Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008242.1 Hibiscus syriacus cultivar Beakdansim tig00110890_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: 16962412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 73
Found at i:6425854 original size:62 final size:60
Alignment explanation
Indices: 6425719--6425881 Score: 152
Period size: 62 Copynumber: 2.6 Consensus size: 60
6425709 ATTAATGATG
* * *
6425719 TAGGGAGGAAAGAGATAAGAGAAGATTTCTATTTTAAAATTTTCACTAAAATTTTAAAAAC
1 TAGGGAGGAAATAGAGAAGAGAATATTTC-ATTTTAAAATTTTCACTAAAATTTTAAAAAC
* * * *
6425780 CA-GGA-GAGAATAGAGAAGAAGAAATATTATCATTTTAAAA-TTTCATTAAAATTTTGAAAAT
1 TAGGGAGGA-AATAGAGAAG-AG-AATATT-TCATTTTAAAATTTTCACTAAAATTTTAAAAAC
* *
6425841 TAGGGAGGAAATAGTGAAGGCAGAATGTTTTCATTTTAAAA
1 TAGGGAGGAAATAGAGAA-G-AGAAT-ATTTCATTTTAAAA
6425882 ACTCAATAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
59 2 0.02
60 11 0.13
61 22 0.27
62 39 0.47
63 9 0.11
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (60 bp):
TAGGGAGGAAATAGAGAAGAGAATATTTCATTTTAAAATTTTCACTAAAATTTTAAAAAC
Found at i:6426319 original size:32 final size:32
Alignment explanation
Indices: 6426283--6426366 Score: 132
Period size: 32 Copynumber: 2.6 Consensus size: 32
6426273 TTGGCCTATG
6426283 TATGTATGTATTTATGTATGTTTTGGTGCATA
1 TATGTATGTATTTATGTATGTTTTGGTGCATA
* *
6426315 TATGTATGTATTTATATATGTTTTGGTGCATG
1 TATGTATGTATTTATGTATGTTTTGGTGCATA
**
6426347 TATGTATGTATACATGTATG
1 TATGTATGTATTTATGTATG
6426367 ATATGTGTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.24, C:0.04, G:0.21, T:0.51
Consensus pattern (32 bp):
TATGTATGTATTTATGTATGTTTTGGTGCATA
Found at i:6438854 original size:44 final size:43
Alignment explanation
Indices: 6438805--6438982 Score: 239
Period size: 44 Copynumber: 4.0 Consensus size: 43
6438795 TTGTTCTAAA
6438805 ATAAATGAAAATGCATAATAGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAAT-GTGCATTATTGGCAGAAAGGTGCC
* * *
6438849 ATAAATGAAAATGCATAACGGTGCATTATTAGCAGAAAGTTGCC
1 ATAAATGAAAATGCATAA-TGTGCATTATTGGCAGAAAGGTGCC
* * * * **
6438893 ATAAATGAAAATACATAACGTCACATTATTGGCAGAAATGTGTT
1 ATAAATGAAAATGCATAATGT-GCATTATTGGCAGAAAGGTGCC
6438937 ATAAATGAAAATGCATAACTGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAA-TGTGCATTATTGGCAGAAAGGTGCC
6438981 AT
1 AT
6438983 TCATGGTATT
Statistics
Matches: 114, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
43 2 0.02
44 110 0.96
45 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.26
Consensus pattern (43 bp):
ATAAATGAAAATGCATAATGTGCATTATTGGCAGAAAGGTGCC
Found at i:6444559 original size:7 final size:7
Alignment explanation
Indices: 6444547--6444572 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6444537 AAGAAGAGAA
6444547 AAAGGGG
1 AAAGGGG
6444554 AAAGGGG
1 AAAGGGG
6444561 AAAGGGG
1 AAAGGGG
6444568 AAAGG
1 AAAGG
6444573 TGAGAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (7 bp):
AAAGGGG
Found at i:6445755 original size:25 final size:25
Alignment explanation
Indices: 6445720--6445800 Score: 68
Period size: 25 Copynumber: 3.5 Consensus size: 25
6445710 TGCATTATTG
*
6445720 GCATAAAGGTGCCATATATGAAAAT
1 GCATAATGGTGCCATATATGAAAAT
*
6445745 GCATAATGGTG-CAT-TATTG-GAA-
1 GCATAATGGTGCCATATA-TGAAAAT
* *
6445767 G-A-AA-GGTTCCATAAATGAAAAT
1 GCATAATGGTGCCATATATGAAAAT
6445789 GCATAATGGTGC
1 GCATAATGGTGC
6445801 ATTATTGGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
19 3 0.07
20 7 0.17
21 4 0.10
22 2 0.05
23 5 0.12
24 7 0.17
25 14 0.33
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (25 bp):
GCATAATGGTGCCATATATGAAAAT
Found at i:6445756 original size:44 final size:44
Alignment explanation
Indices: 6445689--6445902 Score: 311
Period size: 44 Copynumber: 4.9 Consensus size: 44
6445679 TGGCTCTAAA
*
6445689 ATAAATGAAAATGCATAATGGTGCATTATTGGCATAAAGGTGCC
1 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCC
* * *
6445733 ATATATGAAAATGCATAATGGTGCATTATTGGAAGAAAGGTTCC
1 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCC
6445777 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCC
* * * **
6445821 ATAAGTGAAAATGCATAACGGTTCATTATTGGCAGAAAGACGCC
1 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCC
* * * *
6445865 ATAAATGAAAATACATAACGTTACATTATTGGCAGAAA
1 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAA
6445903 TGCACCACTC
Statistics
Matches: 154, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 154 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (44 bp):
ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCC
Found at i:6448402 original size:43 final size:43
Alignment explanation
Indices: 6448337--6448422 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
6448327 TATTCGATGC
*
6448337 ATAGAATTATTAAACCTGTTGTCCATCAACTTAAGTTGATACT
1 ATAGAATTATTAAACCTATTGTCCATCAACTTAAGTTGATACT
6448380 ATAGAATTATTAAACCTATTGTCCATCAACTTAAGTTGATACT
1 ATAGAATTATTAAACCTATTGTCCATCAACTTAAGTTGATACT
6448423 GAAAACTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (43 bp):
ATAGAATTATTAAACCTATTGTCCATCAACTTAAGTTGATACT
Found at i:6451267 original size:18 final size:18
Alignment explanation
Indices: 6451244--6451288 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
6451234 GTCACCCAAA
*
6451244 ATAAATGCAGCTCGGAAG
1 ATAAATACAGCTCGGAAG
*
6451262 ATAAATACAGCTTGGAAG
1 ATAAATACAGCTCGGAAG
6451280 ATAAATACA
1 ATAAATACA
6451289 TTTCAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (18 bp):
ATAAATACAGCTCGGAAG
Found at i:6452805 original size:3 final size:3
Alignment explanation
Indices: 6452797--6452857 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
6452787 TTTATCCATA
*
6452797 TAT TAT TAT TAT TAT TA- TAG TAT TAT TA- TAT TAT TAT T-T TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6452841 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
6452858 AATATATATT
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
2 8 0.15
3 45 0.85
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:6452820 original size:11 final size:10
Alignment explanation
Indices: 6452794--6452873 Score: 74
Period size: 11 Copynumber: 7.6 Consensus size: 10
6452784 ATTTTTATCC
6452794 ATATATTATT
1 ATATATTATT
6452804 AT-TATTATT
1 ATATATTATT
6452813 ATAGTATTATT
1 ATA-TATTATT
6452824 ATATTATTATTTT
1 ATA-TATTA--TT
6452837 ATTATATTATT
1 A-TATATTATT
6452848 AT-TATTATT
1 ATATATTATT
*
6452857 AAATATATATT
1 ATATAT-TATT
*
6452868 AAATAT
1 ATATAT
6452874 ATATATAATA
Statistics
Matches: 61, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
9 17 0.28
10 6 0.10
11 28 0.46
13 8 0.13
14 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (10 bp):
ATATATTATT
Found at i:6452828 original size:8 final size:9
Alignment explanation
Indices: 6452797--6452857 Score: 85
Period size: 8 Copynumber: 7.2 Consensus size: 9
6452787 TTTATCCATA
6452797 TATTATTAT
1 TATTATTAT
6452806 TATTATTA-
1 TATTATTAT
*
6452814 TAGTATTAT
1 TATTATTAT
6452823 TA-TATTAT
1 TATTATTAT
6452831 TATT-TTAT
1 TATTATTAT
6452839 TA-TATTAT
1 TATTATTAT
6452847 TATTATTAT
1 TATTATTAT
6452856 TA
1 TA
6452858 AATATATATT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
7 1 0.02
8 27 0.57
9 19 0.40
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
TATTATTAT
Found at i:6452883 original size:11 final size:11
Alignment explanation
Indices: 6452853--6452877 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6452843 TTATTATTAT
6452853 TATTAAATATA
1 TATTAAATATA
6452864 TATTAAATATA
1 TATTAAATATA
6452875 TAT
1 TAT
6452878 ATAATAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TATTAAATATA
Found at i:6454944 original size:18 final size:18
Alignment explanation
Indices: 6454898--6454945 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
6454888 CTTTTCATTC
6454898 TTTT-TATTATTTATTAT
1 TTTTATATTATTTATTAT
*
6454915 TTTTATAATATTTA-TAT
1 TTTTATATTATTTATTAT
*
6454932 GTTTTATTTTATTT
1 -TTTTATATTATTT
6454946 GCAAGCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTATATTATTTATTAT
Found at i:6465214 original size:19 final size:19
Alignment explanation
Indices: 6465190--6465263 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 19
6465180 ATTATGCTTG
6465190 AAGAAAGAAAAGAAAAAAA
1 AAGAAAGAAAAGAAAAAAA
6465209 AAGAAAGAAAA-AAAAAAA
1 AAGAAAGAAAAGAAAAAAA
6465227 AA-AAA-AAATAGAAATGAAAA
1 AAGAAAGAAA-AGAAA--AAAA
6465247 AAGAGAAGAAAAAGAAA
1 AAGA-AAG-AAAAGAAA
6465264 GGGGTCAAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.06
17 4 0.09
18 12 0.26
19 11 0.23
20 6 0.13
21 1 0.02
22 2 0.04
23 5 0.11
24 3 0.06
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (19 bp):
AAGAAAGAAAAGAAAAAAA
Found at i:6465217 original size:14 final size:14
Alignment explanation
Indices: 6465193--6465248 Score: 71
Period size: 14 Copynumber: 4.0 Consensus size: 14
6465183 ATGCTTGAAG
6465193 AAAGAAAAGAAAAAA
1 AAAG-AAAGAAAAAA
6465208 AAAGAAAGAAAAAA
1 AAAGAAAGAAAAAA
6465222 AAA-AAA-AAAAAA
1 AAAGAAAGAAAAAA
*
6465234 ATAGAAATGAAAAAA
1 AAAGAAA-GAAAAAA
6465249 GAGAAGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
12 8 0.22
13 6 0.16
14 13 0.35
15 10 0.27
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.04
Consensus pattern (14 bp):
AAAGAAAGAAAAAA
Found at i:6465253 original size:14 final size:12
Alignment explanation
Indices: 6465190--6465259 Score: 56
Period size: 13 Copynumber: 5.7 Consensus size: 12
6465180 ATTATGCTTG
6465190 AAGAAAGAAAAG-
1 AAGAAA-AAAAGA
6465202 AA-AAAAAAAGA
1 AAGAAAAAAAGA
*
6465213 AAGAAAAAAAAAA
1 AAG-AAAAAAAGA
*
6465226 AAAAAAAAATAGA
1 AAGAAAAAA-AGA
6465239 AATG-AAAAAAGA
1 AA-GAAAAAAAGA
6465251 GAAGAAAAA
1 -AAGAAAAA
6465260 GAAAGGGGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
10 5 0.11
11 5 0.11
12 12 0.26
13 25 0.53
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:6466551 original size:51 final size:51
Alignment explanation
Indices: 6466468--6466616 Score: 247
Period size: 47 Copynumber: 3.0 Consensus size: 51
6466458 ATTTGCCAAT
6466468 AGCATCTTCT-GAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTT-TCTGATCTGGTTAGACAGAACCA
6466519 AGCATCTTCTGGAAGTGTTCTTTGAGTTTCTGATCT-GTTAGACAGAACC-
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTTCTGATCTGGTTAGACAGAACCA
6466568 A--ATCTTCTGGAAGTGTTCTTTGAG-TTCTGATCTGGTTAGACAGAACCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTTCTGATCTGGTTAGACAGAACCA
6466616 A
1 A
6466617 TCACCGAATT
Statistics
Matches: 95, Mismatches: 0, Indels: 9
0.91 0.00 0.09
Matches are distributed among these distances:
46 9 0.09
47 36 0.38
48 1 0.01
49 1 0.01
50 13 0.14
51 18 0.19
52 17 0.18
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (51 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTTCTGATCTGGTTAGACAGAACCA
Found at i:6467657 original size:107 final size:108
Alignment explanation
Indices: 6467394--6467819 Score: 595
Period size: 107 Copynumber: 4.0 Consensus size: 108
6467384 ATTCAAATCT
* *
6467394 ATCAATTGATGGATTATTTTTTG-AAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCACTTGATGGA-TATTTTTTGCCAGAAAAAGTTCATAATGAGAA-AACTCATCTGAAGAAGGA
* *
6467458 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT-TACCTGAATTC
64 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGT--TTGAATTC
6467504 ATCACTTGATGGATCA-TTTTT-CCAGAAAAAGTTCATAATGAG-AAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGAT-ATTTTTTGCCAGAAAAAGTTCATAATGAGAAAACTCATCTGAAGAAGGAA
6467566 GAAGTTCATAATGAGAAGAACTT-TTCAACCTTTGTTTGAATTC
65 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGTTTGAATTC
* * *
6467609 ATCACTTGATGGATATTTTTTGCCAGAGAAGGTTCATAATGAGAAAACTCGTCTGAAGAAGGAAG
1 ATCACTTGATGGATATTTTTTGCCAGAAAAAGTTCATAATGAGAAAACTCATCTGAAGAAGGAAG
6467674 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTTTGAATTC
66 AAGTTCATAATGAGAAGAACTTGTTCAACC-TTTGTTTGAATTC
* * *
6467718 ATCACTTGATGGAT-TATTTTGCCAG---AGGTTCATAATGAGAGAACTCATCTGAAGAAGGAAG
1 ATCACTTGATGGATATTTTTTGCCAGAAAAAGTTCATAATGAGAAAACTCATCTGAAGAA-G--G
*
6467779 AAGAAGTTCATAATGAGAAGAGCTTGTTC-ACCTTTGTTTGA
63 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGTTTGA
6467820 TACAAGAGGA
Statistics
Matches: 294, Mismatches: 11, Indels: 26
0.89 0.03 0.08
Matches are distributed among these distances:
104 1 0.00
105 55 0.19
106 39 0.13
107 87 0.30
108 47 0.16
109 52 0.18
110 13 0.04
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (108 bp):
ATCACTTGATGGATATTTTTTGCCAGAAAAAGTTCATAATGAGAAAACTCATCTGAAGAAGGAAG
AAGTTCATAATGAGAAGAACTTGTTCAACCTTTGTTTGAATTC
Found at i:6468069 original size:3 final size:3
Alignment explanation
Indices: 6468061--6468142 Score: 139
Period size: 3 Copynumber: 27.7 Consensus size: 3
6468051 TTTTTATCCA
*
6468061 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
6468108 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6468143 AATATATATT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 72 0.97
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:6468154 original size:11 final size:11
Alignment explanation
Indices: 6468138--6468167 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
6468128 TTATTATTAT
6468138 TATTAAATATA
1 TATTAAATATA
6468149 TATTAAATATA
1 TATTAAATATA
6468160 TA-TAAATA
1 TATTAAATA
6468168 ATAAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:6474341 original size:24 final size:25
Alignment explanation
Indices: 6474295--6474349 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
6474285 ATAGTTATGC
*
6474295 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
6474319 CACTTGAAGTGCCATAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
6474344 CA-TTGA
1 CACTTGA
6474350 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:6476963 original size:40 final size:40
Alignment explanation
Indices: 6476915--6476996 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
6476905 TGCAGGTTTA
6476915 TAATACACTTCAGTGTATATGGTGGGCACGACCTTATATG
1 TAATACACTTCAGTGTATATGGTGGGCACGACCTTATATG
** *
6476955 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCAGTGTATATGGTGGGCACGACCTTATATG
6476995 TA
1 TA
6476997 GCATTACGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (40 bp):
TAATACACTTCAGTGTATATGGTGGGCACGACCTTATATG
Found at i:6477151 original size:44 final size:44
Alignment explanation
Indices: 6477101--6477319 Score: 312
Period size: 44 Copynumber: 5.0 Consensus size: 44
6477091 TTAAACATGC
** **
6477101 AAATAAGCTTTTGAGCTTATGGAATAATGACAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
6477145 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
*
6477189 AAATAAGCTTACGATCTTATGGAATAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
* * * *
6477233 AAATAAGCTTACGAGCTTATAGAATAATGGTAATTATGTTTGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
* * * *
6477277 AAATAGGCTTATGAGCTTATGGGATAAATGGTAAATATATTGG
1 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGG
6477320 ATATGCATGT
Statistics
Matches: 157, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
44 143 0.91
45 14 0.09
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.34
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
Found at i:6486178 original size:22 final size:22
Alignment explanation
Indices: 6486150--6486193 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6486140 GCCTATGAGC
6486150 CTACCCAAGGGTCTCCATAGGT
1 CTACCCAAGGGTCTCCATAGGT
*
6486172 CTACCCAAGGTTCTCCATAGGT
1 CTACCCAAGGGTCTCCATAGGT
6486194 GTATAAGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (22 bp):
CTACCCAAGGGTCTCCATAGGT
Found at i:6488749 original size:13 final size:13
Alignment explanation
Indices: 6488731--6488774 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
6488721 TAACTTTTTA
6488731 GGTCAAAGTCAAT
1 GGTCAAAGTCAAT
*
6488744 GGTCAACGATCAAT
1 GGTCAAAG-TCAAT
*
6488758 -GTCAAAGTCAAC
1 GGTCAAAGTCAAT
6488770 GGTCA
1 GGTCA
6488775 GGTCAAAGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.15
13 17 0.65
14 5 0.19
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (13 bp):
GGTCAAAGTCAAT
Found at i:6488769 original size:19 final size:18
Alignment explanation
Indices: 6488745--6488786 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6488735 AAAGTCAATG
*
6488745 GTCAACGATCAATGTCAAA
1 GTCAACGATC-AGGTCAAA
*
6488764 GTCAACGGTCAGGTCAAA
1 GTCAACGATCAGGTCAAA
6488782 GTCAA
1 GTCAA
6488787 TGGGTTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (18 bp):
GTCAACGATCAGGTCAAA
Found at i:6493691 original size:144 final size:145
Alignment explanation
Indices: 6493431--6493719 Score: 571
Period size: 144 Copynumber: 2.0 Consensus size: 145
6493421 GATTTATGCA
6493431 AGAGTTTCCTACTCCGACACAATCCGCCCAATATGAATACACAGCTTCGCAATGACATTCCGAGT
1 AGAGTTTCCTACTCCGACACAATCCGCCCAATATGAATACACAGCTTCGCAATGACATTCCGAGT
6493496 TTTTTTCCAATGAGATGATGAATCAATGTAAGAATGTTGGGATAGGTACAAAAGTCGACTTTGT-
66 TTTTTTCCAATGAGATGATGAATCAATGTAAGAATGTTGGGATAGGTACAAAAGTCGACTTTGTA
6493560 AATGTGTTAACCATG
131 AATGTGTTAACCATG
6493575 AGAGTTTCCTACTCCGACACAATCCGCCCAATATGAATACACAGCTTCGCAATGACATTCCGAGT
1 AGAGTTTCCTACTCCGACACAATCCGCCCAATATGAATACACAGCTTCGCAATGACATTCCGAGT
6493640 TTTTTTCCAATGAGATGATGAATCAATGTAAGAATGTTGGGATAGGTACAAAAGTCGACTTTGTA
66 TTTTTTCCAATGAGATGATGAATCAATGTAAGAATGTTGGGATAGGTACAAAAGTCGACTTTGTA
6493705 AATGTGTTAACCATG
131 AATGTGTTAACCATG
6493720 GATTTCATGA
Statistics
Matches: 144, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
144 129 0.90
145 15 0.10
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (145 bp):
AGAGTTTCCTACTCCGACACAATCCGCCCAATATGAATACACAGCTTCGCAATGACATTCCGAGT
TTTTTTCCAATGAGATGATGAATCAATGTAAGAATGTTGGGATAGGTACAAAAGTCGACTTTGTA
AATGTGTTAACCATG
Found at i:6494404 original size:24 final size:20
Alignment explanation
Indices: 6494347--6494396 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
6494337 TATTGCAGAA
6494347 ATTTATGGCCACAACGAAAG
1 ATTTATGGCCACAACGAAAG
6494367 ATTTATGGCCACAACGAAAG
1 ATTTATGGCCACAACGAAAG
6494387 ATTTCATGGC
1 ATTT-ATGGC
6494397 ATCCACAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (20 bp):
ATTTATGGCCACAACGAAAG
Found at i:6496688 original size:14 final size:14
Alignment explanation
Indices: 6496669--6496697 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6496659 TGCCCAAACG
6496669 AGGATCAATTAATT
1 AGGATCAATTAATT
6496683 AGGATCAATTAATT
1 AGGATCAATTAATT
6496697 A
1 A
6496698 TTCTTACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (14 bp):
AGGATCAATTAATT
Found at i:6500608 original size:21 final size:22
Alignment explanation
Indices: 6500569--6500622 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
6500559 AAGCTTAGGG
6500569 GAGAA-GAATGAAGAAAAGA-AA
1 GAGAAGGAA-GAAGAAAAGAGAA
6500590 TGAGAAGGAAGAA-AAAAGAGAA
1 -GAGAAGGAAGAAGAAAAGAGAA
*
6500612 GACAAGGAAGA
1 GAGAAGGAAGA
6500623 TATTGTTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 16 0.55
22 10 0.34
23 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.31, T:0.04
Consensus pattern (22 bp):
GAGAAGGAAGAAGAAAAGAGAA
Found at i:6501988 original size:36 final size:36
Alignment explanation
Indices: 6501948--6502016 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
6501938 GACTATACAC
* *
6501948 ATAATCATTAGTAGCAAGTAAATGTATATCATGTAT
1 ATAATCATTACTAGCAAGCAAATGTATATCATGTAT
**
6501984 ATAATCATTACTAGCAAGCACTTGTATATCATG
1 ATAATCATTACTAGCAAGCAAATGTATATCATG
6502017 CACAATACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (36 bp):
ATAATCATTACTAGCAAGCAAATGTATATCATGTAT
Found at i:6503071 original size:51 final size:48
Alignment explanation
Indices: 6502951--6503071 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 48
6502941 TGAGACAAAT
6502951 ACATAATTTCAGCATTGAACTTAAATAGACTTACACTAGTGAAATTTA
1 ACATAATTTCAGCATTGAACTTAAATAGACTTACACTAGTGAAATTTA
* * * *
6502999 ACATATTATTCAAGCAGTGAACTT-ATTACCGACTTATACTAGTGAAATTTA
1 ACATAAT-TTC-AGCATTGAACTTAAATA--GACTTACACTAGTGAAATTTA
6503050 TCACATAATTTCAGCATTGAAC
1 --ACATAATTTCAGCATTGAAC
6503072 ACATCTTAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
48 6 0.10
49 6 0.10
50 11 0.18
51 29 0.48
52 3 0.05
53 6 0.10
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (48 bp):
ACATAATTTCAGCATTGAACTTAAATAGACTTACACTAGTGAAATTTA
Found at i:6503117 original size:51 final size:51
Alignment explanation
Indices: 6502975--6503363 Score: 149
Period size: 51 Copynumber: 7.6 Consensus size: 51
6502965 TTGAACTTAA
* * * * * * * **
6502975 ATAGACTTACACTAGTGAAATTTAACATATTATTCAAGCAGTGAACTTATT
1 ATAGACTTACACCAGTCAAATTTAACATATAAATCTAGCATTAAACACATT
** * * * * * * *
6503026 ACCGACTTATACTAGTGAAATTTATCACAT-AATTTCAGCATTGAACACATCT
1 ATAGACTTACACCAGTCAAATTTAACATATAAATCT-AGCATTAAACACAT-T
* * *
6503078 -TAGAGTTATACCAGTCAAATTTAACATATAAATCTAGCATTAAACTCATT
1 ATAGACTTACACCAGTCAAATTTAACATATAAATCTAGCATTAAACACATT
* * * * * *
6503128 ATAGACTTACACCAGTCAAATTTAACATATAATTCCAACACTAAACTCATC
1 ATAGACTTACACCAGTCAAATTTAACATATAAATCTAGCATTAAACACATT
* * * * * * * * ** * * *
6503179 ATAAACTTAGACTAATCAGATTTCACATTTAATTCTATAACTAAACTCATC
1 ATAGACTTACACCAGTCAAATTTAACATATAAATCTAGCATTAAACACATT
* * * * * * *
6503230 ACT-TA-TCTACACCAGTCAAATTTAACACATAATTC-ATTCATTAATCTCATC
1 A-TAGACT-TACACCAGTCAAATTTAACATATAAATCTA-GCATTAAACACATT
* * * * * * * * * *
6503281 ATAGACTTACACTAGTAAAATTTAATATGTAATTCCAACACTAAACTCATC
1 ATAGACTTACACCAGTCAAATTTAACATATAAATCTAGCATTAAACACATT
* * * *
6503332 ACAAACTTACACTAATCAAATTTAACATATAA
1 ATAGACTTACACCAGTCAAATTTAACATATAA
6503364 TTCAAACGCT
Statistics
Matches: 264, Mismatches: 64, Indels: 20
0.76 0.18 0.06
Matches are distributed among these distances:
50 6 0.02
51 250 0.95
52 8 0.03
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (51 bp):
ATAGACTTACACCAGTCAAATTTAACATATAAATCTAGCATTAAACACATT
Found at i:6503149 original size:102 final size:101
Alignment explanation
Indices: 6502951--6503365 Score: 235
Period size: 102 Copynumber: 4.1 Consensus size: 101
6502941 TGAGACAAAT
** * * * *
6502951 ACATAATTTCAGCATTGAACTTAAATAGACTTACACTAGTGAAATTTAACATATTATTCAAGCAG
1 ACATAATTTCAGCATTGAACACAAATAGACTTACACCAGTCAAATTTAACATATAAATCAAGCAG
* * * * * * *
6503016 TGAACTTATTACCGACTTATACTAGTGAAATTTATC
66 TAAACTCATTACAGACTTACACCAGTCAAATTTAAC
** * * *
6503052 ACATAATTTCAGCATTGAACACATCTTAGAGTTATACCAGTCAAATTTAACATATAAATCTAGCA
1 ACATAATTTCAGCATTGAACACA-AATAGACTTACACCAGTCAAATTTAACATATAAATCAAGCA
* *
6503117 TTAAACTCATTATAGACTTACACCAGTCAAATTTAAC
65 GTAAACTCATTACAGACTTACACCAGTCAAATTTAAC
* * * * * * * * * * * * * * * * **
6503154 ATATAATTCCAACACTAAACTCATCATAAACTTAGACTAATCAGATTTCACATTTAATTCTATAA
1 ACATAATTTCAGCATTGAACACA-AATAGACTTACACCAGTCAAATTTAACATATAAATCAAGCA
* * **
6503219 CTAAACTCATCACTTA-TCTACACCAGTCAAATTTAAC
65 GTAAACTCATTACAGACT-TACACCAGTCAAATTTAAC
* * * * * * * *
6503256 ACATAA-TTCATTCATT-AATCTCATCATAGACTTACACTAGTAAAATTTAATATGTAATTCCAA
1 ACATAATTTCA-GCATTGAA-CACA-AATAGACTTACACCAGTCAAATTTAACATATAAAT-CAA
* * * * *
6503319 -CACTAAACTCATCACAAACTTACACTAATCAAATTTAAC
62 GCAGTAAACTCATTACAGACTTACACCAGTCAAATTTAAC
*
6503358 ATATAATT
1 ACATAATT
6503366 CAAACGCTGA
Statistics
Matches: 245, Mismatches: 62, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
101 27 0.11
102 214 0.87
103 4 0.02
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (101 bp):
ACATAATTTCAGCATTGAACACAAATAGACTTACACCAGTCAAATTTAACATATAAATCAAGCAG
TAAACTCATTACAGACTTACACCAGTCAAATTTAAC
Found at i:6503253 original size:153 final size:153
Alignment explanation
Indices: 6503087--6503366 Score: 418
Period size: 153 Copynumber: 1.8 Consensus size: 153
6503077 TTAGAGTTAT
* * *
6503087 ACCAGTCAAATTTAACATATAAATC-TAGCATTAAACTCATTATAGACTTACACCAGTCAAATTT
1 ACCAGTCAAATTTAACACATAAATCAT-GCATTAAACTCATCATAGACTTACACCAGTAAAATTT
* * * * *
6503151 AACATATAATTCCAACACTAAACTCATCATAAACTTAGACTAATCAGATTTCACATTTAATTCTA
65 AACATATAATTCCAACACTAAACTCATCACAAACTTACACTAATCAAATTTAACATATAATTCTA
6503216 TAACTAAACTCATCACTTATCTAC
130 TAACTAAACTCATCACTTATCTAC
* * * *
6503240 ACCAGTCAAATTTAACACATAATTCATTCATTAATCTCATCATAGACTTACACTAGTAAAATTTA
1 ACCAGTCAAATTTAACACATAAATCATGCATTAAACTCATCATAGACTTACACCAGTAAAATTTA
* *
6503305 ATATGTAATTCCAACACTAAACTCATCACAAACTTACACTAATCAAATTTAACATATAATTC
66 ACATATAATTCCAACACTAAACTCATCACAAACTTACACTAATCAAATTTAACATATAATTC
6503367 AAACGCTGAA
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
153 111 0.99
154 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.32
Consensus pattern (153 bp):
ACCAGTCAAATTTAACACATAAATCATGCATTAAACTCATCATAGACTTACACCAGTAAAATTTA
ACATATAATTCCAACACTAAACTCATCACAAACTTACACTAATCAAATTTAACATATAATTCTAT
AACTAAACTCATCACTTATCTAC
Found at i:6503365 original size:51 final size:51
Alignment explanation
Indices: 6503090--6503366 Score: 272
Period size: 51 Copynumber: 5.4 Consensus size: 51
6503080 GAGTTATACC
* * * * * * *
6503090 AGTCAAATTTAACATATAAATCTAGCATTAAACTCATTATAGACTTACACC
1 AGTCAAATTTAACATATAATTCCAACACTAAACTCATCATAAACTTACACT
*
6503141 AGTCAAATTTAACATATAATTCCAACACTAAACTCATCATAAACTTAGACT
1 AGTCAAATTTAACATATAATTCCAACACTAAACTCATCATAAACTTACACT
* * * * * * * *
6503192 AATCAGATTTCACATTTAATTCTATA-ACTAAACTCATCACTTATC-TACACC
1 AGTCAAATTTAACATATAATTCCA-ACACTAAACTCATCA-TAAACTTACACT
* * * * *
6503243 AGTCAAATTTAACACATAATT-CATTCATTAATCTCATCATAGACTTACACT
1 AGTCAAATTTAACATATAATTCCA-ACACTAAACTCATCATAAACTTACACT
* * * *
6503294 AGTAAAATTTAATATGTAATTCCAACACTAAACTCATCACAAACTTACACT
1 AGTCAAATTTAACATATAATTCCAACACTAAACTCATCATAAACTTACACT
*
6503345 AATCAAATTTAACATATAATTC
1 AGTCAAATTTAACATATAATTC
6503367 AAACGCTGAA
Statistics
Matches: 178, Mismatches: 43, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
50 4 0.02
51 168 0.94
52 6 0.03
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (51 bp):
AGTCAAATTTAACATATAATTCCAACACTAAACTCATCATAAACTTACACT
Found at i:6503852 original size:41 final size:41
Alignment explanation
Indices: 6503750--6503889 Score: 140
Period size: 41 Copynumber: 3.4 Consensus size: 41
6503740 CTAAGGACTG
* * ** *
6503750 ATACTTTAGTGGCGTTTTTAGACAAACACCACTCTAAACTC
1 ATACTTTAGTGGCATTTTTATACAAACTTCACTATAAACTC
* * *
6503791 GTACTTTTGTGGCTTTTTTATACAAACTTCACTATAAACTC
1 ATACTTTAGTGGCATTTTTATACAAACTTCACTATAAACTC
* *
6503832 ATACTTTAGTGGCATTTTTATA-AAAATGTCGCTA-AAGACTC
1 ATACTTTAGTGGCATTTTTATACAAACT-TCACTATAA-ACTC
* *
6503873 GTACTTTAGTGGTATTT
1 ATACTTTAGTGGCATTT
6503890 GTGTTTATAA
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 6 0.07
41 77 0.93
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (41 bp):
ATACTTTAGTGGCATTTTTATACAAACTTCACTATAAACTC
Found at i:6504969 original size:18 final size:17
Alignment explanation
Indices: 6504946--6504988 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
6504936 ATATATACAT
6504946 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
6504964 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
6504981 ATAA-AATA
1 ATAATAATA
6504989 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:6505395 original size:37 final size:37
Alignment explanation
Indices: 6505345--6505449 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
6505335 GTGCTTGTGG
* * *
6505345 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * * * *
6505382 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
6505419 ATCCAATTTTTAGGAGTTTAAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
6505450 GACGAAAATG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:6506296 original size:105 final size:105
Alignment explanation
Indices: 6505992--6506622 Score: 914
Period size: 105 Copynumber: 6.0 Consensus size: 105
6505982 GCATTGTTCC
* * * ** *
6505992 GAGTCCAATATCCTCCATCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
6506056 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
6506098 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
6506158 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
6506198 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAGATTGGGAGGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
6506263 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
6506303 GAGTCCAATATCCTTCTTTGTCAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
6506368 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
6506408 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
6506473 TAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
6506513 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
6506578 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
6506619 GAGT
1 GAGT
6506623 GTCACGATAT
Statistics
Matches: 481, Mismatches: 37, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
100 83 0.17
101 1 0.00
102 7 0.01
104 4 0.01
105 303 0.63
106 83 0.17
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:6506868 original size:36 final size:36
Alignment explanation
Indices: 6506821--6506896 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
6506811 ATTTTGGAGA
* *
6506821 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGGGAGACAAAATTCATTTCAAGG
*
6506857 GAAACTATCTCAAGGGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGGGAGACAAAATTCATTTCAAGG
6506893 GAAA
1 GAAA
6506897 TGTTTTCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGGGAGACAAAATTCATTTCAAGG
Found at i:6506992 original size:104 final size:104
Alignment explanation
Indices: 6506797--6507113 Score: 518
Period size: 104 Copynumber: 3.1 Consensus size: 104
6506787 TTCGTTAAAT
* ** *
6506797 TGTTTTCAAAGTTTAT-TTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
6506858 AAACTATCTCAAGGGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
6506897 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
6506962 AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
6507001 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
6507066 AAACTATCT-AAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAA-GAGAGAAAAAATTCATTTCAAGGGAAA
6507105 TGTTTTCAA
1 TGTTTTCAA
6507114 GAGAAACTGT
Statistics
Matches: 203, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
100 15 0.07
101 30 0.15
103 5 0.02
104 153 0.75
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:6507070 original size:39 final size:39
Alignment explanation
Indices: 6507016--6507090 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
6507006 TCAATGTTTA
* *
6507016 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCT-AAGGAGAGAAAAAATTTTC
* *
6507055 TGTTTCGAGGGAAACTATCTAAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTAAGGAGAGAAAAAATT
6507091 AATTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 4 0.13
39 27 0.87
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTAAGGAGAGAAAAAATTTTC
Found at i:6507269 original size:36 final size:36
Alignment explanation
Indices: 6507229--6507342 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 36
6507219 CTTTCGAGTG
* *
6507229 AAAACGGTCTCAAGAGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* ** * * * **
6507265 AAAACAATCTTGAGTGAAATAAATCTTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
*
6507301 AAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TCTTGTTTTAAGA
6507337 AAAACA
1 AAAACA
6507343 AATTTGAGTG
Statistics
Matches: 58, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
36 57 0.98
37 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:6507320 original size:72 final size:75
Alignment explanation
Indices: 6507184--6507353 Score: 217
Period size: 72 Copynumber: 2.3 Consensus size: 75
6507174 TAAAATCTTC
* * * *
6507184 TTAA-AAAAACAACCATGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGAGAGA
1 TTAAGAAAAACAATCTTGAGTGAAATGAAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGAGAGA
*
6507248 CAAA-TCTTGTT
65 CAAAGT-ATGTT
*
6507259 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGAC
1 TTAAGAAAAACAATCTTGAGTGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGAGAGAC
6507321 AAAGTATGTT
66 AAAGTATGTT
6507331 TTAAGAAAAACAAAT-TTGAGTGA
1 TTAAGAAAAAC-AATCTTGAGTGA
6507354 GATTGTTGAG
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
72 44 0.51
73 15 0.17
75 8 0.09
76 19 0.22
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (75 bp):
TTAAGAAAAACAATCTTGAGTGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGAGAGAC
AAAGTATGTT
Found at i:6508794 original size:17 final size:17
Alignment explanation
Indices: 6508772--6508805 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6508762 TCCATAAATC
*
6508772 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
*
6508789 CAAAATCAAACATTCCA
1 CAAAATCAAACAATCCA
6508806 AAATATTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:6510773 original size:21 final size:21
Alignment explanation
Indices: 6510748--6510828 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
6510738 CAGAACCCCA
* *
6510748 GGGGGTATCGATTCCCTTGTG
1 GGGGGAATCGATTCCCTTATG
* **
6510769 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCCTT-ATG
* *
6510792 GGGGGAATCGGTTCCCTCATG
1 GGGGGAATCGATTCCCTTATG
6510813 GGGGG-ATCGATTCCCT
1 GGGGGAATCGATTCCCT
6510829 CTGCACCAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 10 0.20
21 17 0.35
22 9 0.18
23 13 0.27
ACGTcount: A:0.15, C:0.23, G:0.36, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTATG
Found at i:6514705 original size:22 final size:21
Alignment explanation
Indices: 6514663--6514702 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6514653 GAGTTTATTT
*
6514663 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
6514684 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
6514703 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:6518403 original size:183 final size:183
Alignment explanation
Indices: 6518095--6518448 Score: 629
Period size: 183 Copynumber: 1.9 Consensus size: 183
6518085 ATCAGGTTTA
6518095 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
6518160 GCCAAGTGTCTGAGCAATGTCATGATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATGATTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
6518225 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * *
6518278 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACATCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
6518343 GCCAAGTGTCCGAGCAGTGTCAT-AGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAATGTCATGA-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
6518407 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
6518449 CGGATTTAAT
Statistics
Matches: 163, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 1 0.01
183 162 0.99
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATGATTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:6523486 original size:19 final size:19
Alignment explanation
Indices: 6523454--6523513 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
6523444 ATATATATGT
**
6523454 ATATTAGACTTATAGTAAA
1 ATATTAGAAATATAGTAAA
*
6523473 ATATTAGAAATATATATATATA
1 ATATTAGAAATATA-GTA-A-A
*
6523495 ATAATA-AAATATAGTAAA
1 ATATTAGAAATATAGTAAA
6523513 A
1 A
6523514 AATAAATGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 2 0.06
19 13 0.39
20 4 0.12
21 8 0.24
22 6 0.18
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (19 bp):
ATATTAGAAATATAGTAAA
Found at i:6523568 original size:15 final size:14
Alignment explanation
Indices: 6523545--6523587 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
6523535 ATATATATAT
*
6523545 ACATAAATAATAATA
1 ACATGAATAA-AATA
*
6523560 ACATGAATAAAAAA
1 ACATGAATAAAATA
*
6523574 ATATGAATAAAATA
1 ACATGAATAAAATA
6523588 CCATATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (14 bp):
ACATGAATAAAATA
Found at i:6526688 original size:51 final size:50
Alignment explanation
Indices: 6526547--6526762 Score: 165
Period size: 51 Copynumber: 4.3 Consensus size: 50
6526537 AGTGCACCAA
* * * * * * *
6526547 TCAAATTTAATACATAA-TTCAAGCATTGAACCTATGACAGACTTACAAAG
1 TCAAATTTAACACATAACTCCAA-CAATAAACCTATCATAGACTTACACAG
* * * *
6526597 TCAAATTTAACACATAATTCCAGC----AACCTATCACACACTTACACTAG
1 TCAAATTTAACACATAACTCCAACAATAAACCTATCATAGACTTACAC-AG
* * *
6526644 TTAAATTTAACACATGA-TGCCAACAATAAACCTATCATTGACTTACAACAG
1 TCAAATTTAACACATAACT-CCAACAATAAACCTATCATAGACTTAC-ACAG
* * * *
6526695 TCAAATTTAACTCATAACTCCAACATTGAACCTATCATAGACTTACACCCG
1 TCAAATTTAACACATAACTCCAACAATAAACCTATCATAGACTTACA-CAG
* *
6526746 TCAAAGTTAACATATAA
1 TCAAATTTAACACATAA
6526763 TAAGGTAAAT
Statistics
Matches: 134, Mismatches: 22, Indels: 19
0.77 0.13 0.11
Matches are distributed among these distances:
46 18 0.13
47 21 0.16
50 18 0.13
51 74 0.55
52 3 0.02
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (50 bp):
TCAAATTTAACACATAACTCCAACAATAAACCTATCATAGACTTACACAG
Found at i:6535925 original size:18 final size:18
Alignment explanation
Indices: 6535899--6535937 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6535889 GCTTCACTTC
*
6535899 CTTAGAAGTCATGAATCT
1 CTTAAAAGTCATGAATCT
* *
6535917 CTTAAAAGTTATTAATCT
1 CTTAAAAGTCATGAATCT
6535935 CTT
1 CTT
6535938 GAATCTTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (18 bp):
CTTAAAAGTCATGAATCT
Found at i:6545784 original size:20 final size:20
Alignment explanation
Indices: 6545761--6545810 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
6545751 TTAACTTTTT
6545761 CTTTTATCTTTC-TTTCTTAA
1 CTTTTATCTTTCATTT-TTAA
* *
6545781 CTTTTCTATTTCATTTTTAA
1 CTTTTATCTTTCATTTTTAA
6545801 CTTTTA-CTTT
1 CTTTTATCTTT
6545811 TTATCTCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (20 bp):
CTTTTATCTTTCATTTTTAA
Found at i:6555335 original size:34 final size:32
Alignment explanation
Indices: 6555273--6555342 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
6555263 ACCTTACACC
* *
6555273 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
6555305 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
6555339 TCCC
1 TCCC
6555343 CTTTACAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:6555823 original size:20 final size:21
Alignment explanation
Indices: 6555780--6555839 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
6555770 AAACCATTCA
*
6555780 GGGGGAATCTGTACCCCATGG
1 GGGGGAATCTGTACCCCCTGG
*
6555801 GGGGGAATCTGTTCCCCCT-G
1 GGGGGAATCTGTACCCCCTGG
6555821 GGGGGAATCTGTACCCCCT
1 GGGGGAATCTGTACCCCCT
6555840 AGGCAATCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.15, C:0.28, G:0.35, T:0.22
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:6558865 original size:21 final size:20
Alignment explanation
Indices: 6558826--6558863 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6558816 AAACCATTCA
*
6558826 GGGGGGAATTTGTACCCCTG
1 GGGGGGAATCTGTACCCCTG
6558846 GGGGGGAATCTGTACCCC
1 GGGGGGAATCTGTACCCC
6558864 CTAGGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.24, G:0.39, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCTG
Found at i:6559368 original size:19 final size:20
Alignment explanation
Indices: 6559284--6559373 Score: 148
Period size: 20 Copynumber: 4.5 Consensus size: 20
6559274 ATGTTTTTAT
6559284 GAAGATTCATGATTTCTAAA
1 GAAGATTCATGATTTCTAAA
6559304 GAAGATTCATGATTTCTAAA
1 GAAGATTCATGATTTCTAAA
6559324 GAAGATTCATGATTTCTAAA
1 GAAGATTCATGATTTCTAAA
*
6559344 AAAGATTCATGATTT-TAATA
1 GAAGATTCATGATTTCTAA-A
6559364 -AAGATTCATG
1 GAAGATTCATG
6559374 CCCTTACGCT
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
19 13 0.19
20 55 0.81
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (20 bp):
GAAGATTCATGATTTCTAAA
Found at i:6563150 original size:77 final size:79
Alignment explanation
Indices: 6563020--6563174 Score: 210
Period size: 77 Copynumber: 2.0 Consensus size: 79
6563010 ATATAGTAAG
* *
6563020 TAAACATTAAAAGAATGTAATTCTAATTACAACTCTTTTAATGGTTATTTAATTCAGAA-TAATT
1 TAAACATTAAAAGAATGTAATTCAAATTACAACTCTTTTAATGGATATTTAATT-AGAATTAATT
6563084 AAATAAGAGTTTAAA
65 AAATAAGAGTTTAAA
* * * *
6563099 TAAACATT-AAAGAGTGTAATT-AAGATTATAAGTC-TTTAATGGATATTTAATTTGAATTAATT
1 TAAACATTAAAAGAATGTAATTCAA-ATTACAACTCTTTTAATGGATATTTAATTAGAATTAATT
6563161 AAATAAGAGTTTAA
65 AAATAAGAGTTTAA
6563175 TTAATTCGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
76 3 0.04
77 37 0.54
78 20 0.29
79 8 0.12
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTCAAATTACAACTCTTTTAATGGATATTTAATTAGAATTAATTA
AATAAGAGTTTAAA
Found at i:6571207 original size:37 final size:37
Alignment explanation
Indices: 6571166--6571237 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
6571156 GAAACAAAAT
*
6571166 ATGGAAAACATTGATATAAATATAAAACACAAGAAAC
1 ATGGAAAACATTGATATAAAGATAAAACACAAGAAAC
** * * *
6571203 ATGGAAAATGTTGATATGAAGATAAAGCTCAAGAA
1 ATGGAAAACATTGATATAAAGATAAAACACAAGAA
6571238 GCACTGGATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.21
Consensus pattern (37 bp):
ATGGAAAACATTGATATAAAGATAAAACACAAGAAAC
Found at i:6576022 original size:24 final size:21
Alignment explanation
Indices: 6575987--6576029 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
6575977 GGCTCATTCT
*
6575987 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
6576010 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
6576030 ATCTTATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:6577274 original size:15 final size:15
Alignment explanation
Indices: 6577238--6577267 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6577228 GTGCTTCAAC
6577238 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
6577252 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
6577267 T
1 T
6577268 CTTTTTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:6586804 original size:13 final size:13
Alignment explanation
Indices: 6586786--6586810 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6586776 AAATAAAAAA
6586786 TTTATTTTTATTT
1 TTTATTTTTATTT
6586799 TTTATTTTTATT
1 TTTATTTTTATT
6586811 ATTCATGGAT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTATTTTTATTT
Found at i:6590776 original size:21 final size:22
Alignment explanation
Indices: 6590733--6590780 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
6590723 AACTTCAAGA
*
6590733 AAGTATCGATGTCACATACTAG
1 AAGTATCGATGTCACAAACTAG
*
6590755 AAGTATCGAT-TCTCAAACTAG
1 AAGTATCGATGTCACAAACTAG
6590776 -AGTAT
1 AAGTAT
6590781 TGATACCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.21
21 9 0.38
22 10 0.42
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (22 bp):
AAGTATCGATGTCACAAACTAG
Found at i:6593826 original size:21 final size:21
Alignment explanation
Indices: 6593802--6593844 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6593792 ATTAAAAATC
6593802 ATGATAAACATTATCAAACAA
1 ATGATAAACATTATCAAACAA
6593823 ATGATAAACATTATCAAACAA
1 ATGATAAACATTATCAAACAA
6593844 A
1 A
6593845 ATAATCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.14, G:0.05, T:0.23
Consensus pattern (21 bp):
ATGATAAACATTATCAAACAA
Found at i:6602117 original size:19 final size:19
Alignment explanation
Indices: 6602093--6602133 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
6602083 TAAATTAAAG
6602093 TAATTATATAATAATGAAT
1 TAATTATATAATAATGAAT
6602112 TAATTATATAATAATGAAT
1 TAATTATATAATAATGAAT
6602131 TAA
1 TAA
6602134 AGTTGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TAATTATATAATAATGAAT
Found at i:6603346 original size:29 final size:29
Alignment explanation
Indices: 6603313--6603368 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
6603303 GAATTAGACC
**
6603313 GTCCAGTCAGTGCCAACTTCTAGAAGGCA
1 GTCCAGTCAGCACCAACTTCTAGAAGGCA
* *
6603342 GTCCAGTCTGCACCAGCTTCTAGAAGG
1 GTCCAGTCAGCACCAACTTCTAGAAGG
6603369 TAGTTCATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.21
Consensus pattern (29 bp):
GTCCAGTCAGCACCAACTTCTAGAAGGCA
Found at i:6609626 original size:84 final size:84
Alignment explanation
Indices: 6609436--6609627 Score: 207
Period size: 84 Copynumber: 2.3 Consensus size: 84
6609426 AGAGCAGTAC
* * * *
6609436 TTAGCGGCGTTTTTATACAAACGCCGCAATAGGGTAAGTATATAATGGAGTTTTTTTCAACAAAT
1 TTAGAGGCATTTTTATACAAATGCCGCAATAGGGTAAGTATATAATGGAGTTTTTTTCAAAAAAT
*
6609501 ATCGCAATAGAGTAGTAAT
66 ATCGCAATAGAGTACTAAT
* * * *
6609520 TTA-ATGGTATTTTTATTA-AAATGCCGTAATAGGGTTAA-TCTATAGTGGCA-TTTTTTTCAAA
1 TTAGA-GGCATTTTTA-TACAAATGCCGCAATAGGG-TAAGTATATAATGG-AGTTTTTTTCAAA
6609581 AAATGA-CGCAATAGAGTACTACA-
62 AAAT-ATCGCAATAGAGTACTA-AT
6609604 TTAGAGGCATTTTTATACAAATGC
1 TTAGAGGCATTTTTATACAAATGC
6609628 ATCAATGAGT
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
83 2 0.02
84 79 0.88
85 9 0.10
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (84 bp):
TTAGAGGCATTTTTATACAAATGCCGCAATAGGGTAAGTATATAATGGAGTTTTTTTCAAAAAAT
ATCGCAATAGAGTACTAAT
Found at i:6609822 original size:82 final size:83
Alignment explanation
Indices: 6609708--6609863 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 83
6609698 TTGATGTATA
* * *
6609708 GTGGCATTTTTTGATCAAATGCCGCAAAAGACTCTTA-TATTAGAGGCGTTTGTATACAAATGTC
1 GTGGCATTTTTTGATCAAATGCCGCAAAAGACTCGTACT-TTAGAGGCATTTGTATACAAATGCC
6609772 ACTAAAGACTAAGACTTTC
65 ACTAAAGACTAAGACTTTC
* * * * * * *
6609791 GTGGCCTTTTTTTA-CAAATGTCGCTATAGACTCGTACTTTAGTGGCATTTTTATACAAATGCCA
1 GTGGCATTTTTTGATCAAATGCCGCAAAAGACTCGTACTTTAGAGGCATTTGTATACAAATGCCA
*
6609855 CTATAGACT
66 CTAAAGACT
6609864 TTACTTTAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
82 48 0.79
83 13 0.21
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (83 bp):
GTGGCATTTTTTGATCAAATGCCGCAAAAGACTCGTACTTTAGAGGCATTTGTATACAAATGCCA
CTAAAGACTAAGACTTTC
Found at i:6609869 original size:40 final size:41
Alignment explanation
Indices: 6609706--6609882 Score: 135
Period size: 41 Copynumber: 4.3 Consensus size: 41
6609696 CCTTGATGTA
* *
6609706 TAGTGGCATTTTT-TGATCAAATGCCGCAAAAGACTCTTA-TAT
1 TAGTGGCATTTTTAT-A-CAAATGCCACTAAAGACTCTTACT-T
* * * * ***
6609748 TAGAGGCGTTTGTATACAAATGTCACTAAAGACTAAGACTT
1 TAGTGGCATTTTTATACAAATGCCACTAAAGACTCTTACTT
* * * * * * *
6609789 TCGTGGCCTTTTTTTACAAATGTCGCTATAGACTCGTACTT
1 TAGTGGCATTTTTATACAAATGCCACTAAAGACTCTTACTT
*
6609830 TAGTGGCATTTTTATACAAATGCCACTATAGACT-TTACTT
1 TAGTGGCATTTTTATACAAATGCCACTAAAGACTCTTACTT
* *
6609870 TAGTTGCTTTTTT
1 TAGTGGCATTTTT
6609883 GTTTAAACAC
Statistics
Matches: 106, Mismatches: 27, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
40 16 0.15
41 77 0.73
42 12 0.11
43 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (41 bp):
TAGTGGCATTTTTATACAAATGCCACTAAAGACTCTTACTT
Found at i:6612006 original size:46 final size:46
Alignment explanation
Indices: 6611938--6612355 Score: 583
Period size: 46 Copynumber: 9.1 Consensus size: 46
6611928 AATCCATCAA
*
6611938 TAAAATGCATGAAAGGACGCATTAAGGCATGAAAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * *
6611984 TAAAATGCATGAAATGATGCATTAAGGCATGAACGAATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* *
6612030 TAAAATGCATGAAAGGATGCATTAAGGTATGAACA-AATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAA-AGGATGCCATAAT
*
6612076 TAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * *
6612122 T-AAATGCATGAAACGATGCATTAAGGCGTGAACA-GATGTCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAA-AGGATGCCATAAT
* * * * *
6612167 CAAAATGCATGAAAGGATGCATCAAGGAATGAAAGGATTCCATCAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * *
6612213 TAAAATACATGAAATGATGCATTAAGGCATAAAAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
** * *
6612259 T-AAATGCATGAAAGGATGCATTATTGCATGAACGGATGCCATATT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
*
6612304 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAC
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
6612350 TAAAAT
1 TAAAAT
6612356 TTACAAGAAA
Statistics
Matches: 324, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
45 78 0.24
46 246 0.76
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
Found at i:6612015 original size:20 final size:20
Alignment explanation
Indices: 6611944--6612343 Score: 120
Period size: 20 Copynumber: 17.7 Consensus size: 20
6611934 TCAATAAAAT
*
6611944 GCATGAAAGGACGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
6611964 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
6611990 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
6612010 GCATGAACGAATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
6612036 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
6612056 GTATGAACA-AATGCCATAATTAAAAT
1 GCATGAA-AGGATG-C---ATT--AAG
6612082 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
6612102 GCATGAACGGATGCCATAATTAAAT
1 GCATGAAAGGATG-C---ATT-AAG
*
6612127 GCATGAAACGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
6612147 GCGTGAACA-GATGTCATAATCAAAAT
1 GCATGAA-AGGATG-CAT--T---AAG
*
6612173 GCATGAAAGGATGCATCAAG
1 GCATGAAAGGATGCATTAAG
* * *
6612193 GAATGAAAGGATTCCATCATTAAAAT
1 GCATGAAAGGA-T---GCATT--AAG
* *
6612219 ACATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
6612239 GCATAAAAGGATGCCATAATTAAAT
1 GCATGAAAGGATG-C---ATT-AAG
**
6612264 GCATGAAAGGATGCATTATT
1 GCATGAAAGGATGCATTAAG
* *
6612284 GCATGAACGGATGCCATATTTAAAAT
1 GCATGAAAGGATG-C--A-TT--AAG
6612310 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
6612330 GCATGAAAGGATGC
1 GCATGAAAGGATGC
6612344 CATAACTAAA
Statistics
Matches: 284, Mismatches: 46, Indels: 100
0.66 0.11 0.23
Matches are distributed among these distances:
20 115 0.40
21 18 0.06
22 15 0.05
23 3 0.01
24 22 0.08
25 37 0.13
26 74 0.26
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.23
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:6612088 original size:26 final size:26
Alignment explanation
Indices: 6612010--6612088 Score: 64
Period size: 26 Copynumber: 3.3 Consensus size: 26
6612000 ATGCATTAAG
*
6612010 GCATGAACGAATGCCATAATTAAAAT
1 GCATGAACAAATGCCATAATTAAAAT
* *
6612036 GCATGAA-AGGATG-C---ATT--AAG
1 GCATGAACA-AATGCCATAATTAAAAT
*
6612056 GTATGAACAAATGCCATAATTAAAAT
1 GCATGAACAAATGCCATAATTAAAAT
6612082 GCATGAA
1 GCATGAA
6612089 AGGATGCATT
Statistics
Matches: 38, Mismatches: 7, Indels: 16
0.62 0.11 0.26
Matches are distributed among these distances:
20 11 0.29
21 2 0.05
22 3 0.08
24 3 0.08
25 1 0.03
26 18 0.47
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.23
Consensus pattern (26 bp):
GCATGAACAAATGCCATAATTAAAAT
Found at i:6612095 original size:26 final size:26
Alignment explanation
Indices: 6611964--6612049 Score: 94
Period size: 26 Copynumber: 3.5 Consensus size: 26
6611954 ACGCATTAAG
6611964 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCCATAATTAAAAT
* *
6611990 GCATGAAATGATG-C---ATT--AAG
1 GCATGAAAGGATGCCATAATTAAAAT
* *
6612010 GCATGAACGAATGCCATAATTAAAAT
1 GCATGAAAGGATGCCATAATTAAAAT
6612036 GCATGAAAGGATGC
1 GCATGAAAGGATGC
6612050 ATTAAGGTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
20 12 0.26
21 1 0.02
22 3 0.07
24 3 0.07
25 1 0.02
26 26 0.57
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAATTAAAAT
Found at i:6612181 original size:91 final size:93
Alignment explanation
Indices: 6611938--6612355 Score: 598
Period size: 91 Copynumber: 4.6 Consensus size: 93
6611928 AATCCATCAA
* *
6611938 TAAAATGCATGAAAGGACGCATTAAGGCATGAA-AGGATGCCATAATTAAAATGCATGAAATGAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAACAGGATGCCATAATTAAAATGCATGAAAGGAT
*
6612002 GCATTAAGGCATGAACGAATGCCATAAT
66 GCATTAAGGCATGAACGGATGCCATAAT
* *
6612030 TAAAATGCATGAAAGGATGCATTAAGGTATGAACA-AATGCCATAATTAAAATGCATGAAAGGAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAACAGGATGCCATAATTAAAATGCATGAAAGGAT
6612094 GCATTAAGGCATGAACGGATGCCATAAT
66 GCATTAAGGCATGAACGGATGCCATAAT
* * * *
6612122 T-AAATGCATGAAACGATGCATTAAGGCGTGAACA-GATGTCATAATCAAAATGCATGAAAGGAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAACAGGATGCCATAATTAAAATGCATGAAAGGAT
* * * * *
6612185 GCATCAAGGAATGAAAGGATTCCATCAT
66 GCATTAAGGCATGAACGGATGCCATAAT
* * *
6612213 TAAAATACATGAAATGATGCATTAAGGCAT-AAAAGGATGCCATAATT-AAATGCATGAAAGGAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAACAGGATGCCATAATTAAAATGCATGAAAGGAT
** *
6612276 GCATTATTGCATGAACGGATGCCATATT
66 GCATTAAGGCATGAACGGATGCCATAAT
*
6612304 TAAAATGCATGAAAGGATGCATTAAGGCATGAA-AGGATGCCATAACTAAAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAACAGGATGCCATAATTAAAAT
6612356 TTACAAGAAA
Statistics
Matches: 288, Mismatches: 33, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
91 160 0.56
92 127 0.44
93 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (93 bp):
TAAAATGCATGAAAGGATGCATTAAGGCATGAACAGGATGCCATAATTAAAATGCATGAAAGGAT
GCATTAAGGCATGAACGGATGCCATAAT
Found at i:6612185 original size:137 final size:136
Alignment explanation
Indices: 6611938--6612355 Score: 604
Period size: 137 Copynumber: 3.0 Consensus size: 136
6611928 AATCCATCAA
* *
6611938 TAAAATGCATGAAAGGACGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAAATGATG
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATT-AAATGCATGAAACGATG
* *
6612003 CATTAAGGCATGAACGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGTATGAACA-AA
65 CATTAAGGCATGAACG-ATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAA-AGGA
6612067 TGCCATAAT
128 TGCCATAAT
*
6612076 TAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTAAATGCATGAAACGATGC
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAATGCATGAAACGATGC
* * * * *
6612141 ATTAAGGCGTGAACAGATGTCATAATCAAAATGCATGAAAGGATGCATCAAGGAATGAAAGGATT
66 ATTAAGGCATGAAC-GATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATG
*
6612206 CCATCAT
130 CCATAAT
* * * *
6612213 TAAAATACATGAAATGATGCATTAAGGCATAAAAGGATGCCATAATTAAATGCATGAAAGGATGC
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAATGCATGAAACGATGC
** * *
6612278 ATTATTGCATGAACGGATGCCATATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
66 ATTAAGGCATGAAC-GATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATG
*
6612343 CCATAAC
130 CCATAAT
6612350 TAAAAT
1 TAAAAT
6612356 TTACAAGAAA
Statistics
Matches: 250, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
136 1 0.00
137 203 0.81
138 46 0.18
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (136 bp):
TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAATGCATGAAACGATGC
ATTAAGGCATGAACGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGC
CATAAT
Found at i:6620952 original size:21 final size:21
Alignment explanation
Indices: 6620923--6620972 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
6620913 TGATTTATTA
*
6620923 TTATTGATTTCAAGTTGGTTG
1 TTATGGATTTCAAGTTGGTTG
* **
6620944 TTATGGATTTGAAGTTTTTTG
1 TTATGGATTTCAAGTTGGTTG
6620965 TTATGGAT
1 TTATGGAT
6620973 GTCATGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.02, G:0.24, T:0.54
Consensus pattern (21 bp):
TTATGGATTTCAAGTTGGTTG
Found at i:6620981 original size:21 final size:21
Alignment explanation
Indices: 6620923--6620981 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
6620913 TGATTTATTA
* * **
6620923 TTATTGATTTCAAGTTGGTTG
1 TTATGGATGTCAAGTTTTTTG
* *
6620944 TTATGGATTTGAAGTTTTTTG
1 TTATGGATGTCAAGTTTTTTG
*
6620965 TTATGGATGTCATGTTT
1 TTATGGATGTCAAGTTT
6620982 ATTGGATAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.03, G:0.24, T:0.54
Consensus pattern (21 bp):
TTATGGATGTCAAGTTTTTTG
Found at i:6623498 original size:54 final size:55
Alignment explanation
Indices: 6623385--6623490 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 55
6623375 CATAACGGTG
* **
6623385 CATTTTCGGCACTAAATGTGCAACCCATGGTATTCATAATGTGTTTATGAATAAT
1 CATTTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAAT
** * *
6623440 CATTTT-GGCACTATGTGTGCAATCCATGGAATTCATAATAAGTTTGTGAAT
1 CATTTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAAT
6623491 TTCCATTTCA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
54 38 0.86
55 6 0.14
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (55 bp):
CATTTTCGGCACTAAATGTGCAACCCATGGAATTCATAATAAGTTTATGAATAAT
Found at i:6623505 original size:54 final size:54
Alignment explanation
Indices: 6623401--6623505 Score: 122
Period size: 54 Copynumber: 1.9 Consensus size: 54
6623391 CGGCACTAAA
* ** **
6623401 TGTGCAACCCATGGTATTCATAATGTGTTTATGAATAATCATTTTGGCACTATG
1 TGTGCAACCCATGGAATTCATAATAAGTTTATGAATAATCATTTCAGCACTATG
* * *
6623455 TGTGCAATCCATGGAATTCATAATAAGTTTGTGAAT-TTCCATTTCAGCACT
1 TGTGCAACCCATGGAATTCATAATAAGTTTATGAATAAT-CATTTCAGCACT
6623506 TCGGTGCAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.02
54 41 0.98
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (54 bp):
TGTGCAACCCATGGAATTCATAATAAGTTTATGAATAATCATTTCAGCACTATG
Found at i:6627142 original size:16 final size:16
Alignment explanation
Indices: 6627121--6627166 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
6627111 AGTCTTCGGG
6627121 ATTTATAAATAATAAT
1 ATTTATAAATAATAAT
* *
6627137 ATTTAT-AATATTATT
1 ATTTATAAATAATAAT
*
6627152 A-TTATATATAATAAT
1 ATTTATAAATAATAAT
6627167 GTATAATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTATAAATAATAAT
Found at i:6627804 original size:128 final size:128
Alignment explanation
Indices: 6627641--6627949 Score: 413
Period size: 128 Copynumber: 2.3 Consensus size: 128
6627631 TCCACTACTC
* * *
6627641 TTTCGTGGAGTTCAGATTTACTTCTGCTTCACTACTCTTCCTTGAAGATTGAATTTGATTGACTT
1 TTTCGTGGAGTTCAGATTTACCTCTGCTTCACTACTCTTCCGTGAAGATTGAATTTGATTAACTT
* * * *
6627706 GACAATAATCTAATTTCACTACTTTTCCGTGAAGATTTCATACTTTGCTGAAAAATTCATTTT
66 GACAAGAATCTAATTTCACTACTCTTCCATGAAGATTTCATACTTTGCTAAAAAATTCATTTT
* *
6627769 TTTCGTGGAGTTCAGATTTACCTCTGCTTCGCTACTCTTTCGTGAAGATTGAATTTGATTAACTT
1 TTTCGTGGAGTTCAGATTTACCTCTGCTTCACTACTCTTCCGTGAAGATTGAATTTGATTAACTT
*
6627834 GACAAGAATCTAATTTCACTACTCTTCCATGAAGATTTCATACTTTTCTAAAAAAAATAT-ATTC
66 GACAAGAATCTAATTTCACTACTCTTCCATGAAGATTTCATACTTTGCT--AAAAAAT-TCATT-
6627898 CACTACT
127 ---T--T
* *
6627905 CTTTCGTGGAGTTCAGATTTACTTCTGCTTCACTACTCTTTCGTG
1 -TTTCGTGGAGTTCAGATTTACCTCTGCTTCACTACTCTTCCGTG
6627950 GAGTTCAGTT
Statistics
Matches: 159, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
128 105 0.66
130 9 0.06
131 1 0.01
134 1 0.01
136 1 0.01
137 42 0.26
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (128 bp):
TTTCGTGGAGTTCAGATTTACCTCTGCTTCACTACTCTTCCGTGAAGATTGAATTTGATTAACTT
GACAAGAATCTAATTTCACTACTCTTCCATGAAGATTTCATACTTTGCTAAAAAATTCATTTT
Found at i:6627969 original size:36 final size:37
Alignment explanation
Indices: 6627898--6627980 Score: 159
Period size: 36 Copynumber: 2.3 Consensus size: 37
6627888 AAATATATTC
6627898 CACTACTCTTTCGTGGAGTTCAGATTTACTTCTGCTT
1 CACTACTCTTTCGTGGAGTTCAGATTTACTTCTGCTT
6627935 CACTACTCTTTCGTGGAGTTCAG-TTTACTTCTGCTT
1 CACTACTCTTTCGTGGAGTTCAGATTTACTTCTGCTT
6627971 CACTACTCTT
1 CACTACTCTT
6627981 CCATTAAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 23 0.50
37 23 0.50
ACGTcount: A:0.16, C:0.27, G:0.14, T:0.43
Consensus pattern (37 bp):
CACTACTCTTTCGTGGAGTTCAGATTTACTTCTGCTT
Found at i:6629525 original size:22 final size:22
Alignment explanation
Indices: 6629497--6629546 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
6629487 CTTGTTGCAT
* *
6629497 GAGATTGAAGGAAAAGAGGGTA
1 GAGATTGAAGAAAAACAGGGTA
*
6629519 GAGATTGAATAAAAACAGGGTA
1 GAGATTGAAGAAAAACAGGGTA
6629541 GAGATT
1 GAGATT
6629547 CCCTTGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.34, T:0.18
Consensus pattern (22 bp):
GAGATTGAAGAAAAACAGGGTA
Found at i:6636220 original size:27 final size:26
Alignment explanation
Indices: 6636184--6636267 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 26
6636174 TATATTTTTA
6636184 AATA-AAAATATTTTTAAATTAAGTC
1 AATATAAAATATTTTTAAATTAAGTC
* *
6636209 AATAGTAAAATATATTT-AA-TAAGTT
1 AATA-TAAAATATTTTTAAATTAAGTC
6636234 AATATAAAATA-TTTTAAATTAA-T-
1 AATATAAAATATTTTTAAATTAAGTC
6636257 ATATATAAAAT
1 A-ATATAAAAT
6636268 TATATTATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
23 4 0.08
24 19 0.37
25 16 0.31
26 2 0.04
27 10 0.20
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (26 bp):
AATATAAAATATTTTTAAATTAAGTC
Found at i:6636259 original size:20 final size:24
Alignment explanation
Indices: 6636184--6636250 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 24
6636174 TATATTTTTA
* *
6636184 AATA-AAAATATTTTTAAATTAAGTC
1 AATATAAAATATATTT-AA-TAAGTT
6636209 AATAGTAAAATATATTTAATAAGTT
1 AATA-TAAAATATATTTAATAAGTT
6636234 AATATAAAATAT-TTTAA
1 AATATAAAATATATTTAA
6636251 ATTAATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.13
24 8 0.21
25 13 0.34
26 2 0.05
27 10 0.26
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (24 bp):
AATATAAAATATATTTAATAAGTT
Found at i:6637077 original size:31 final size:30
Alignment explanation
Indices: 6637019--6637086 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
6637009 GGAGTGACTG
*
6637019 TATCTTAATTAAATAAAAATAAAGTGATAA
1 TATCTTAAATAAATAAAAATAAAGTGATAA
*
6637049 TATCTTAAATAAATAATAACA-AAAGTGATTA
1 TATCTTAAATAAATAA-AA-ATAAAGTGATAA
6637080 TATCTTA
1 TATCTTA
6637087 TATTCTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 15 0.44
31 18 0.53
32 1 0.03
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (30 bp):
TATCTTAAATAAATAAAAATAAAGTGATAA
Found at i:6637626 original size:15 final size:15
Alignment explanation
Indices: 6637606--6637637 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6637596 TTCTCAGGTA
6637606 TCTCTCGTTTCATCT
1 TCTCTCGTTTCATCT
*
6637621 TCTCTCTTTTCATCT
1 TCTCTCGTTTCATCT
6637636 TC
1 TC
6637638 CTTGATCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.34, G:0.03, T:0.56
Consensus pattern (15 bp):
TCTCTCGTTTCATCT
Found at i:6639090 original size:17 final size:18
Alignment explanation
Indices: 6639062--6639095 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6639052 GTTTGATGTA
6639062 TTTATAAAAATATAATTT
1 TTTATAAAAATATAATTT
6639080 TTTAT-AAAATATAATT
1 TTTATAAAAATATAATT
6639096 ATATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATAAAAATATAATTT
Found at i:6639105 original size:17 final size:17
Alignment explanation
Indices: 6639067--6639109 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
6639057 ATGTATTTAT
* *
6639067 AAAAATATAATTTTTTA
1 AAAAATATAATTATATA
*
6639084 TAAAATATAATTATATA
1 AAAAATATAATTATATA
6639101 AAAAA-ATAA
1 AAAAATATAA
6639110 AATGAACCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAATATAATTATATA
Found at i:6646797 original size:21 final size:22
Alignment explanation
Indices: 6646771--6646821 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
6646761 CCAAGGGGTG
6646771 TCGGTACTCCT-AAAAAGAGTA
1 TCGGTACTCCTAAAAAAGAGTA
6646792 TCGGTACTCCTAAAAAAGAGTA
1 TCGGTACTCCTAAAAAAGAGTA
6646814 TCGGTACT
1 TCGGTACT
6646822 TCCTTTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (22 bp):
TCGGTACTCCTAAAAAAGAGTA
Found at i:6648396 original size:19 final size:19
Alignment explanation
Indices: 6648369--6648405 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6648359 AAAATTTTAT
6648369 TTTGATTTTCAAAATCAAC
1 TTTGATTTTCAAAATCAAC
*
6648388 TTTGGTTTTCAAAATCAA
1 TTTGATTTTCAAAATCAA
6648406 ATCATTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (19 bp):
TTTGATTTTCAAAATCAAC
Found at i:6650961 original size:13 final size:13
Alignment explanation
Indices: 6650943--6650971 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
6650933 TTTTTTTTTA
6650943 ATTTATCTTCTTT
1 ATTTATCTTCTTT
6650956 ATTTATCTTCTTT
1 ATTTATCTTCTTT
6650969 ATT
1 ATT
6650972 ATATATTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTATCTTCTTT
Found at i:6657112 original size:5 final size:5
Alignment explanation
Indices: 6657104--6657330 Score: 382
Period size: 5 Copynumber: 47.0 Consensus size: 5
6657094 GATAAGATAA
6657104 AATAT AATAT AATAT AATAT AATAT AATAT -A-AT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
6657152 -A-AT AATAT AATAT AATAT AATAT AATAT -ATAT AATAT AATAT -A-AT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
6657197 AATAT AATAT AATAT AATAT AATAT AATAT ATATAT AATAT AATAT -ATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT
6657247 -ATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
6657296 AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT
6657331 TTAAACTAAA
Statistics
Matches: 213, Mismatches: 0, Indels: 18
0.92 0.00 0.08
Matches are distributed among these distances:
3 6 0.03
4 18 0.08
5 184 0.86
6 5 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:6658474 original size:28 final size:28
Alignment explanation
Indices: 6658434--6658488 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
6658424 ATCAAGAAGG
6658434 AAATATGTAGTCTATATAGGTGCATCTA
1 AAATATGTAGTCTATATAGGTGCATCTA
6658462 AAATATGTAGTCTATATAGGTGCATCT
1 AAATATGTAGTCTATATAGGTGCATCT
6658489 CATAATAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (28 bp):
AAATATGTAGTCTATATAGGTGCATCTA
Found at i:6659889 original size:12 final size:12
Alignment explanation
Indices: 6659872--6659915 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
6659862 TATCTTTTAC
6659872 TGTATTGTTTCA
1 TGTATTGTTTCA
*
6659884 TGTATTTTTTCA
1 TGTATTGTTTCA
*
6659896 TGTATTGTATCA
1 TGTATTGTTTCA
*
6659908 TTTATTGT
1 TGTATTGT
6659916 ATTGTATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.18, C:0.07, G:0.14, T:0.61
Consensus pattern (12 bp):
TGTATTGTTTCA
Found at i:6660164 original size:66 final size:66
Alignment explanation
Indices: 6660072--6660402 Score: 375
Period size: 66 Copynumber: 5.1 Consensus size: 66
6660062 GTAGCCGATG
* * * * * * *
6660072 CACTTCACCTCGTGTACCACTAAGGTACACGAGTTATATCGAGTGATCTATATAATATTTAATTA
1 CACTCCACCTCATGCACCACAAAGGTACACGAGTCATATCGAGTGATCTATACAATATTCAATTA
6660137 T
66 T
* * * *
6660138 CACTCTACCTCATGCACCACAAAGGTACACTAGTCATATCGAGTGATCTGTACAGTATTCAATTA
1 CACTCCACCTCATGCACCACAAAGGTACACGAGTCATATCGAGTGATCTATACAATATTCAATTA
6660203 T
66 T
* * *
6660204 CACTCCACTTCATGCACCACAAAGGTATACGAGTC---TCGAGTGATCTATACAGTATTCAATTA
1 CACTCCACCTCATGCACCACAAAGGTACACGAGTCATATCGAGTGATCTATACAATATTCAATTA
6660266 T
66 T
* * * * * * *
6660267 CACTCCACCTCATGCATCACAAATGTACACGAGCCACATCGAGTAATCTTGTGCAATATTCAATT
1 CACTCCACCTCATGCACCACAAAGGTACACGAGTCATATCGAGTGATC-TATACAATATTCAATT
6660332 AT
65 AT
* * * * *
6660334 CACTCCACCTCATGTACCA-TAAGGTACACGAGTCACT-TCGATTGATCAATACAATATTCAATA
1 CACTCCACCTCATGCACCACAAAGGTACACGAGTCA-TATCGAGTGATCTATACAATATTCAATT
6660397 AT
65 AT
6660399 CACT
1 CACT
6660403 TTGCCTTGTG
Statistics
Matches: 223, Mismatches: 37, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
63 57 0.26
65 18 0.08
66 116 0.52
67 32 0.14
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (66 bp):
CACTCCACCTCATGCACCACAAAGGTACACGAGTCATATCGAGTGATCTATACAATATTCAATTA
T
Found at i:6660265 original size:129 final size:131
Alignment explanation
Indices: 6660093--6660402 Score: 385
Period size: 129 Copynumber: 2.4 Consensus size: 131
6660083 GTGTACCACT
* * *
6660093 AAGGTACACGAGTTA-TATCGAGTGATCTATATAATATTTAATTATCACTCTACCTCATGCACCA
1 AAGGTACACGAG-TACT-TCGAGTGATCTATACAATATTCAATTATCACTCCACCTCATGCACCA
* * * * * *
6660157 CAAAGGTACACTAGTCATATCGAGTGATC-TGTACAGTATTCAATTATCACTCCACTTCATGCAC
64 CAAAGGTACACGAGCCACATCGAGTAATCTTGTACAATATTCAATTATCACTCCACCTCATGCAC
6660221 CACA
129 CA-A
* * *
6660225 AAGGTATACGAGT-C-TCGAGTGATCTATACAGTATTCAATTATCACTCCACCTCATGCATCACA
1 AAGGTACACGAGTACTTCGAGTGATCTATACAATATTCAATTATCACTCCACCTCATGCACCACA
* * *
6660288 AATGTACACGAGCCACATCGAGTAATCTTGTGCAATATTCAATTATCACTCCACCTCATGTACCA
66 AAGGTACACGAGCCACATCGAGTAATCTTGTACAATATTCAATTATCACTCCACCTCATGCACCA
*
6660353 T
131 A
* * *
6660354 AAGGTACACGAGTCACTTCGATTGATCAATACAATATTCAATAATCACT
1 AAGGTACACGAGT-ACTTCGAGTGATCTATACAATATTCAATTATCACT
6660403 TTGCCTTGTG
Statistics
Matches: 152, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
129 78 0.51
130 33 0.22
131 2 0.01
132 39 0.26
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (131 bp):
AAGGTACACGAGTACTTCGAGTGATCTATACAATATTCAATTATCACTCCACCTCATGCACCACA
AAGGTACACGAGCCACATCGAGTAATCTTGTACAATATTCAATTATCACTCCACCTCATGCACCA
A
Found at i:6661091 original size:3 final size:3
Alignment explanation
Indices: 6661083--6661140 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
6661073 TTTGTTTTAT
* * *
6661083 TTA TTA TTA TTG TT- TTG TT- TTA ATA TTA TTA -TA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6661126 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
6661141 AATAATTAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
2 10 0.21
3 37 0.79
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:6661095 original size:18 final size:18
Alignment explanation
Indices: 6661074--6661133 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
6661064 TTTATTTCAT
6661074 TTGTTTTATTTATTATTA
1 TTGTTTTATTTATTATTA
* *
6661092 TTGTTTTGTTTTAATATTA
1 TTGTTTT-ATTTATTATTA
*
6661111 TTATATTATATTATATTATTA
1 TTGT-TT-TATT-TATTATTA
6661132 TT
1 TT
6661134 ATTATTAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
18 7 0.21
19 12 0.36
20 4 0.12
21 10 0.30
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTGTTTTATTTATTATTA
Found at i:6661135 original size:6 final size:6
Alignment explanation
Indices: 6661083--6661140 Score: 54
Period size: 5 Copynumber: 10.5 Consensus size: 6
6661073 TTTGTTTTAT
* * *
6661083 TTATTA TTATTG TT-TTG TT-TTA ATATTA TTA-TA TTA-TA TTA-TA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
6661126 TTATTA TTATTA TTA
1 TTATTA TTATTA TTA
6661141 AATAATTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
5 23 0.50
6 23 0.50
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (6 bp):
TTATTA
Found at i:6663374 original size:20 final size:21
Alignment explanation
Indices: 6663340--6663389 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
6663330 TATATATACT
6663340 TATTATTTTCATAAT-ATTTA
1 TATTATTTTCATAATGATTTA
*
6663360 TATTATTTT-ATTAATGTTTTA
1 TATTATTTTCA-TAATGATTTA
*
6663381 TTTTATTTT
1 TATTATTTT
6663390 TCAAGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 13 0.50
21 12 0.46
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTATTTTCATAATGATTTA
Found at i:6665635 original size:15 final size:15
Alignment explanation
Indices: 6665615--6665646 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6665605 GATCAATACC
6665615 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
6665630 TTTTGCATACATTCA
1 TTTTGCATACATGCA
6665645 TT
1 TT
6665647 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:6667777 original size:14 final size:14
Alignment explanation
Indices: 6667758--6667787 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6667748 TACCTTGGAA
6667758 TTATACTACTAATG
1 TTATACTACTAATG
6667772 TTATACTACTAATG
1 TTATACTACTAATG
6667786 TT
1 TT
6667788 TCAATGGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (14 bp):
TTATACTACTAATG
Found at i:6670055 original size:36 final size:35
Alignment explanation
Indices: 6670010--6670103 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 35
6670000 TAATATAAGT
6670010 TTATATATAAACTATATTTATAT-TATAACATGTATGA
1 TTAT-TATAAACTATATTTATATATATAA-AT-TATGA
* *
6670047 TTATTATAAGCTATATATATATATATATAAATTATGT
1 TTATTATAAACTATAT-T-TATATATATAAATTATGA
* *
6670084 TTA-TATGAACTATATATATA
1 TTATTATAAACTATATTTATA
6670104 AATTATCTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
34 4 0.08
36 21 0.43
37 12 0.24
38 7 0.14
39 5 0.10
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (35 bp):
TTATTATAAACTATATTTATATATATAAATTATGA
Found at i:6670101 original size:13 final size:13
Alignment explanation
Indices: 6670066--6670298 Score: 90
Period size: 12 Copynumber: 17.8 Consensus size: 13
6670056 GCTATATATA
*
6670066 TATATATATAAAT
1 TATATATATAAAC
* *
6670079 TATGTTTATATGAAC
1 TA--TATATATAAAC
*
6670094 TATATATATAAAT
1 TATATATATAAAC
*
6670107 TATCTATATAAAC
1 TATATATATAAAC
* **
6670120 TCTATATATGTA-
1 TATATATATAAAC
* * *
6670132 TAAACTATAAAAAG
1 TATA-TATATAAAC
6670146 TATATAGTTTATAAAC
1 TATATA---TATAAAC
*
6670162 TATAATTATATTAA-
1 TAT-A-TATATAAAC
*
6670176 TATAGTGCATATATA-
1 TATA-T--ATATAAAC
*
6670191 TATATATATATA-
1 TATATATATAAAC
*
6670203 TATATATATATA-
1 TATATATATAAAC
*
6670215 TATATATATATA-
1 TATATATATAAAC
*
6670227 TATATATATATA-
1 TATATATATAAAC
*
6670239 TATATATAATATA-
1 TATATAT-ATAAAC
*
6670252 TATATATATATA-
1 TATATATATAAAC
*
6670264 TATATATATATA-
1 TATATATATAAAC
* *
6670276 TATATATATATAT
1 TATATATATAAAC
6670289 TATATATATA
1 TATATATATA
6670299 TGTATGTATG
Statistics
Matches: 183, Mismatches: 24, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
12 81 0.44
13 60 0.33
14 7 0.04
15 24 0.13
16 8 0.04
17 1 0.01
18 2 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:6670103 original size:15 final size:15
Alignment explanation
Indices: 6670064--6670299 Score: 111
Period size: 14 Copynumber: 16.7 Consensus size: 15
6670054 AAGCTATATA
*
6670064 TATATATATATAAAT
1 TATATATATATAAAC
* * *
6670079 TATGTTTATATGAAC
1 TATATATATATAAAC
6670094 --TATATATATAAA-
1 TATATATATATAAAC
*
6670106 T-TATCTATATAAACTC
1 TATATATATATAAA--C
*
6670122 TATATATGTATAAAC
1 TATATATATATAAAC
*
6670137 ----TATA-A-AAAG
1 TATATATATATAAAC
*
6670146 TATATAGTTTATAAAC
1 TATATA-TATATAAAC
*
6670162 TATA-ATTATATTAA-
1 TATATA-TATATAAAC
*
6670176 TATAGTGCATATATATA-
1 TATA-T--ATATATAAAC
*
6670193 TATATATATATATA-
1 TATATATATATAAAC
*
6670207 TATATATATATATA-
1 TATATATATATAAAC
*
6670221 TATATATATATATA-
1 TATATATATATAAAC
6670235 TATATATATAT-AA-
1 TATATATATATAAAC
6670248 TATATATATAT--A-
1 TATATATATATAAAC
*
6670260 TATATATATATATA-
1 TATATATATATAAAC
* *
6670274 TATATATATATATAT
1 TATATATATATAAAC
6670289 TATATATATAT
1 TATATATATAT
6670300 GTATGTATGT
Statistics
Matches: 182, Mismatches: 20, Indels: 38
0.76 0.08 0.16
Matches are distributed among these distances:
9 3 0.02
10 1 0.01
11 3 0.02
12 12 0.07
13 34 0.19
14 68 0.37
15 31 0.17
16 9 0.05
17 20 0.11
18 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:6670114 original size:26 final size:27
Alignment explanation
Indices: 6670057--6670128 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
6670047 TTATTATAAG
*
6670057 CTATATATA-TATATATATAAATTATGT
1 CTATATAAACTATATATATAAATTA-GT
* *
6670084 TTATATGAACTATATATATAAATTA-T
1 CTATATAAACTATATATATAAATTAGT
*
6670110 CTATATAAACTCTATATAT
1 CTATATAAACTATATATAT
6670129 GTATAAACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 17 0.45
27 6 0.16
28 15 0.39
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (27 bp):
CTATATAAACTATATATATAAATTAGT
Found at i:6670191 original size:2 final size:2
Alignment explanation
Indices: 6670184--6670433 Score: 264
Period size: 2 Copynumber: 126.5 Consensus size: 2
6670174 AATATAGTGC
6670184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6670226 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
6670267 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT GT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * *
6670308 GT AA ACT AT AT AA AT AT AC AGT TT AT AA AT -T AA AT TT AT AT AT
1 AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* ** *
6670351 AGT AT AT AT AT GT AT GC AT ACT -T A- AT AT A- AGT A- AT CT AT
1 A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT
*
6670390 AG AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6670431 AT A
1 AT A
6670434 GCTTATAGAA
Statistics
Matches: 205, Mismatches: 30, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
1 8 0.04
2 192 0.94
3 5 0.02
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6670540 original size:21 final size:21
Alignment explanation
Indices: 6670516--6670556 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6670506 TCTTATATTG
*
6670516 TAAACCCTAAATCATAAACTC
1 TAAACCCTAAACCATAAACTC
* *
6670537 TAAACTCTAAACCATGAACT
1 TAAACCCTAAACCATAAACT
6670557 ATATATGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACTC
Found at i:6670641 original size:16 final size:16
Alignment explanation
Indices: 6670620--6670650 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6670610 TAATTCATAT
6670620 ATAGTTTATATAAATA
1 ATAGTTTATATAAATA
6670636 ATAGTTTATATAAAT
1 ATAGTTTATATAAAT
6670651 TATATATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
ATAGTTTATATAAATA
Found at i:6670773 original size:20 final size:20
Alignment explanation
Indices: 6670750--6670861 Score: 69
Period size: 18 Copynumber: 6.0 Consensus size: 20
6670740 TATAGTACAT
* *
6670750 GTATGTATAAACTATGTATA
1 GTATATATAAACTATATATA
6670770 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
** * *
6670790 -TA-ACCTATAGTATATATA
1 GTATATATAAACTATATATA
* * *
6670808 -TATATACAATCTATA-GT-
1 GTATATATAAACTATATATA
*
6670825 GTATATATATA-TATATATA
1 GTATATATAAACTATATATA
*
6670844 -TATATATATA-TATATATA
1 GTATATATAAACTATATATA
6670862 ATGAAAATAT
Statistics
Matches: 71, Mismatches: 17, Indels: 10
0.72 0.17 0.10
Matches are distributed among these distances:
17 4 0.06
18 41 0.58
19 8 0.11
20 18 0.25
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:6670778 original size:2 final size:2
Alignment explanation
Indices: 6670766--6670861 Score: 88
Period size: 2 Copynumber: 47.0 Consensus size: 2
6670756 ATAAACTATG
* **
6670766 TA TA GTA TA TA TA AA CTA TA TA TA TA -A CC TA TA GTA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
6670808 TA TA TA CA -A TC TA TA GTG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
6670850 TA TA TA TA TA TA
1 TA TA TA TA TA TA
6670862 ATGAAAATAT
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
1 2 0.03
2 70 0.90
3 6 0.08
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:6670809 original size:24 final size:23
Alignment explanation
Indices: 6670782--6670862 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 23
6670772 ATATATAAAC
6670782 TATATATATAACCTATAGTATATA
1 TATATATATAA-CTATAGTATATA
* *
6670806 TATATATACAATCTATAGTGTATA
1 TATATATATAA-CTATAGTATATA
6670830 TATATATATATA-TATA-TATATA
1 TATATATATA-ACTATAGTATATA
6670852 TATATATATAA
1 TATATATATAA
6670863 TGAAAATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.02
22 15 0.29
23 4 0.08
24 30 0.59
25 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (23 bp):
TATATATATAACTATAGTATATA
Found at i:6671943 original size:23 final size:24
Alignment explanation
Indices: 6671915--6671968 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
6671905 TTATTTTTTC
6671915 TTTACATAAATTAAACTATA-TAA
1 TTTACATAAATTAAACTATATTAA
6671938 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
6671962 TTTACAT
1 TTTACAT
6671969 TTAATCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:6677026 original size:45 final size:45
Alignment explanation
Indices: 6676962--6677229 Score: 446
Period size: 45 Copynumber: 6.0 Consensus size: 45
6676952 TTTATTGGTT
* *
6676962 AATAAATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
*
6677007 AATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA
1 AATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
* *
6677052 AATAAATGACAAGTATATTGGTAAAATAAACTTACGAGCTTATGG
1 AATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
*
6677097 AATAAATGGCAAATATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
**
6677142 AATAAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
1 AATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
* *
6677187 AATAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTAT
1 AATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
6677230 AAGTTAAATG
Statistics
Matches: 209, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 209 1.00
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (45 bp):
AATAAATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG
Found at i:6677078 original size:24 final size:24
Alignment explanation
Indices: 6677051--6677170 Score: 62
Period size: 24 Copynumber: 5.2 Consensus size: 24
6677041 CGAGCTTATG
6677051 AAATAAATGACAAGTATATTGGTA
1 AAATAAATGACAAGTATATTGGTA
* *
6677075 AAATAAACTTACGAGCT-TA-TGG--
1 AAATAAA-TGACAAG-TATATTGGTA
* *
6677097 -AATAAATGGCAAATATATTGGTA
1 AAATAAATGACAAGTATATTGGTA
* * *
6677120 AAATAAGCTTACGAGCT-TA-TGG--
1 AAATAA-ATGACAAG-TATATTGGTA
*
6677142 -AATAAATGATAAGTATATTGGTA
1 AAATAAATGACAAGTATATTGGTA
6677165 AAATAA
1 AAATAA
6677171 GCTTACGAGC
Statistics
Matches: 67, Mismatches: 15, Indels: 28
0.61 0.14 0.25
Matches are distributed among these distances:
19 2 0.03
20 11 0.16
21 17 0.25
24 23 0.34
25 12 0.18
26 2 0.03
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (24 bp):
AAATAAATGACAAGTATATTGGTA
Found at i:6677637 original size:2 final size:2
Alignment explanation
Indices: 6677630--6677686 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
6677620 TTTTATGAGT
6677630 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6677670 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
6677687 TGCTGAAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6679846 original size:6 final size:6
Alignment explanation
Indices: 6679825--6679964 Score: 124
Period size: 6 Copynumber: 22.8 Consensus size: 6
6679815 ATATAAGAGA
* * *
6679825 AAAAAG AAAGAAG AAAAAG AAATAT AAAAA- AAATAG AAAAAG AAAAAG
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * * * *
6679873 AGAAAAC TAAAAG AAAGAAG AAAGAA- AATAAG AAAAAT AAAAAT AAAAAG
1 A-AAAAG AAAAAG AAA-AAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG
*
6679923 AAAAA- AAAACAG AAAAAG AAAAAG AAAAGAA AAAAAG AAAAA
1 AAAAAG AAAA-AG AAAAAG AAAAAG AAAA-AG AAAAAG AAAAA
6679965 ATGAGAGATA
Statistics
Matches: 111, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
5 10 0.09
6 73 0.66
7 28 0.25
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:6679961 original size:55 final size:57
Alignment explanation
Indices: 6679824--6679964 Score: 155
Period size: 61 Copynumber: 2.4 Consensus size: 57
6679814 AATATAAGAG
* * *
6679824 AAAAAAG-AAAGAAGAAAAAGAAATATAAAAAAAATAGAAAAAGAAAAAGAGAAAACTA
1 AAAAAAGAAAAGAA-AAAAAGAAAAATAAAAAAAAAAGAAAAAGAAAAACAGAAAAC-A
*
6679882 AAAGAAAGAAGAAAGAAAATAAGAAAAATAAAAATAAAAAG-AAAA-AAAAACAGAAAA-A
1 AAA-AAAG-A-AAAGAAAAAAAGAAAAATAAAAA-AAAAAGAAAAAGAAAAACAGAAAACA
*
6679940 GAAAAAGAAAAGAAAAAAAGAAAAA
1 AAAAAAGAAAAGAAAAAAAGAAAAA
6679965 ATGAGAGATA
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
55 16 0.22
56 1 0.01
57 4 0.06
58 6 0.08
59 4 0.06
60 11 0.15
61 19 0.26
62 11 0.15
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.05
Consensus pattern (57 bp):
AAAAAAGAAAAGAAAAAAAGAAAAATAAAAAAAAAAGAAAAAGAAAAACAGAAAACA
Done.