAATGCAAGTTAAATGCA
* * *
2502903 TAACAGTGCATTTTTGACAGAAAGGTGCTACTAATGCAAGTAAAATGCGTAATGGTGCATTCTTG
64 TAACAGTGCATTTTTGACAGAAAAGTGCCACTAATGCAAGTAAAATGCATAATGGTGCATTCTTG
** * *
2502968 GTGGAAATGTGCCACTAATGCAAGTTAAATGCATAATGGTACATTTTTGGCAGAAAGGTGCCCCT
129 GCAGAAAGGTGCCACTAATGCAAGTTAAATGCATAATGGTACATTTTTGGCAGAAAGGTGCCACT
2503033 AA
194 AA
* * * * *
2503035 TGTAAGTTAAATGCATAAAGGTGCATTTTGGCAGAATGGTGCCCCTAATGCAAGTTAAATGCATA
1 TGCAAGTTAAATGAATAAAGGTGCATTTTGGCAGAAAGGTACCACTAATGCAAGTTAAATGCATA
* * * * *
2503100 A-AGGTGCATTTTTGGCAGAAAAGTTCCACTAATGTAAGTTAAATGCATAATGGTGCATTTTTGG
66 ACA-GTGCATTTTTGACAGAAAAGTGCCACTAATGCAAGTAAAATGCATAATGGTGCATTCTTGG
* * * * * * *
2503164 CAGAAAGGTGCCCCTAATGGAAGTTAAATGCATAATGGTTCTTTTTTGTCAGAATGGTGTCACTA
130 CAGAAAGGTGCCACTAATGCAAGTTAAATGCATAATGGTACATTTTTGGCAGAAAGGTGCCACTA
2503229 A
195 A
* * *
2503230 TGCGAGTTAAATGAATAACGATGCATTTT
1 TGCAAGTTAAATGAATAAAGGTGCATTTT
2503259 TAGTAGAAAG
Statistics
Matches: 190, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
194 1 0.01
195 168 0.88
196 21 0.11
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (195 bp):
TGCAAGTTAAATGAATAAAGGTGCATTTTGGCAGAAAGGTACCACTAATGCAAGTTAAATGCATA
ACAGTGCATTTTTGACAGAAAAGTGCCACTAATGCAAGTAAAATGCATAATGGTGCATTCTTGGC
AGAAAGGTGCCACTAATGCAAGTTAAATGCATAATGGTACATTTTTGGCAGAAAGGTGCCACTAA
Found at i:2503259 original size:49 final size:49
Alignment explanation
Indices: 2502839--2503268 Score: 502
Period size: 49 Copynumber: 8.8 Consensus size: 49
2502829 TGCTCTATAG
* * * * *
2502839 TGCAAGTTAAATGTATAATAGTGCATTTTTTGTAGAAAGGTACCACTAA
1 TGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAA
* ** * *
2502888 TGCGAGTTAAATGCATAACAGTGCATTTTTGACAGAAAGGTGCTACTAA
1 TGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAA
* * * ** *
2502937 TGCAAGTAAAATGCGTAATGGTGCATTCTTGGTGGAAATGTGCCACTAA
1 TGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAA
* *
2502986 TGCAAGTTAAATGCATAATGGTACATTTTTGGCAGAAAGGTGCCCCTAA
1 TGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAA
* * * *
2503035 TGTAAGTTAAATGCATAAAGGTGCA-TTTTGGCAGAATGGTGCCCCTAA
1 TGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAA
* * *
2503083 TGCAAGTTAAATGCATAAAGGTGCATTTTTGGCAGAAAAGTTCCACTAA
1 TGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAA
* *
2503132 TGTAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCCCTAA
1 TGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAA
* * * * * *
2503181 TGGAAGTTAAATGCATAATGGTTCTTTTTTGTCAGAATGGTGTCACTAA
1 TGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAA
* * * * * *
2503230 TGCGAGTTAAATGAATAACGATGCATTTTTAGTAGAAAG
1 TGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAG
2503269 TGGCCATTTT
Statistics
Matches: 321, Mismatches: 59, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
48 46 0.14
49 275 0.86
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (49 bp):
TGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAA
Found at i:2505492 original size:22 final size:22
Alignment explanation
Indices: 2505467--2505508 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2505457 AATACTCAGG
*
2505467 ATTTATCTTTTTATTATTTTGA
1 ATTTATCTTTTGATTATTTTGA
*
2505489 ATTTATCTTTTGGTTATTTT
1 ATTTATCTTTTGATTATTTT
2505509 TAGGATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.69
Consensus pattern (22 bp):
ATTTATCTTTTGATTATTTTGA
Found at i:2505707 original size:16 final size:17
Alignment explanation
Indices: 2505677--2505709 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2505667 GAAGTTATTT
2505677 TTTTAACTTTATTTTTA
1 TTTTAACTTTATTTTTA
*
2505694 TTTT-ACTTTCTTTTTA
1 TTTTAACTTTATTTTTA
2505710 GAAAAATCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTAACTTTATTTTTA
Found at i:2507817 original size:326 final size:324
Alignment explanation
Indices: 2507222--2507875 Score: 1227
Period size: 326 Copynumber: 2.0 Consensus size: 324
2507212 CTTTAAGCTA
2507222 CATTATTACTAATGACGATAGTTGTGGTTAGTTCAAGTAATAACTAAATTCCAAACATAGACTTG
1 CATTATTACTAATGACGATAGTTGTGGTTAGTTCAAGTAATAACTAAATTCCAAACATAGACTTG
*
2507287 GGAATATTGGTTTAGAAAAGAAAAAAATAAGTTACAGGGGTTGAACCTTTTATACTGTAACCGAC
66 GGAATATTGGTTTAGAAAAGAAAAAAATAAGTTACAAGGGTTGAACCTTTTATACTGTAACCGAC
* *
2507352 AAGTATCCAGAGTAAAACTCTTTTGACGATGAATTGAATTGAGGTGAAGCGAAGCCTGAGGCACC
131 AAGTATCCAGAGTAAAACTCTTTTGACGATGAATTGAATTCAGGTGAAGCGAAGCCAGAGGCACC
2507417 TTTTTATTCATTTTATTTTCTTTAAAAGATTTACCTTATTTTACTTTCTTTCAATTCTTGAATTC
196 TTTTTATTCATTTTATTTTCTTTAAAAGATTTACCTTATTTTACTTTCTTTCAATTCTTGAATTC
*
2507482 TTACTTTTCAATTTTAAAACCCTTTTTTTATTTATTTTATGCTATGATTTTGGTTGTTTTGAGT
261 TTACTTTTCAATTTTAAAACCCCTTTTTTATTTATTTTATGCTATGATTTTGGTTGTTTTGAGT
2507546 CATTATTACTAATGACGATAGTTGTGGTTAGTTCAAGTAATAACTAAATTCCAAACATAGACTTG
1 CATTATTACTAATGACGATAGTTGTGGTTAGTTCAAGTAATAACTAAATTCCAAACATAGACTTG
*
2507611 GGAATATTGGTTTAGAAAAGAAAAAAAATAAGTTACAAGGGTTGAGCCTTTTATACTGTAACCGA
66 GGAATATTGGTTTAGAAAAG-AAAAAAATAAGTTACAAGGGTTGAACCTTTTATACTGTAACCGA
2507676 CAAGTATCCAGAGTAAAACTCTTTTGACGATGAATTGGAATTCAGGTGAAGCGAAGCCAGAGGCA
130 CAAGTATCCAGAGTAAAACTCTTTTGACGATGAATT-GAATTCAGGTGAAGCGAAGCCAGAGGCA
2507741 CCTTTTTATTCATTTTATTTTCTTTAAAAGATTTACCTTATTTTACTTTCTTTCAATTCTTGAAT
194 CCTTTTTATTCATTTTATTTTCTTTAAAAGATTTACCTTATTTTACTTTCTTTCAATTCTTGAAT
* *
2507806 TCTTTCTTTTCAATTTTAAAACCCCTTTTTTATTTATTTTATGCTATGATTTTGGTTGTTTTGAT
259 TCTTACTTTTCAATTTTAAAACCCCTTTTTTATTTATTTTATGCTATGATTTTGGTTGTTTTGAG
2507871 T
324 T
2507872 CATT
1 CATT
2507876 TTTGTGCAGG
Statistics
Matches: 321, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
324 85 0.26
325 78 0.24
326 158 0.49
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (324 bp):
CATTATTACTAATGACGATAGTTGTGGTTAGTTCAAGTAATAACTAAATTCCAAACATAGACTTG
GGAATATTGGTTTAGAAAAGAAAAAAATAAGTTACAAGGGTTGAACCTTTTATACTGTAACCGAC
AAGTATCCAGAGTAAAACTCTTTTGACGATGAATTGAATTCAGGTGAAGCGAAGCCAGAGGCACC
TTTTTATTCATTTTATTTTCTTTAAAAGATTTACCTTATTTTACTTTCTTTCAATTCTTGAATTC
TTACTTTTCAATTTTAAAACCCCTTTTTTATTTATTTTATGCTATGATTTTGGTTGTTTTGAGT
Found at i:2513886 original size:46 final size:46
Alignment explanation
Indices: 2513833--2513996 Score: 211
Period size: 46 Copynumber: 3.6 Consensus size: 46
2513823 TTTTTTGTTA
* * * * *
2513833 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCAGCATTTCATAC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
2513879 ATTTTATTTGTGGCATCATTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
2513925 ATTTCATTTATGACATCCTTTCAAGCTTTAGTGCATCCTTTCATGC
1 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
2513971 ATTTCATTTATAACATCCTTTCATGC
1 ATTTCATTTATGACATCCTTTCATGC
2513997 ATTTCATTTA
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 104 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (46 bp):
ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:2513920 original size:20 final size:20
Alignment explanation
Indices: 2513891--2513970 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 20
2513881 TTTATTTGTG
*
2513891 GCATCATTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
2513911 GCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
* * *
2513936 GACATCCTTTCAAGCTTTAGT
1 G-CATCCTTTCATGCCTTAAT
2513957 GCATCCTTTCATGC
1 GCATCCTTTCATGC
2513971 ATTTCATTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
20 25 0.53
21 4 0.09
24 1 0.02
25 5 0.11
26 12 0.26
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:2513992 original size:72 final size:72
Alignment explanation
Indices: 2513912--2514068 Score: 215
Period size: 72 Copynumber: 2.2 Consensus size: 72
2513902 TGCCTTAATG
* * * *
2513912 CATCCTTTCATGCATTTCATTTATGACATCCTTTCAAGCTTTAGTGCATCCTTTCATGCATTTCA
1 CATCCTTTCATGCATTTCATTTATGACATCATTTCAAGCCTTAATGCATCATTTCATGCATTTCA
2513977 TTTATAA
66 TTTATAA
* * * * *
2513984 CATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGCATCATTTTATGTATTTTA
1 CATCCTTTCATGCATTTCATTTATGACATCATTTCAAGCCTTAATGCATCATTTCATGCATTTCA
*
2514049 TTTATGA
66 TTTATAA
*
2514056 CATACTTTCATGC
1 CATCCTTTCATGC
2514069 CTTAATGCAT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.46
Consensus pattern (72 bp):
CATCCTTTCATGCATTTCATTTATGACATCATTTCAAGCCTTAATGCATCATTTCATGCATTTCA
TTTATAA
Found at i:2514011 original size:118 final size:118
Alignment explanation
Indices: 2513871--2514099 Score: 350
Period size: 118 Copynumber: 1.9 Consensus size: 118
2513861 TAATGCAGCA
* * *
2513871 TTTCATACATTTTATTTGTGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTAT
1 TTTCATACATTTCATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATGCATTTCATTTAT
* * * *
2513936 GACATCCTTTCAAGCTTTAGTGCATCCTTTCATGCATTTCATTTATAACATCC
66 GACATACTTTCAAGCCTTAATGCATCATTTCATGCATTTCATTTATAACATCC
* * * *
2513989 TTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGCATCATTTTATGTATTTTATTTAT
1 TTTCATACATTTCATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATGCATTTCATTTAT
*
2514054 GACATACTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTAT
66 GACATACTTTCAAGCCTTAATGCATCATTTCATGCATTTCATTTAT
2514100 GGCAACCTTT
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
118 99 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.47
Consensus pattern (118 bp):
TTTCATACATTTCATTTATGGCATCATTTCATGCCTTAATGCATCATTTCATGCATTTCATTTAT
GACATACTTTCAAGCCTTAATGCATCATTTCATGCATTTCATTTATAACATCC
Found at i:2514034 original size:20 final size:20
Alignment explanation
Indices: 2514009--2514180 Score: 76
Period size: 20 Copynumber: 7.7 Consensus size: 20
2513999 TTCATTTATG
2514009 GCATCATTTCATGCCTTAAT
1 GCATCATTTCATGCCTTAAT
* **
2514029 GCATCATTTTATGTATTTTATTTAT
1 GCATCATTTCATG--CCTTA---AT
2514054 GACAT-ACTTTCATGCCTTAAT
1 G-CATCA-TTTCATGCCTTAAT
*
2514075 GCATCATTTCATGCATTTCATTTAT
1 GCATCATTTCATGC----C-TTAAT
* * *
2514100 GGCAACCTTTCATTCCTTAAT
1 -GCATCATTTCATGCCTTAAT
*
2514121 GCATCATTTCATGCTTTTCATTTAT
1 GCATCATTTCATGC----C-TTAAT
* *
2514146 GGTATCCTTTCATGCCTTAAT
1 -GCATCATTTCATGCCTTAAT
2514167 GCATCATTTCATGC
1 GCATCATTTCATGC
2514181 ATTTCATTTA
Statistics
Matches: 112, Mismatches: 20, Indels: 40
0.65 0.12 0.23
Matches are distributed among these distances:
20 46 0.41
21 12 0.11
22 5 0.04
24 5 0.04
25 12 0.11
26 32 0.29
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (20 bp):
GCATCATTTCATGCCTTAAT
Found at i:2514066 original size:46 final size:46
Alignment explanation
Indices: 2513984--2514194 Score: 309
Period size: 46 Copynumber: 4.6 Consensus size: 46
2513974 TCATTTATAA
*
2513984 CATCCTTTCATGCATTTCATTTATGGCAT-CATTTCATGCCTTAATG
1 CATCATTTCATGCATTTCATTTATGGCATAC-TTTCATGCCTTAATG
* * * *
2514030 CATCATTTTATGTATTTTATTTATGACATACTTTCATGCCTTAATG
1 CATCATTTCATGCATTTCATTTATGGCATACTTTCATGCCTTAATG
*
2514076 CATCATTTCATGCATTTCATTTATGGCA-ACCTTTCATTCCTTAATG
1 CATCATTTCATGCATTTCATTTATGGCATA-CTTTCATGCCTTAATG
* * *
2514122 CATCATTTCATGCTTTTCATTTATGGTATCCTTTCATGCCTTAATG
1 CATCATTTCATGCATTTCATTTATGGCATACTTTCATGCCTTAATG
2514168 CATCATTTCATGCATTTCATTTATGGC
1 CATCATTTCATGCATTTCATTTATGGC
2514195 TTCGTTTTAG
Statistics
Matches: 146, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
45 1 0.01
46 144 0.99
47 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (46 bp):
CATCATTTCATGCATTTCATTTATGGCATACTTTCATGCCTTAATG
Found at i:2514092 original size:164 final size:164
Alignment explanation
Indices: 2513833--2514160 Score: 460
Period size: 164 Copynumber: 2.0 Consensus size: 164
2513823 TTTTTTGTTA
* * * *
2513833 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCAGCATTTCATACATTTTATTTGTGGCATCAT
1 ATTTCATTTATGGCATCATTTCATGCCTTAATGCAGCATTTCATACATTTTATTTATGACATCAT
* * * * *
2513898 TTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGACATCCTTTCAAGCTTTAGTGCATCC
66 TTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGACAACCTTTCAAGCCTTAATGCATCA
2513963 TTTCATGCATTTCATTTATAACATCCTTTCATGC
131 TTTCATGCATTTCATTTATAACATCCTTTCATGC
* * **
2513997 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCATTTTATGTATTTTATTTATGACAT-AC
1 ATTTCATTTATGGCATCATTTCATGCCTTAATGCAGCATTTCATACATTTTATTTATGACATCA-
* **
2514061 TTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCAACCTTTCATTCCTTAATGCATC
65 TTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGACAACCTTTCAAGCCTTAATGCATC
* ***
2514126 ATTTCATGCTTTTCATTTATGGTATCCTTTCATGC
130 ATTTCATGCATTTCATTTATAACATCCTTTCATGC
2514161 CTTAATGCAT
Statistics
Matches: 143, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
163 1 0.01
164 142 0.99
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (164 bp):
ATTTCATTTATGGCATCATTTCATGCCTTAATGCAGCATTTCATACATTTTATTTATGACATCAT
TTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGACAACCTTTCAAGCCTTAATGCATCA
TTTCATGCATTTCATTTATAACATCCTTTCATGC
Found at i:2515833 original size:51 final size:51
Alignment explanation
Indices: 2515772--2515875 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
2515762 GCCAGGATCC
2515772 GTATTAGTTCTTCCTCATAAGTTAAATCTGATCGGATCTCTATCTTTTCTG
1 GTATTAGTTCTTCCTCATAAGTTAAATCTGATCGGATCTCTATCTTTTCTG
2515823 GTATTAGTTCTTCCTCATAAGTTAAATCTGATCGGATCTCTATCTTTTCTG
1 GTATTAGTTCTTCCTCATAAGTTAAATCTGATCGGATCTCTATCTTTTCTG
2515874 GT
1 GT
2515876 GTGATAATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.45
Consensus pattern (51 bp):
GTATTAGTTCTTCCTCATAAGTTAAATCTGATCGGATCTCTATCTTTTCTG
Found at i:2521002 original size:46 final size:46
Alignment explanation
Indices: 2520935--2521314 Score: 523
Period size: 46 Copynumber: 8.3 Consensus size: 46
2520925 TTATTTGTTA
* * *
2520935 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGT
1 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * *
2520981 ATTTTATATATGGAATCCTTTCATGCCTTAATTCATCATTTCATGC
1 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGC
** * *
2521027 ATTTCATTTATGGTTTCCTTTCATGCCTTAGTGCATACTTTCATGC
1 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
2521073 A-TTCATTTAT-GACATCCTTTCATGCCTTAATGCGTCCATTCATGC
1 ATTTCATTTATGGA-ATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
2521118 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGC
1 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
2521164 ATTTCATTTATGGTATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
2521210 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATTCTTTCATGC
1 ATTTCATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
2521256 ATTTCATTTAT-GACATCCTTTCATTCCTTAGTGCATCCTTTCATGC
1 ATTTCATTTATGGA-ATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
2521302 ATTTGATTTATGG
1 ATTTCATTTATGG
2521315 GATTCAATCT
Statistics
Matches: 297, Mismatches: 32, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
44 1 0.00
45 38 0.13
46 256 0.86
47 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (46 bp):
ATTTCATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:2521253 original size:183 final size:184
Alignment explanation
Indices: 2520935--2521314 Score: 591
Period size: 183 Copynumber: 2.1 Consensus size: 184
2520925 TTATTTGTTA
* * * *
2520935 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGTATTTTATATATGGAATCCT
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTCATATATGGAATCCT
* ** * *
2521000 TTCATGCCTTAATTCATCATTTCATGCATTTCATTTATGGTTTCCTTTCATGCCTTAGTGCATAC
66 TTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGCATAC
*
2521065 TTTCATGCA-TTCATTTATGACATCCTTTCATGCCTTAATGCGTCCATTCATGC
131 TTTCATGCATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCATTCATGC
* *
2521118 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTCATTTATGGTATCCT
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTCATATATGGAATCCT
* *
2521183 TTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGCATTC
66 TTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGCATAC
* * *
2521248 TTTCATGCATTTCATTTATGACATCCTTTCATTCCTTAGTGCATCCTTTCATGC
131 TTTCATGCATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCATTCATGC
*
2521302 ATTTGATTTATGG
1 ATTTCATTTATGG
2521315 GATTCAATCT
Statistics
Matches: 178, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
183 126 0.71
184 52 0.29
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (184 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCATTCATGCATTTCATATATGGAATCCT
TTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAATGCATAC
TTTCATGCATTTCATTTATGACATCCTTTCATGCCTTAATGCATCCATTCATGC
Found at i:2522881 original size:3 final size:3
Alignment explanation
Indices: 2522873--2522910 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2522863 ATTATCTAAG
* *
2522873 GAA GAA GAA GAA GAA CAA TAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2522911 TTTGTTGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:2530491 original size:28 final size:28
Alignment explanation
Indices: 2530460--2530515 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2530450 AACACCACCA
2530460 TAAATTTATCCAAGTATGGTAGAAATAC
1 TAAATTTATCCAAGTATGGTAGAAATAC
2530488 TAAATTTATCCAAGTATGGTAGAAATAC
1 TAAATTTATCCAAGTATGGTAGAAATAC
2530516 ACCACCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (28 bp):
TAAATTTATCCAAGTATGGTAGAAATAC
Found at i:2531698 original size:16 final size:16
Alignment explanation
Indices: 2531651--2531709 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 16
2531641 ATTGAAAATC
*
2531651 AATAAAACCTTTATAT
1 AATATAACCTTTATAT
2531667 AATATTAAGTCACTTTTATAT
1 AATA-TAA--C-C-TTTATAT
2531688 AA-ATAACCTTTATAT
1 AATATAACCTTTATAT
2531703 AATATAA
1 AATATAA
2531710 ACTTACCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
15 9 0.25
16 9 0.25
17 3 0.08
19 4 0.11
20 2 0.06
21 9 0.25
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (16 bp):
AATATAACCTTTATAT
Found at i:2537003 original size:24 final size:24
Alignment explanation
Indices: 2536942--2537003 Score: 56
Period size: 24 Copynumber: 2.6 Consensus size: 24
2536932 TAGTACGGTA
*
2536942 AAATCATACTAT-GTACACTAATC
1 AAATCATACTATAGTAAACTAATC
* * * *
2536965 AAATGATAGTTTAGTAAATCTCAT-
1 AAATCATACTATAGTAAA-CTAATC
2536989 AAATCATACTATAGT
1 AAATCATACTATAGT
2537004 GGAGCTTTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
23 9 0.31
24 16 0.55
25 4 0.14
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (24 bp):
AAATCATACTATAGTAAACTAATC
Found at i:2539854 original size:9 final size:9
Alignment explanation
Indices: 2539840--2539869 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
2539830 ATCGGGTTTG
2539840 ACCGGTCAA
1 ACCGGTCAA
2539849 ACCGGTCAA
1 ACCGGTCAA
2539858 ACCGGTCAA
1 ACCGGTCAA
2539867 ACC
1 ACC
2539870 AGTTTTACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.37, G:0.20, T:0.10
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:2563632 original size:20 final size:21
Alignment explanation
Indices: 2563588--2563632 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
2563578 GATTTAATCA
* *
2563588 ATATCGATACCGAATGGGGAG
1 ATATCGATACCGAAAGGGAAG
2563609 -TATCGATACC-AAAGGGAAG
1 ATATCGATACCGAAAGGGAAG
2563628 ATATC
1 ATATC
2563633 ATTACCATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (21 bp):
ATATCGATACCGAAAGGGAAG
Found at i:2563713 original size:20 final size:20
Alignment explanation
Indices: 2563663--2563732 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
2563653 GCAAAAATGG
* *
2563663 TATCGATACCATAGTAGGGT
1 TATCGATACCATGGTAAGGT
* *
2563683 AAT-GGTACCATGGTAAGGT
1 TATCGATACCATGGTAAGGT
2563702 TATCGATACCATGGTAATGG-
1 TATCGATACCATGGTAA-GGT
2563722 TATCGATACCA
1 TATCGATACCA
2563733 AAGAACCAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
19 15 0.36
20 25 0.60
21 2 0.05
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
TATCGATACCATGGTAAGGT
Found at i:2564164 original size:58 final size:58
Alignment explanation
Indices: 2564060--2564337 Score: 432
Period size: 58 Copynumber: 4.8 Consensus size: 58
2564050 TGGCACTAAC
* *
2564060 TGTGCAAAAAGTTAA-AAAATCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTG
1 TGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
** * *
2564117 TGTGCAAAAAGTTAAGAAATTTGTACTAAGTGTATGAATTTCTGTATTAGGCACTTTG
1 TGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
* *
2564175 TGTGCAAAAAGTGAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGTACTTTG
1 TGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
* *
2564233 TGTGAAAAAAGTTAAGAAATTCATACTAAGTGCATGAATTTCCGTATTGGGCACTTTG
1 TGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
* * *
2564291 TGTGCAAAAAGTTAAGAGATTCATACTAAGTCTATGAATATCCGTAT
1 TGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
2564338 GGAAAATATG
Statistics
Matches: 199, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
57 15 0.08
58 184 0.92
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (58 bp):
TGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
Found at i:2566067 original size:23 final size:23
Alignment explanation
Indices: 2566021--2566088 Score: 109
Period size: 23 Copynumber: 2.9 Consensus size: 23
2566011 TCTTTAATGT
*
2566021 ATATTTAATTTGAATTAATTAAATA
1 ATATTT-ATTTG-ATTTATTAAATA
2566046 ATATTTATTTGATTTATTAAATA
1 ATATTTATTTGATTTATTAAATA
2566069 ATATTTATTTGATTTATTAA
1 ATATTTATTTGATTTATTAA
2566089 TTCGAAATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
23 31 0.74
24 5 0.12
25 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
ATATTTATTTGATTTATTAAATA
Found at i:2579650 original size:17 final size:17
Alignment explanation
Indices: 2579624--2579656 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2579614 TCTTTGAAAC
*
2579624 AATTCTTATATAAGAGG
1 AATTCCTATATAAGAGG
2579641 AATTCCTATATAAGAG
1 AATTCCTATATAAGAG
2579657 AAGAGGGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (17 bp):
AATTCCTATATAAGAGG
Found at i:2581037 original size:3 final size:3
Alignment explanation
Indices: 2581029--2581054 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2581019 TCTATTACTA
2581029 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2581055 AACCCTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2584915 original size:17 final size:19
Alignment explanation
Indices: 2584893--2584930 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2584883 ATACTTTGTA
2584893 TTTTATA-TTT-CATGTTT
1 TTTTATATTTTCCATGTTT
2584910 TTTTATATTTTCCATGTTT
1 TTTTATATTTTCCATGTTT
2584929 TT
1 TT
2584931 ACATTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 9 0.47
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTATATTTTCCATGTTT
Found at i:2601391 original size:20 final size:20
Alignment explanation
Indices: 2601366--2601407 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2601356 TATATTGGGC
* *
2601366 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
2601386 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
2601406 TA
1 TA
2601408 AGGAATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.55
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:2609029 original size:16 final size:16
Alignment explanation
Indices: 2608998--2609050 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2608988 CTTTTTATTC
* *
2608998 TTATTTTTGTTCTTAT
1 TTATTTTTATTATTAT
2609014 TTATTTTTATTATTAT
1 TTATTTTTATTATTAT
*
2609030 TCTCTTTTTATTATCTAT
1 T-TATTTTTATTAT-TAT
2609048 TTA
1 TTA
2609051 ATTTAACATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 15 0.48
17 12 0.39
18 4 0.13
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTTTATTATTAT
Found at i:2609032 original size:22 final size:23
Alignment explanation
Indices: 2608991--2609041 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
2608981 TGTTTACCTT
* *
2608991 TTTATTCTTATTTTTGTTCT-TA
1 TTTATTCTTATTATTATTCTCTA
* *
2609013 TTTATTTTTATTATTATTCTCTT
1 TTTATTCTTATTATTATTCTCTA
2609036 TTTATT
1 TTTATT
2609042 ATCTATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTATTCTTATTATTATTCTCTA
Found at i:2609102 original size:5 final size:5
Alignment explanation
Indices: 2609085--2609316 Score: 58
Period size: 5 Copynumber: 46.2 Consensus size: 5
2609075 TATTTTTATT
* * * *
2609085 TTTTA TTCT- TTTTA TTTT- CTTTA TCTTTC TTTTA TTTATT TCTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTT-TA T-TTTA
* * * *
2609131 TATTTA -TTT- TTTTC CTTTA TTTTA -TTTG TTTTA TTTTC TTTATA TTTTTA
1 T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA -TTTTA
* * *
2609181 TTTT- CTTTA TCTTCA TTTTA -TTTA TTTTA TTCATT- TATTA TCTTTA
1 TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TT--TTA TTTTA T-TTTA
* * * * *
2609227 CTTTA TTTT- TTTATT TTTTA TTTT- CTTTA TCTTTCT TTTTA TTTCA
1 TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA T-TTT-A TTTTA TTTTA
* * * * *
2609273 TTTT- TTTTC TTTCA CTTT- CTTTA TTTTA TTTCT- TTTCA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA TTTTA T
2609317 CCCTATCTAA
Statistics
Matches: 163, Mismatches: 38, Indels: 52
0.64 0.15 0.21
Matches are distributed among these distances:
4 38 0.23
5 84 0.52
6 33 0.20
7 8 0.05
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:2609113 original size:10 final size:9
Alignment explanation
Indices: 2609086--2609309 Score: 101
Period size: 9 Copynumber: 24.0 Consensus size: 9
2609076 ATTTTTATTT
2609086 TTTATTCTT-
1 TTTATT-TTC
2609095 TTTATTTTC
1 TTTATTTTC
2609104 TTTATCTTTC
1 TTTAT-TTTC
*
2609114 TTT-TATTTA
1 TTTAT-TTTC
* *
2609123 TTTCTTTATA
1 TTTATTT-TC
2609133 TTTATTTT-
1 TTTATTTTC
*
2609141 TTTCCTTTAT-
1 TTT-ATTT-TC
2609151 TTTATTTGT-
1 TTTATTT-TC
2609160 TTTATTTTC
1 TTTATTTTC
*
2609169 TTTATATT-
1 TTTATTTTC
2609177 TTTATTTTC
1 TTTATTTTC
*
2609186 TTTATCTTC
1 TTTATTTTC
2609195 ATTTTATTTAT-
1 --TTTATTT-TC
2609206 TTTATTCATT-
1 TTTATT--TTC
2609216 TATTATCTTTAC
1 T-TTAT-TTT-C
2609228 TTTATTTT-
1 TTTATTTTC
2609236 TTTA-TTT-
1 TTTATTTTC
2609243 TTTATTTTC
1 TTTATTTTC
2609252 TTTATCTTTC
1 TTTAT-TTTC
*
2609262 TTTTTATTTC
1 TTTAT-TTTC
*
2609272 ATTTTTTTTC
1 -TTTATTTTC
*
2609282 TTTCACTTTC
1 TTT-ATTTTC
*
2609292 TTTATTTTA
1 TTTATTTTC
*
2609301 TTTCTTTTC
1 TTTATTTTC
2609310 ATTTTATCCC
Statistics
Matches: 175, Mismatches: 18, Indels: 44
0.74 0.08 0.19
Matches are distributed among these distances:
7 7 0.04
8 20 0.11
9 75 0.43
10 50 0.29
11 20 0.11
12 3 0.02
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATTTTC
Found at i:2609130 original size:23 final size:24
Alignment explanation
Indices: 2609086--2609309 Score: 99
Period size: 24 Copynumber: 9.8 Consensus size: 24
2609076 ATTTTTATTT
*
2609086 TTTATTCTT-TTTATTTTCTTTATC
1 TTTATT-TTATTTATTTTCTTTATA
*
2609110 TTTCTTTTATTTA-TTTCTTTATA
1 TTTATTTTATTTATTTTCTTTATA
*
2609133 TTTA---T-TTT-TTTCCTTTAT-
1 TTTATTTTATTTATTTTCTTTATA
2609151 TTTATTTGT-TTTATTTTCTTTATA
1 TTTATTT-TATTTATTTTCTTTATA
* *
2609175 TTTTTATTTTCTTTATCTTCATTT-TA
1 --TTTATTTTATTTATTTTC-TTTATA
* * *
2609201 TTTATTTTATTCA-TTT-ATTATC
1 TTTATTTTATTTATTTTCTTTATA
* *
2609223 TTTACTTTATTT-TTTT-ATT-T-
1 TTTATTTTATTTATTTTCTTTATA
* *
2609243 TTTATTTTCTTTATCTTTCTTTTTA
1 TTTATTTTATTTAT-TTTCTTTATA
* *
2609268 TTTCATTTT-TTT-TCTTTCACTT-TC
1 TTT-ATTTTATTTAT-TTTC-TTTATA
*
2609292 TTTATTTTATTTCTTTTC
1 TTTATTTTATTTATTTTC
2609310 ATTTTATCCC
Statistics
Matches: 159, Mismatches: 18, Indels: 46
0.71 0.08 0.21
Matches are distributed among these distances:
18 4 0.03
19 11 0.07
20 11 0.07
21 4 0.03
22 24 0.15
23 32 0.20
24 38 0.24
25 10 0.06
26 22 0.14
27 3 0.02
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTATTTTATTTATTTTCTTTATA
Found at i:2609164 original size:9 final size:8
Alignment explanation
Indices: 2609077--2609279 Score: 106
Period size: 9 Copynumber: 22.6 Consensus size: 8
2609067 TATATGTGTA
2609077 TTTTTA-T
1 TTTTTATT
2609084 TTTTTATT
1 TTTTTATT
2609092 CTTTTTATT
1 -TTTTTATT
2609101 TTCTTTATCTT
1 TT-TTTA--TT
2609112 TCTTTTATT
1 T-TTTTATT
* *
2609121 TATTTCTT
1 TTTTTATT
2609129 TATATTTATT
1 T-T-TTTATT
*
2609139 TTTTTCCTT
1 TTTTT-ATT
2609148 TATTTTATT
1 T-TTTTATT
2609157 TGTTTTATT
1 T-TTTTATT
*
2609166 TTCTTTATA
1 TT-TTTATT
2609175 TTTTTATT
1 TTTTTATT
2609183 TTCTTTATCT
1 TT-TTTAT-T
2609193 TCATTTTATT
1 T--TTTTATT
2609203 TATTTTATT
1 T-TTTTATT
2609212 CATTTATTATCT
1 --TTT-TTAT-T
2609224 TTACTTTATT
1 TT--TTTATT
2609234 TTTTTA-T
1 TTTTTATT
2609241 TTTTTATT
1 TTTTTATT
2609249 TTCTTTATCT
1 TT-TTTAT-T
2609259 TTCTTT-TT
1 TT-TTTATT
* *
2609267 ATTTCATT
1 TTTTTATT
2609275 TTTTT
1 TTTTT
2609280 TCTTTCACTT
Statistics
Matches: 158, Mismatches: 13, Indels: 49
0.72 0.06 0.22
Matches are distributed among these distances:
7 15 0.09
8 34 0.22
9 56 0.35
10 28 0.18
11 21 0.13
12 4 0.03
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTATT
Found at i:2609200 original size:82 final size:83
Alignment explanation
Indices: 2609093--2609256 Score: 228
Period size: 82 Copynumber: 2.0 Consensus size: 83
2609083 TTTTTTATTC
* * *
2609093 TTTTTATTTTCTTTATCTTTCTTTTATTTATTTCT-TTATATTTATT-TTTTTCCTTTATTTTAT
1 TTTTTATTTTCTTTATCTTTCTTTTATTTATTT-TATT-CATTTATTATCTTTACTTTATTTTAT
2609156 T-TGTTTTATTTTCTTTATA
64 TATGTTTTATTTTCTTTATA
*
2609175 TTTTTATTTTCTTTATC-TTCATTTTATTTATTTTATTCATTTATTATCTTTACTTTATTTTTTT
1 TTTTTATTTTCTTTATCTTTC-TTTTATTTATTTTATTCATTTATTATCTTTACTTTATTTTATT
*
2609239 ATTTTTTATTTTCTTTAT
65 ATGTTTTATTTTCTTTAT
2609257 CTTTCTTTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
81 11 0.15
82 46 0.63
83 16 0.22
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.75
Consensus pattern (83 bp):
TTTTTATTTTCTTTATCTTTCTTTTATTTATTTTATTCATTTATTATCTTTACTTTATTTTATTA
TGTTTTATTTTCTTTATA
Found at i:2609241 original size:30 final size:31
Alignment explanation
Indices: 2609187--2609302 Score: 105
Period size: 30 Copynumber: 3.8 Consensus size: 31
2609177 TTTATTTTCT
* *
2609187 TTATCTTCATTTTATTTATTTTATTCATTTA
1 TTATCTTTACTTTATTTATTTTATTCATTTA
*
2609218 TTATCTTTACTTTATTT-TTTTATT-TTTTA
1 TTATCTTTACTTTATTTATTTTATTCATTTA
* * * *
2609247 TTTTCTTTATCTTTCTTT-TTAT-TTCATTTT
1 TTATCTTTA-CTTTATTTATTTTATTCATTTA
* *
2609277 TTTTCTTTCACTTTCTTTATTTTATT
1 TTATCTTT-ACTTTATTTATTTTATT
2609303 TCTTTTCATT
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
29 14 0.20
30 36 0.51
31 19 0.27
32 2 0.03
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (31 bp):
TTATCTTTACTTTATTTATTTTATTCATTTA
Found at i:2609273 original size:59 final size:57
Alignment explanation
Indices: 2609095--2609307 Score: 196
Period size: 59 Copynumber: 3.6 Consensus size: 57
2609085 TTTTATTCTT
* * * *
2609095 TTTATTTTCTTTATCTTTCTTTTATTTATTTCTTTATATTTATTTTTTTCCTTTATTTTA
1 TTTATTTTCTTTA-CTTTATTTT-TTTATTTCTTTAT-TTTCTTTTTTTCTTTTATTTCA
* * * * * *
2609155 TTTGTTTTATTTTCTTTATATTTTTATTTTCTTTATCTTCATTTTATTTATTTTA-TTCA
1 TTTATTTTCTTTACTTTATTTTTTTA-TTTCTTTATTTTC-TTTT-TTTCTTTTATTTCA
*
2609214 TTTATTATCTTTACTTTATTTTTTTATTT-TTTATTTTCTTTATCTTTCTTTTTATTTCA
1 TTTATTTTCTTTACTTTATTTTTTTATTTCTTTATTTTCTTT-T-TTTC-TTTTATTTCA
* *
2609273 TTTTTTTTCTTTCACTTTCTTTATTTTATTTCTTT
1 TTTATTTTCTTT-ACTTTATTT-TTTTATTTCTTT
2609308 TCATTTTATC
Statistics
Matches: 123, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
56 3 0.02
57 12 0.10
58 14 0.11
59 58 0.47
60 25 0.20
61 8 0.07
62 3 0.02
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (57 bp):
TTTATTTTCTTTACTTTATTTTTTTATTTCTTTATTTTCTTTTTTTCTTTTATTTCA
Found at i:2609895 original size:10 final size:9
Alignment explanation
Indices: 2609880--2610052 Score: 58
Period size: 9 Copynumber: 18.7 Consensus size: 9
2609870 TTAGATAGGG
2609880 AATAAATGAA
1 AATAAAT-AA
2609890 AATAAATAA
1 AATAAATAA
2609899 AATAAATAA
1 AATAAATAA
* *
2609908 AAGGAAAGGAA
1 AA-TAAA-TAA
*
2609919 AA-AAA-CA
1 AATAAATAA
2609926 AATGAAATAAA
1 AAT-AAAT-AA
*
2609937 AAGAAAGTTAA
1 AATAAA--TAA
2609948 AA-AAA-AA
1 AATAAATAA
*
2609955 TAAAAAAT-A
1 -AATAAATAA
2609964 AATAAAGTAA
1 AATAAA-TAA
2609974 AGAT-AA-AA
1 A-ATAAATAA
2609982 AATAAATAA
1 AATAAATAA
*
2609991 AATGTAGATAA
1 AA--TAAATAA
*
2610002 AA-ATATAA
1 AATAAATAA
*
2610010 AAAAATATAA
1 AATAA-ATAA
**
2610020 AATAAAGGA
1 AATAAATAA
2610029 AATAAATTAA
1 AATAAA-TAA
*
2610039 TATAAAT-A
1 AATAAATAA
2610047 AATAAA
1 AATAAA
2610053 AGAAAGAAAG
Statistics
Matches: 126, Mismatches: 16, Indels: 44
0.68 0.09 0.24
Matches are distributed among these distances:
7 7 0.06
8 25 0.20
9 38 0.30
10 34 0.27
11 21 0.17
12 1 0.01
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (9 bp):
AATAAATAA
Found at i:2609906 original size:23 final size:22
Alignment explanation
Indices: 2609880--2610053 Score: 64
Period size: 23 Copynumber: 7.9 Consensus size: 22
2609870 TTAGATAGGG
2609880 AATAAATGAAAATAAATAAAATA
1 AATAAAT-AAAATAAATAAAATA
* *
2609903 AATAAA-AGGAAAGGAAA-AAAACA
1 AATAAATA--AAA-TAAATAAAATA
*
2609926 AATGAAATAAAAAGAAAGTTAAAA-A
1 AAT-AAAT-AAAATAAA--TAAAATA
* *
2609951 AA-AATAAAAAATAAATAAAGTA
1 AATAA-ATAAAATAAATAAAATA
*
2609973 AAGATAA-AAAATAAATAAAAT-
1 AATA-AATAAAATAAATAAAATA
* * *
2609994 -GTAGATAAAA-ATATAAAA-A
1 AATAAATAAAATAAATAAAATA
**
2610013 AAT--ATAAAATAAAGGAAATA
1 AATAAATAAAATAAATAAAATA
*
2610033 AATTAATATAAATAAATAAAA
1 AATAAATA-AAATAAATAAAA
2610054 GAAAGAAAGA
Statistics
Matches: 114, Mismatches: 16, Indels: 42
0.66 0.09 0.24
Matches are distributed among these distances:
18 6 0.05
19 13 0.11
20 10 0.09
21 5 0.04
22 19 0.17
23 42 0.37
24 11 0.10
25 3 0.03
26 5 0.04
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (22 bp):
AATAAATAAAATAAATAAAATA
Found at i:2609960 original size:11 final size:11
Alignment explanation
Indices: 2609930--2609992 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
2609920 AAAACAAATG
*
2609930 AAATAAAAAGA
1 AAATAAAAAAA
* *
2609941 AAGTTAAAAAA
1 AAATAAAAAAA
*
2609952 AAATAAAAAAT
1 AAATAAAAAAA
**
2609963 AAATAAAGTAA
1 AAATAAAAAAA
* *
2609974 AGATAAAAAAT
1 AAATAAAAAAA
2609985 AAATAAAA
1 AAATAAAA
2609993 TGTAGATAAA
Statistics
Matches: 38, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (11 bp):
AAATAAAAAAA
Found at i:2609966 original size:4 final size:4
Alignment explanation
Indices: 2609952--2610052 Score: 50
Period size: 4 Copynumber: 24.8 Consensus size: 4
2609942 AGTTAAAAAA
** *
2609952 AAAT AAA- AAAT AAAT AAAGT AAAGAT AAA- AAAT AAAT AAA- ATGT AGAT
1 AAAT AAAT AAAT AAAT AAA-T -AA-AT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
2610000 AAA- AATAT AAAA AAAT ATA- AAAT AAAGG AAAT AAATT AATAT AAAT
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAA-T AAAT AAA-T AA-AT AAAT
2610046 AAAT AAA
1 AAAT AAA
2610053 AGAAAGAAAG
Statistics
Matches: 74, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
3 11 0.15
4 44 0.59
5 14 0.19
6 4 0.05
7 1 0.01
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2609967 original size:33 final size:33
Alignment explanation
Indices: 2609917--2609992 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
2609907 AAAGGAAAGG
* *
2609917 AAAAA-AACAAATGAAATAAAAAG-AAAGTTAAAA
1 AAAAATAAAAAATGAAAT--AAAGTAAAGATAAAA
2609950 AAAAATAAAAAAT-AAATAAAGTAAAGATAAAA
1 AAAAATAAAAAATGAAATAAAGTAAAGATAAAA
2609982 AATAAATAAAA
1 AA-AAATAAAA
2609993 TGTAGATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 4 0.11
32 11 0.29
33 17 0.45
34 6 0.16
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.14
Consensus pattern (33 bp):
AAAAATAAAAAATGAAATAAAGTAAAGATAAAA
Found at i:2609970 original size:27 final size:26
Alignment explanation
Indices: 2609897--2609992 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 26
2609887 GAAAATAAAT
* * *
2609897 AAAATAAATAAAAGGAAAGGAAAAAA
1 AAAATAAAAAAAAAGAAAGTAAAAAA
* *
2609923 ACAAATGAAATAAAAAGAAAGTTAAAAA
1 A-AAAT-AAAAAAAAAGAAAGTAAAAAA
*
2609951 AAAATAAAAAATAAATAAAGTAAAGATAA
1 AAAATAAAAAA-AAAGAAAGTAAA-A-AA
*
2609980 AAAATAAATAAAA
1 AAAATAAAAAAAA
2609993 TGTAGATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
26 6 0.10
27 18 0.31
28 22 0.38
29 12 0.21
ACGTcount: A:0.76, C:0.01, G:0.09, T:0.14
Consensus pattern (26 bp):
AAAATAAAAAAAAAGAAAGTAAAAAA
Found at i:2609979 original size:22 final size:22
Alignment explanation
Indices: 2609945--2610078 Score: 93
Period size: 22 Copynumber: 6.2 Consensus size: 22
2609935 AAAAGAAAGT
*
2609945 TAAAA-AAAAATAAAAAATAAA
1 TAAAATAAAGATAAAAAATAAA
*
2609966 TAAAGTAAAGATAAAAAATAAA
1 TAAAATAAAGATAAAAAATAAA
**
2609988 TAAAATGTAGATAAAAATATAAA
1 TAAAATAAAGATAAAAA-ATAAA
* **
2610011 -AAAATATAA-A-ATAAAGGAAA
1 TAAAATA-AAGATAAAAAATAAA
* *
2610031 T-AAATTAATATAAATAAATAAA
1 TAAAATAAAGATAAA-AAATAAA
*
2610053 -AGAAAGAAAGATAAAAAA-AAA
1 TA-AAATAAAGATAAAAAATAAA
2610074 TAAAA
1 TAAAA
2610079 CTATACATAT
Statistics
Matches: 86, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
19 2 0.02
20 8 0.09
21 16 0.19
22 44 0.51
23 16 0.19
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.19
Consensus pattern (22 bp):
TAAAATAAAGATAAAAAATAAA
Found at i:2610002 original size:33 final size:31
Alignment explanation
Indices: 2609936--2610078 Score: 88
Period size: 33 Copynumber: 4.8 Consensus size: 31
2609926 AATGAAATAA
*
2609936 AAAGAAAGTTAAAAAAAAATAAAAAATAAAT
1 AAAGAAAGATAAAAAAAAATAAAAAATAAAT
** *
2609967 AAAGTAAAGATAAAAAATAAATAAAATGTAGAT
1 AAAG-AAAGATAAAAAA-AAATAAAAAATAAAT
* *
2610000 --A-AAA-ATATAAAAAAAT---ATA-AAAT
1 AAAGAAAGATAAAAAAAAATAAAAAATAAAT
* ** * *
2610023 AAAGGAA-ATAAATTAATATAAATAAATAAAAG
1 AAAGAAAGATAAAAAAAAATAAA-AAAT-AAAT
2610055 AAAGAAAGATAAAAAAAAATAAAA
1 AAAGAAAGATAAAAAAAAATAAAA
2610079 CTATACATAT
Statistics
Matches: 82, Mismatches: 18, Indels: 23
0.67 0.15 0.19
Matches are distributed among these distances:
23 3 0.04
24 2 0.02
25 1 0.01
26 10 0.12
27 4 0.05
28 7 0.09
29 3 0.04
30 2 0.02
31 5 0.06
32 21 0.26
33 24 0.29
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (31 bp):
AAAGAAAGATAAAAAAAAATAAAAAATAAAT
Found at i:2610156 original size:12 final size:10
Alignment explanation
Indices: 2609880--2610165 Score: 67
Period size: 10 Copynumber: 27.6 Consensus size: 10
2609870 TTAGATAGGG
*
2609880 AATAAATGAA
1 AATAAATAAA
2609890 AATAAAT-AA
1 AATAAATAAA
2609899 AATAAATAAA
1 AATAAATAAA
** **
2609909 AGGAAA-GGA
1 AATAAATAAA
*
2609918 AA-AAA-ACA
1 AATAAATAAA
2609926 AATGAAATAAA
1 AAT-AAATAAA
*
2609937 AAGAAAGTTAAA
1 AATAAA--TAAA
*
2609949 AAAAAATAAAA
1 AATAAAT-AAA
2609960 AATAAATAAA
1 AATAAATAAA
*
2609970 GTAA-AGATAAAA
1 --AATAAAT-AAA
2609982 AATAAATAAA
1 AATAAATAAA
* *
2609992 ATGTAGATAAA
1 A-ATAAATAAA
2610003 AAT--AT-AA
1 AATAAATAAA
2610010 AA-AAATATAA
1 AATAAATA-AA
*
2610020 AATAAAGGAAATA
1 AATAAA--TAA-A
* *
2610033 AATTAATATA
1 AATAAATAAA
2610043 AATAAAT-AA
1 AATAAATAAA
* *
2610052 AAGAAAGAAA
1 AATAAATAAA
* *
2610062 GATAAAAAAA
1 AATAAATAAA
2610072 AATAAAACTATACA
1 AAT-AAA-TA-A-A
*
2610086 TATAAATAAA
1 AATAAATAAA
*
2610096 AATGTTAAAT-TA
1 AA---TAAATAAA
*
2610108 AATAGATAATA
1 AATAAATAA-A
* *
2610119 AA-AGGATAAT
1 AATA-AATAAA
2610129 AAT-AATAAA
1 AATAAATAAA
2610138 AATAAATAAA
1 AATAAATAAA
2610148 AACTGAAATAAA
1 AA-T-AAATAAA
2610160 AATAAA
1 AATAAA
2610166 AAGGTCAACA
Statistics
Matches: 204, Mismatches: 37, Indels: 70
0.66 0.12 0.23
Matches are distributed among these distances:
7 4 0.02
8 10 0.05
9 28 0.14
10 68 0.33
11 45 0.22
12 30 0.15
13 16 0.08
14 3 0.01
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.20
Consensus pattern (10 bp):
AATAAATAAA
Found at i:2612667 original size:14 final size:14
Alignment explanation
Indices: 2612630--2612659 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2612620 AACAATAATA
*
2612630 ATTTTAATTTATTT
1 ATTTTATTTTATTT
2612644 ATTTTATTTTATTT
1 ATTTTATTTTATTT
2612658 AT
1 AT
2612660 CTTTTTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTATTTTATTT
Found at i:2623242 original size:31 final size:31
Alignment explanation
Indices: 2623206--2623314 Score: 96
Period size: 31 Copynumber: 3.4 Consensus size: 31
2623196 TCAATCGCTG
2623206 ATGGTAATTCCTTCTATAGGTTCTGCACCGA
1 ATGGTAATTCCTTCTATAGGTTCTGCACCGA
* * * * *
2623237 CTGGTAATTCCTATCCCTACATGTTCAGTCACTG-
1 ATGGTAATTCCT-T--CTATAGGTTCTG-CACCGA
* *
2623271 GTGGTAATTCCTTTTATAGGTT-TAGCACCGA
1 ATGGTAATTCCTTCTATAGGTTCT-GCACCGA
2623302 ATGGTAATTCCTT
1 ATGGTAATTCCTT
2623315 AGGAACCTAA
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
30 4 0.07
31 30 0.50
32 1 0.02
33 1 0.02
34 20 0.33
35 4 0.07
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (31 bp):
ATGGTAATTCCTTCTATAGGTTCTGCACCGA
Found at i:2624342 original size:19 final size:21
Alignment explanation
Indices: 2624300--2624347 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2624290 ATGATAATGG
2624300 TTAATTTTATTTATTATGATT
1 TTAATTTTATTTATTATGATT
2624321 TTAATTTT-TTT-TT-TGTATT
1 TTAATTTTATTTATTATG-ATT
2624340 TT-ATTTTA
1 TTAATTTTA
2624348 ATAAAGATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.28
19 7 0.28
20 3 0.12
21 8 0.32
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (21 bp):
TTAATTTTATTTATTATGATT
Found at i:2624935 original size:19 final size:19
Alignment explanation
Indices: 2624903--2624941 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2624893 AATTGAATTT
*
2624903 AAATTTAAATAAAGA-ATA
1 AAATTTAAACAAAGAGATA
2624921 AAATTTAAAACAAAGAGATA
1 AAATTT-AAACAAAGAGATA
2624941 A
1 A
2624942 TCAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.23
Consensus pattern (19 bp):
AAATTTAAACAAAGAGATA
Found at i:2626324 original size:5 final size:5
Alignment explanation
Indices: 2626316--2626412 Score: 56
Period size: 5 Copynumber: 18.4 Consensus size: 5
2626306 TTTATTTTGC
* * * *
2626316 TTATT TTATT TGTTTT TTCTT TTCTT TTTTT TTATT CTT-TT CTTATT
1 TTATT TTATT T-TATT TTATT TTATT TTATT TTATT -TTATT -TTATT
*
2626363 TTA-T TT-TT TTATA TTAGTT TTATT TATATAT TTATTT TTATT TGTATT
1 TTATT TTATT TTATT TTA-TT TTATT T-TAT-T TTA-TT TTATT T-TATT
2626411 TT
1 TT
2626413 CCTCTTGTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 20
0.75 0.06 0.20
Matches are distributed among these distances:
4 6 0.08
5 41 0.54
6 26 0.34
7 3 0.04
ACGTcount: A:0.15, C:0.04, G:0.03, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:2626348 original size:26 final size:26
Alignment explanation
Indices: 2626319--2626448 Score: 77
Period size: 26 Copynumber: 4.7 Consensus size: 26
2626309 ATTTTGCTTA
* *
2626319 TTTTATTTGTTTTTTCTTTTCTTTTT
1 TTTTATTTGTTTTTTATTTTATTTTT
*
2626345 TTTTATTCT-TTTCTTATTTTATTTTT
1 TTTTATT-TGTTTTTTATTTTATTTTT
* *
2626371 TTATATTAG--TTTTATTTATATATTTAT
1 TTTTATTTGTTTTTTATTT-TAT-TTT-T
*
2626398 TTTTATTTGTATTTTCCTCTTGTTATTTATT
1 TTTTATTTGT-TTTT--TATT-TTATTT-TT
*
2626429 TATTTATTTATTTATTTATT
1 T-TTTATTTGTTT-TTTATT
2626449 ATTTATATAC
Statistics
Matches: 79, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
24 7 0.09
25 3 0.04
26 30 0.38
27 9 0.11
30 6 0.08
31 6 0.08
32 17 0.22
33 1 0.01
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.75
Consensus pattern (26 bp):
TTTTATTTGTTTTTTATTTTATTTTT
Found at i:2626355 original size:18 final size:18
Alignment explanation
Indices: 2626321--2626370 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
2626311 TTTGCTTATT
2626321 TTATTTGTTTTTTCTTTTC
1 TTATTT-TTTTTTCTTTTC
2626340 TT-TTTTTTTATTCTTTTC
1 TTATTTTTTT-TTCTTTTC
2626358 TTATTTTATTTTT
1 TTATTTT-TTTTT
2626371 TTATATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.14
18 13 0.46
19 8 0.29
20 3 0.11
ACGTcount: A:0.08, C:0.08, G:0.02, T:0.82
Consensus pattern (18 bp):
TTATTTTTTTTTCTTTTC
Found at i:2626429 original size:4 final size:4
Alignment explanation
Indices: 2626420--2626454 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
2626410 TTTCCTCTTG
2626420 TTAT TTAT TTAT TTAT TTAT TTAT TTA- TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
2626455 ATACAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:2626490 original size:6 final size:5
Alignment explanation
Indices: 2626475--2626607 Score: 52
Period size: 5 Copynumber: 26.6 Consensus size: 5
2626465 TAGTATTTCC
* *
2626475 TTTAT TTTAT TCTTAT TCTTAT TTTAT TTTGCT CGTTAT CTTTAT TTTGA-
1 TTTAT TTTAT T-TTAT T-TTAT TTTAT TTT-AT -TTTAT -TTTAT TTT-AT
* *
2626525 -TTAT TTTA- TTTAT TTT-T CTTCA- TTT-T TTTA- TTTCT TTT-T TTTAT
1 TTTAT TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
* *
2626569 GTT-C TTTAT TTTA- TTTAGTT TTTAT CTTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTA--T TTTAT -TTTAT TTTAT TTT
2626608 TTTATGTATT
Statistics
Matches: 99, Mismatches: 11, Indels: 36
0.68 0.08 0.25
Matches are distributed among these distances:
3 1 0.01
4 25 0.25
5 43 0.43
6 24 0.24
7 6 0.06
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:2626530 original size:9 final size:9
Alignment explanation
Indices: 2626529--2626632 Score: 63
Period size: 9 Copynumber: 11.3 Consensus size: 9
2626519 TTTTGATTAT
2626529 TTTA-TTTA
1 TTTATTTTA
2626537 TTT-TTCTTCA
1 TTTATT-TT-A
2626547 TTT-TTTTA
1 TTTATTTTA
* *
2626555 TTTCTTTTT
1 TTTATTTTA
* *
2626564 TTTATGTTC
1 TTTATTTTA
2626573 TTTATTTTA
1 TTTATTTTA
2626582 TTTAGTTTTTA
1 TTTA--TTTTA
2626593 TCTTTATTTTA
1 --TTTATTTTA
2626604 TTT-TTTTA
1 TTTATTTTA
* *
2626612 TGTATTTTC
1 TTTATTTTA
*
2626621 TTTATCTTA
1 TTTATTTTA
2626630 TTT
1 TTT
2626633 TCCTTTTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
8 15 0.20
9 41 0.54
10 6 0.08
11 10 0.13
13 4 0.05
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2626555 original size:27 final size:26
Alignment explanation
Indices: 2626525--2626622 Score: 69
Period size: 26 Copynumber: 3.7 Consensus size: 26
2626515 TTTATTTTGA
2626525 TTATTTTATTTATTTTTCTTCATTTTT
1 TTATTTTATTT-TTTTTCTTCATTTTT
*
2626552 TTATTTCT-TTTTTTTATGTTC-TTTATT
1 TTATTT-TATTTTTTT-TCTTCATTT-TT
* * *
2626579 TTA-TTTAGTTTTTATCTTTATTTTAT
1 TTATTTTATTTTTTTTCTTCATTTT-T
* *
2626605 TT-TTTTATGTATTTTCTT
1 TTATTTTATTTTTTTTCTT
2626623 TATCTTATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
25 5 0.09
26 31 0.56
27 18 0.33
28 1 0.02
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (26 bp):
TTATTTTATTTTTTTTCTTCATTTTT
Found at i:2626568 original size:49 final size:48
Alignment explanation
Indices: 2626515--2626689 Score: 165
Period size: 49 Copynumber: 3.5 Consensus size: 48
2626505 GCTCGTTATC
**
2626515 TTTATTTTGATTATTTTATTTATTTTTCTTCATTTTTTTATTTCTTTTT
1 TTTATTTTCTTTATTTTATTTATTTTT-TTCATTTTTTTATTTCTTTTT
* * *
2626564 TTTATGTTCTTTATTTTATTTAGTTTTTATC-TTTATTTTATTT-TTTTA
1 TTTATTTTCTTTATTTTATTTA-TTTTTTTCATTT-TTTTATTTCTTTTT
* * *
2626612 TGTATTTTCTTTATCTTATTTTCCTTTTTTTCATTTATTTTTATTTCCTTTATT
1 TTTATTTTCTTTATTTTA-TTT-ATTTTTTTCA-TT-TTTTTATTT-CTTT-TT
*
2626666 TTTATCTTTCTTTAGTTTATTTAT
1 TTTAT-TTTCTTTATTTTATTTAT
2626690 CTTCATTGCC
Statistics
Matches: 100, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
48 22 0.22
49 39 0.39
50 5 0.05
51 10 0.10
52 1 0.01
53 4 0.04
54 8 0.08
55 11 0.11
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (48 bp):
TTTATTTTCTTTATTTTATTTATTTTTTTCATTTTTTTATTTCTTTTT
Found at i:2626590 original size:26 final size:23
Alignment explanation
Indices: 2626529--2626657 Score: 81
Period size: 22 Copynumber: 5.5 Consensus size: 23
2626519 TTTTGATTAT
* * *
2626529 TTTA-TTTATTTTTCTTCATTTT
1 TTTATTTTATTTTTTTTTATTTC
*
2626551 TTTA-TTT-CTTTTTTTTATGTTC
1 TTTATTTTATTTTTTTTTAT-TTC
*
2626573 TTTATTTTATTTAGTTTTTA--TC
1 TTTATTTTATTT-TTTTTTATTTC
2626595 TTTATTTTATTTTTTTATGTATTTTC
1 TTTATTTTATTTTTTT-T-TA-TTTC
* *
2626621 TTTATCTTATTTTCCTTTT-TTTC
1 TTTATTTTATTTT-TTTTTATTTC
2626644 ATTTATTTTTATTT
1 -TTTA-TTTTATTT
2626658 CCTTTATTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
21 11 0.13
22 28 0.33
23 9 0.11
24 6 0.07
25 14 0.16
26 15 0.18
27 2 0.02
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTATTTTATTTTTTTTTATTTC
Found at i:2626640 original size:32 final size:33
Alignment explanation
Indices: 2626589--2626652 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
2626579 TTATTTAGTT
2626589 TTTATCTTTATTTTATTTTTTT-ATGTATTTTC
1 TTTATCTTTATTTTATTTTTTTCATGTATTTTC
* *
2626621 TTTATC-TTATTTTCCTTTTTTTCATTTATTTT
1 TTTATCTTTATTTT-ATTTTTTTCATGTATTTT
2626653 TATTTCCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 7 0.25
32 13 0.46
33 8 0.29
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (33 bp):
TTTATCTTTATTTTATTTTTTTCATGTATTTTC
Found at i:2630852 original size:13 final size:13
Alignment explanation
Indices: 2630836--2630870 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2630826 TTGTTTTCCA
*
2630836 TTTTTTTCATGTCT
1 TTTTTTTC-TCTCT
2630850 TTTTTTTCTCTCT
1 TTTTTTTCTCTCT
2630863 TTTTTTTC
1 TTTTTTTC
2630871 GAACAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTTTCTCTCT
Found at i:2633843 original size:13 final size:13
Alignment explanation
Indices: 2633825--2633849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2633815 CTTGATCGAA
2633825 TAAAAATAAAAAG
1 TAAAAATAAAAAG
2633838 TAAAAATAAAAA
1 TAAAAATAAAAA
2633850 TTTAACAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAG
Found at i:2636376 original size:76 final size:75
Alignment explanation
Indices: 2636287--2636503 Score: 299
Period size: 75 Copynumber: 2.9 Consensus size: 75
2636277 ATTTTAAACA
*
2636287 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGATTTTTAGTATTTTAATTAAGTTTT
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG-TTTTTAGTATTTTAATTAAGATTT
* * *
2636352 AGGATATTTTT
65 AGAAAATTATT
* *
2636363 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTTAGTATTTTAATTAAGATTTA
*
2636428 TAAAATTATT
66 GAAAATTATT
* * * * * *
2636438 TTAAATATTATTTTTGTTTTGGGTATTTTAGTTTAAATAGTTTTTAAGTGTTTTAATTAGGATTT
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTT-AGTATTTTAATTAAGATTT
2636503 A
65 A
2636504 AGATGTTTTA
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
75 68 0.54
76 59 0.46
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.59
Consensus pattern (75 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTTAGTATTTTAATTAAGATTTA
GAAAATTATT
Found at i:2636543 original size:21 final size:21
Alignment explanation
Indices: 2636478--2636544 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
2636468 GTTTAAATAG
2636478 TTTTTAAG-TGTTTTA-ATTA
1 TTTTTAAGATGTTTTAGATTA
** *
2636497 GGATTTAAGATGTTTTAGCTTA
1 -TTTTTAAGATGTTTTAGATTA
2636519 TTTTTAAGATGTTTTACGATT-
1 TTTTTAAGATGTTTTA-GATTA
2636540 TTTTT
1 TTTTT
2636545 CGAAGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 6 0.16
21 26 0.68
22 6 0.16
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (21 bp):
TTTTTAAGATGTTTTAGATTA
Found at i:2644293 original size:30 final size:30
Alignment explanation
Indices: 2644229--2644373 Score: 119
Period size: 30 Copynumber: 4.7 Consensus size: 30
2644219 CAATACATCG
* * * * **
2644229 AGTGTCCTTACACACCACAGTGCTACACTG
1 AGTGTCCTTACACACTATAGTACTATACAA
* ** * *
2644259 AGTGTCCTTACACATTATAGTGTTGTACTA
1 AGTGTCCTTACACACTATAGTACTATACAA
*
2644289 AGTGTCCTTATACACTATAGTACTATACAA
1 AGTGTCCTTACACACTATAGTACTATACAA
* *
2644319 AGTGTCCTTACACACTATAATACCATATGAACTA
1 AGTGTCCTTACACACTATAGTA-C-TAT--ACAA
*
2644353 AGTGTCCTTACACACGATAGT
1 AGTGTCCTTACACACTATAGT
2644374 GCTAATCTGA
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
30 67 0.72
31 1 0.01
32 3 0.03
34 22 0.24
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (30 bp):
AGTGTCCTTACACACTATAGTACTATACAA
Found at i:2647139 original size:29 final size:29
Alignment explanation
Indices: 2647077--2647140 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
2647067 AAAATACCTT
* * *
2647077 TTTTGTCCCTAAACTTTACAAACTTTATA
1 TTTTGGCCCTAAACTTTACAAAATTTAAA
*
2647106 CTTTGGCCACTAAACTTT-CAAAATTTAAA
1 TTTTGGCC-CTAAACTTTACAAAATTTAAA
2647135 TTTTGG
1 TTTTGG
2647141 TCATTAACCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (29 bp):
TTTTGGCCCTAAACTTTACAAAATTTAAA
Found at i:2651690 original size:30 final size:30
Alignment explanation
Indices: 2651627--2651692 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2651617 ACACTGAGTG
* * *
2651627 TCCTTACACACCATAGTGTTGCACTGAGCA
1 TCCTTACACACCACAGTGATGCACTAAGCA
* * *
2651657 TCCTTACACACTACAGTGATGTACTAAGTA
1 TCCTTACACACCACAGTGATGCACTAAGCA
2651687 TCCTTA
1 TCCTTA
2651693 TACATTATAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (30 bp):
TCCTTACACACCACAGTGATGCACTAAGCA
Found at i:2654075 original size:44 final size:44
Alignment explanation
Indices: 2654026--2654327 Score: 428
Period size: 44 Copynumber: 6.9 Consensus size: 44
2654016 CTACTCTAAA
* *
2654026 ATAAATGAAAATGCATAATGGTGCATTATTGGGAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTC
* *
2654070 ATAAATGAAAATACATAACAGTGCATTATTGGCAGAAAGGTAG-C
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGT-GTC
*
2654114 ATAAATTAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTC
* * *
2654158 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTC
* * *
2654202 ATAAATGAAAATGCATAACGGTGCATTATTGACAGTAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTC
*
2654246 ATAAATGAAAATGTATAACGGTGCATTATTGGCAGAAAGGT-TCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGT-C
* * * *
2654290 ATAAATGAAAATGTATAACGGTACACTATTGACAGAAA
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAA
2654328 TATGCCACTC
Statistics
Matches: 233, Mismatches: 22, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
43 1 0.00
44 231 0.99
45 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.25
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTC
Found at i:2656279 original size:29 final size:30
Alignment explanation
Indices: 2656223--2656286 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
2656213 CTTTTGATCC
*
2656223 CTAAACTTTTACAAAATTTATACTTTGGCCA
1 CTAAACTTTTA-AAAATTTAAACTTTGGCCA
* * *
2656254 CTAAACTTTT-AGAATTTAAATTTTGGTCA
1 CTAAACTTTTAAAAATTTAAACTTTGGCCA
2656283 CTAA
1 CTAA
2656287 CCTAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 19 0.66
31 10 0.34
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.41
Consensus pattern (30 bp):
CTAAACTTTTAAAAATTTAAACTTTGGCCA
Found at i:2657921 original size:22 final size:21
Alignment explanation
Indices: 2657892--2657932 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2657882 TTTATACTAA
* *
2657892 TTTAATTTTTATTTTTAGTAT
1 TTTAATTTATAATTTTAGTAT
2657913 TTTATATTTATAATTTTAGT
1 TTTA-ATTTATAATTTTAGT
2657933 GTATTTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTAATTTATAATTTTAGTAT
Found at i:2657928 original size:23 final size:24
Alignment explanation
Indices: 2657862--2657929 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 24
2657852 AATATATATA
*
2657862 TATA-TATATATATTTA-AATTTT
1 TATACTATTTATATTTATAATTTT
*
2657884 TATACTAATTTA-ATTT-TTATTTT
1 TATACT-ATTTATATTTATAATTTT
2657907 TAGTA-T-TTTATATTTATAATTTT
1 TA-TACTATTTATATTTATAATTTT
2657930 AGTGTATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
21 4 0.11
22 8 0.22
23 19 0.51
24 6 0.16
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (24 bp):
TATACTATTTATATTTATAATTTT
Found at i:2659396 original size:62 final size:61
Alignment explanation
Indices: 2659223--2659396 Score: 160
Period size: 62 Copynumber: 2.9 Consensus size: 61
2659213 TAAACTACGT
* * * * **
2659223 ATTTAGAACCTAAACTATCAATTTTGATCAGTTTTAGTACCTAAACTTTTAATATTTTCAA
1 ATTTAGTACCTAAACTATCAGTTTTGATCCGTTTTAGTACCTAAACTTTAAATATTAACAA
* * * * *
2659284 AATCA-TACCT-AACGT-TTAGTTTTTG-TCTCATTTTAGTACC-ACAACATTAAATACTTAACA
1 ATTTAGTACCTAAAC-TATCAG-TTTTGATC-CGTTTTAGTACCTA-AACTTTAAATA-TTAACA
*
2659344 C
61 A
2659345 ATTTAGTACCTAAACTATCAGTTTTGATCCGTTTTAGTACCTAAACTTTAAA
1 ATTTAGTACCTAAACTATCAGTTTTGATCCGTTTTAGTACCTAAACTTTAAA
2659397 AAAAATTCAA
Statistics
Matches: 86, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
59 8 0.09
60 29 0.34
61 10 0.12
62 30 0.35
63 9 0.10
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.40
Consensus pattern (61 bp):
ATTTAGTACCTAAACTATCAGTTTTGATCCGTTTTAGTACCTAAACTTTAAATATTAACAA
Found at i:2660580 original size:14 final size:14
Alignment explanation
Indices: 2660561--2660606 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2660551 TTGAATACTT
2660561 AAAAATATCTTTTA
1 AAAAATATCTTTTA
*
2660575 AAAAATA-ATTTTA
1 AAAAATATCTTTTA
2660588 AGAAAA-ATCATTTTA
1 A-AAAATATC-TTTTA
2660603 AAAA
1 AAAA
2660607 CACAAAATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 7 0.26
14 14 0.52
15 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (14 bp):
AAAAATATCTTTTA
Found at i:2666100 original size:23 final size:23
Alignment explanation
Indices: 2666073--2666128 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2666063 TGGTTGCTCA
* *
2666073 TTTGATTTTTGGCATGCATGAGT
1 TTTGATCTTAGGCATGCATGAGT
*
2666096 TTTGATCTTAGGCATGTATGAGT
1 TTTGATCTTAGGCATGCATGAGT
2666119 TTTGATCTTA
1 TTTGATCTTA
2666129 AATGGTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.48
Consensus pattern (23 bp):
TTTGATCTTAGGCATGCATGAGT
Found at i:2667219 original size:20 final size:21
Alignment explanation
Indices: 2667194--2667233 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
2667184 CTCTACATAG
2667194 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
2667214 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
2667234 CACAACAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:2672733 original size:23 final size:23
Alignment explanation
Indices: 2672690--2672740 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2672680 AAGTTTAATT
* *
2672690 CTAAACTTAAAATAATTTAAAAA
1 CTAAACTTAAAAGAATGTAAAAA
*
2672713 CTAAA-TTAAAAGAATAGTAAAAT
1 CTAAACTTAAAAGAAT-GTAAAAA
2672736 CTAAA
1 CTAAA
2672741 GGACCTAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.27
Consensus pattern (23 bp):
CTAAACTTAAAAGAATGTAAAAA
Found at i:2674259 original size:22 final size:24
Alignment explanation
Indices: 2674218--2674261 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2674208 TTACATAAAA
2674218 TATTATTTTTATACTGAAAATGCT
1 TATTATTTTTATACTGAAAATGCT
*
2674242 TATTTTTTTTA-ACT-AAAATG
1 TATTATTTTTATACTGAAAATG
2674262 AATATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 3 0.16
24 10 0.53
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (24 bp):
TATTATTTTTATACTGAAAATGCT
Found at i:2674267 original size:22 final size:24
Alignment explanation
Indices: 2674216--2674269 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
2674206 TATTACATAA
*
2674216 AATATTATTTTTATACTGAAAATG
1 AATATTTTTTTTATACTGAAAATG
**
2674240 CTTATTTTTTTTA-ACT-AAAATG
1 AATATTTTTTTTATACTGAAAATG
2674262 AATATTTT
1 AATATTTT
2674270 CAATAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 12 0.48
23 3 0.12
24 10 0.40
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.52
Consensus pattern (24 bp):
AATATTTTTTTTATACTGAAAATG
Found at i:2674472 original size:221 final size:221
Alignment explanation
Indices: 2674049--2674496 Score: 860
Period size: 221 Copynumber: 2.0 Consensus size: 221
2674039 TTAATGCACC
*
2674049 CAATAAATAAGTGAAGGGCCCACTATGCATCTTCGCACCAAAAATCAAAATTCCCTCTACAAAAA
1 CAATAAATAAGTGAAGGGCCCACTATGCATCTTCGCACCAAAAATCAAAATTCCCTCAACAAAAA
2674114 AGTCAAAGGTATTTCTGTTATACGGTATCTTAATATGAGACGAAAGAAATAAATTATCGAAATTA
66 AGTCAAAGGTATTTCTGTTATACGGTATCTTAATATGAGACGAAAGAAATAAATTATCGAAATTA
2674179 TTAATATTTTTTAATTTTTTAATAGAGTATTACATAAAATATTATTTTTATACTGAAAATGCTTA
131 TTAATATTTTTTAATTTTTTAATAGAGTATTACATAAAATATTATTTTTATACTGAAAATGCTTA
2674244 TTTTTTTTAACTAAAATGAATATTTT
196 TTTTTTTTAACTAAAATGAATATTTT
2674270 CAATAAATAAGTGAAGGGCCCACTATGCATCTTCGCACCAAAAATCAAAATTCCCTCAACAAAAA
1 CAATAAATAAGTGAAGGGCCCACTATGCATCTTCGCACCAAAAATCAAAATTCCCTCAACAAAAA
2674335 AGTCAAAGGTATTTCTGTTATACGGTATCTTAATATGAGACGAAAGAAATAAATTATCGAAATTA
66 AGTCAAAGGTATTTCTGTTATACGGTATCTTAATATGAGACGAAAGAAATAAATTATCGAAATTA
*
2674400 TTAATATTTTTTAATTTTTTTAATAGAGTATTACATAAAATATTATTTTTATATTGAAAATGCTT
131 TTAATATTTTTTAA-TTTTTTAATAGAGTATTACATAAAATATTATTTTTATACTGAAAATGCTT
2674465 ATTTTTTTTAACTAAAATGAATATTTT
195 ATTTTTTTTAACTAAAATGAATATTTT
*
2674492 TAATA
1 CAATA
2674497 TTAATATTTT
Statistics
Matches: 223, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
221 143 0.64
222 80 0.36
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (221 bp):
CAATAAATAAGTGAAGGGCCCACTATGCATCTTCGCACCAAAAATCAAAATTCCCTCAACAAAAA
AGTCAAAGGTATTTCTGTTATACGGTATCTTAATATGAGACGAAAGAAATAAATTATCGAAATTA
TTAATATTTTTTAATTTTTTAATAGAGTATTACATAAAATATTATTTTTATACTGAAAATGCTTA
TTTTTTTTAACTAAAATGAATATTTT
Found at i:2676869 original size:33 final size:33
Alignment explanation
Indices: 2676764--2676869 Score: 90
Period size: 33 Copynumber: 3.2 Consensus size: 33
2676754 TATAATATGT
2676764 ATTTAATGCGTAATACTAATAAAACAACTATAC
1 ATTTAATGCGTAATACTAATAAAACAACTATAC
** * * * * * **
2676797 ATTTAACAC-AAAAACCTTATATTATATAA-TATGT
1 ATTTAATGCGTAATA-C-TA-ATAAAACAACTATAC
2676831 ATTTAATGCGTAATACTAATAAAACAACTATAC
1 ATTTAATGCGTAATACTAATAAAACAACTATAC
2676864 ATTTAA
1 ATTTAA
2676870 CACAAAAACT
Statistics
Matches: 50, Mismatches: 18, Indels: 10
0.64 0.23 0.13
Matches are distributed among these distances:
32 9 0.18
33 19 0.38
34 13 0.26
35 9 0.18
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (33 bp):
ATTTAATGCGTAATACTAATAAAACAACTATAC
Found at i:2676885 original size:67 final size:67
Alignment explanation
Indices: 2676740--2676878 Score: 278
Period size: 67 Copynumber: 2.1 Consensus size: 67
2676730 ATGTAATATG
2676740 AAAACCTTATATTATATAATATGTATTTAATGCGTAATACTAATAAAACAACTATACATTTAACA
1 AAAACCTTATATTATATAATATGTATTTAATGCGTAATACTAATAAAACAACTATACATTTAACA
2676805 CA
66 CA
2676807 AAAACCTTATATTATATAATATGTATTTAATGCGTAATACTAATAAAACAACTATACATTTAACA
1 AAAACCTTATATTATATAATATGTATTTAATGCGTAATACTAATAAAACAACTATACATTTAACA
2676872 CA
66 CA
2676874 AAAAC
1 AAAAC
2676879 TATATATCAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 72 1.00
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (67 bp):
AAAACCTTATATTATATAATATGTATTTAATGCGTAATACTAATAAAACAACTATACATTTAACA
CA
Found at i:2676914 original size:67 final size:65
Alignment explanation
Indices: 2676740--2676918 Score: 175
Period size: 67 Copynumber: 2.7 Consensus size: 65
2676730 ATGTAATATG
* ***
2676740 AAAACCTTATATTATATAATATGTATTTAATGCGTAATACTAATAAAACAACTATACATTTAACA
1 AAAACCTTATATCATATAATATGTAAAAAAT--GTAATACTAATAAAACAACTATACATTTAACA
2676805 CA
64 CA
* ***
2676807 AAAACCTTATATTATATAATATGTATTTAATGCGTAATACTAATAAAACAACTATACATTTAACA
1 AAAACCTTATATCATATAATATGTAAAAAAT--GTAATACTAATAAAACAACTATACATTTAACA
2676872 CA
64 CA
*
2676874 AAAA-CTATATATCACTATTATAT-TCACAAAAAT-TACATACTAATA
1 AAAACCT-TATATCA-TATAATATGT-A-AAAAATGTA-ATACTAATA
2676919 CTAATATTAT
Statistics
Matches: 102, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
66 4 0.04
67 87 0.85
68 8 0.08
69 3 0.03
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (65 bp):
AAAACCTTATATCATATAATATGTAAAAAATGTAATACTAATAAAACAACTATACATTTAACACA
Found at i:2679708 original size:55 final size:54
Alignment explanation
Indices: 2679623--2679975 Score: 496
Period size: 55 Copynumber: 6.5 Consensus size: 54
2679613 GAAATGTATA
* **
2679623 CACTTAGTAT-ACATTTCCT-AGTTTGTACATAAAGTGCCCATACATAAATTCATC
1 CACTTAGTATGA-ATTTCTTAAGTTTACACATAAAGTGCCCATACA-AAATTCATC
* * *
2679677 CACTTAGTCTGAATTCCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATT
1 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC-AAAATTCATC
* *
2679732 CACTTAGTATGAATTTCTTAAGTTTACACGTAAAGTGCCCATACGAAAATTCATA
1 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC-AAAATTCATC
*
2679787 GACTTAGTATGAATTTCTTAAGTTTACACATAAAGTG-CCATACGAAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC-AAAATTCATC
*
2679841 CATTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC-AAAATTCATC
* *
2679896 CACTTAGTATTAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATAC-AAAATTCATC
* *
2679951 CACTTAATATGAATTTCATAAGTTT
1 CACTTAGTATGAATTTCTTAAGTTT
2679976 TTGCACATTT
Statistics
Matches: 271, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
54 65 0.24
55 205 0.76
56 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (54 bp):
CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAAAATTCATC
Found at i:2679863 original size:164 final size:165
Alignment explanation
Indices: 2679620--2679975 Score: 540
Period size: 164 Copynumber: 2.2 Consensus size: 165
2679610 ACGGAAATGT
* **
2679620 ATACACTTAGTAT-ACATTTCCT-AGTTTGTACATAAAGTGCCCATACATAAATTCATCCACTTA
1 ATACACTTAGTATGA-ATTTCATAAGTTTACACATAAAGTGCCCATACATAAATTCATCCACTTA
* *
2679683 GTCTGAATTCCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATTCACTTAGTATGAATTT
65 GTATGAATTCCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATCCACTTAGTATGAATTT
*
2679748 CTTAAGTTTACACGTAAAGTGCCCATACGAAAATTC
130 CTTAAGTTTACACATAAAGTGCCCATACGAAAATTC
* * *
2679784 ATAGACTTAGTATGAATTTCTTAAGTTTACACATAAAGTG-CCATACGA-AAATTCATCCATTTA
1 ATACACTTAGTATGAATTTCATAAGTTTACACATAAAGTGCCCATAC-ATAAATTCATCCACTTA
* *
2679847 GTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATCCACTTAGTATTAATTT
65 GTATGAATTCCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATCCACTTAGTATGAATTT
*
2679912 CTTAAGTTTACACATAAAGTGCCCATACGGAAATTC
130 CTTAAGTTTACACATAAAGTGCCCATACGAAAATTC
* *
2679948 ATCCACTTAATATGAATTTCATAAGTTT
1 ATACACTTAGTATGAATTTCATAAGTTT
2679976 TTGCACATTT
Statistics
Matches: 174, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
164 157 0.90
165 17 0.10
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (165 bp):
ATACACTTAGTATGAATTTCATAAGTTTACACATAAAGTGCCCATACATAAATTCATCCACTTAG
TATGAATTCCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATCCACTTAGTATGAATTTC
TTAAGTTTACACATAAAGTGCCCATACGAAAATTC
Found at i:2679890 original size:109 final size:110
Alignment explanation
Indices: 2679623--2679975 Score: 523
Period size: 109 Copynumber: 3.2 Consensus size: 110
2679613 GAAATGTATA
* ** * *
2679623 CACTTAGTAT-ACATTTCCT-AGTTTGTACATAAAGTGCCCATACATAAATTCATCCACTTAGTC
1 CACTTAGTATGA-ATTTCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATCCACTTAGTA
* * *
2679686 TGAATTCCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATT
65 TGAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATC
* * **
2679732 CACTTAGTATGAATTTCTTAAGTTTACACGTAAAGTGCCCATACGAAAATTCATAGACTTAGTAT
1 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATCCACTTAGTAT
2679797 GAATTTCTTAAGTTTACACATAAAGTG-CCATACGAAAATTCATC
66 GAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATC
*
2679841 CATTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATCCACTTAGTAT
1 CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATCCACTTAGTAT
* *
2679906 TAATTTCTTAAGTTTACACATAAAGTGCCCATACGGAAATTCATC
66 GAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATC
* *
2679951 CACTTAATATGAATTTCATAAGTTT
1 CACTTAGTATGAATTTCTTAAGTTT
2679976 TTGCACATTT
Statistics
Matches: 219, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
109 117 0.53
110 102 0.47
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (110 bp):
CACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACAAAAATTCATCCACTTAGTAT
GAATTTCTTAAGTTTACACATAAAGTGCCCATACGAAAATTCATC
Found at i:2686658 original size:55 final size:53
Alignment explanation
Indices: 2686554--2686972 Score: 529
Period size: 55 Copynumber: 7.7 Consensus size: 53
2686544 TACCAATACG
* * * * * *
2686554 AAAATTTATACACTTAGTATGCATTTCCT-ATTTTGCACATAAAGTGCCCATA
1 AAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA
* * *
2686606 TAATAATTCATACACTTAGTATGAATTCCTTAAGTTTATACATAAAGTGCCCATA
1 -AA-AATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA
* * *
2686661 TGGAATTTCATCCACTTAGTATGAATTTCTTAAGTTTACA-AGTAAAGTGACCATA
1 --AAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACA-TAAAGTGCCCATA
* *
2686716 CATATATTCATCCACTTAGAATGAATTTCTTAAGTTTACACATAAAGTGCCCATA
1 -A-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA
* *
2686771 CAGAAA-TCTATCCACTTAGTATGAATTTCTTAAGTTTACACGTAAACTGCCCATA
1 -A-AAATTC-ATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA
2686826 AGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA
1 A--AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA
2686881 CAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA
1 -A-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA
2686936 CGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
1 --AAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
2686973 TTGCACACTT
Statistics
Matches: 327, Mismatches: 28, Indels: 20
0.87 0.07 0.05
Matches are distributed among these distances:
53 2 0.01
54 27 0.08
55 292 0.89
56 6 0.02
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (53 bp):
AAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATA
Found at i:2686861 original size:165 final size:165
Alignment explanation
Indices: 2686589--2686972 Score: 596
Period size: 165 Copynumber: 2.3 Consensus size: 165
2686579 TCCTATTTTG
* * * * *
2686589 CACATAAAGTGCCCATATA-ATAATTCATACACTTAGTATGAATTCCTTAAGTTTATACATAAAG
1 CACATAAAGTGCCCATACAGA-AATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAC
* *
2686653 TGCCCATATGGAATTTCATCCACTTAGTATGAATTTCTTAAGTTTACA-AGTAAAGTGACCATAC
65 TGCCCATAAGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACA-TAAAGTGACCATAC
* *
2686717 ATATATTCATCCACTTAGAATGAATTTCTTAAGTTTA
129 AGAAATTCATCCACTTAGAATGAATTTCTTAAGTTTA
*
2686754 CACATAAAGTGCCCATACAGAAA-TCTATCCACTTAGTATGAATTTCTTAAGTTTACACGTAAAC
1 CACATAAAGTGCCCATACAGAAATTC-ATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAC
*
2686818 TGCCCATAAGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCCATACA
65 TGCCCATAAGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGACCATACA
*
2686883 GAAATTCATCCACTTAGTATGAATTTCTTAAGTTTA
130 GAAATTCATCCACTTAGAATGAATTTCTTAAGTTTA
2686919 CACATAAAGTGCCCATAC-GAAAATTCATCCACTTAGTATGAATTTCTTAAGTTT
1 CACATAAAGTGCCCATACAG-AAATTCATCCACTTAGTATGAATTTCTTAAGTTT
2686973 TTGCACACTT
Statistics
Matches: 202, Mismatches: 12, Indels: 10
0.90 0.05 0.04
Matches are distributed among these distances:
164 3 0.01
165 195 0.97
166 4 0.02
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (165 bp):
CACATAAAGTGCCCATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAACT
GCCCATAAGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGACCATACAG
AAATTCATCCACTTAGAATGAATTTCTTAAGTTTA
Found at i:2687440 original size:20 final size:20
Alignment explanation
Indices: 2687417--2687456 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2687407 CATGGATACC
2687417 TTCCCTTTGGTATCGATATT
1 TTCCCTTTGGTATCGATATT
2687437 TTCCCTTTGGTATCGATATT
1 TTCCCTTTGGTATCGATATT
2687457 GATTGCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (20 bp):
TTCCCTTTGGTATCGATATT
Found at i:2692312 original size:15 final size:15
Alignment explanation
Indices: 2692292--2692324 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2692282 AGTGACAATT
*
2692292 TGTGTACATATTATG
1 TGTGTACATAATATG
2692307 TGTGTACATAATATG
1 TGTGTACATAATATG
2692322 TGT
1 TGT
2692325 CGCAATGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.45
Consensus pattern (15 bp):
TGTGTACATAATATG
Found at i:2692767 original size:19 final size:19
Alignment explanation
Indices: 2692726--2692768 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
2692716 TGAGCTTCTT
* ** *
2692726 AAAAAATAAAATCAATGTT
1 AAAAAATAAAATAAAAATA
2692745 AAAAAATAAAATAAAAATA
1 AAAAAATAAAATAAAAATA
2692764 AAAAA
1 AAAAA
2692769 GTATTAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAAAATAAAATAAAAATA
Found at i:2694121 original size:24 final size:23
Alignment explanation
Indices: 2694081--2694126 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
2694071 GACCTAAAAC
2694081 AAAACAAAATAAAAATAAATAAA
1 AAAACAAAATAAAAATAAATAAA
* *
2694104 AAAACAATAATAATAATATATAA
1 AAAACAA-AATAAAAATAAATAA
2694127 TATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAACAAAATAAAAATAAATAAA
Found at i:2694263 original size:33 final size:33
Alignment explanation
Indices: 2694189--2694289 Score: 94
Period size: 33 Copynumber: 3.3 Consensus size: 33
2694179 TATATTTAAA
* *
2694189 ATATATA-ATATGTATATATTCCAAAACTATAT
1 ATATATATATATATTTATATTCCAAAACTATAT
*
2694221 ATATATATATATATTTATATT-C-AAA--A-GT
1 ATATATATATATATTTATATTCCAAAACTATAT
* *
2694249 ATCTA-ATATGTA--TATATTCCAAAACTATAT
1 ATATATATATATATTTATATTCCAAAACTATAT
2694279 ATATATATATA
1 ATATATATATA
2694290 GTCAAAAGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
25 6 0.11
26 1 0.02
27 9 0.17
28 5 0.09
29 2 0.04
30 5 0.09
31 7 0.13
32 8 0.15
33 11 0.20
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.43
Consensus pattern (33 bp):
ATATATATATATATTTATATTCCAAAACTATAT
Found at i:2694314 original size:50 final size:49
Alignment explanation
Indices: 2694224--2694328 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 49
2694214 ACTATATATA
* * ** *
2694224 TATATATATATTTATATTCAAAAGTATCTAATATGTATATATTCCAAAAC
1 TATATATATATATATAGTCAAAAGTA-CTAATATCCATATATACCAAAAC
*
2694274 TATATATATATATATAGTCAAAAGTA-TAATGTATCCATATATACCAAAAT
1 TATATATATATATATAGTCAAAAGTACTAA--TATCCATATATACCAAAAC
2694324 TATAT
1 TATAT
2694329 GTTTGCAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 3 0.06
50 44 0.94
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.40
Consensus pattern (49 bp):
TATATATATATATATAGTCAAAAGTACTAATATCCATATATACCAAAAC
Found at i:2694330 original size:25 final size:23
Alignment explanation
Indices: 2694254--2694330 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 23
2694244 AAAGTATCTA
2694254 ATATGTATATAT-T-CCAAAACT
1 ATATGTATATATATACCAAAACT
* * *
2694275 ATATATATATATATAGTCAAAAGT
1 ATATGTATATATATA-CCAAAACT
*
2694299 ATAATGTATCCATATATACCAAAATT
1 AT-ATGTAT--ATATATACCAAAACT
2694325 ATATGT
1 ATATGT
2694331 TTGCAAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 11 0.25
22 1 0.02
24 8 0.18
25 9 0.20
26 8 0.18
27 7 0.16
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.38
Consensus pattern (23 bp):
ATATGTATATATATACCAAAACT
Found at i:2695225 original size:74 final size:73
Alignment explanation
Indices: 2695140--2695373 Score: 225
Period size: 74 Copynumber: 3.2 Consensus size: 73
2695130 CATTTCGCGA
* * *
2695140 GTTTAAGTCAAGTGAGATGACTCCCATTCGTGGTTTAAGCCAGACTTAATACTTCAGATGAATCC
1 GTTTAAGTCAAGTGAGATGACTCCC-TTCGCGGTTTAAGCCAGTCTTAATACTTCAGATGACTCC
*
2695205 CCTTCACAG
65 CCTTCACGG
* * * **** * **
2695214 GTTTAAGTCAAGTGATATGACTCCTCTTCACGGTTTCATTTGGTCTTGATACTTTGGATGACTCC
1 GTTTAAGTCAAGTGAGATGACTCC-CTTCGCGGTTTAAGCCAGTCTTAATACTTCAGATGACTCC
* **
2695279 TCTTCGTGG
65 CCTTCACGG
* * ** *
2695288 GATTAAGTCAAGTGAGGTGACTCCCCTTCGCGGTTTAAGCCAGTCTTAATTTTTCAGATGACTTC
1 GTTTAAGTCAAGTGAGATGACT-CCCTTCGCGGTTTAAGCCAGTCTTAATACTTCAGATGACTCC
*
2695353 CATTCACGG
65 CCTTCACGG
*
2695362 GTTTAAGCCAAG
1 GTTTAAGTCAAG
2695374 CGAAATGTTT
Statistics
Matches: 120, Mismatches: 38, Indels: 4
0.74 0.23 0.02
Matches are distributed among these distances:
74 117 0.98
75 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.34
Consensus pattern (73 bp):
GTTTAAGTCAAGTGAGATGACTCCCTTCGCGGTTTAAGCCAGTCTTAATACTTCAGATGACTCCC
CTTCACGG
Found at i:2695491 original size:2 final size:2
Alignment explanation
Indices: 2695484--2695517 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
2695474 TACAAAATTG
2695484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
2695518 CATGAATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2699923 original size:32 final size:32
Alignment explanation
Indices: 2699881--2699950 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
2699871 CTACCCGAAC
*
2699881 ATAATTTCTATCCTGCATAGATTCTGAAATTA
1 ATAATCTCTATCCTGCATAGATTCTGAAATTA
*
2699913 ATAATCTCTATCCTGCATGGATTCTGAAATTA
1 ATAATCTCTATCCTGCATAGATTCTGAAATTA
2699945 ATAATC
1 ATAATC
2699951 CTAATCGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (32 bp):
ATAATCTCTATCCTGCATAGATTCTGAAATTA
Found at i:2702266 original size:25 final size:27
Alignment explanation
Indices: 2702238--2702300 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 27
2702228 AATTACATAA
* *
2702238 TATATATATTTTTAATAAAA-CTAT-C
1 TATATATATTTATAATAAAATATATAC
* *
2702263 TATATATATATATATTAAAATATATAC
1 TATATATATTTATAATAAAATATATAC
2702290 TATATATATTT
1 TATATATATTT
2702301 CAAAGCTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 17 0.55
26 3 0.10
27 11 0.35
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (27 bp):
TATATATATTTATAATAAAATATATAC
Found at i:2702378 original size:22 final size:23
Alignment explanation
Indices: 2702210--2702383 Score: 87
Period size: 22 Copynumber: 7.7 Consensus size: 23
2702200 CAACAATAGT
2702210 AATATA-ATATATA-TTTTAAATTA
1 AATATATATATATATTTTTAAA--A
*
2702233 CATA-ATATATATATTTTTAATAA
1 AATATATATATATATTTTTAA-AA
* * * *
2702256 AACTATCTATATATATATATATTAA
1 AA-TATATATATATATTTTTA-AAA
* *
2702281 AATATATACTATATATATTT--CA
1 AATATATA-TATATATTTTTAAAA
** * ***
2702303 AAGCTATATATGT-TTTCGCAAA
1 AATATATATATATATTTTTAAAA
*
2702325 TATATA-ATATATATTTTTAAAA
1 AATATATATATATATTTTTAAAA
*
2702347 ACTACT-TATAT-TATTTTTAAAA
1 AATA-TATATATATATTTTTAAAA
2702369 AATATATATATATAT
1 AATATATATATATAT
2702384 ATATATATAT
Statistics
Matches: 111, Mismatches: 26, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
20 2 0.02
21 10 0.09
22 39 0.35
23 20 0.18
24 13 0.12
25 27 0.24
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
AATATATATATATATTTTTAAAA
Found at i:2702380 original size:24 final size:25
Alignment explanation
Indices: 2702322--2702459 Score: 83
Period size: 22 Copynumber: 5.6 Consensus size: 25
2702312 ATGTTTTCGC
2702322 AAATATATA-ATATATATTTTTAAA
1 AAATATATATATATATATTTTTAAA
* *
2702346 AACTA-CT-TATAT-TATTTTTAAA
1 AAATATATATATATATATTTTTAAA
* **
2702368 AAATATATATATATATATATATATATTC
1 AAATATATATATATATAT-T-TTTA-AA
* *
2702396 CAA-A-AT-TATATATATTTTGAAA
1 AAATATATATATATATATTTTTAAA
* *
2702418 AAATTATAATGTACATATATTCTTTAAA
1 AAA-TAT-ATATATATATATT-TTTAAA
*
2702446 AACTATATATATAT
1 AAATATATATATAT
2702460 TCCAAAACTA
Statistics
Matches: 83, Mismatches: 18, Indels: 24
0.66 0.14 0.19
Matches are distributed among these distances:
22 16 0.19
23 8 0.10
24 11 0.13
25 12 0.14
26 11 0.13
27 16 0.19
28 9 0.11
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (25 bp):
AAATATATATATATATATTTTTAAA
Done.