Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008876.1 Hibiscus syriacus cultivar Beakdansim tig00112114_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: 1683876
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1387280 original size:15 final size:15
Alignment explanation
Indices: 1387247--1387290 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
1387237 AAAATGAGTG
*
1387247 AAAATGAAAAAAGAA
1 AAAATGAAAAAAAAA
*
1387262 AAAATAAAAAAAAATAA
1 AAAAT-GAAAAAAA-AA
1387279 AAAATGAAAAAA
1 AAAATGAAAAAA
1387291 TGGAAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (15 bp):
AAAATGAAAAAAAAA
Found at i:1388401 original size:53 final size:55
Alignment explanation
Indices: 1388301--1389078 Score: 288
Period size: 53 Copynumber: 14.7 Consensus size: 55
1388291 AGATTTCCCA
1388301 GCAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 GCAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * ** *
1388356 GCAATTGA-TGAAGATTG-T-GGGTCTTATACTCTCTGAAGATGTAGGGGGCAGA-
1 GCAATT-ATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
1388408 -C--------ACGATCGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 GCAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * * * *
1388454 ACGATTGTTGAAGA-TATTCGAGT-TC-TATTCTCCTTAGAGAAAGAAGGAGC-GAAC
1 GCAATTATTGAAGATTGTTCGAGTCTCATACTCT-CTGA-AGAAATAGGGAGCAG-AC
** * * * *
1388508 -C-CGT-TTGAAGAGATG-TCTAAGT-TCCATACTCCCT-AGAGAAAGAGGGAGC-GAAC
1 GCAATTATTGAAGA-TTGTTC-GAGTCT-CATACTCTCTGA-AGAAATAGGGAGCAG-AC
** * * * * * * *
1388561 -C-CGT-GTGAAGA-TATCCGAGTCCCGTACTC-CGTAAAGAAAAAGGGAGC-GAAC
1 GCAATTATTGAAGATTGTTCGAGTCTCATACTCTC-TGAAGAAATAGGGAGCAG-AC
* * * *
1388612 -CCA--GTTGAAGA-TGTTCGAGT-TCTATACTCCCTGAAGAAAGAGGGAG-AGAAC
1 GCAATTATTGAAGATTGTTCGAGTCTC-ATACTCTCTGAAGAAATAGGGAGCAG-AC
* ** *** * *
1388663 CCGTTTGCAGAAGATT-TTCAAGT-TCTATACTCCCTGAAGAAATAGGGAGCAGAC
1 GCAATTATTGAAGATTGTTCGAGTCTC-ATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * *
1388717 GCGATTGA-TGAAAATTG-T-GGGTCTTATACTCTCTGCAGAAATAGGGAGCCGAC
1 GCAATT-ATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * * *
1388770 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGAAGAC
1 GCAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
** * * *
1388825 GTGATTGA-TGAGGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 GCAATT-ATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * *
1388878 GCGATTGA-TGAAAATTG-T-GGGTCTTATACTCTCTGCAGAAATAGGGAGCCGAC
1 GCAATT-ATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * * *
1388931 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGAAGAC
1 GCAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
** * * * *
1388986 GTGATTGA-TGAGGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1 GCAATT-ATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * *
1389039 GCGATTGTTAAAGATTGTTCGGGTCTTATACTCTCTGAAG
1 GCAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAG
1389079 GACTATGGAG
Statistics
Matches: 582, Mismatches: 92, Indels: 98
0.75 0.12 0.13
Matches are distributed among these distances:
43 5 0.01
44 1 0.00
45 29 0.05
47 1 0.00
50 2 0.00
51 71 0.12
52 12 0.02
53 249 0.43
54 80 0.14
55 131 0.23
56 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (55 bp):
GCAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:1388610 original size:51 final size:50
Alignment explanation
Indices: 1388460--1388667 Score: 182
Period size: 51 Copynumber: 4.1 Consensus size: 50
1388450 AGACACGATT
* * * * * * *
1388460 GTTGAAGATATTCGAGTTCTATTCTCCTTAGAGAAAGAAGGAGCGAACCC
1 GTTGAAGATATCCGAGTCCCATACTCCCTAAAGAAAGAGGGAGCGAACCC
* ** * *
1388510 GTTTGAAGAGATGTCTAAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC
1 G-TTG-A-AGATATCCGAGTCCCATACTCCCTAAAGAAAGAGGGAGCGAACCC
* * *
1388563 GTGTGAAGATATCCGAGTCCCGTACTCCGTAAAGAAAAAGGGAGCGAACCC
1 GT-TGAAGATATCCGAGTCCCATACTCCCTAAAGAAAGAGGGAGCGAACCC
* * * * * *
1388614 AGTTGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGAGAACCC
1 -GTTGAAGATATCCGAGTCCCATACTCCCTAAAGAAAGAGGGAGCGAACCC
1388665 GTT
1 GTT
1388668 TGCAGAAGAT
Statistics
Matches: 128, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
50 4 0.03
51 79 0.62
52 5 0.04
53 40 0.31
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (50 bp):
GTTGAAGATATCCGAGTCCCATACTCCCTAAAGAAAGAGGGAGCGAACCC
Found at i:1388825 original size:108 final size:108
Alignment explanation
Indices: 1388688--1389078 Score: 522
Period size: 108 Copynumber: 3.6 Consensus size: 108
1388678 TTTCAAGTTC
*
1388688 TATACTCCCTGAAGAAATAGGGAGCAGACGCGATTGATGAAAATTG-T-GGGTCTTATACTCTCT
1 TATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGATGAAAATTGTTCGGGTCTTATACTCTCT
* * * *
1388751 GCAGAAATAGGGAGCCGACACGATTGTTGAAGATTGTTCGGGTCT
66 GAAGAAATAGGGAGCAGACGCGATTGATGAAGATTG-T-GGGTCT
* * * **
1388796 TATACTCTCTGAAGAAATAGGGGGAAGACGTGATTGATGAGGATTG-T-GGGTCTTATACTCTCT
1 TATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGATGAAAATTGTTCGGGTCTTATACTCTCT
*
1388859 GAAGAAATAGGGAGCAGACGCGATTGATGAAAATTGTGGGTCT
66 GAAGAAATAGGGAGCAGACGCGATTGATGAAGATTGTGGGTCT
* * * * *
1388902 TATACTCTCTGCAGAAATAGGGAGCCGACACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCT
1 TATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGATGAAAATTGTTCGGGTCTTATACTCTCT
* * * *
1388967 GAAGAAATAGGGGGAAGACGTGATTGATGAGGATTGTGGGTCT
66 GAAGAAATAGGGAGCAGACGCGATTGATGAAGATTGTGGGTCT
* *
1389010 TATACTCTCTGAAGAAATAGGGGGCAGACGCGATTG-TTAAAGATTGTTCGGGTCTTATACTCTC
1 TATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGATGAAA-ATTGTTCGGGTCTTATACTCTC
1389074 TGAAG
65 TGAAG
1389079 GACTATGGAG
Statistics
Matches: 250, Mismatches: 30, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
106 44 0.18
107 5 0.02
108 201 0.80
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.28
Consensus pattern (108 bp):
TATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGATGAAAATTGTTCGGGTCTTATACTCTCT
GAAGAAATAGGGAGCAGACGCGATTGATGAAGATTGTGGGTCT
Found at i:1388863 original size:161 final size:161
Alignment explanation
Indices: 1388688--1389075 Score: 715
Period size: 161 Copynumber: 2.4 Consensus size: 161
1388678 TTTCAAGTTC
*
1388688 TATACTCCCTGAAGAAATAGGGAGCAGACGCGATTGATGAAAATTGTGGGTCTTATACTCTCTGC
1 TATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGATGAAAATTGTGGGTCTTATACTCTCTGC
1388753 AGAAATAGGGAGCCGACACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGG
66 AGAAATAGGGAGCCGACACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGG
1388818 GGAAGACGTGATTGATGAGGATTGTGGGTCT
131 GGAAGACGTGATTGATGAGGATTGTGGGTCT
1388849 TATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGATGAAAATTGTGGGTCTTATACTCTCTGC
1 TATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGATGAAAATTGTGGGTCTTATACTCTCTGC
1388914 AGAAATAGGGAGCCGACACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGG
66 AGAAATAGGGAGCCGACACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGG
1388979 GGAAGACGTGATTGATGAGGATTGTGGGTCT
131 GGAAGACGTGATTGATGAGGATTGTGGGTCT
* *
1389010 TATACTCTCTGAAGAAATAGGGGGCAGACGCGATTG-TTAAAGATTGTTCGGGTCTTATACTCTC
1 TATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGATGAAA-ATTG-T-GGGTCTTATACTCTC
1389074 TG
63 TG
1389076 AAGGACTATG
Statistics
Matches: 221, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
160 4 0.02
161 199 0.90
162 1 0.00
163 17 0.08
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.28
Consensus pattern (161 bp):
TATACTCTCTGAAGAAATAGGGAGCAGACGCGATTGATGAAAATTGTGGGTCTTATACTCTCTGC
AGAAATAGGGAGCCGACACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGG
GGAAGACGTGATTGATGAGGATTGTGGGTCT
Found at i:1389782 original size:17 final size:17
Alignment explanation
Indices: 1389758--1389800 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1389748 CTCCCTGAAG
1389758 CCCGTGACCAGCTCGCA
1 CCCGTGACCAGCTCGCA
*
1389775 CTCGTGACCAGCTCGCA
1 CCCGTGACCAGCTCGCA
1389792 CCCGTGACC
1 CCCGTGACC
1389801 TGCAAGCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.16, C:0.47, G:0.23, T:0.14
Consensus pattern (17 bp):
CCCGTGACCAGCTCGCA
Found at i:1391289 original size:13 final size:13
Alignment explanation
Indices: 1391271--1391295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1391261 GTATATAGTT
1391271 TTTTTATTTATTC
1 TTTTTATTTATTC
1391284 TTTTTATTTATT
1 TTTTTATTTATT
1391296 TCAAATTACA
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:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTATTC
Found at i:1401562 original size:19 final size:19
Alignment explanation
Indices: 1401538--1401598 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
1401528 GTTTAATCTT
1401538 AATTTAAAATGATTCAATA
1 AATTTAAAATGATTCAATA
*
1401557 AATTT---A-GCCTTCAATTA
1 AATTTAAAATG-ATTCAA-TA
1401574 AATTTAAAATGATTCAATA
1 AATTTAAAATGATTCAATA
1401593 AATTTA
1 AATTTA
1401599 GCCTTCAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 1 0.03
16 6 0.18
17 7 0.21
19 13 0.38
20 6 0.18
21 1 0.03
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (19 bp):
AATTTAAAATGATTCAATA
Found at i:1401571 original size:16 final size:16
Alignment explanation
Indices: 1401550--1401607 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
1401540 TTTAAAATGA
1401550 TTCAATAAATTTAGCC
1 TTCAATAAATTTAGCC
*
1401566 TTCAATTAAATTTAAAATG-A
1 TTCAA-TAAATTT---A-GCC
1401586 TTCAATAAATTTAGCC
1 TTCAATAAATTTAGCC
1401602 TTCAAT
1 TTCAAT
1401608 TAAAAAATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 1 0.03
16 12 0.35
17 7 0.21
19 7 0.21
20 6 0.18
21 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (16 bp):
TTCAATAAATTTAGCC
Found at i:1401585 original size:36 final size:36
Alignment explanation
Indices: 1401538--1401611 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1401528 GTTTAATCTT
1401538 AATTTAAAATGATTCAATAAATTTAGCCTTCAATTA
1 AATTTAAAATGATTCAATAAATTTAGCCTTCAATTA
1401574 AATTTAAAATGATTCAATAAATTTAGCCTTCAATTA
1 AATTTAAAATGATTCAATAAATTTAGCCTTCAATTA
1401610 AA
1 AA
1401612 AAATTCGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (36 bp):
AATTTAAAATGATTCAATAAATTTAGCCTTCAATTA
Found at i:1403313 original size:17 final size:18
Alignment explanation
Indices: 1403293--1403336 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1403283 AAGGTTAATT
*
1403293 TTTTATATATAAT-TATA
1 TTTTATATAAAATATATA
*
1403310 TTTTATA-AAAATATGTA
1 TTTTATATAAAATATATA
1403327 TTTTATATAA
1 TTTTATATAA
1403337 TATTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 17 0.74
18 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTATATAAAATATATA
Found at i:1404290 original size:34 final size:33
Alignment explanation
Indices: 1404252--1404355 Score: 121
Period size: 34 Copynumber: 3.2 Consensus size: 33
1404242 CAGTTGAGAT
1404252 TAAACAAACCCAAATTGAAATTTCACAGAAACTA
1 TAAACAAACCC-AATTGAAATTTCACAGAAACTA
**
1404286 TAAACAAAATC-A--GAAA--TCGA-AGAAACTA
1 TAAACAAACCCAATTGAAATTTC-ACAGAAACTA
1404314 TAAACAAACCCAGATTGAAATTTCACAGAAACTA
1 TAAACAAACCCA-ATTGAAATTTCACAGAAACTA
1404348 TAAACAAA
1 TAAACAAA
1404356 ATCAGAAATC
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
28 19 0.33
29 1 0.02
30 5 0.09
32 5 0.09
33 1 0.02
34 27 0.47
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (33 bp):
TAAACAAACCCAATTGAAATTTCACAGAAACTA
Found at i:1404309 original size:28 final size:28
Alignment explanation
Indices: 1404278--1404371 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 28
1404268 GAAATTTCAC
1404278 AGAAACTATAAACAAAATCAGAAATCGA
1 AGAAACTATAAACAAAATCAGAAATCGA
**
1404306 AGAAACTATAAACAAACCCAGATTGAAATTTC-A
1 AGAAACTATAAACAAAATC--A--GAAA--TCGA
1404339 CAGAAACTATAAACAAAATCAGAAATCGA
1 -AGAAACTATAAACAAAATCAGAAATCGA
1404368 AGAA
1 AGAA
1404372 GTGAAATAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
28 23 0.43
29 1 0.02
30 5 0.09
32 5 0.09
33 1 0.02
34 19 0.35
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (28 bp):
AGAAACTATAAACAAAATCAGAAATCGA
Found at i:1404318 original size:62 final size:62
Alignment explanation
Indices: 1404252--1404371 Score: 231
Period size: 62 Copynumber: 1.9 Consensus size: 62
1404242 CAGTTGAGAT
1404252 TAAACAAACCCAAATTGAAATTTCACAGAAACTATAAACAAAATCAGAAATCGAAGAAACTA
1 TAAACAAACCCAAATTGAAATTTCACAGAAACTATAAACAAAATCAGAAATCGAAGAAACTA
*
1404314 TAAACAAACCCAGATTGAAATTTCACAGAAACTATAAACAAAATCAGAAATCGAAGAA
1 TAAACAAACCCAAATTGAAATTTCACAGAAACTATAAACAAAATCAGAAATCGAAGAA
1404372 GTGAAATAAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.56, C:0.17, G:0.09, T:0.17
Consensus pattern (62 bp):
TAAACAAACCCAAATTGAAATTTCACAGAAACTATAAACAAAATCAGAAATCGAAGAAACTA
Found at i:1405328 original size:14 final size:13
Alignment explanation
Indices: 1405296--1405329 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1405286 AAATTTTTAT
1405296 TAAAAAAATAAAA
1 TAAAAAAATAAAA
1405309 TGAAAAAAATAAAAA
1 T-AAAAAAAT-AAAA
1405324 TAAAAA
1 TAAAAA
1405330 TAGAAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 13 0.68
15 5 0.26
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (13 bp):
TAAAAAAATAAAA
Found at i:1407408 original size:23 final size:23
Alignment explanation
Indices: 1407382--1407450 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1407372 CACCACAGCT
*
1407382 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
1407405 CGTAGAATTGCACCGGAGTGTCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1407428 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1407451 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1407894 original size:17 final size:17
Alignment explanation
Indices: 1407872--1407905 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1407862 CACATATCTC
*
1407872 ATAGTCATGTATTTCAT
1 ATAGTCATATATTTCAT
*
1407889 ATAGTCTTATATTTCAT
1 ATAGTCATATATTTCAT
1407906 TATCTTATTA
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:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (17 bp):
ATAGTCATATATTTCAT
Found at i:1407913 original size:15 final size:17
Alignment explanation
Indices: 1407881--1407913 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1407871 CATAGTCATG
1407881 TATTTCATATAGTCTTA
1 TATTTCATATAGTCTTA
1407898 TATTTCAT-TA-TCTTA
1 TATTTCATATAGTCTTA
1407913 T
1 T
1407914 TACTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.27, C:0.12, G:0.03, T:0.58
Consensus pattern (17 bp):
TATTTCATATAGTCTTA
Found at i:1408313 original size:18 final size:18
Alignment explanation
Indices: 1408290--1408327 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1408280 GATTCTTGAA
1408290 CTCGTTCAGGCTCTAAAT
1 CTCGTTCAGGCTCTAAAT
* *
1408308 CTCGTTTAGGCTCTGAAT
1 CTCGTTCAGGCTCTAAAT
1408326 CT
1 CT
1408328 TTTATCTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.37
Consensus pattern (18 bp):
CTCGTTCAGGCTCTAAAT
Found at i:1419976 original size:28 final size:29
Alignment explanation
Indices: 1419924--1419981 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
1419914 TCTTTGTGGT
1419924 GTAGTAAGTGGTTTTTCATGTTTTAACCA
1 GTAGTAAGTGGTTTTTCATGTTTTAACCA
1419953 GTAGTAAGTGG-TTTTCATGTTTTAACCA
1 GTAGTAAGTGGTTTTTCATGTTTTAACCA
1419981 G
1 G
1419982 GAGTGACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.43
Consensus pattern (29 bp):
GTAGTAAGTGGTTTTTCATGTTTTAACCA
Found at i:1423101 original size:21 final size:21
Alignment explanation
Indices: 1423077--1423123 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1423067 AGTTAGATCT
1423077 CATG-AATTTTTCATAAATATA
1 CATGCAATTTTTC-TAAATATA
*
1423098 CATGCCATTTTTCTAAATA-A
1 CATGCAATTTTTCTAAATATA
1423118 -ATGCAA
1 CATGCAA
1423124 ACAAGTCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.22
20 1 0.04
21 10 0.43
22 7 0.30
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.38
Consensus pattern (21 bp):
CATGCAATTTTTCTAAATATA
Found at i:1440320 original size:26 final size:26
Alignment explanation
Indices: 1440291--1440347 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1440281 ACTCATTATG
*
1440291 TCGTCAAC-ATTATCATCATATCATCA
1 TCGTC-ACTATTATCATCACATCATCA
*
1440317 TCGTCACTATTATTATCACATCATCA
1 TCGTCACTATTATCATCACATCATCA
1440343 TCGTC
1 TCGTC
1440348 GTCGTCATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (26 bp):
TCGTCACTATTATCATCACATCATCA
Found at i:1446707 original size:2 final size:2
Alignment explanation
Indices: 1446700--1446724 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1446690 AATCATACTC
1446700 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1446725 AGCATATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1450412 original size:29 final size:29
Alignment explanation
Indices: 1450365--1450421 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1450355 GTCCCAACAC
*
1450365 ATAGGTCGCCATACCCTCCGGGCGACCTT
1 ATAGGTCGCCATACACTCCGGGCGACCTT
**
1450394 ATAGGTCGCCATGTACTCCGGGCGACCT
1 ATAGGTCGCCATACACTCCGGGCGACCT
1450422 ACCATCGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (29 bp):
ATAGGTCGCCATACACTCCGGGCGACCTT
Found at i:1450513 original size:14 final size:14
Alignment explanation
Indices: 1450491--1450523 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1450481 CCTCGCATAG
*
1450491 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
1450505 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1450519 CTCGG
1 CTCGG
1450524 ATGTTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:1451343 original size:2 final size:2
Alignment explanation
Indices: 1451338--1451365 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1451328 ATTTTCCCAT
1451338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1451366 CTTTTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1451460 original size:10 final size:10
Alignment explanation
Indices: 1451445--1451475 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1451435 ATGATAAATA
1451445 AAAAAATTAG
1 AAAAAATTAG
1451455 AAAAAATTAG
1 AAAAAATTAG
*
1451465 AATAAATTAG
1 AAAAAATTAG
1451475 A
1 A
1451476 TATAAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (10 bp):
AAAAAATTAG
Found at i:1455165 original size:23 final size:24
Alignment explanation
Indices: 1455138--1455197 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
1455128 TATATAACGA
1455138 ACAAGCTCGTTTATC-ACTCGTTT
1 ACAAGCTCGTTTATCGACTCGTTT
1455161 ACAAGCTCGTTTATCGACTCGTTT
1 ACAAGCTCGTTTATCGACTCGTTT
*
1455185 ACAAGCTCATTTA
1 ACAAGCTCGTTTA
1455198 AGTATTGGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 15 0.43
24 20 0.57
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (24 bp):
ACAAGCTCGTTTATCGACTCGTTT
Found at i:1455171 original size:12 final size:12
Alignment explanation
Indices: 1455138--1455197 Score: 63
Period size: 12 Copynumber: 5.1 Consensus size: 12
1455128 TATATAACGA
1455138 ACAAGCTCGTTT
1 ACAAGCTCGTTT
1455150 ATC-A-CTCGTTT
1 A-CAAGCTCGTTT
1455161 ACAAGCTCGTTT
1 ACAAGCTCGTTT
*
1455173 ATCGA-CTCGTTT
1 A-CAAGCTCGTTT
*
1455185 ACAAGCTCATTT
1 ACAAGCTCGTTT
1455197 A
1 A
1455198 AGTATTGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 1 0.03
11 11 0.28
12 25 0.62
13 3 0.08
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (12 bp):
ACAAGCTCGTTT
Found at i:1455365 original size:23 final size:23
Alignment explanation
Indices: 1455339--1455412 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
1455329 GTTTGGTTAT
1455339 CGAACATGTTCACAAACGTTAAA
1 CGAACATGTTCACAAACGTTAAA
* *
1455362 CGAATATGTTCACAAGCGTTAAA
1 CGAACATGTTCACAAACGTTAAA
* ** *
1455385 TGAACATGTTCTTAAATGTTAAA
1 CGAACATGTTCACAAACGTTAAA
1455408 CGAAC
1 CGAAC
1455413 CTACAAAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.27
Consensus pattern (23 bp):
CGAACATGTTCACAAACGTTAAA
Found at i:1460356 original size:362 final size:365
Alignment explanation
Indices: 1459729--1460457 Score: 1387
Period size: 362 Copynumber: 2.0 Consensus size: 365
1459719 AAACAATTAC
1459729 TTTTAGTTTAAGGAAATTGGAGATTTATTGCCAATAATAATATATTGGGTCCATATTATTTTCCG
1 TTTTAGTTTAAGGAAATTGGAGATTTATTGCCAATAATAATATATTGGGTCCATATTATTTTCCG
1459794 ACACTCAATAATTTATCCACTCCATTTAAGGAAGTATCTTAGGGATGGGAGGGGGCTCTCCTCAT
66 ACACTCAATAATTTAT-CACTCCATTTAAGGAAGTATCTTAGGGATGGGAGGGGGCTCTCCTCAT
1459859 GTTTTGGGTTAACTATCTTTACGGTCCTCGTTAATTTTAAAACTAGATAAATTAAATCCCATGTT
130 GTTTTGGGTTAACTATCTTTACGGTCCTCGTTAATTTTAAAACTAGATAAATTAAATCCCATGTT
1459924 TCGGTTTAAATACTACTTGAAAATTGTGATATTAGTAAAATTTAGCTTTGGCTTCATTTTTGTTC
195 TCGGTTTAAATACTACTTGAAAATTGTGATATTAGTAAAATTTAGCTTTGGCTTCATTTTTGTTC
1459989 AAATACTTC-TAGATTTCTGTCAATTTTAAAATGATATAATGTCAAAAATATTCATGATATTTTG
260 AAATACTTCTTAGATTTCTGTCAATTTTAAAATGATATAATGTCAAAAATATTCATGATA-TTTG
1460053 ATTAAGTAGTC-ATTGACCTCTATTCGAGTATTTTGATTCTT
324 ATTAAGTAGTCAATTGACCTCTATTCGAGTATTTTGATTCTT
1460094 TTTTAGTTTAAGGAAATTGGAGAATTTATTGCCAATAATAATATATTGGGTCCATATTATTTTCC
1 TTTTAGTTTAAGGAAATTGGAG-ATTTATTGCCAATAATAATATATTGGGTCCATATTATTTTCC
1460159 GACACTCAATAATTT-T-ACTCCATTTAAGGAAGTATCTTAGGGATGGGAGGGGGCTCTCCTCAT
65 GACACTCAATAATTTATCACTCCATTTAAGGAAGTATCTTAGGGATGGGAGGGGGCTCTCCTCAT
1460222 G-TTTGGGTTAACTATCTTTACGGTCCTCGTTAATTTTAAAACTAGATAAATTAAATCCCATGTT
130 GTTTTGGGTTAACTATCTTTACGGTCCTCGTTAATTTTAAAACTAGATAAATTAAATCCCATGTT
1460286 TCGGTTTAAATACTACTTGAAAATTGTGATATTAGTAAAATTTAGCTTTGGCTTCATTTTTGTTC
195 TCGGTTTAAATACTACTTGAAAATTGTGATATTAGTAAAATTTAGCTTTGGCTTCATTTTTGTTC
1460351 AAATACTTCTTAGATTTCTGTCAATTTTAAAATGATATAATGTCAAAAATATTCATGATATTTGA
260 AAATACTTCTTAGATTTCTGTCAATTTTAAAATGATATAATGTCAAAAATATTCATGATATTTGA
1460416 TTAAGTAGTCATATTGACCTCTATTCGAGTATTTTGATTCTT
325 TTAAGTAGTCA-ATTGACCTCTATTCGAGTATTTTGATTCTT
1460458 AATTTTTTTT
Statistics
Matches: 360, Mismatches: 0, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
362 152 0.42
363 98 0.27
364 30 0.08
365 23 0.06
366 57 0.16
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (365 bp):
TTTTAGTTTAAGGAAATTGGAGATTTATTGCCAATAATAATATATTGGGTCCATATTATTTTCCG
ACACTCAATAATTTATCACTCCATTTAAGGAAGTATCTTAGGGATGGGAGGGGGCTCTCCTCATG
TTTTGGGTTAACTATCTTTACGGTCCTCGTTAATTTTAAAACTAGATAAATTAAATCCCATGTTT
CGGTTTAAATACTACTTGAAAATTGTGATATTAGTAAAATTTAGCTTTGGCTTCATTTTTGTTCA
AATACTTCTTAGATTTCTGTCAATTTTAAAATGATATAATGTCAAAAATATTCATGATATTTGAT
TAAGTAGTCAATTGACCTCTATTCGAGTATTTTGATTCTT
Found at i:1471070 original size:20 final size:20
Alignment explanation
Indices: 1471045--1471089 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1471035 TATAATCAAT
*
1471045 AAAATAGGTAGTAATTGAAG
1 AAAATAAGTAGTAATTGAAG
1471065 AAAATAAGTAGTAATTGAAG
1 AAAATAAGTAGTAATTGAAG
1471085 AAAAT
1 AAAAT
1471090 TCAATTCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (20 bp):
AAAATAAGTAGTAATTGAAG
Found at i:1473127 original size:60 final size:60
Alignment explanation
Indices: 1473061--1473224 Score: 179
Period size: 60 Copynumber: 2.7 Consensus size: 60
1473051 ATGAATTTGA
* * * ** *
1473061 GGATGAAATTGGAATGTTCAAAACTTTAGGGACCAATTTAGAAA-GAGGGTTGTAGTTTAG
1 GGATGAAATTGGAATATTTAAAACTTTAGGGACCAATTTA-AAATGAGAGTCATAATTTAG
* **
1473121 GGATGAAATTGGAATATTTAAAAGTTTAAGGG-TTAATTTAAAATGAGAGTCATAATTTAG
1 GGATGAAATTGGAATATTTAAAACTTT-AGGGACCAATTTAAAATGAGAGTCATAATTTAG
* * * *
1473181 GGATAAAATTAGAATATTTAAAATTTTAAGGACCAATTTAAAAT
1 GGATGAAATTGGAATATTTAAAACTTTAGGGACCAATTTAAAAT
1473225 AAGGATTATA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
59 6 0.07
60 76 0.88
61 4 0.05
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.33
Consensus pattern (60 bp):
GGATGAAATTGGAATATTTAAAACTTTAGGGACCAATTTAAAATGAGAGTCATAATTTAG
Found at i:1474426 original size:16 final size:16
Alignment explanation
Indices: 1474405--1474436 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1474395 ACGCGTTTAG
1474405 ATTTAAAATAAAAATT
1 ATTTAAAATAAAAATT
1474421 ATTTAAAATAAAAATT
1 ATTTAAAATAAAAATT
1474437 GTTAAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTAAAATAAAAATT
Found at i:1474441 original size:15 final size:16
Alignment explanation
Indices: 1474407--1474442 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1474397 GCGTTTAGAT
*
1474407 TTAAAATAAAAATTAT
1 TTAAAATAAAAATTAG
1474423 TTAAAATAAAAATT-G
1 TTAAAATAAAAATTAG
1474438 TTAAA
1 TTAAA
1474443 TTCAAGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TTAAAATAAAAATTAG
Found at i:1474530 original size:17 final size:17
Alignment explanation
Indices: 1474489--1474548 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
1474479 ATTTAATTTT
*
1474489 TATTTTTAGTATTTT-AT
1 TATTTTTA-TATTTTAAA
* *
1474506 TATATTTACT-TTTTGAA
1 TATTTTTA-TATTTTAAA
1474523 TATTTTTATATTTTAAA
1 TATTTTTATATTTTAAA
1474540 TATTTTTAT
1 TATTTTTAT
1474549 TTAAAAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 5 0.14
17 31 0.86
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (17 bp):
TATTTTTATATTTTAAA
Found at i:1505732 original size:277 final size:277
Alignment explanation
Indices: 1505238--1505775 Score: 1013
Period size: 277 Copynumber: 1.9 Consensus size: 277
1505228 CTTTCATCAC
1505238 ATAGTTATTGAACTTTGACAATTGAGTGACCGTTTTGTTAGGAAAAAAATATTAGTGACTATATT
1 ATAGTTATTGAACTTTGACAATTGAGTGACCGTTTTGTTAGGAAAAAAATATTAGTGACTATATT
1505303 ATAACTTTTGAAACGTCAGTGATAAAAAGCAAAACTTACTTAAAATTTAGTGATCTTTTATGTAA
66 ATAACTTTTGAAACGTCAGTGATAAAAAGCAAAACTTACTTAAAATTTAGTGATCTTTTATGTAA
* **
1505368 TTGACCCTAAATATAAATTTTGATTAATATAGATTAACAATTAAAATATAATTTAAACTTTTTGT
131 TTGACCCTAAATATAAATTTTAATTAATATAGATTAACAATTAAAATATAATTTAAACTTTAAGT
1505433 TTATTGTATAAACTATTTTTAAAAAAAATATCTAGAACTGAACTTACGTACACACAGACTATATT
196 TTATTGTATAAACTATTTTTAAAAAAAATATCTAGAACTGAACTTACGTACACACAGACTATATT
1505498 ATAACTTTTGTTATAAT
261 ATAACTTTTGTTATAAT
* *
1505515 ATAGTTATTGAACTTTGACAATTGAGTGACCGTTTTGTTAGGAAAAAAATGTTAGTGACTATTTT
1 ATAGTTATTGAACTTTGACAATTGAGTGACCGTTTTGTTAGGAAAAAAATATTAGTGACTATATT
1505580 ATAACTTTTGAAACGTCAGTGATAAAAAGCAAAACTTACTTAAAATTTAGTGATCTTTTATGTAA
66 ATAACTTTTGAAACGTCAGTGATAAAAAGCAAAACTTACTTAAAATTTAGTGATCTTTTATGTAA
*
1505645 TTGTCCCTAAATATAAATTTTAATTAATATAGATTAACAATTAAAATATAATTTAAACTTTAAGT
131 TTGACCCTAAATATAAATTTTAATTAATATAGATTAACAATTAAAATATAATTTAAACTTTAAGT
*
1505710 TTATTGTATAAACTATTTTTAAAAAAAATATTTAGAACTGAACTTACGTACACACAGACTATATT
196 TTATTGTATAAACTATTTTTAAAAAAAATATCTAGAACTGAACTTACGTACACACAGACTATATT
1505775 A
261 A
1505776 CTCGAATTTG
Statistics
Matches: 254, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
277 254 1.00
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.39
Consensus pattern (277 bp):
ATAGTTATTGAACTTTGACAATTGAGTGACCGTTTTGTTAGGAAAAAAATATTAGTGACTATATT
ATAACTTTTGAAACGTCAGTGATAAAAAGCAAAACTTACTTAAAATTTAGTGATCTTTTATGTAA
TTGACCCTAAATATAAATTTTAATTAATATAGATTAACAATTAAAATATAATTTAAACTTTAAGT
TTATTGTATAAACTATTTTTAAAAAAAATATCTAGAACTGAACTTACGTACACACAGACTATATT
ATAACTTTTGTTATAAT
Found at i:1512974 original size:2 final size:2
Alignment explanation
Indices: 1512967--1513008 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1512957 AGAATTATGA
1512967 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
1513009 TAAAAAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1513048 original size:20 final size:19
Alignment explanation
Indices: 1512999--1513050 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 19
1512989 ATATATATAT
1512999 ATATATATATTAAAAAATG
1 ATATATATATTAAAAAATG
*
1513018 ATATCACATATTAAAAAATATG
1 ATAT-ATATATT-AAAAA-ATG
1513040 AATATATATAT
1 -ATATATATAT
1513051 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 6 0.22
21 5 0.19
22 8 0.30
23 4 0.15
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (19 bp):
ATATATATATTAAAAAATG
Found at i:1513441 original size:110 final size:110
Alignment explanation
Indices: 1513316--1513517 Score: 359
Period size: 110 Copynumber: 1.8 Consensus size: 110
1513306 TCCTCGACTA
* *
1513316 TTTTTTTGGAACAATCCCATAAAGAAAGTCATATTGCCCAATAACTAAGCCAGATGAATTTTCTT
1 TTTTTTTGGAACAATCCCATAAAGAAAGTCACATTACCCAATAACTAAGCCAGATGAATTTTCTT
1513381 TTTCTCCTTCCCCAGTAGAAAAGGAGGTCATCGACGTGTTTTTTT
66 TTTCTCCTTCCCCAGTAGAAAAGGAGGTCATCGACGTGTTTTTTT
* * *
1513426 TTTTTTTTGAACAATCCCATAAAGAAAGTCACATTATCCAATAACTAAGCTAGATGAATTTTCTT
1 TTTTTTTGGAACAATCCCATAAAGAAAGTCACATTACCCAATAACTAAGCCAGATGAATTTTCTT
1513491 TTTCTCCTTCCCCAGTAGAAAAGGAGG
66 TTTCTCCTTCCCCAGTAGAAAAGGAGG
1513518 GATGCGTGGA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 87 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (110 bp):
TTTTTTTGGAACAATCCCATAAAGAAAGTCACATTACCCAATAACTAAGCCAGATGAATTTTCTT
TTTCTCCTTCCCCAGTAGAAAAGGAGGTCATCGACGTGTTTTTTT
Found at i:1516411 original size:33 final size:32
Alignment explanation
Indices: 1516353--1516451 Score: 139
Period size: 33 Copynumber: 3.1 Consensus size: 32
1516343 TAAGTGAAAA
*
1516353 AATTTGATAAA-TTTAATGATCATTTTGTAAC
1 AATTTGATAAACTTCAATGATCATTTTGTAAC
* *
1516384 AATTTGATAAAACTTCAATGATAATTTTGTAGC
1 AATTTGAT-AAACTTCAATGATCATTTTGTAAC
*
1516417 AATTTGATAAACCTCAATGATCATTTTGT-AC
1 AATTTGATAAACTTCAATGATCATTTTGTAAC
1516448 AATT
1 AATT
1516452 CAAAAATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
31 13 0.22
32 22 0.37
33 25 0.42
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (32 bp):
AATTTGATAAACTTCAATGATCATTTTGTAAC
Found at i:1516443 original size:32 final size:31
Alignment explanation
Indices: 1516353--1516451 Score: 137
Period size: 32 Copynumber: 3.1 Consensus size: 31
1516343 TAAGTGAAAA
*
1516353 AATTTGATAAA-TTTAATGATCATTTTGTAAC
1 AATTTGATAAACTTCAATGATCATTTTGT-AC
*
1516384 AATTTGATAAAACTTCAATGATAATTTTGTAGC
1 AATTTGAT-AAACTTCAATGATCATTTTGTA-C
*
1516417 AATTTGATAAACCTCAATGATCATTTTGTAC
1 AATTTGATAAACTTCAATGATCATTTTGTAC
1516448 AATT
1 AATT
1516452 CAAAAATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
31 13 0.21
32 24 0.39
33 24 0.39
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (31 bp):
AATTTGATAAACTTCAATGATCATTTTGTAC
Found at i:1518196 original size:13 final size:13
Alignment explanation
Indices: 1518178--1518202 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1518168 TTAAATTCAA
1518178 TATTCAATTATAT
1 TATTCAATTATAT
1518191 TATTCAATTATA
1 TATTCAATTATA
1518203 AAATTTTATT
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:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTCAATTATAT
Found at i:1520882 original size:25 final size:25
Alignment explanation
Indices: 1520854--1520912 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
1520844 ATAAAAATCA
1520854 TAAAAATTTAAAATATAAAGGAATT
1 TAAAAATTTAAAATATAAAGGAATT
*
1520879 TAAAATTTTAAAATATAAAGGAATT
1 TAAAAATTTAAAATATAAAGGAATT
1520904 TAAAAATTT
1 TAAAAATTT
1520913 CAAAGGCGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (25 bp):
TAAAAATTTAAAATATAAAGGAATT
Found at i:1521014 original size:17 final size:17
Alignment explanation
Indices: 1520992--1521025 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1520982 CATATAACAT
1520992 AGTGTCAATTATTGAAA
1 AGTGTCAATTATTGAAA
1521009 AGTGTCAATTATTGAAA
1 AGTGTCAATTATTGAAA
1521026 TGTGCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
AGTGTCAATTATTGAAA
Found at i:1525669 original size:12 final size:12
Alignment explanation
Indices: 1525652--1525677 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1525642 CCGATGCTCT
1525652 GCTATGCAGAAA
1 GCTATGCAGAAA
1525664 GCTATGCAGAAA
1 GCTATGCAGAAA
1525676 GC
1 GC
1525678 CTTAGATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.15
Consensus pattern (12 bp):
GCTATGCAGAAA
Found at i:1531139 original size:18 final size:18
Alignment explanation
Indices: 1531116--1531151 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1531106 TGGAGATCTG
1531116 CTCCCTAATATCGGGTGC
1 CTCCCTAATATCGGGTGC
*
1531134 CTCCCTATTATCGGGTGC
1 CTCCCTAATATCGGGTGC
1531152 AGGAGACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.33, G:0.22, T:0.31
Consensus pattern (18 bp):
CTCCCTAATATCGGGTGC
Found at i:1533349 original size:57 final size:57
Alignment explanation
Indices: 1533280--1533438 Score: 263
Period size: 57 Copynumber: 2.8 Consensus size: 57
1533270 AAGTCAATGC
* *
1533280 AGCATTTTAAGCTCATCTTATGGTGATCGAGTTTAGAGTGTTAACTCCTCCACCTGT
1 AGCATCTTAAGCTCATCTTATGGTGATAGAGTTTAGAGTGTTAACTCCTCCACCTGT
1533337 AGCATCTTAAGCTCATCTTATGGTGATAGAGTTTAGAGTGTTAAC-CCTCCACCTGT
1 AGCATCTTAAGCTCATCTTATGGTGATAGAGTTTAGAGTGTTAACTCCTCCACCTGT
1533393 AGCATC-T--GCTCATCTTATGGTGATAGAGTTTAGAGTGTTACACTCC
1 AGCATCTTAAGCTCATCTTATGGTGATAGAGTTTAGAGTGTTA-ACTCC
1533439 ACGTAATTCT
Statistics
Matches: 98, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
53 33 0.34
54 2 0.02
55 3 0.03
56 17 0.17
57 43 0.44
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (57 bp):
AGCATCTTAAGCTCATCTTATGGTGATAGAGTTTAGAGTGTTAACTCCTCCACCTGT
Found at i:1535949 original size:30 final size:30
Alignment explanation
Indices: 1535913--1536014 Score: 195
Period size: 30 Copynumber: 3.4 Consensus size: 30
1535903 GAGGCAAATC
*
1535913 ACAATAACAATAACCATATCTGAATTATGA
1 ACAATAACAATAAGCATATCTGAATTATGA
1535943 ACAATAACAATAAGCATATCTGAATTATGA
1 ACAATAACAATAAGCATATCTGAATTATGA
1535973 ACAATAACAATAAGCATATCTGAATTATGA
1 ACAATAACAATAAGCATATCTGAATTATGA
1536003 ACAATAACAATA
1 ACAATAACAATA
1536015 TATAAAGGAG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (30 bp):
ACAATAACAATAAGCATATCTGAATTATGA
Found at i:1545125 original size:17 final size:19
Alignment explanation
Indices: 1545099--1545136 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1545089 GAAAAAGATT
1545099 ATTTGAAA-TTATTA-ATA
1 ATTTGAAATTTATTATATA
*
1545116 ATTTGGAATTTATTATATA
1 ATTTGAAATTTATTATATA
1545135 AT
1 AT
1545137 ATGTATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (19 bp):
ATTTGAAATTTATTATATA
Found at i:1546287 original size:2 final size:2
Alignment explanation
Indices: 1546282--1546312 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1546272 TATATAAAGT
1546282 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1546313 TCAAGTTCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1551009 original size:2 final size:2
Alignment explanation
Indices: 1551002--1551033 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1550992 ATACTAACCC
1551002 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
1551034 GAGCTCTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1552891 original size:18 final size:18
Alignment explanation
Indices: 1552856--1552909 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
1552846 TTTGAATTTG
*
1552856 AATAGTATTTTTATTTTT
1 AATAGTATTTTAATTTTT
1552874 AATAGT-TTTTAATTTTT
1 AATAGTATTTTAATTTTT
** *
1552891 TTTAATATTTTAATATTTT
1 AATAGTATTTTAAT-TTTT
1552910 TTCTTAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 13 0.43
18 13 0.43
19 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
AATAGTATTTTAATTTTT
Found at i:1552894 original size:20 final size:19
Alignment explanation
Indices: 1552869--1552911 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
1552859 AGTATTTTTA
1552869 TTTTTAATAGTTTTTAAT-TT
1 TTTTTAATA--TTTTAATATT
1552889 TTTTTAATATTTTAATATT
1 TTTTTAATATTTTAATATT
1552908 TTTT
1 TTTT
1552912 CTTAAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 6 0.27
20 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTTAATATTTTAATATT
Found at i:1552910 original size:18 final size:19
Alignment explanation
Indices: 1552869--1552911 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1552859 AGTATTTTTA
*
1552869 TTTTTAATAGTTTTTAATTT
1 TTTTTAATAG-TTTTAATAT
1552889 TTTTTAATA-TTTTAATAT
1 TTTTTAATAGTTTTAATAT
1552907 TTTTT
1 TTTTT
1552912 CTTAAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.59
20 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTTAATAGTTTTAATAT
Found at i:1552911 original size:10 final size:10
Alignment explanation
Indices: 1552869--1552911 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
1552859 AGTATTTTTA
*
1552869 TTTTTAATAG
1 TTTTTAATAT
*
1552879 TTTTTAATTT
1 TTTTTAATAT
1552889 TTTTTAATA-
1 TTTTTAATAT
1552898 -TTTTAATAT
1 TTTTTAATAT
1552907 TTTTT
1 TTTTT
1552912 CTTAAAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 8 0.29
10 20 0.71
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:1563099 original size:46 final size:46
Alignment explanation
Indices: 1562998--1563099 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
1562988 AACAAGGGGA
* *
1562998 TATGGATATCCCATATCCCACATCAGCAAGAAAATTAATAAGAGGT
1 TATGGATATCCCATATCCCACATAAGCAAGAAAATTAATAAGAGGC
* * * * *
1563044 TGTGAATATCCCATATCCCACATAAGGAA-ATGAATTAGTAAGAGGC
1 TATGGATATCCCATATCCCACATAAGCAAGA-AAATTAATAAGAGGC
1563090 TATGGATATC
1 TATGGATATC
1563100 ATTTATAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
45 1 0.02
46 45 0.98
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (46 bp):
TATGGATATCCCATATCCCACATAAGCAAGAAAATTAATAAGAGGC
Found at i:1563237 original size:32 final size:32
Alignment explanation
Indices: 1563195--1563276 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
1563185 TATTTCTTTA
*
1563195 TTTAT-GTATTTTTATTTAGCTCTAATTAATG
1 TTTATGGTATTTTTATTTAGCTATAATTAATG
* *
1563226 TTTCTGGTATTTTTATTTAGCTATGATTAATG
1 TTTATGGTATTTTTATTTAGCTATAATTAATG
*
1563258 TTTATGGTATTTTCATTTA
1 TTTATGGTATTTTTATTTA
1563277 TTTGCTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 4 0.09
32 41 0.91
ACGTcount: A:0.23, C:0.06, G:0.12, T:0.59
Consensus pattern (32 bp):
TTTATGGTATTTTTATTTAGCTATAATTAATG
Found at i:1564406 original size:2 final size:2
Alignment explanation
Indices: 1564399--1564424 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1564389 ACAAGTTTCT
1564399 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1564425 GTACATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1564723 original size:170 final size:170
Alignment explanation
Indices: 1564440--1564770 Score: 554
Period size: 170 Copynumber: 1.9 Consensus size: 170
1564430 TATGATTGTA
*
1564440 ATATAACATTTTAAATAAAAAACGCAGATACAATATGCACAAATTTCAAATGAAATTTTTCATGA
1 ATATAACATTTTAAATAAAAAACGCAGATACAATATGCACAAATTTCAAATGAAATTTTCCATGA
* * *
1564505 CGAAATTTATATTCTAAAACTGCTTTTAACTATTAGTTTAAGTTGGTTCATCTTTCCATTTGCTT
66 CGAAATTTATATTCTAAAACTGCTTTCAACTATTACTTTAAATTGGTTCATCTTTCCATTTGCTT
1564570 TTAACTAGTAGTTTAAATTTGTCATAGTTGTGAATGTAAT
131 TTAACTAGTAGTTTAAATTTGTCATAGTTGTGAATGTAAT
* * *
1564610 ATATAACATTTTAAATAAAAAACGCATATGCAATATGTACAAATTTCAAATGAAATTTTCCATGA
1 ATATAACATTTTAAATAAAAAACGCAGATACAATATGCACAAATTTCAAATGAAATTTTCCATGA
* * *
1564675 TGAAATTTATATTCTAAAATTGCTTTCATCTATTACTTTAAATTGGTTCATCTTTCCATTTGCTT
66 CGAAATTTATATTCTAAAACTGCTTTCAACTATTACTTTAAATTGGTTCATCTTTCCATTTGCTT
**
1564740 TTAGTTAGTAGTTTAAATTTGTCATAGTTGT
131 TTAACTAGTAGTTTAAATTTGTCATAGTTGT
1564771 ATTCATAATG
Statistics
Matches: 149, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
170 149 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.42
Consensus pattern (170 bp):
ATATAACATTTTAAATAAAAAACGCAGATACAATATGCACAAATTTCAAATGAAATTTTCCATGA
CGAAATTTATATTCTAAAACTGCTTTCAACTATTACTTTAAATTGGTTCATCTTTCCATTTGCTT
TTAACTAGTAGTTTAAATTTGTCATAGTTGTGAATGTAAT
Found at i:1575483 original size:16 final size:16
Alignment explanation
Indices: 1575438--1575476 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1575428 TTCAGAACTT
**
1575438 GAAATGACATGAATCC
1 GAAATGACACAAATCC
1575454 GAAATGACACAAATCC
1 GAAATGACACAAATCC
1575470 GAAATGA
1 GAAATGA
1575477 TTTAAATGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (16 bp):
GAAATGACACAAATCC
Found at i:1577035 original size:13 final size:13
Alignment explanation
Indices: 1577017--1577043 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1577007 AAAATCTCAA
1577017 GGGAACTTCTAAG
1 GGGAACTTCTAAG
1577030 GGGAACTTCTAAG
1 GGGAACTTCTAAG
1577043 G
1 G
1577044 TGATTTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (13 bp):
GGGAACTTCTAAG
Found at i:1581289 original size:17 final size:17
Alignment explanation
Indices: 1581267--1581304 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1581257 TTATCAATAG
1581267 AAAATACTAA-AAAATTT
1 AAAATA-TAAGAAAATTT
*
1581284 AAAATATAAGAGAATTT
1 AAAATATAAGAAAATTT
1581301 AAAA
1 AAAA
1581305 GTTTTAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (17 bp):
AAAATATAAGAAAATTT
Found at i:1588419 original size:24 final size:22
Alignment explanation
Indices: 1588374--1588419 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1588364 TCATGATTCG
* *
1588374 ATTATAAATATCAACAATTTAA
1 ATTATAAAAATCAACAAATTAA
1588396 ATTATAAAAATCAATTCAAATTAA
1 ATTATAAAAATCAA--CAAATTAA
1588420 TACGTAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTATAAAAATCAACAAATTAA
Found at i:1595328 original size:122 final size:122
Alignment explanation
Indices: 1595111--1595356 Score: 492
Period size: 122 Copynumber: 2.0 Consensus size: 122
1595101 GACCATCCAG
1595111 CTCAGTTGATAGAGCATAAGACTCTTAATCTTGGGGTTGTGGGATCGAGTCCCACGGAGAGCATT
1 CTCAGTTGATAGAGCATAAGACTCTTAATCTTGGGGTTGTGGGATCGAGTCCCACGGAGAGCATT
1595176 TCATAATTTGAAGGTCTCATACGGAAGTTGCTCTCAACCTGACGTTGGGGCAGTCTA
66 TCATAATTTGAAGGTCTCATACGGAAGTTGCTCTCAACCTGACGTTGGGGCAGTCTA
1595233 CTCAGTTGATAGAGCATAAGACTCTTAATCTTGGGGTTGTGGGATCGAGTCCCACGGAGAGCATT
1 CTCAGTTGATAGAGCATAAGACTCTTAATCTTGGGGTTGTGGGATCGAGTCCCACGGAGAGCATT
1595298 TCATAATTTGAAGGTCTCATACGGAAGTTGCTCTCAACCTGACGTTGGGGCAGTCTA
66 TCATAATTTGAAGGTCTCATACGGAAGTTGCTCTCAACCTGACGTTGGGGCAGTCTA
1595355 CT
1 CT
1595357 ATCTTACCTC
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (122 bp):
CTCAGTTGATAGAGCATAAGACTCTTAATCTTGGGGTTGTGGGATCGAGTCCCACGGAGAGCATT
TCATAATTTGAAGGTCTCATACGGAAGTTGCTCTCAACCTGACGTTGGGGCAGTCTA
Found at i:1595999 original size:28 final size:28
Alignment explanation
Indices: 1595959--1596016 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1595949 CTAAAAATCT
1595959 TAGATTTAAACAATTACGTCTGAAAGTG
1 TAGATTTAAACAATTACGTCTGAAAGTG
1595987 TAGATTTAAACAATTACGTCTGAAAGTG
1 TAGATTTAAACAATTACGTCTGAAAGTG
1596015 TA
1 TA
1596017 TGTACATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (28 bp):
TAGATTTAAACAATTACGTCTGAAAGTG
Found at i:1602602 original size:2 final size:2
Alignment explanation
Indices: 1602595--1602625 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1602585 CAGCACCTCG
1602595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1602626 ATTTCTTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1605774 original size:13 final size:13
Alignment explanation
Indices: 1605755--1605815 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 13
1605745 GTCATAACCC
1605755 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
1605768 TACCCGACCAGTT
1 GACCCGACCCGTT
1605781 GATCCGACCCGACCCGTT
1 G-----ACCCGACCCGTT
*
1605799 GACCCGACCCATT
1 GACCCGACCCGTT
1605812 GACC
1 GACC
1605816 TGTTGATTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
13 26 0.68
18 12 0.32
ACGTcount: A:0.20, C:0.44, G:0.20, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1605774 original size:18 final size:18
Alignment explanation
Indices: 1605751--1605808 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
1605741 ACCGGTCATA
*
1605751 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
1605769 ACCCGA-CC-A---GTTG
1 ACCCGACCCGACCCGTTG
*
1605782 ATCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1605800 ACCCGACCC
1 ACCCGACCC
1605809 ATTGACCTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
13 8 0.25
14 2 0.06
15 1 0.03
16 1 0.03
17 2 0.06
18 18 0.56
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1608195 original size:24 final size:23
Alignment explanation
Indices: 1608136--1608214 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 23
1608126 AATTTTGTTA
1608136 TGATACATGACCTGGATTCTGA-
1 TGATACATGACCTGGATTCTGAT
* *
1608158 T-ATA-TTGACATGGATTCTGAT
1 TGATACATGACCTGGATTCTGAT
1608179 CTGATACATGACCTGGATTCTGAT
1 -TGATACATGACCTGGATTCTGAT
*
1608203 ATGATACTTGAC
1 -TGATACATGAC
1608215 TTGAATTATG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 14 0.30
21 3 0.06
22 2 0.04
23 3 0.06
24 25 0.53
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (23 bp):
TGATACATGACCTGGATTCTGAT
Found at i:1608200 original size:19 final size:19
Alignment explanation
Indices: 1608136--1608203 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 19
1608126 AATTTTGTTA
1608136 TGATACATGACCTGGATTC
1 TGATACATGACCTGGATTC
* *
1608155 TGATATATTGACATGGATTCTGATC
1 TGATACA-TGACCTGGA---T--TC
1608180 TGATACATGACCTGGATTC
1 TGATACATGACCTGGATTC
1608199 TGATA
1 TGATA
1608204 TGATACTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
19 13 0.33
20 8 0.21
21 1 0.03
23 1 0.03
24 8 0.21
25 8 0.21
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (19 bp):
TGATACATGACCTGGATTC
Found at i:1610733 original size:15 final size:15
Alignment explanation
Indices: 1610713--1610757 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
1610703 TAGTATCAAA
*
1610713 GGTAATCAATCGAAC
1 GGTAATCAATCCAAC
1610728 GGTAATCAATCCAAC
1 GGTAATCAATCCAAC
*
1610743 GGTAACCAATCCAAC
1 GGTAATCAATCCAAC
1610758 AGTATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.18
Consensus pattern (15 bp):
GGTAATCAATCCAAC
Found at i:1610986 original size:21 final size:21
Alignment explanation
Indices: 1610959--1611028 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
1610949 TAGCACGGTC
1610959 CTCCGCAGCATCAGCTCGCTG
1 CTCCGCAGCATCAGCTCGCTG
* *
1610980 TTCCGCAGCATCAGCTCGCTC
1 CTCCGCAGCATCAGCTCGCTG
*
1611001 CTCTGCAGCATCAGCTCGCTG
1 CTCCGCAGCATCAGCTCGCTG
1611022 CTCCGCA
1 CTCCGCA
1611029 TCACAAGCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.14, C:0.43, G:0.21, T:0.21
Consensus pattern (21 bp):
CTCCGCAGCATCAGCTCGCTG
Found at i:1611844 original size:191 final size:190
Alignment explanation
Indices: 1611592--1611967 Score: 610
Period size: 192 Copynumber: 2.0 Consensus size: 190
1611582 GTGGATGCCA
* * *
1611592 TGGAAGCTTTAATTAAACCGAATGTAATTAACGATATTACTTAATCACCCTACACTGTTTAGCTA
1 TGGAAGCTTTAATTAAACCGAATATAATTAACAATATTACTTAATCACCCTAAACTGTTTAGCTA
* * * * *
1611657 TTGCTTATTTAAACATTGGTTTTGAATTGAAAATTGATCATCTT-TACATCATTGAATTTCAATT
66 TTGCTTATTTAAACACTGGTTTTGAATTGAAAATTGATCATATTCTAAATCATTCAATTTCAATG
1611721 AATATACATATACATGCAAATTTGGATGCCAAAACTCATTATTCAGTAGGTTCCATAATT
131 AATATACATATACATGCAAATTTGGATGCCAAAACTCATTATTCAGTAGGTTCCATAATT
* * *
1611781 TGGAAGCTTTAATTCAACCGAAATATAATTAACAATATTACTTACTTCACCCTAAATTGTTTAGC
1 TGGAAGCTTTAATTAAACCG-AATATAATTAACAATATTACTTA-ATCACCCTAAACTGTTTAGC
1611846 TATTGCTTATTTAAACACTGGTTTTGAATTGAAAATTGATCATATTCTAAATCATTCAATTTCAA
64 TATTGCTTATTTAAACACTGGTTTTGAATTGAAAATTGATCATATTCTAAATCATTCAATTTCAA
* *
1611911 TGAATATACATATTCATGCAATTTTGGATGCCAAAACTCATTATTCAGTAGGTTCCA
129 TGAATATACATATACATGCAAATTTGGATGCCAAAACTCATTATTCAGTAGGTTCCA
1611968 CATTACATTT
Statistics
Matches: 171, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
189 19 0.11
190 21 0.12
191 61 0.36
192 70 0.41
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (190 bp):
TGGAAGCTTTAATTAAACCGAATATAATTAACAATATTACTTAATCACCCTAAACTGTTTAGCTA
TTGCTTATTTAAACACTGGTTTTGAATTGAAAATTGATCATATTCTAAATCATTCAATTTCAATG
AATATACATATACATGCAAATTTGGATGCCAAAACTCATTATTCAGTAGGTTCCATAATT
Found at i:1614619 original size:45 final size:44
Alignment explanation
Indices: 1614545--1614633 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 44
1614535 TGGAAGAATC
1614545 AATCATCGTTATGATTGTTGGTCTCTAAGAAAAGCAAGGAGATA
1 AATCATCGTTATGATTGTTGGTCTCTAAGAAAAGCAAGGAGATA
1614589 AATCATCGTTATGATTTGTTGGTCTCTAAGAAAAGCAAGGAGATA
1 AATCATCGTTATGA-TTGTTGGTCTCTAAGAAAAGCAAGGAGATA
1614634 TTGCTCTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 14 0.32
45 30 0.68
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.30
Consensus pattern (44 bp):
AATCATCGTTATGATTGTTGGTCTCTAAGAAAAGCAAGGAGATA
Found at i:1615826 original size:189 final size:189
Alignment explanation
Indices: 1615503--1616072 Score: 1014
Period size: 189 Copynumber: 3.0 Consensus size: 189
1615493 GTGGATCCCA
* *
1615503 TGGAAGCTTTAATTCAACCGAAATGTAATTAACAATATTACTGAATCACCCTACATTGTTTACCT
1 TGGAAGCTTTAATTCAACCGAAATATAATTAACAATATTACT---TCACCCTACATTGTTTAGCT
*
1615568 ATTGCTTATTTAAACACTAGTTTTTAATTGAAAATTGATCATCTTTTAAATCATTCAATTTCAAT
63 ATTGCTTATTTAAACACTAGTTTTGAATTGAAAATTGATCATCTTTTAAATCATTCAATTTCAAT
1615633 GAATATACATATTCATGCAAATTTGGATGCCAAAACTCATTATTCAGTAGGTTCCATAATTT
128 GAATATACATATTCATGCAAATTTGGATGCCAAAACTCATTATTCAGTAGGTTCCATAATTT
1615695 TGGAAGCTTTAATTCAACCGAAATATAATTAACAATATTACTTCACCCTACATTGTTTAGCTATT
1 TGGAAGCTTTAATTCAACCGAAATATAATTAACAATATTACTTCACCCTACATTGTTTAGCTATT
**
1615760 GCTTATTTAAACACCGGTTTTGAATTGAAAATTGATCATCTTTTAAATCATTCAATTTCAATGAA
66 GCTTATTTAAACACTAGTTTTGAATTGAAAATTGATCATCTTTTAAATCATTCAATTTCAATGAA
*
1615825 TATACATAGTCATGCAAATTTGGATGCCAAAACTCATTATTCAGTAGGTTCCATAATTT
131 TATACATATTCATGCAAATTTGGATGCCAAAACTCATTATTCAGTAGGTTCCATAATTT
1615884 TGGAAGCTTTAATTCAACCGAAATATAATTAACAATATTACTTCACCCTACATTGTTTAGCTATT
1 TGGAAGCTTTAATTCAACCGAAATATAATTAACAATATTACTTCACCCTACATTGTTTAGCTATT
*
1615949 GCTTATTTAAACACTAGTTTTGAATTGAAAATTGATCATATTTCTAAATCATTCAATTTCAATGA
66 GCTTATTTAAACACTAGTTTTGAATTGAAAATTGATCATCTTT-TAAATCATTCAATTTCAATGA
* * *
1616014 ATATACATATTCATTCAATTTTGGATGCCAAAACTCATTATTCAGTAGGTTCCACAATT
130 ATATACATATTCATGCAAATTTGGATGCCAAAACTCATTATTCAGTAGGTTCCATAATT
1616073 ACATTTTACA
Statistics
Matches: 364, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
189 247 0.68
190 76 0.21
192 41 0.11
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (189 bp):
TGGAAGCTTTAATTCAACCGAAATATAATTAACAATATTACTTCACCCTACATTGTTTAGCTATT
GCTTATTTAAACACTAGTTTTGAATTGAAAATTGATCATCTTTTAAATCATTCAATTTCAATGAA
TATACATATTCATGCAAATTTGGATGCCAAAACTCATTATTCAGTAGGTTCCATAATTT
Found at i:1621138 original size:40 final size:37
Alignment explanation
Indices: 1621093--1621176 Score: 93
Period size: 37 Copynumber: 2.3 Consensus size: 37
1621083 TCCAATTGAC
1621093 TAATAATTAAAAAAATAGCTTTAATATAATTTTATAAAAA
1 TAATAATTAAAAAAATAGC--TAATATAATTTT-TAAAAA
***
1621133 TAATAATT-TGTAAATAGCTAATATAATTTTTAAAAA
1 TAATAATTAAAAAAATAGCTAATATAATTTTTAAAAA
1621169 -AAT-ATTAA
1 TAATAATTAA
1621177 GCAAATTATC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
34 3 0.08
35 3 0.08
36 6 0.15
37 12 0.31
39 7 0.18
40 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (37 bp):
TAATAATTAAAAAAATAGCTAATATAATTTTTAAAAA
Found at i:1628562 original size:15 final size:15
Alignment explanation
Indices: 1628542--1628571 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1628532 TTTGTATCCG
1628542 ATTTTGTATTAGACT
1 ATTTTGTATTAGACT
1628557 ATTTTGTATTAGACT
1 ATTTTGTATTAGACT
1628572 CGTCTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (15 bp):
ATTTTGTATTAGACT
Found at i:1629788 original size:27 final size:27
Alignment explanation
Indices: 1629758--1629818 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
1629748 CAACGTTAAG
*
1629758 CAATCCCCAAACAGTATAAAAAATAAA
1 CAATCCCCAAACAATATAAAAAATAAA
* * * *
1629785 CAATCCACAAACAATATTAAAAGTAAG
1 CAATCCCCAAACAATATAAAAAATAAA
1629812 CAATCCC
1 CAATCCC
1629819 ACCAGTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.54, C:0.25, G:0.05, T:0.16
Consensus pattern (27 bp):
CAATCCCCAAACAATATAAAAAATAAA
Found at i:1629994 original size:21 final size:21
Alignment explanation
Indices: 1629968--1630050 Score: 148
Period size: 21 Copynumber: 4.0 Consensus size: 21
1629958 GTTTTAACAA
*
1629968 GCTCCTCCGCAGAACGAGCAT
1 GCTCCTCCGCAGAACGAGCAC
1629989 GCTCCTCCGCAGAACGAGCAC
1 GCTCCTCCGCAGAACGAGCAC
*
1630010 GTTCCTCCGCAGAACGAGCAC
1 GCTCCTCCGCAGAACGAGCAC
1630031 GCTCCTCCGCAGAACGAGCA
1 GCTCCTCCGCAGAACGAGCA
1630051 AGCTTCACTG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (21 bp):
GCTCCTCCGCAGAACGAGCAC
Found at i:1630066 original size:21 final size:21
Alignment explanation
Indices: 1630042--1630110 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
1630032 CTCCTCCGCA
*
1630042 GAACGAGCAAGCTTCACTGTG
1 GAACGAGCAAGCTCCACTGTG
*
1630063 GAACGAGCAAGCTCCTCTGTG
1 GAACGAGCAAGCTCCACTGTG
*
1630084 GAACGAAGGC-A-CTCCTCTGTG
1 GAACG-A-GCAAGCTCCACTGTG
1630105 GAACGA
1 GAACGA
1630111 AGACGCTCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 1 0.02
21 39 0.89
22 2 0.05
23 2 0.05
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (21 bp):
GAACGAGCAAGCTCCACTGTG
Found at i:1630067 original size:42 final size:41
Alignment explanation
Indices: 1629965--1630079 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 41
1629955 ATTGTTTTAA
* *
1629965 CAAGCTCCTCCGCAGAACGAGCATGCTCCTCCGCAGAACGAG
1 CAAGTTCCT-CGCAGAACGAGCAAGCTCCTCCGCAGAACGAG
* *
1630007 CACGTTCCTCCGCAGAACGAGCACGCTCCTCCGCAGAACGAG
1 CAAGTTCCT-CGCAGAACGAGCAAGCTCCTCCGCAGAACGAG
**
1630049 CAAGCTTCACT-GTGGAACGAGCAAGCTCCTC
1 CAAG-TTC-CTCGCAGAACGAGCAAGCTCCTC
1630080 TGTGGAACGA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
42 59 0.92
43 3 0.05
44 2 0.03
ACGTcount: A:0.25, C:0.37, G:0.23, T:0.14
Consensus pattern (41 bp):
CAAGTTCCTCGCAGAACGAGCAAGCTCCTCCGCAGAACGAG
Found at i:1630111 original size:21 final size:21
Alignment explanation
Indices: 1630058--1630121 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
1630048 GCAAGCTTCA
1630058 CTGTGGAACG-A-GCAAGCTCCT
1 CTGTGGAACGAAGGC-A-CTCCT
1630079 CTGTGGAACGAAGGCACTCCT
1 CTGTGGAACGAAGGCACTCCT
* *
1630100 CTGTGGAACGAAGACGCTCCT
1 CTGTGGAACGAAGGCACTCCT
1630121 C
1 C
1630122 AAAAGAACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
21 35 0.90
22 2 0.05
23 2 0.05
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (21 bp):
CTGTGGAACGAAGGCACTCCT
Found at i:1630205 original size:21 final size:21
Alignment explanation
Indices: 1630161--1630221 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1630151 GAAGAAGCGT
* ***
1630161 CTCCAAAGAACAAAGACTTTC
1 CTCCAAAGAACGAAGACGCCC
* *
1630182 CTCCAGAGAATGAAGACGCCC
1 CTCCAAAGAACGAAGACGCCC
*
1630203 CTCCAAAGAACGAGGACGC
1 CTCCAAAGAACGAAGACGC
1630222 TTCTTAGCAG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.31, G:0.20, T:0.11
Consensus pattern (21 bp):
CTCCAAAGAACGAAGACGCCC
Found at i:1635388 original size:21 final size:21
Alignment explanation
Indices: 1635362--1635433 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
1635352 AGCACGGTCC
*
1635362 TCCGCAGCATCAGCTCGTTGT
1 TCCGCAGCATCAGCTCGCTGT
*
1635383 TCCGCAACATCAGCTCGCTGT
1 TCCGCAGCATCAGCTCGCTGT
* *
1635404 TCCGCAGCATCAGCACGCTGC
1 TCCGCAGCATCAGCTCGCTGT
1635425 TCCGCAGCA
1 TCCGCAGCA
1635434 CAAGCCATCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.18, C:0.39, G:0.22, T:0.21
Consensus pattern (21 bp):
TCCGCAGCATCAGCTCGCTGT
Found at i:1637613 original size:18 final size:18
Alignment explanation
Indices: 1637584--1637620 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1637574 TATCATTGAA
1637584 TTTTATTCACT-AACTTT
1 TTTTATTCACTAAACTTT
1637601 TTTTATATCACTAAACTTT
1 TTTTAT-TCACTAAACTTT
1637620 T
1 T
1637621 AATTTTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATTCACTAAACTTT
Found at i:1642441 original size:22 final size:23
Alignment explanation
Indices: 1642403--1642451 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
1642393 GTAAATCATA
*
1642403 CATTAATTTAATTATAA-AATAT
1 CATTAATTTAATAATAATAATAT
1642425 CATT-ATTTAAATAATAATTAATAT
1 CATTAATTT-AATAATAA-TAATAT
1642449 CAT
1 CAT
1642452 CATAGTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 11 0.48
24 8 0.35
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (23 bp):
CATTAATTTAATAATAATAATAT
Found at i:1646439 original size:27 final size:27
Alignment explanation
Indices: 1646409--1646469 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
1646399 CAACGTTAAG
*
1646409 CAATCCCCAAACAGTATAAAAAATAAA
1 CAATCCCCAAACAATATAAAAAATAAA
* * * *
1646436 CAATCCACAAACAATATTAAAAGTAAG
1 CAATCCCCAAACAATATAAAAAATAAA
1646463 CAATCCC
1 CAATCCC
1646470 ACCAGTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.54, C:0.25, G:0.05, T:0.16
Consensus pattern (27 bp):
CAATCCCCAAACAATATAAAAAATAAA
Found at i:1646719 original size:42 final size:42
Alignment explanation
Indices: 1646617--1646773 Score: 140
Period size: 42 Copynumber: 3.7 Consensus size: 42
1646607 ATTGTTTTAA
* ** *
1646617 CAAGCTCCTCCGCAGAACGAGCATGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACGAG
* * * **
1646659 CACGTTCCTCCGCAGAACGAGCACGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACGAG
* * * **
1646701 CAAGCTCCACTGTGGAACGAGCAAGCTCCTCTGTGGAACGAAG
1 CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACG-AG
1646744 -ACA-CTCCTCTGTGGAACGAAG-ACGCTCCTC
1 CA-AGCTCCTCTGTGGAACG-AGCACGCTCCTC
1646774 AAAAGAACGA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 92 0.95
43 5 0.05
ACGTcount: A:0.25, C:0.36, G:0.24, T:0.15
Consensus pattern (42 bp):
CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACGAG
Found at i:1646741 original size:21 final size:21
Alignment explanation
Indices: 1646617--1646731 Score: 158
Period size: 21 Copynumber: 5.5 Consensus size: 21
1646607 ATTGTTTTAA
1646617 CAAGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
*
1646638 CATGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
* *
1646659 CACGTTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
*
1646680 CACGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
* * **
1646701 CAAGCTCCACTGTGGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
1646722 CAAGCTCCTC
1 CAAGCTCCTC
1646732 TGTGGAACGA
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 84 1.00
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.13
Consensus pattern (21 bp):
CAAGCTCCTCCGCAGAACGAG
Found at i:1646750 original size:21 final size:21
Alignment explanation
Indices: 1646705--1646773 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
1646695 AACGAGCAAG
*
1646705 CTCCACTGTGGAACG-AG-CAA
1 CTCCTCTGTGGAACGAAGAC-A
1646725 GCTCCTCTGTGGAACGAAGACA
1 -CTCCTCTGTGGAACGAAGACA
*
1646747 CTCCTCTGTGGAACGAAGACG
1 CTCCTCTGTGGAACGAAGACA
1646768 CTCCTC
1 CTCCTC
1646774 AAAAGAACGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 40 0.91
22 3 0.07
23 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.19
Consensus pattern (21 bp):
CTCCTCTGTGGAACGAAGACA
Found at i:1646866 original size:21 final size:21
Alignment explanation
Indices: 1646813--1646873 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1646803 GAAGAAGCGT
* ***
1646813 CTCCAAAGAACAAAGACTTTC
1 CTCCAAAGAACGAAGACGCCC
*
1646834 CTCCAGAGAACGAAGACGCCC
1 CTCCAAAGAACGAAGACGCCC
*
1646855 CTCCAAAGAACGAGGACGC
1 CTCCAAAGAACGAAGACGC
1646874 TTCTTAGCAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.38, C:0.33, G:0.20, T:0.10
Consensus pattern (21 bp):
CTCCAAAGAACGAAGACGCCC
Found at i:1652074 original size:21 final size:21
Alignment explanation
Indices: 1652048--1652119 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
1652038 AGCACGGTCC
*
1652048 TCCGCAGCATCAGCTCGTTGT
1 TCCGCAGCATCAGCTCGCTGT
*
1652069 TCCGCAACATCAGCTCGCTGT
1 TCCGCAGCATCAGCTCGCTGT
*
1652090 TCCGCAGCATCAGCTCGCTGC
1 TCCGCAGCATCAGCTCGCTGT
1652111 TCCGCAGCA
1 TCCGCAGCA
1652120 CAAGCCATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.22
Consensus pattern (21 bp):
TCCGCAGCATCAGCTCGCTGT
Found at i:1654313 original size:18 final size:18
Alignment explanation
Indices: 1654284--1654320 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1654274 TATCATTGAA
1654284 TTTTATTCACT-AACTTT
1 TTTTATTCACTAAACTTT
1654301 TTTTATATCACTAAACTTT
1 TTTTAT-TCACTAAACTTT
1654320 T
1 T
1654321 AATTTTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATTCACTAAACTTT
Found at i:1659183 original size:22 final size:23
Alignment explanation
Indices: 1659145--1659193 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
1659135 GTAAATCATA
*
1659145 CATTAATTTAATTATAA-AATAT
1 CATTAATTTAATAATAATAATAT
1659167 CATT-ATTTAAATAATAATTAATAT
1 CATTAATTT-AATAATAA-TAATAT
1659191 CAT
1 CAT
1659194 CATAGTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 11 0.48
24 8 0.35
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (23 bp):
CATTAATTTAATAATAATAATAT
Found at i:1663186 original size:27 final size:27
Alignment explanation
Indices: 1663156--1663216 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
1663146 CAACGTTAAG
*
1663156 CAATCCCCAAACAGTATAAAAAATAAA
1 CAATCCCCAAACAATATAAAAAATAAA
* * * *
1663183 CAATCCACAAACAATATTAAAAGTAAG
1 CAATCCCCAAACAATATAAAAAATAAA
1663210 CAATCCC
1 CAATCCC
1663217 ACCAGTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.54, C:0.25, G:0.05, T:0.16
Consensus pattern (27 bp):
CAATCCCCAAACAATATAAAAAATAAA
Found at i:1663465 original size:42 final size:42
Alignment explanation
Indices: 1663363--1663519 Score: 140
Period size: 42 Copynumber: 3.7 Consensus size: 42
1663353 ATTGTTTTAA
* ** *
1663363 CAAGCTCCTCCGCAGAACGAGCATGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACGAG
* * * **
1663405 CACGTTCCTCCGCAGAACGAGCACGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACGAG
* * * **
1663447 CAAGCTCCACTGTGGAACGAGCAAGCTCCTCTGTGGAACGAAG
1 CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACG-AG
1663490 -ACA-CTCCTCTGTGGAACGAAG-ACGCTCCTC
1 CA-AGCTCCTCTGTGGAACG-AGCACGCTCCTC
1663520 AAAAGAACGA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 92 0.95
43 5 0.05
ACGTcount: A:0.25, C:0.36, G:0.24, T:0.15
Consensus pattern (42 bp):
CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACGAG
Found at i:1663487 original size:21 final size:21
Alignment explanation
Indices: 1663363--1663477 Score: 158
Period size: 21 Copynumber: 5.5 Consensus size: 21
1663353 ATTGTTTTAA
1663363 CAAGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
*
1663384 CATGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
* *
1663405 CACGTTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
*
1663426 CACGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
* * **
1663447 CAAGCTCCACTGTGGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
1663468 CAAGCTCCTC
1 CAAGCTCCTC
1663478 TGTGGAACGA
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 84 1.00
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.13
Consensus pattern (21 bp):
CAAGCTCCTCCGCAGAACGAG
Found at i:1663496 original size:21 final size:21
Alignment explanation
Indices: 1663451--1663519 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
1663441 AACGAGCAAG
*
1663451 CTCCACTGTGGAACG-AG-CAA
1 CTCCTCTGTGGAACGAAGAC-A
1663471 GCTCCTCTGTGGAACGAAGACA
1 -CTCCTCTGTGGAACGAAGACA
*
1663493 CTCCTCTGTGGAACGAAGACG
1 CTCCTCTGTGGAACGAAGACA
1663514 CTCCTC
1 CTCCTC
1663520 AAAAGAACGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 40 0.91
22 3 0.07
23 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.19
Consensus pattern (21 bp):
CTCCTCTGTGGAACGAAGACA
Found at i:1663612 original size:21 final size:21
Alignment explanation
Indices: 1663559--1663619 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1663549 GAAGAAGCGT
* ***
1663559 CTCCAAAGAACAAAGACTTTC
1 CTCCAAAGAACGAAGACGCCC
*
1663580 CTCCAGAGAACGAAGACGCCC
1 CTCCAAAGAACGAAGACGCCC
*
1663601 CTCCAAAGAACGAGGACGC
1 CTCCAAAGAACGAAGACGC
1663620 TTCTTAGCAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.38, C:0.33, G:0.20, T:0.10
Consensus pattern (21 bp):
CTCCAAAGAACGAAGACGCCC
Found at i:1668820 original size:21 final size:21
Alignment explanation
Indices: 1668794--1668865 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
1668784 AGCACGGTCC
*
1668794 TCCGCAGCATCAGCTCGTTGT
1 TCCGCAGCATCAGCTCGCTGT
*
1668815 TCCGCAACATCAGCTCGCTGT
1 TCCGCAGCATCAGCTCGCTGT
*
1668836 TCCGCAGCATCAGCTCGCTGC
1 TCCGCAGCATCAGCTCGCTGT
1668857 TCCGCAGCA
1 TCCGCAGCA
1668866 CAAGCCATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.22
Consensus pattern (21 bp):
TCCGCAGCATCAGCTCGCTGT
Found at i:1671056 original size:18 final size:18
Alignment explanation
Indices: 1671027--1671063 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1671017 TATCATTGAA
1671027 TTTTATTCACT-AACTTT
1 TTTTATTCACTAAACTTT
1671044 TTTTATATCACTAAACTTT
1 TTTTAT-TCACTAAACTTT
1671063 T
1 T
1671064 AATTTTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATTCACTAAACTTT
Found at i:1675912 original size:22 final size:23
Alignment explanation
Indices: 1675874--1675922 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
1675864 GTAAATCATA
*
1675874 CATTAATTTAATTATAA-AATAT
1 CATTAATTTAATAATAATAATAT
1675896 CATT-ATTTAAATAATAATTAATAT
1 CATTAATTT-AATAATAA-TAATAT
1675920 CAT
1 CAT
1675923 CATAGTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.17
22 11 0.48
24 8 0.35
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (23 bp):
CATTAATTTAATAATAATAATAT
Found at i:1679885 original size:27 final size:27
Alignment explanation
Indices: 1679855--1679916 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
1679845 CAACGTTAAG
* *
1679855 CAATCCCCAAACAGTATAAAAAATAAA
1 CAATCCACAAACAATATAAAAAATAAA
* * *
1679882 CAATCCACAAACAATATTAAAAGTAAG
1 CAATCCACAAACAATATAAAAAATAAA
1679909 CAATCCAC
1 CAATCCAC
1679917 CAGTAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.55, C:0.24, G:0.05, T:0.16
Consensus pattern (27 bp):
CAATCCACAAACAATATAAAAAATAAA
Found at i:1680163 original size:42 final size:42
Alignment explanation
Indices: 1680061--1680217 Score: 140
Period size: 42 Copynumber: 3.7 Consensus size: 42
1680051 ATTGTTTTAA
* ** *
1680061 CAAGCTCCTCCGCAGAACGAGCATGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACGAG
* * * **
1680103 CACGTTCCTCCGCAGAACGAGCACGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACGAG
* * * **
1680145 CAAGCTCCACTGTGGAACGAGCAAGCTCCTCTGTGGAACGAAG
1 CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACG-AG
1680188 -ACA-CTCCTCTGTGGAACGAAG-ACGCTCCTC
1 CA-AGCTCCTCTGTGGAACG-AGCACGCTCCTC
1680218 AAAAGAACGA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 92 0.95
43 5 0.05
ACGTcount: A:0.25, C:0.36, G:0.24, T:0.15
Consensus pattern (42 bp):
CAAGCTCCTCTGTGGAACGAGCACGCTCCTCCGCAGAACGAG
Found at i:1680185 original size:21 final size:21
Alignment explanation
Indices: 1680061--1680175 Score: 158
Period size: 21 Copynumber: 5.5 Consensus size: 21
1680051 ATTGTTTTAA
1680061 CAAGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
*
1680082 CATGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
* *
1680103 CACGTTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
*
1680124 CACGCTCCTCCGCAGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
* * **
1680145 CAAGCTCCACTGTGGAACGAG
1 CAAGCTCCTCCGCAGAACGAG
1680166 CAAGCTCCTC
1 CAAGCTCCTC
1680176 TGTGGAACGA
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 84 1.00
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.13
Consensus pattern (21 bp):
CAAGCTCCTCCGCAGAACGAG
Found at i:1680194 original size:21 final size:21
Alignment explanation
Indices: 1680149--1680217 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
1680139 AACGAGCAAG
*
1680149 CTCCACTGTGGAACG-AG-CAA
1 CTCCTCTGTGGAACGAAGAC-A
1680169 GCTCCTCTGTGGAACGAAGACA
1 -CTCCTCTGTGGAACGAAGACA
*
1680191 CTCCTCTGTGGAACGAAGACG
1 CTCCTCTGTGGAACGAAGACA
1680212 CTCCTC
1 CTCCTC
1680218 AAAAGAACGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 40 0.91
22 3 0.07
23 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.19
Consensus pattern (21 bp):
CTCCTCTGTGGAACGAAGACA
Found at i:1680310 original size:21 final size:21
Alignment explanation
Indices: 1680257--1680317 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1680247 GAAGAAGCGT
* ***
1680257 CTCCAAAGAACAAAGACTTTC
1 CTCCAAAGAACGAAGACGCCC
*
1680278 CTCCAGAGAACGAAGACGCCC
1 CTCCAAAGAACGAAGACGCCC
*
1680299 CTCCAAAGAACGAGGACGC
1 CTCCAAAGAACGAAGACGC
1680318 TTCTTAGCAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.38, C:0.33, G:0.20, T:0.10
Consensus pattern (21 bp):
CTCCAAAGAACGAAGACGCCC
Done.