Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001574.1 Hibiscus syriacus cultivar Beakdansim tig00003126_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: 1705968
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 7 of 7
Found at i:1528893 original size:21 final size:20
Alignment explanation
Indices: 1528853--1528894 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1528843 TATACTTATC
* *
1528853 TATGAGCTATGGATTAATGA
1 TATGAGCTAAGGAATAATGA
1528873 TATGAGCTAAGGAAATAATGA
1 TATGAGCTAAGG-AATAATGA
1528894 T
1 T
1528895 GCAAAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (20 bp):
TATGAGCTAAGGAATAATGA
Found at i:1530413 original size:33 final size:33
Alignment explanation
Indices: 1530334--1530437 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
1530324 ATACAATCTG
* *
1530334 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
1530370 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
1530403 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
1530436 TC
1 TC
1530438 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:1530562 original size:16 final size:17
Alignment explanation
Indices: 1530535--1530567 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1530525 CATCTTTGAT
1530535 AAATTCCTTTCCATTTC
1 AAATTCCTTTCCATTTC
1530552 AAATT-CTTTCCATTTC
1 AAATTCCTTTCCATTTC
1530568 TATTTACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATTCCTTTCCATTTC
Found at i:1537154 original size:12 final size:11
Alignment explanation
Indices: 1537127--1537170 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
1537117 GTCCTACAAC
1537127 AAAAAGCAACAAG
1 AAAAAG-AA-AAG
1537140 AAAGAAGAAAAG
1 AAA-AAGAAAAG
1537152 AAAAGAGAAAAG
1 AAAA-AGAAAAG
1537164 AAAAAGA
1 AAAAAGA
1537171 CTCCTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.14
12 17 0.59
13 5 0.17
14 3 0.10
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:1542397 original size:36 final size:36
Alignment explanation
Indices: 1542350--1542451 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
1542340 GATACAATCT
1542350 GTCCATCACCATTATCACGCCTATATCATCAACATA
1 GTCCATCACCATTATCACGCCTATATCATCAACATA
* *
1542386 GTCCATCACCATTATCACGCTTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCAACATA
* *
1542422 TTCCATCACCA-TATCACGCCTATATTATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
1542452 CCAACTTATA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 17 0.28
36 44 0.72
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCAACATA
Found at i:1544638 original size:24 final size:25
Alignment explanation
Indices: 1544602--1544650 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
1544592 TTTAGCAATG
* *
1544602 AAATTGAAGCACTC-AAAAGAAGAA
1 AAATTCAAACACTCAAAAAGAAGAA
1544626 AAATTCAAACACTCAAAAAGAAGAA
1 AAATTCAAACACTCAAAAAGAAGAA
1544651 GAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.61, C:0.14, G:0.12, T:0.12
Consensus pattern (25 bp):
AAATTCAAACACTCAAAAAGAAGAA
Found at i:1545989 original size:24 final size:25
Alignment explanation
Indices: 1545943--1545997 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1545933 ACAGTTATGC
*
1545943 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
1545967 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
1545992 CA-TTGA
1 CACTTGA
1545998 GACTACAAGT
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:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:1558470 original size:20 final size:18
Alignment explanation
Indices: 1558435--1558497 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
1558425 AAATTTGAGT
1558435 ACAAAAAG-A-AAGAAAA
1 ACAAAAAGAAGAAGAAAA
1558451 GACAAAAAGAAGAAGAAAA
1 -ACAAAAAGAAGAAGAAAA
*
1558470 ATCAGAAAAGAAGAA-AAGA
1 A-CA-AAAAGAAGAAGAAAA
1558489 A-AAAAAGAA
1 ACAAAAAGAA
1558498 AAATTCAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
16 7 0.17
17 9 0.22
18 2 0.05
19 13 0.32
20 10 0.24
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (18 bp):
ACAAAAAGAAGAAGAAAA
Found at i:1568690 original size:19 final size:20
Alignment explanation
Indices: 1568649--1568699 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1568639 GAAACCCCTT
* *
1568649 TGAAAATATATGATTTTTGA
1 TGAAAATACATGATTTTTAA
1568669 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1568688 TGAAGATACATG
1 TGAAAATACATG
1568700 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1569649 original size:30 final size:31
Alignment explanation
Indices: 1569609--1569668 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1569599 ACATGCTGCC
**
1569609 ATGATATCTAAATGAAATGTAAACATAATAA
1 ATGATATCTAAAACAAATGTAAACATAATAA
*
1569640 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGTAAACATAATA
1569669 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGTAAACATAATAA
Found at i:1570140 original size:23 final size:23
Alignment explanation
Indices: 1570110--1570157 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1570100 TTGAACCTCC
1570110 TTGTCCTGAAAAAAAAGAAGACT
1 TTGTCCTGAAAAAAAAGAAGACT
*
1570133 TTGTCCTGAAAAGAAAGAAGACT
1 TTGTCCTGAAAAAAAAGAAGACT
1570156 TT
1 TT
1570158 CATAAGTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (23 bp):
TTGTCCTGAAAAAAAAGAAGACT
Found at i:1577996 original size:8 final size:8
Alignment explanation
Indices: 1577966--1578009 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
1577956 TCTTTTTGAA
1577966 CTTCTCTTT
1 CTTCT-TTT
1577975 -TTCTTTT
1 CTTCTTTT
1577982 CTTTTCTTTT
1 C--TTCTTTT
1577992 CTTCTTTT
1 CTTCTTTT
1578000 CTTCTTTT
1 CTTCTTTT
1578008 CT
1 CT
1578010 GATTTTTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.09
8 21 0.66
10 8 0.25
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (8 bp):
CTTCTTTT
Found at i:1579710 original size:30 final size:31
Alignment explanation
Indices: 1579670--1579729 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
1579660 ACATGCTGCC
**
1579670 ATGACATCTAAATGAAATGCAAACATAATAA
1 ATGACATCTAAAACAAATGCAAACATAATAA
* *
1579701 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGACATCTAAAACAAATGCAAACATAATA
1579730 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (31 bp):
ATGACATCTAAAACAAATGCAAACATAATAA
Found at i:1583159 original size:34 final size:34
Alignment explanation
Indices: 1583121--1583194 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
1583111 TTTACCATCC
1583121 CTTAAAGAAGCAATATAAAGTATGGGTCTTTGTT
1 CTTAAAGAAGCAATATAAAGTATGGGTCTTTGTT
*
1583155 CTTAAAGAAGCAATATAAAGTCTGGGTCTTTGTT
1 CTTAAAGAAGCAATATAAAGTATGGGTCTTTGTT
1583189 CTTAAA
1 CTTAAA
1583195 CATTGGTTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (34 bp):
CTTAAAGAAGCAATATAAAGTATGGGTCTTTGTT
Found at i:1583861 original size:41 final size:41
Alignment explanation
Indices: 1583804--1583885 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
1583794 GCCCATGGAG
1583804 ATGCATTTTCATCCAAGAGCACGTTGGTGAAGAAATTGCAA
1 ATGCATTTTCATCCAAGAGCACGTTGGTGAAGAAATTGCAA
1583845 ATGCATTTTCATCCAAGAGCACGTTGGTGAAGAAATTGCAA
1 ATGCATTTTCATCCAAGAGCACGTTGGTGAAGAAATTGCAA
1583886 CCATTGGAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (41 bp):
ATGCATTTTCATCCAAGAGCACGTTGGTGAAGAAATTGCAA
Found at i:1584494 original size:15 final size:15
Alignment explanation
Indices: 1584474--1584514 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
1584464 TCTATTTCAA
1584474 CATCAACATCAACAC
1 CATCAACATCAACAC
1584489 CATCAACATCAACAC
1 CATCAACATCAACAC
1584504 CATCAACATCA
1 CATCAACATCA
1584515 TCCACCAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (15 bp):
CATCAACATCAACAC
Found at i:1586868 original size:17 final size:17
Alignment explanation
Indices: 1586829--1586871 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
1586819 AAAGTGCTAC
1586829 AAAA-AAAACAACAAGA
1 AAAAGAAAACAACAAGA
1586845 AAGAAGAAAACAA-AAGA
1 AA-AAGAAAACAACAAGA
1586862 GAAAAGAAAA
1 -AAAAGAAAA
1586872 AGACTCCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAGAAAACAACAAGA
Found at i:1602416 original size:13 final size:13
Alignment explanation
Indices: 1602398--1602429 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1602388 GCAAGCACTC
1602398 AAAGAAGAAAAAA
1 AAAGAAGAAAAAA
*
1602411 AAAGAAGAAAAGA
1 AAAGAAGAAAAAA
1602424 AAAGAA
1 AAAGAA
1602430 AATTGCAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAA
Found at i:1614270 original size:8 final size:8
Alignment explanation
Indices: 1614259--1614283 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1614249 TCTTTTTCTT
1614259 TTCTTTTC
1 TTCTTTTC
1614267 TTCTTTTC
1 TTCTTTTC
1614275 TTCTTTTC
1 TTCTTTTC
1614283 T
1 T
1614284 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:1620866 original size:36 final size:36
Alignment explanation
Indices: 1620819--1620923 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
1620809 GATACAATCT
1620819 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
1620855 GTCCATCACCATTATCACGCCTATATCGTCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
1620891 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
1620924 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1620891 original size:11 final size:11
Alignment explanation
Indices: 1620822--1620906 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
1620812 ACAATCTGTC
1620822 CATCACCATTAT
1 CATCACCA-TAT
*
1620834 CA-CGCCTATAT
1 CATCACC-ATAT
1620845 CATCACCATAGT
1 CATCACCATA-T
1620857 CCATCACCATTAT
1 -CATCACCA-TAT
*
1620870 CA-CGCCTATAT
1 CATCACC-ATAT
*
1620881 CGTCACCATATT
1 CATCACCATA-T
1620893 CCATCACCATAT
1 -CATCACCATAT
1620905 CA
1 CA
1620907 CGCCTATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
11 23 0.40
12 15 0.26
13 18 0.31
14 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1622470 original size:19 final size:19
Alignment explanation
Indices: 1622446--1622483 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1622436 GAATGAAGTT
1622446 GAAGTG-GATTGAAATGAAA
1 GAAGTGTGA-TGAAATGAAA
*
1622465 GAAGTGTGATGTAATGAAA
1 GAAGTGTGATGAAATGAAA
1622484 ATGGTGAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.24
Consensus pattern (19 bp):
GAAGTGTGATGAAATGAAA
Found at i:1623289 original size:25 final size:25
Alignment explanation
Indices: 1623260--1623310 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1623250 GAAAATGAAT
1623260 AACCCTTGGTTTGAATGATTAAATC
1 AACCCTTGGTTTGAATGATTAAATC
*
1623285 AACCCTTGGTTTGGATGATTAAATC
1 AACCCTTGGTTTGAATGATTAAATC
1623310 A
1 A
1623311 GTCTTGAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (25 bp):
AACCCTTGGTTTGAATGATTAAATC
Found at i:1623736 original size:17 final size:17
Alignment explanation
Indices: 1623714--1623747 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1623704 AATTAAGATT
*
1623714 TAGTTTGTTAAATGAAC
1 TAGTTTGATAAATGAAC
*
1623731 TAGTTTGATGAATGAAC
1 TAGTTTGATAAATGAAC
1623748 AACTAGTTTA
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:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (17 bp):
TAGTTTGATAAATGAAC
Found at i:1623753 original size:20 final size:21
Alignment explanation
Indices: 1623728--1623772 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1623718 TTGTTAAATG
*
1623728 AACTAGTTTGATGAATGAAC-
1 AACTAGTTTAATGAATGAACT
*
1623748 AACTAGTTTAATTAATGAACT
1 AACTAGTTTAATGAATGAACT
1623769 AACT
1 AACT
1623773 TTATTCAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (21 bp):
AACTAGTTTAATGAATGAACT
Found at i:1626742 original size:24 final size:25
Alignment explanation
Indices: 1626707--1626761 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1626697 ACTTGGAGCC
*
1626707 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* * *
1626731 TCAAGTGA-CACATCTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
1626755 TCAAGTG
1 TCAAGTG
1626762 GCATAACTGT
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:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:1630631 original size:21 final size:21
Alignment explanation
Indices: 1630592--1630631 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1630582 CTCATTTTTA
*
1630592 CTCTCAATTCTCTTTTCAATG
1 CTCTCAATTCTCTTATCAATG
1630613 CTCTCAATGTCT-TTATCAA
1 CTCTCAAT-TCTCTTATCAA
1630632 CTCTCATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.23, C:0.28, G:0.05, T:0.45
Consensus pattern (21 bp):
CTCTCAATTCTCTTATCAATG
Found at i:1630637 original size:19 final size:19
Alignment explanation
Indices: 1630591--1630642 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
1630581 GCTCATTTTT
*
1630591 ACTCTCAATTCTCTTTTCA
1 ACTCTCAATTCTCTTATCA
1630610 ATGCTCTCAATGTCT-TTATCA
1 A--CTCTCAAT-TCTCTTATCA
*
1630631 ACTCTCATTTCT
1 ACTCTCAATTCT
1630643 TCTTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 3 0.11
19 8 0.29
21 14 0.50
22 3 0.11
ACGTcount: A:0.21, C:0.29, G:0.04, T:0.46
Consensus pattern (19 bp):
ACTCTCAATTCTCTTATCA
Found at i:1632593 original size:25 final size:25
Alignment explanation
Indices: 1632564--1632612 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1632554 TTATGAACAT
1632564 CCCTTGGTTTGAATGATTAAATCAA
1 CCCTTGGTTTGAATGATTAAATCAA
*
1632589 CCCTTGGTTTGGATGATTAAATCA
1 CCCTTGGTTTGAATGATTAAATCA
1632613 GCCTTGAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (25 bp):
CCCTTGGTTTGAATGATTAAATCAA
Found at i:1634745 original size:13 final size:13
Alignment explanation
Indices: 1634724--1634757 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
1634714 AAAAAAACAA
1634724 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
1634738 AAAAAAAAAAGGC
1 AAAAAAAAAAGGC
1634751 AAAAAAA
1 AAAAAAA
1634758 CAAAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:1634783 original size:20 final size:20
Alignment explanation
Indices: 1634739--1634776 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1634729 AAAAAAGGCA
*
1634739 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
1634759 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
1634777 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:1644405 original size:17 final size:17
Alignment explanation
Indices: 1644383--1644444 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
1644373 TATTTTATTA
*
1644383 AATGAACTAGTTTGATG
1 AATGAACTAGTTTAATG
* *
1644400 AATGAACAAGTTTAATT
1 AATGAACTAGTTTAATG
* * *
1644417 AATGAACTAACTTTATTC
1 AATGAACT-AGTTTAATG
1644435 AATGAACTAG
1 AATGAACTAG
1644445 ATGCATGAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
17 22 0.61
18 14 0.39
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.34
Consensus pattern (17 bp):
AATGAACTAGTTTAATG
Found at i:1644438 original size:18 final size:18
Alignment explanation
Indices: 1644400--1644443 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1644390 TAGTTTGATG
*
1644400 AATGAAC-AAGTTTAATT
1 AATGAACTAACTTTAATT
1644417 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
1644434 CAATGAACTA
1 -AATGAACTA
1644444 GATGCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:1647937 original size:6 final size:6
Alignment explanation
Indices: 1647926--1647966 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
1647916 GTGTTACAAC
*
1647926 AAAAGA AAAAGA AAGAATAA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AA-AA-GA AAAAGA AAAAGA AAAAGA AAA
1647967 GACTCCTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 24 0.77
7 4 0.13
8 3 0.10
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:1647942 original size:10 final size:10
Alignment explanation
Indices: 1647927--1647959 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1647917 TGTTACAACA
1647927 AAAGAAAAAG
1 AAAGAAAAAG
1647937 AAAGAATAAA-
1 AAAGAA-AAAG
1647947 AAAGAAAAAG
1 AAAGAAAAAG
1647957 AAA
1 AAA
1647960 AAGAAAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.14
10 15 0.71
11 3 0.14
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:1650269 original size:17 final size:17
Alignment explanation
Indices: 1650249--1650307 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
1650239 TTTAGAGAAG
1650249 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
1650266 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
1650282 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
1650299 TAGTTCATT
1 TAGTTCATT
1650308 GAATAATGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:1653798 original size:18 final size:18
Alignment explanation
Indices: 1653772--1653810 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1653762 ATTAATTAAA
1653772 TAACATTATTCAATGAAC
1 TAACATTATTCAATGAAC
*
1653790 TAACTTTATTCAATGAAC
1 TAACATTATTCAATGAAC
1653808 TAA
1 TAA
1653811 ATGCATGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (18 bp):
TAACATTATTCAATGAAC
Found at i:1653886 original size:17 final size:17
Alignment explanation
Indices: 1653844--1653907 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
1653834 AAACAACTAG
*
1653844 ATGCATAAATGAAATAC
1 ATGCTTAAATGAAATAC
* * *
1653861 TTCCCTAAATGAAATAC
1 ATGCTTAAATGAAATAC
* *
1653878 ATGCTTAAATGCAATGC
1 ATGCTTAAATGAAATAC
*
1653895 ATGCTTTAATGAA
1 ATGCTTAAATGAA
1653908 CAACAAACTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (17 bp):
ATGCTTAAATGAAATAC
Found at i:1658476 original size:5 final size:5
Alignment explanation
Indices: 1658439--1658491 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
1658429 ACTTGCTTCA
*
1658439 CTTTT CTTTT GCTTTT GCTTTT CTTCT -TTTT CTTTT CTTTT -TTTT -TTTT
1 CTTTT CTTTT -CTTTT -CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1658488 -TTTT
1 CTTTT
1658492 GCACTCCAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
4 15 0.34
5 18 0.41
6 11 0.25
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (5 bp):
CTTTT
Found at i:1658480 original size:20 final size:19
Alignment explanation
Indices: 1658440--1658493 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 19
1658430 CTTGCTTCAC
*
1658440 TTTTCTTTTGCTTTTGCTT
1 TTTTCTTTTTCTTTTGCTT
1658459 TTCTTCTTTTTCTTTT-CTT
1 TT-TTCTTTTTCTTTTGCTT
*
1658478 TTTT-TTTTTTTTTTGC
1 TTTTCTTTTTCTTTTGC
1658494 ACTCCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 9 0.29
18 3 0.10
19 7 0.23
20 12 0.39
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTTCTTTTGCTT
Found at i:1658488 original size:14 final size:14
Alignment explanation
Indices: 1658450--1658486 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1658440 TTTTCTTTTG
*
1658450 CTTTTGCTTTTCTT
1 CTTTTTCTTTTCTT
1658464 CTTTTTCTTTTCTT
1 CTTTTTCTTTTCTT
1658478 -TTTTT-TTTT
1 CTTTTTCTTTT
1658487 TTTTTGCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 4 0.18
13 5 0.23
14 13 0.59
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (14 bp):
CTTTTTCTTTTCTT
Found at i:1668874 original size:13 final size:13
Alignment explanation
Indices: 1668856--1668888 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1668846 CATAGCTGAC
1668856 TTGAGCTGGACGT
1 TTGAGCTGGACGT
1668869 TTGAGCTGGACGT
1 TTGAGCTGGACGT
1668882 TTGAGCT
1 TTGAGCT
1668889 AGCTAGAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.36, T:0.33
Consensus pattern (13 bp):
TTGAGCTGGACGT
Found at i:1669774 original size:13 final size:11
Alignment explanation
Indices: 1669754--1669910 Score: 97
Period size: 11 Copynumber: 13.2 Consensus size: 11
1669744 AATATAGGCG
1669754 TGATATGGTGA
1 TGATATGGTGA
1669765 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
1669778 TGATATAGGCG-
1 TGATAT-GGTGA
1669789 TGATAATGGTGA
1 TGAT-ATGGTGA
1669801 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
1669814 TGATATAGG-CA
1 TGATAT-GGTGA
1669825 TGATAATGGTGA
1 TGAT-ATGGTGA
1669837 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
1669850 TGATATAGGCG-
1 TGATAT-GGTGA
*
1669861 TGATAATGGTGC
1 TGAT-ATGGTGA
1669873 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
1669886 TGATATAGGCG-
1 TGATAT-GGTGA
1669897 TGATAATGGTGA
1 TGAT-ATGGTGA
1669909 TG
1 TG
1669911 GACAGATTGT
Statistics
Matches: 117, Mismatches: 9, Indels: 39
0.71 0.05 0.24
Matches are distributed among these distances:
11 43 0.37
12 32 0.27
13 38 0.32
14 4 0.03
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:1669799 original size:23 final size:23
Alignment explanation
Indices: 1669771--1669871 Score: 68
Period size: 25 Copynumber: 4.3 Consensus size: 23
1669761 GTGATGGAAT
1669771 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
*
1669794 ATGGTGATGGACTAT-GGTGATGAT-
1 ATGGTGAT-GA-TATAGGCG-TGATA
* *
1669818 ATAGG-CATGATA-ATG-GTGATGGAA
1 AT-GGTGATGATATAGGCGTGAT---A
1669842 TATGGTGATGATATAGGCGTGATA
1 -ATGGTGATGATATAGGCGTGATA
1669866 ATGGTG
1 ATGGTG
1669872 CTGGACTATG
Statistics
Matches: 60, Mismatches: 5, Indels: 26
0.66 0.05 0.29
Matches are distributed among these distances:
20 4 0.07
21 1 0.02
22 3 0.05
23 16 0.27
24 12 0.20
25 17 0.28
26 2 0.03
27 5 0.08
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.31
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:1669810 original size:36 final size:36
Alignment explanation
Indices: 1669737--1669913 Score: 302
Period size: 36 Copynumber: 4.9 Consensus size: 36
1669727 ATTTATAAGT
* *
1669737 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1669772 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
1669808 TGGTGATGATATAGGCATGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
1669844 TGGTGATGATATAGGCGTGATAATGGTGCTGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1669880 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1669914 AGATTGTATC
Statistics
Matches: 133, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
35 20 0.15
36 113 0.85
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:1669906 original size:23 final size:23
Alignment explanation
Indices: 1669807--1669910 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
1669797 GTGATGGACT
*
1669807 ATGGTGATGATATAGGCATGATA
1 ATGGTGATGATATAGGCGTGATA
*
1669830 ATGGTGATGGA-ATATG-GTGATGA
1 ATGGTGAT-GATATAGGCGTGAT-A
* *
1669853 TATAGGCG-TGATA-ATGGTGCTGGACT-
1 -AT-GGTGATGATATA-GGCG-T-GA-TA
1669879 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
1669902 ATGGTGATG
1 ATGGTGATG
1669911 GACAGATTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 26
0.66 0.06 0.28
Matches are distributed among these distances:
22 5 0.08
23 27 0.44
24 11 0.18
25 14 0.23
26 2 0.03
27 2 0.03
28 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.31
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:1670294 original size:19 final size:20
Alignment explanation
Indices: 1670252--1670301 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1670242 GAAATCCCTT
*
1670252 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTAAA
1670272 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1670291 TGAAGATACAT
1 TGAAAATACAT
1670302 ACTCTTGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1674011 original size:22 final size:23
Alignment explanation
Indices: 1673983--1674034 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
1673973 ATTTATAAGT
1673983 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
* *
1674005 TGGTGATGATATAGGCGTTATAA
1 TGGTGATAATATAGGCGTGATAA
1674028 TGGTGAT
1 TGGTGAT
1674035 GGACTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.35
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:1674043 original size:36 final size:36
Alignment explanation
Indices: 1674003--1674146 Score: 270
Period size: 36 Copynumber: 4.0 Consensus size: 36
1673993 ATAGGCGTGA
*
1674003 TATGGTGATGATATAGGCGTTATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
1674039 TATGGTGATGATATAGGCGTGATAATGGTGATGGAA
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1674075 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1674111 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1674147 AGATTGTATC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 105 1.00
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:1674045 original size:13 final size:11
Alignment explanation
Indices: 1674027--1674143 Score: 78
Period size: 11 Copynumber: 9.8 Consensus size: 11
1674017 AGGCGTTATA
1674027 ATGGTGATGGACT
1 ATGGTGAT-GA-T
1674040 ATGGTGATGAT
1 ATGGTGATGAT
*
1674051 ATAGGCG-TGAT
1 AT-GGTGATGAT
1674062 AATGGTGATGGAAT
1 -ATGGTGAT-G-AT
1674076 ATGGTGATGAT
1 ATGGTGATGAT
*
1674087 ATAGGCG-TGAT
1 AT-GGTGATGAT
1674098 AATGGTGATGGACT
1 -ATGGTGAT-GA-T
1674112 ATGGTGATGAT
1 ATGGTGATGAT
*
1674123 ATAGGCG-TGAT
1 AT-GGTGATGAT
1674134 AATGGTGATG
1 -ATGGTGATG
1674144 GACAGATTGT
Statistics
Matches: 85, Mismatches: 6, Indels: 27
0.72 0.05 0.23
Matches are distributed among these distances:
11 31 0.36
12 24 0.28
13 27 0.32
14 3 0.04
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.31
Consensus pattern (11 bp):
ATGGTGATGAT
Found at i:1674063 original size:72 final size:74
Alignment explanation
Indices: 1673985--1674136 Score: 242
Period size: 72 Copynumber: 2.1 Consensus size: 74
1673975 TTATAAGTTG
*
1673985 GTGATAATATAGGCG-T-G-ATATGGTGATGATATAGGCGTTATAATGGTGATGGACTATGGTGA
1 GTGATAATAT-GGCGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGA
1674047 TGATATAGGC
65 TGATATAGGC
*
1674057 GTGAT-A-ATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGAT
1 GTGATAATATGGCGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGAT
1674120 GATATAGGC
66 GATATAGGC
1674129 GTGATAAT
1 GTGATAAT
1674137 GGTGATGGAC
Statistics
Matches: 73, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
69 3 0.04
70 3 0.04
71 2 0.03
72 64 0.88
73 1 0.01
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.32
Consensus pattern (74 bp):
GTGATAATATGGCGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGAT
GATATAGGC
Found at i:1674070 original size:23 final size:24
Alignment explanation
Indices: 1674029--1674143 Score: 82
Period size: 23 Copynumber: 4.8 Consensus size: 24
1674019 GCGTTATAAT
1674029 GGTGATGGACTATGGTGATGATATAG
1 GGTGAT-GA-TATGGTGATGATATAG
*
1674055 GCGTGAT-A-ATGGTGATGGA-ATAT
1 G-GTGATGATATGGTGAT-GATATAG
* *
1674078 GGTGATGATATAGGCG-TGATA-AT
1 GGTGATGATAT-GGTGATGATATAG
1674101 GGTGATGGACTATGGTGATGATATAG
1 GGTGAT-GA-TATGGTGATGATATAG
1674127 GCGTGAT-A-ATGGTGATG
1 G-GTGATGATATGGTGATG
1674144 GACAGATTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
22 5 0.07
23 32 0.43
24 11 0.15
25 13 0.18
26 3 0.04
27 10 0.14
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.30
Consensus pattern (24 bp):
GGTGATGATATGGTGATGATATAG
Found at i:1674532 original size:19 final size:20
Alignment explanation
Indices: 1674485--1674535 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1674475 GAAATCCCTT
**
1674485 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1674505 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1674524 TGAAGATACATG
1 TGAAAATACATG
1674536 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1677739 original size:13 final size:11
Alignment explanation
Indices: 1677719--1677875 Score: 106
Period size: 11 Copynumber: 13.2 Consensus size: 11
1677709 AATATAGGCG
1677719 TGATATGGTGA
1 TGATATGGTGA
1677730 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
1677743 TGATATAGGCG-
1 TGATAT-GGTGA
1677754 TGATAATGGTGA
1 TGAT-ATGGTGA
1677766 TGGATTATGGTGA
1 T-GA-TATGGTGA
*
1677779 TGATATAGGCG-
1 TGATAT-GGTGA
1677790 TGATAATGGTGA
1 TGAT-ATGGTGA
1677802 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
1677815 TGATATAGGCG-
1 TGATAT-GGTGA
1677826 TGATAATGGTGA
1 TGAT-ATGGTGA
1677838 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
1677851 TGATATAGGCG-
1 TGATAT-GGTGA
1677862 TGATAATGGTGA
1 TGAT-ATGGTGA
1677874 TG
1 TG
1677876 GACAGATTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 39
0.72 0.05 0.24
Matches are distributed among these distances:
11 43 0.36
12 32 0.27
13 39 0.33
14 4 0.03
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:1677871 original size:23 final size:24
Alignment explanation
Indices: 1677702--1677875 Score: 102
Period size: 23 Copynumber: 7.3 Consensus size: 24
1677692 ATTTATAAGT
* *
1677702 TGGTGATAATATA-GGCG-TGATA
1 TGGTGATGATATAGGGTGATGATA
*
1677724 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATAGGGTGATGATA
* *
1677748 TAGGCG-TGATA-ATGGTGATGGATTA
1 T-GGTGATGATATAGGGTGAT-GA-TA
1677773 TGGTGATGATATAGGCGTGAT-A-A
1 TGGTGATGATATAGG-GTGATGATA
*
1677796 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATAGGGTGATGATA
* *
1677820 TAGGCG-TGATA-ATGGTGATGGACTA
1 T-GGTGATGATATAGGGTGAT-GA-TA
1677845 TGGTGATGATATAGGCGTGAT-A-A
1 TGGTGATGATATAGG-GTGATGATA
1677868 TGGTGATG
1 TGGTGATG
1677876 GACAGATTGT
Statistics
Matches: 123, Mismatches: 9, Indels: 39
0.72 0.05 0.23
Matches are distributed among these distances:
22 15 0.12
23 46 0.37
24 24 0.20
25 24 0.20
26 4 0.03
27 10 0.08
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (24 bp):
TGGTGATGATATAGGGTGATGATA
Found at i:1677878 original size:36 final size:36
Alignment explanation
Indices: 1677702--1677877 Score: 318
Period size: 36 Copynumber: 4.9 Consensus size: 36
1677692 ATTTATAAGT
*
1677702 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
1677737 TGGTGATGATATAGGCGTGATAATGGTGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1677773 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
1677809 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1677845 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1677878 CAGATTGTAT
Statistics
Matches: 136, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.15
36 116 0.85
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:1681756 original size:22 final size:23
Alignment explanation
Indices: 1681728--1681779 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
1681718 ATTTATAAGT
1681728 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
1681750 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
1681773 TGGTGAT
1 TGGTGAT
1681780 GGACTATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:1681771 original size:36 final size:36
Alignment explanation
Indices: 1681748--1681891 Score: 270
Period size: 36 Copynumber: 4.0 Consensus size: 36
1681738 ATAGGCGTGA
1681748 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
1681784 TATGGTGATGATATAGGCGTGATAATGGTGATGGAA
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1681820 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
1681856 TATGGTGATGATATAGGTGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1681892 AGATTGTATC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 105 1.00
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:1681790 original size:13 final size:11
Alignment explanation
Indices: 1681745--1681888 Score: 107
Period size: 11 Copynumber: 12.2 Consensus size: 11
1681735 AATATAGGCG
1681745 TGATATGGTGA
1 TGATATGGTGA
*
1681756 TGATATAGGCG-
1 TGATAT-GGTGA
1681767 TGATAATGGTGA
1 TGAT-ATGGTGA
1681779 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
1681792 TGATATAGGCG-
1 TGATAT-GGTGA
1681803 TGATAATGGTGA
1 TGAT-ATGGTGA
1681815 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
1681828 TGATATAGGCG-
1 TGATAT-GGTGA
1681839 TGATAATGGTGA
1 TGAT-ATGGTGA
1681851 TGGACTATGGTGA
1 T-GA-TATGGTGA
1681864 TGATATAGGTG-
1 TGATAT-GGTGA
1681875 TGATAATGGTGA
1 TGAT-ATGGTGA
1681887 TG
1 TG
1681889 GACAGATTGT
Statistics
Matches: 109, Mismatches: 6, Indels: 35
0.73 0.04 0.23
Matches are distributed among these distances:
11 45 0.41
12 31 0.28
13 29 0.27
14 4 0.04
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:1681887 original size:23 final size:24
Alignment explanation
Indices: 1681747--1681888 Score: 113
Period size: 23 Copynumber: 5.9 Consensus size: 24
1681737 TATAGGCGTG
*
1681747 ATATGGTGATGATATAGGCG-TGAT
1 ATATGGTGATGATAT-GGTGATGAT
1681771 A-ATGGTGATGGACTATGGTGATGAT
1 ATATGGTGAT-GA-TATGGTGATGAT
*
1681796 ATA-GGCG-TGATAATGGTGATGGA-
1 ATATGGTGATGAT-ATGGTGAT-GAT
*
1681819 ATATGGTGATGATATAGGCG-TGAT
1 ATATGGTGATGATAT-GGTGATGAT
1681843 A-ATGGTGATGGACTATGGTGATGAT
1 ATATGGTGAT-GA-TATGGTGATGAT
1681868 ATA-GGTG-TGATAATGGTGATG
1 ATATGGTGATGAT-ATGGTGATG
1681889 GACAGATTGT
Statistics
Matches: 98, Mismatches: 5, Indels: 31
0.73 0.04 0.23
Matches are distributed among these distances:
22 2 0.02
23 42 0.43
24 22 0.22
25 30 0.31
26 2 0.02
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.32
Consensus pattern (24 bp):
ATATGGTGATGATATGGTGATGAT
Found at i:1686851 original size:35 final size:37
Alignment explanation
Indices: 1686782--1686861 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
1686772 ATACTATTTC
* * *
1686782 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCAGTATCACACCTATAT
*
1686819 CATCACCATAGTCCATC-ACC-GTATCACACCTATAT
1 CATCACCATAATCCATCTACCAGTATCACACCTATAT
1686854 CATCACCA
1 CATCACCA
1686862 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 2 0.05
37 16 0.41
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCAGTATCACACCTATAT
Found at i:1687334 original size:14 final size:15
Alignment explanation
Indices: 1687299--1687346 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
1687289 AAATTTGGAG
1687299 AGCAAAAGAAAGAAA
1 AGCAAAAGAAAGAAA
*
1687314 AGAAAAAG-AAGAAA
1 AGCAAAAGAAAGAAA
*
1687328 ATCAAAAGCAAAAGAAA
1 AGCAAAAG--AAAGAAA
1687345 AG
1 AG
1687347 TGAAGCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.46
15 7 0.27
17 7 0.27
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
AGCAAAAGAAAGAAA
Found at i:1687731 original size:29 final size:29
Alignment explanation
Indices: 1687689--1687752 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
1687679 CGAGAGGGTG
1687689 AGATCAGAAGGGGGATCCGAAAAAGCCAA
1 AGATCAGAAGGGGGATCCGAAAAAGCCAA
*
1687718 AGATCAGAAGGGGGATCCGAAATAGCCAA
1 AGATCAGAAGGGGGATCCGAAAAAGCCAA
*
1687747 GGATCA
1 AGATCA
1687753 TATCCTCGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.31, T:0.09
Consensus pattern (29 bp):
AGATCAGAAGGGGGATCCGAAAAAGCCAA
Found at i:1691492 original size:22 final size:22
Alignment explanation
Indices: 1691459--1691511 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
1691449 TTGGAGGAGA
1691459 CACATG-CACGCCTAAGAAGAAG
1 CACATGAC-CGCCTAAGAAGAAG
1691481 CACATGACCGCCTAAGAAGAAG
1 CACATGACCGCCTAAGAAGAAG
1691503 CACATGACC
1 CACATGACC
1691512 AGCCATCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.40, C:0.30, G:0.21, T:0.09
Consensus pattern (22 bp):
CACATGACCGCCTAAGAAGAAG
Found at i:1692448 original size:23 final size:24
Alignment explanation
Indices: 1692422--1692474 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
1692412 AAATCAAGCA
1692422 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATCAAAGCACTCGAAAAG
* *
1692445 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATCAAAGCACTCGAAAAG
1692469 AAGAAA
1 AAGAAA
1692475 CAGAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.60, C:0.13, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTCGAAAAG
Found at i:1692480 original size:24 final size:23
Alignment explanation
Indices: 1692431--1692481 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
1692421 AAAGAAAATC
**
1692431 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAACAG
1692454 AAAGCACTCGAAAAGAAGAAACAG
1 AAAGCACTC-AAAAGAAGAAACAG
1692478 AAAG
1 AAAG
1692482 AAAGAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.59, C:0.14, G:0.20, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAACAG
Found at i:1693768 original size:24 final size:25
Alignment explanation
Indices: 1693722--1693776 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1693712 ACAGTTATGC
*
1693722 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
1693746 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
1693771 CA-TTGA
1 CACTTGA
1693777 GGCTCTAAGT
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:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:1696321 original size:23 final size:23
Alignment explanation
Indices: 1696284--1696335 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 23
1696274 AAATCCAGCA
1696284 AAGAAATCAAAGCACTC-AAAAG
1 AAGAAATCAAAGCACTCGAAAAG
*
1696306 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAA-TCAAAGCACTCGAAAAG
1696330 AAGAAA
1 AAGAAA
1696336 CAGAAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 6 0.22
23 10 0.37
24 11 0.41
ACGTcount: A:0.60, C:0.13, G:0.17, T:0.10
Consensus pattern (23 bp):
AAGAAATCAAAGCACTCGAAAAG
Found at i:1696341 original size:24 final size:23
Alignment explanation
Indices: 1696292--1696342 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
1696282 CAAAGAAATC
**
1696292 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAACAG
1696315 AAAGCACTCGAAAAGAAGAAACAG
1 AAAGCACTC-AAAAGAAGAAACAG
1696339 AAAG
1 AAAG
1696343 AAAGAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.59, C:0.14, G:0.20, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAACAG
Found at i:1697629 original size:24 final size:25
Alignment explanation
Indices: 1697583--1697637 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1697573 ACAGTTATGC
*
1697583 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
1697607 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
1697632 CA-TTGA
1 CACTTGA
1697638 GGCTCTAAGT
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:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:1700169 original size:22 final size:23
Alignment explanation
Indices: 1700144--1700195 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
1700134 GAATCCAGCA
1700144 AAGAAAATCAAAGCACTC-AAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
1700166 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATCAAAGCACTC-AAAAG
1700190 AAGAAA
1 AAGAAA
1700196 CAGAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 16 0.62
24 10 0.38
ACGTcount: A:0.60, C:0.13, G:0.17, T:0.10
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Found at i:1700201 original size:24 final size:22
Alignment explanation
Indices: 1700153--1700202 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
1700143 AAAGAAAATC
**
1700153 AAAGCACTCAAAGAAGAAATTG
1 AAAGCACTCAAAGAAGAAACAG
1700175 AAAGCACTCGAAAAGAAGAAACAG
1 AAAGCACTC--AAAGAAGAAACAG
1700199 AAAG
1 AAAG
1700203 AAAGAAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.38
24 15 0.62
ACGTcount: A:0.58, C:0.14, G:0.20, T:0.08
Consensus pattern (22 bp):
AAAGCACTCAAAGAAGAAACAG
Found at i:1701482 original size:24 final size:25
Alignment explanation
Indices: 1701436--1701490 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1701426 ACAGTTATTC
*
1701436 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
1701460 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
1701485 CA-TTGA
1 CACTTGA
1701491 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:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Done.