Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 51 of 91
Found at i:11146201 original size:24 final size:25
Alignment explanation
Indices: 11146159--11146213 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
11146149 ACAGTTATGC
*
11146159 CACTTGAAGTTCAAAAAGTTGTG-T
1 CACTTGAAGTGCAAAAAGTTGTGAT
* *
11146183 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGTTGTGAT
11146208 CA-TTGA
1 CACTTGA
11146214 GGCTCCAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGTTGTGAT
Found at i:11149569 original size:31 final size:32
Alignment explanation
Indices: 11149534--11149608 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
11149524 GAGTGCAAAA
* * *
11149534 AGAAAAGAAAAGACAAAAAGAAGAA-AAATTC
1 AGAAAAGAAAAGAAAAAAAGAAAAAGAAAATC
11149565 AGAAAAGAAGAA-AAAAAAAGAAAAAGAAAATC
1 AGAAAAGAA-AAGAAAAAAAGAAAAAGAAAATC
11149597 A-AAAAGAGAAAG
1 AGAAAAGA-AAAG
11149609 CAAGCCAAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
31 28 0.76
32 9 0.24
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (32 bp):
AGAAAAGAAAAGAAAAAAAGAAAAAGAAAATC
Found at i:11149600 original size:18 final size:18
Alignment explanation
Indices: 11149529--11149608 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 18
11149519 AATTGGAGTG
*
11149529 CAAAAAG-AAAAGAAAAGA
1 CAAAAAGAAAAAGAAAA-T
* *
11149547 CAAAAAGAAGAA-AAATT
1 CAAAAAGAAAAAGAAAAT
11149564 CAGAAAAG---AAGAAAA-
1 CA-AAAAGAAAAAGAAAAT
11149579 -AAAAAGAAAAAGAAAAT
1 CAAAAAGAAAAAGAAAAT
*
11149596 CAAAAAGAGAAAG
1 CAAAAAGAAAAAG
11149609 CAAGCCAAGG
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
13 5 0.10
14 1 0.02
15 2 0.04
16 10 0.20
17 2 0.04
18 26 0.53
19 3 0.06
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (18 bp):
CAAAAAGAAAAAGAAAAT
Found at i:11158352 original size:23 final size:23
Alignment explanation
Indices: 11158326--11158375 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
11158316 CCAGAAGTAT
11158326 CAAGGAGAAAGGGGTTGACGCCA
1 CAAGGAGAAAGGGGTTGACGCCA
11158349 CAAGGAGAAAGGGGTTGACGCCA
1 CAAGGAGAAAGGGGTTGACGCCA
11158372 CAAG
1 CAAG
11158376 TATTAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.38, T:0.08
Consensus pattern (23 bp):
CAAGGAGAAAGGGGTTGACGCCA
Found at i:11160231 original size:19 final size:20
Alignment explanation
Indices: 11160190--11160240 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
11160180 GAAACCCCTT
*
11160190 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
11160210 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
11160229 TGAAGATACATG
1 TGAAAATACATG
11160241 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:11161178 original size:30 final size:31
Alignment explanation
Indices: 11161137--11161196 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
11161127 ACATGCTTCC
**
11161137 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
11161168 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
11161197 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:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:11164104 original size:24 final size:23
Alignment explanation
Indices: 11164046--11164105 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
11164036 AAATCCAGCA
*
11164046 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATGAAAGCACTCAAAAG
*
11164069 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATGAAAGCACTC-AAAAG
*
11164093 AAGAAAAAGAAAG
1 AAGAAAATGAAAG
11164106 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGCACTCAAAAG
Found at i:11169891 original size:12 final size:12
Alignment explanation
Indices: 11169874--11169937 Score: 69
Period size: 12 Copynumber: 5.4 Consensus size: 12
11169864 ATTTTTTTTC
11169874 AAAAAAAC-AAA
1 AAAAAAACAAAA
11169885 AAAAAAAC-AAA
1 AAAAAAACAAAA
**
11169896 AAAAATGCAAAA
1 AAAAAAACAAAA
*
11169908 AAAAAAGGCAAAA
1 AAAAAA-ACAAAA
*
11169921 AAAAAACCAAAA
1 AAAAAAACAAAA
11169933 AAAAA
1 AAAAA
11169938 CCAAAAAAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
11 17 0.36
12 18 0.38
13 12 0.26
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.02
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:11169944 original size:12 final size:11
Alignment explanation
Indices: 11169874--11169945 Score: 90
Period size: 11 Copynumber: 6.3 Consensus size: 11
11169864 ATTTTTTTTC
11169874 AAAAAAACAAA
1 AAAAAAACAAA
11169885 AAAAAAACAAA
1 AAAAAAACAAA
**
11169896 AAAAATGCAAA
1 AAAAAAACAAA
11169907 AAAAAAAGGCAAA
1 AAAAAAA--CAAA
11169920 AAAAAAACCAAA
1 AAAAAAA-CAAA
*
11169932 AAAAAACCAAA
1 AAAAAAACAAA
11169943 AAA
1 AAA
11169946 GCCAAAATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
11 32 0.60
12 10 0.19
13 11 0.21
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.01
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:11183539 original size:8 final size:8
Alignment explanation
Indices: 11183528--11183558 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
11183518 TCTTTTTCTT
11183528 TTCTTTTC
1 TTCTTTTC
11183536 TTCTTTTC
1 TTCTTTTC
11183544 TTCTTTTC
1 TTCTTTTC
11183552 TTCTTTT
1 TTCTTTT
11183559 TCTCTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:11183558 original size:35 final size:36
Alignment explanation
Indices: 11183518--11183586 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
11183508 TTTGAACTTC
* *
11183518 TCTTTTTCTTTTCTTTTCT-TCTTTTC-TTCTTTTCT
1 TCTTTTTCTCTTCTTTTGTCT-TTTTCTTTCTTTTCT
11183553 TCTTTTTCTCTTCTTTTGTCTTTTTCTTTCTTTT
1 TCTTTTTCTCTTCTTTTGTCTTTTTCTTTCTTTT
11183587 TGCACTCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 22 0.73
36 8 0.27
ACGTcount: A:0.00, C:0.22, G:0.01, T:0.77
Consensus pattern (36 bp):
TCTTTTTCTCTTCTTTTGTCTTTTTCTTTCTTTTCT
Found at i:11183564 original size:16 final size:16
Alignment explanation
Indices: 11183529--11183579 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
11183519 CTTTTTCTTT
11183529 TCTTTTCTTC-TTTTC
1 TCTTTTCTTCTTTTTC
11183544 TTCTTTTCTTCTTTTTC
1 -TCTTTTCTTCTTTTTC
*
11183561 TCTTCTTTTGTCTTTTTC
1 TCTT-TTCT-TCTTTTTC
11183579 T
1 T
11183580 TTCTTTTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 14 0.45
17 8 0.26
18 9 0.29
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTTTTCTTCTTTTTC
Found at i:11184352 original size:19 final size:20
Alignment explanation
Indices: 11184311--11184359 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
11184301 AAAACCCCTT
*
11184311 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
11184331 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
11184350 TGAAGATACA
1 TGAAAATACA
11184360 AGCTCTTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:11194069 original size:13 final size:13
Alignment explanation
Indices: 11194051--11194076 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11194041 AACACCTCTC
11194051 ACATACCTTTTCA
1 ACATACCTTTTCA
11194064 ACATACCTTTTCA
1 ACATACCTTTTCA
11194077 TCTTTGGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATACCTTTTCA
Found at i:11196849 original size:24 final size:23
Alignment explanation
Indices: 11196821--11196881 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
11196811 ACTTTTCTTT
*
11196821 CTTTCTTTTTCTTTTTTTCAAGTG
1 CTTTCATTTTCTTTTTTT-AAGTG
* * *
11196845 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCATTTTCTTTTTTTAAGTG
*
11196868 CTTTGATTTTCTTT
1 CTTTCATTTTCTTT
11196882 GCTGGATTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 15 0.50
24 15 0.50
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.64
Consensus pattern (23 bp):
CTTTCATTTTCTTTTTTTAAGTG
Found at i:11201362 original size:22 final size:21
Alignment explanation
Indices: 11201330--11201371 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
11201320 CCAACTCCAT
*
11201330 TTCATCATCAACATCATCAAC
1 TTCATCATCAACACCATCAAC
*
11201351 TTCATCCATCAAGACCATCAA
1 TTCAT-CATCAACACCATCAA
11201372 TTACGGAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.26
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:11201724 original size:18 final size:18
Alignment explanation
Indices: 11201671--11201727 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
11201661 GGAGTGCAAA
11201671 AAGAAAAGAAAAGACAAAA-
1 AAGAAAA-AAAAGA-AAAAG
**
11201690 AAGAAAAATTTAG-AAAAG
1 AAGAAAAA-AAAGAAAAAG
11201708 AAGAAAAAAAAGAAAAAG
1 AAGAAAAAAAAGAAAAAG
11201726 AA
1 AA
11201728 AATCAAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 6 0.19
18 16 0.52
19 9 0.29
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (18 bp):
AAGAAAAAAAAGAAAAAG
Found at i:11213721 original size:16 final size:16
Alignment explanation
Indices: 11213700--11213731 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11213690 TCTTCCACCA
11213700 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11213716 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11213732 GAGCTAACTA
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11222648 original size:20 final size:20
Alignment explanation
Indices: 11222623--11222679 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
11222613 GCTGCTGGAA
11222623 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACCAGTTTTG
*
11222643 AACCGGTTTGACCAG-TCTG
1 AACCGGTTTGACCAGTTTTG
*
11222662 AACCGGTTTGACCGGTTT
1 AACCGGTTTGACCAGTTT
11222680 GACCCGACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (20 bp):
AACCGGTTTGACCAGTTTTG
Found at i:11222677 original size:9 final size:9
Alignment explanation
Indices: 11222624--11222683 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
11222614 CTGCTGGAAA
11222624 ACCGGTTTG
1 ACCGGTTTG
*
11222633 ACCAGTTTTG
1 ACC-GGTTTG
11222643 AACCGGTTTG
1 -ACCGGTTTG
* *
11222653 ACCAGTCTG
1 ACCGGTTTG
11222662 AACCGGTTTG
1 -ACCGGTTTG
11222672 ACCGGTTTG
1 ACCGGTTTG
11222681 ACC
1 ACC
11222684 CGACTGTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 22 0.52
10 17 0.40
11 3 0.07
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:11222702 original size:17 final size:17
Alignment explanation
Indices: 11222680--11222746 Score: 107
Period size: 17 Copynumber: 3.9 Consensus size: 17
11222670 TGACCGGTTT
11222680 GACCCGACTGTTGACCC
1 GACCCGACTGTTGACCC
11222697 GACCCGACTGTTGACCC
1 GACCCGACTGTTGACCC
* *
11222714 GACACGAATGTTGACCC
1 GACCCGACTGTTGACCC
*
11222731 GACCCGACCGTTGACC
1 GACCCGACTGTTGACC
11222747 GTTGACTGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.21, C:0.39, G:0.24, T:0.16
Consensus pattern (17 bp):
GACCCGACTGTTGACCC
Found at i:11222760 original size:19 final size:19
Alignment explanation
Indices: 11222736--11222772 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
11222726 GACCCGACCC
11222736 GACCGTTGACCGTTGACTG
1 GACCGTTGACCGTTGACTG
11222755 GACCGTTGACCGTTGACT
1 GACCGTTGACCGTTGACT
11222773 TTCTTTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (19 bp):
GACCGTTGACCGTTGACTG
Found at i:11229978 original size:10 final size:10
Alignment explanation
Indices: 11229949--11230017 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
11229939 GCTGCTGGAA
11229949 AACCGGTTTG
1 AACCGGTTTG
*
11229959 -ACCAGTTTTG
1 AACC-GGTTTG
11229969 AACCGGTTTG
1 AACCGGTTTG
*
11229979 -ACCGGTCTG
1 AACCGGTTTG
11229988 AACCGGTTTG
1 AACCGGTTTG
*
11229998 -ACCGGTCTG
1 AACCGGTTTG
*
11230007 AACCGGGTTG
1 AACCGGTTTG
11230017 A
1 A
11230018 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:11229991 original size:19 final size:19
Alignment explanation
Indices: 11229949--11230019 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
11229939 GCTGCTGGAA
* *
11229949 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
11229969 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
11229988 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
11230007 AACCGGGTTGACC
1 AACCGGTTTGACC
11230020 CGACCCGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 35 0.73
20 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:11230035 original size:17 final size:17
Alignment explanation
Indices: 11230013--11230053 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
11230003 TCTGAACCGG
*
11230013 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
11230030 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
11230047 GTTGACC
1 GTTGACC
11230054 GTTGACTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:11230067 original size:19 final size:19
Alignment explanation
Indices: 11230043--11230079 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11230033 GACCCGACCC
*
11230043 GACCGTTGACCGTTGACTG
1 GACCGTTGACCATTGACTG
11230062 GACCGTTGACCATTGACT
1 GACCGTTGACCATTGACT
11230080 TTCTTTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (19 bp):
GACCGTTGACCATTGACTG
Found at i:11232825 original size:19 final size:19
Alignment explanation
Indices: 11232801--11232850 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
11232791 GAAACCCCTT
*
11232801 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
11232820 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
11232839 TGAAGATACATG
1 TGAAAATACATG
11232851 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:11233786 original size:30 final size:31
Alignment explanation
Indices: 11233747--11233806 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
11233737 AAATGCTTCC
**
11233747 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
11233778 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
11233807 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:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:11235069 original size:19 final size:19
Alignment explanation
Indices: 11235045--11235094 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
11235035 GAAACCCCTT
**
11235045 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTAAA
11235064 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
11235083 TGAAGATACATG
1 TGAAAATACATG
11235095 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:11236926 original size:16 final size:16
Alignment explanation
Indices: 11236905--11236936 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11236895 TCTTCCACCA
11236905 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11236921 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11236937 GAGCTAACTA
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11240497 original size:16 final size:16
Alignment explanation
Indices: 11240476--11240507 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11240466 TCTTCCACCA
11240476 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11240492 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11240508 GAGCTAACTA
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11246018 original size:20 final size:20
Alignment explanation
Indices: 11245993--11246049 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
11245983 GCTGCTGGAA
11245993 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACCAGTTTTG
*
11246013 AACCGGTTTGACCAG-TCTG
1 AACCGGTTTGACCAGTTTTG
*
11246032 AACCGGTTTGACCGGTTT
1 AACCGGTTTGACCAGTTT
11246050 GACCCGACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (20 bp):
AACCGGTTTGACCAGTTTTG
Found at i:11246047 original size:9 final size:9
Alignment explanation
Indices: 11245994--11246053 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
11245984 CTGCTGGAAA
11245994 ACCGGTTTG
1 ACCGGTTTG
*
11246003 ACCAGTTTTG
1 ACC-GGTTTG
11246013 AACCGGTTTG
1 -ACCGGTTTG
* *
11246023 ACCAGTCTG
1 ACCGGTTTG
11246032 AACCGGTTTG
1 -ACCGGTTTG
11246042 ACCGGTTTG
1 ACCGGTTTG
11246051 ACC
1 ACC
11246054 CGACTGTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 22 0.52
10 17 0.40
11 3 0.07
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:11246072 original size:17 final size:17
Alignment explanation
Indices: 11246050--11246116 Score: 107
Period size: 17 Copynumber: 3.9 Consensus size: 17
11246040 TGACCGGTTT
11246050 GACCCGACTGTTGACCC
1 GACCCGACTGTTGACCC
11246067 GACCCGACTGTTGACCC
1 GACCCGACTGTTGACCC
* *
11246084 GACACGAATGTTGACCC
1 GACCCGACTGTTGACCC
*
11246101 GACCCGACCGTTGACC
1 GACCCGACTGTTGACC
11246117 GTTGACTGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.21, C:0.39, G:0.24, T:0.16
Consensus pattern (17 bp):
GACCCGACTGTTGACCC
Found at i:11246130 original size:19 final size:19
Alignment explanation
Indices: 11246106--11246142 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
11246096 GACCCGACCC
11246106 GACCGTTGACCGTTGACTG
1 GACCGTTGACCGTTGACTG
11246125 GACCGTTGACCGTTGACT
1 GACCGTTGACCGTTGACT
11246143 TTCTTTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (19 bp):
GACCGTTGACCGTTGACTG
Found at i:11247088 original size:32 final size:31
Alignment explanation
Indices: 11247041--11247128 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
11247031 ATCATTCTCG
** *
11247041 GGTAGGCCCTGCGGCCCTAAGATGTGTTCTTA
1 GGTAGGCCCCACGGCCCTAAGATGT-ATCTTA
* * * *
11247073 GGTAGGCCCCACGGCCCCAAAATCTATCTTG
1 GGTAGGCCCCACGGCCCTAAGATGTATCTTA
11247104 GGTAGGCTCCCA-GGCCCTAAGATGT
1 GGTAGGC-CCCACGGCCCTAAGATGT
11247129 TCCCTTAGGG
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
31 21 0.47
32 24 0.53
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (31 bp):
GGTAGGCCCCACGGCCCTAAGATGTATCTTA
Found at i:11253367 original size:10 final size:10
Alignment explanation
Indices: 11253338--11253406 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
11253328 GCTGCTGGAA
11253338 AACCGGTTTG
1 AACCGGTTTG
*
11253348 -ACCAGTTTTG
1 AACC-GGTTTG
11253358 AACCGGTTTG
1 AACCGGTTTG
*
11253368 -ACCGGTCTG
1 AACCGGTTTG
11253377 AACCGGTTTG
1 AACCGGTTTG
*
11253387 -ACCGGTCTG
1 AACCGGTTTG
*
11253396 AACCGGGTTG
1 AACCGGTTTG
11253406 A
1 A
11253407 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:11253380 original size:19 final size:19
Alignment explanation
Indices: 11253338--11253408 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
11253328 GCTGCTGGAA
* *
11253338 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
11253358 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
11253377 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
11253396 AACCGGGTTGACC
1 AACCGGTTTGACC
11253409 CGACCCGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 35 0.73
20 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:11253424 original size:17 final size:17
Alignment explanation
Indices: 11253402--11253442 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
11253392 TCTGAACCGG
*
11253402 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
11253419 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
11253436 GTTGACC
1 GTTGACC
11253443 GTTGACTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:11253456 original size:19 final size:19
Alignment explanation
Indices: 11253432--11253468 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11253422 GACCCGACCC
*
11253432 GACCGTTGACCGTTGACTG
1 GACCGTTGACCATTGACTG
11253451 GACCGTTGACCATTGACT
1 GACCGTTGACCATTGACT
11253469 TTCTTTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (19 bp):
GACCGTTGACCATTGACTG
Found at i:11254408 original size:32 final size:31
Alignment explanation
Indices: 11254335--11254411 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
11254325 CTAATGTGAC
* *
11254335 TCTTAGGTAGGCTCTGCGACCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
** * **
11254366 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGACCCTAAGAT-CAT
11254398 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
11254412 CACAGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
Found at i:11256231 original size:19 final size:20
Alignment explanation
Indices: 11256190--11256240 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
11256180 GAAACCCCTT
*
11256190 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
11256210 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
11256229 TGAAGATACATG
1 TGAAAATACATG
11256241 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:11257176 original size:30 final size:31
Alignment explanation
Indices: 11257137--11257196 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
11257127 AAATGCTTCC
**
11257137 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
11257168 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
11257197 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:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:11258485 original size:19 final size:20
Alignment explanation
Indices: 11258438--11258488 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11258428 GAAACCCCTT
**
11258438 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11258458 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11258477 TGAAGATACATG
1 TGAAAATACATG
11258489 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:11260320 original size:16 final size:16
Alignment explanation
Indices: 11260299--11260330 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11260289 TCTTCCACCA
11260299 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11260315 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11260331 GAGCTAACTA
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11263912 original size:16 final size:16
Alignment explanation
Indices: 11263891--11263922 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11263881 TCTTCCACCA
11263891 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11263907 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11263923 GAGCTAACTA
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11266971 original size:20 final size:19
Alignment explanation
Indices: 11266946--11266983 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
11266936 TCTTTTTCTT
11266946 TTCTTTTCTTTTTATTTTTC
1 TTCTTTT-TTTTTATTTTTC
*
11266966 TTCTTTTTTTTTCTTTTT
1 TTCTTTTTTTTTATTTTT
11266984 TTGTTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (19 bp):
TTCTTTTTTTTTATTTTTC
Found at i:11266983 original size:10 final size:10
Alignment explanation
Indices: 11266936--11266985 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
11266926 GATGTAGGAG
11266936 TCTTTTTCTTT
1 TCTTTTT-TTT
11266947 TCTTTTCTTTT
1 TCTTTT-TTTT
* *
11266958 T-ATTTTTCT
1 TCTTTTTTTT
11266967 TCTTTTTTTT
1 TCTTTTTTTT
11266977 TCTTTTTTT
1 TCTTTTTTT
11266986 GTTGCTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 4 0.12
10 18 0.55
11 10 0.30
12 1 0.03
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:11267424 original size:36 final size:36
Alignment explanation
Indices: 11267355--11267451 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
11267345 GTTGGTAATA
*
11267355 ATATAGGCGTGAT-ATGGTGATGGAATATAGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATAGTGATG
*
11267390 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATAGTGATG
11267426 ATATAGGCGTGATAATGGTGATGGAC
1 ATATAGGCGTGATAATGGTGATGGAC
11267452 AGATTGTATC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 13 0.22
36 46 0.78
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGACTATAGTGATG
Found at i:11267837 original size:19 final size:20
Alignment explanation
Indices: 11267790--11267840 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11267780 GAAACCCCTT
**
11267790 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11267810 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11267829 TGAAGATACATG
1 TGAAAATACATG
11267841 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:11271286 original size:24 final size:23
Alignment explanation
Indices: 11271228--11271287 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
11271218 CAATCTAGCA
*
11271228 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATGAAAGCACTCAAAAG
*
11271251 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATGAAAGCACTC-AAAAG
*
11271275 AAGAAAAAGAAAG
1 AAGAAAATGAAAG
11271288 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGCACTCAAAAG
Found at i:11272799 original size:33 final size:33
Alignment explanation
Indices: 11272757--11272825 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
11272747 GTTGATGAAT
*
11272757 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
11272790 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
11272823 GAA
1 GAA
11272826 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:11273248 original size:19 final size:20
Alignment explanation
Indices: 11273201--11273251 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11273191 GAAATCCCTT
**
11273201 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11273221 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11273240 TGAAGATACATG
1 TGAAAATACATG
11273252 CTCTTGGCTG
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:11276824 original size:33 final size:33
Alignment explanation
Indices: 11276782--11276850 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
11276772 GTTGATGAAT
*
11276782 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
11276815 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
11276848 GAA
1 GAA
11276851 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:11277273 original size:19 final size:20
Alignment explanation
Indices: 11277226--11277276 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11277216 GAAATCCCTT
**
11277226 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11277246 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11277265 TGAAGATACATG
1 TGAAAATACATG
11277277 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:11278751 original size:16 final size:16
Alignment explanation
Indices: 11278730--11278761 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11278720 TCTTCCACCA
11278730 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11278746 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11278762 GAGCTAACTA
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11280878 original size:5 final size:5
Alignment explanation
Indices: 11280843--11280871 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
11280833 CTTTTTGAAC
11280843 TTCTT TT-TT TTCTT TTCTT TTCTT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
11280872 CTTTTCTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTCTT
Found at i:11282341 original size:16 final size:16
Alignment explanation
Indices: 11282320--11282351 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11282310 TCTTCCACCA
11282320 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11282336 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11282352 GAGCTAACTA
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11285403 original size:20 final size:19
Alignment explanation
Indices: 11285378--11285415 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
11285368 TCTTTTTCTT
11285378 TTCTTTTCTTTTTATTTTTC
1 TTCTTTT-TTTTTATTTTTC
*
11285398 TTCTTTTTTTTTCTTTTT
1 TTCTTTTTTTTTATTTTT
11285416 TGTTGCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (19 bp):
TTCTTTTTTTTTATTTTTC
Found at i:11285415 original size:10 final size:10
Alignment explanation
Indices: 11285368--11285416 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
11285358 GATGTAGGAG
11285368 TCTTTTTCTTT
1 TCTTTTT-TTT
11285379 TCTTTTCTTTT
1 TCTTTT-TTTT
* *
11285390 T-ATTTTTCT
1 TCTTTTTTTT
11285399 TCTTTTTTTT
1 TCTTTTTTTT
11285409 TCTTTTTT
1 TCTTTTTT
11285417 GTTGCTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
9 4 0.12
10 17 0.53
11 10 0.31
12 1 0.03
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:11285855 original size:36 final size:36
Alignment explanation
Indices: 11285786--11285882 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
11285776 GTTGGTAATA
*
11285786 ATATAGGCGTGAT-ATGGTGATGGAATATAGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATAGTGATG
*
11285821 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATAGTGATG
11285857 ATATAGGCGTGATAATGGTGATGGAC
1 ATATAGGCGTGATAATGGTGATGGAC
11285883 AGATTGTATC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 13 0.22
36 46 0.78
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGACTATAGTGATG
Found at i:11286268 original size:19 final size:20
Alignment explanation
Indices: 11286221--11286271 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11286211 GAAACCCCTT
**
11286221 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11286241 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11286260 TGAAGATACATG
1 TGAAAATACATG
11286272 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:11289717 original size:24 final size:23
Alignment explanation
Indices: 11289659--11289718 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
11289649 CAATCTAGCA
*
11289659 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATGAAAGCACTCAAAAG
*
11289682 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATGAAAGCACTC-AAAAG
*
11289706 AAGAAAAAGAAAG
1 AAGAAAATGAAAG
11289719 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.62, C:0.12, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGCACTCAAAAG
Found at i:11291231 original size:33 final size:33
Alignment explanation
Indices: 11291189--11291257 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
11291179 GTTGATGAAT
*
11291189 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
11291222 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
11291255 GAA
1 GAA
11291258 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:11291680 original size:19 final size:20
Alignment explanation
Indices: 11291633--11291683 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11291623 GAAATCCCTT
**
11291633 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11291653 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11291672 TGAAGATACATG
1 TGAAAATACATG
11291684 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:11295254 original size:33 final size:33
Alignment explanation
Indices: 11295212--11295280 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
11295202 GTTGATGAAT
*
11295212 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
11295245 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
11295278 GAA
1 GAA
11295281 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:11295703 original size:19 final size:20
Alignment explanation
Indices: 11295656--11295706 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11295646 GAAATCCCTT
**
11295656 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11295676 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11295695 TGAAGATACATG
1 TGAAAATACATG
11295707 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:11297181 original size:16 final size:16
Alignment explanation
Indices: 11297160--11297191 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11297150 TCTTCCACCA
11297160 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11297176 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11297192 GAGCTAACTA
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11300760 original size:16 final size:16
Alignment explanation
Indices: 11300739--11300770 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11300729 TCTTCCACCA
11300739 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11300755 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
11300771 GAGCTAACTA
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:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:11306619 original size:30 final size:31
Alignment explanation
Indices: 11306580--11306639 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
11306570 ACATGCTTCC
**
11306580 ATGATATCTAAATGATATACAAACATAATAA
1 ATGATATCTAAAACATATACAAACATAATAA
**
11306611 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATACAAACATAATA
11306640 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:0.10, G:0.07, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATACAAACATAATAA
Found at i:11309715 original size:30 final size:31
Alignment explanation
Indices: 11309675--11309734 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
11309665 ACATGCTGCC
**
11309675 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
11309706 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
11309735 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:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:11314903 original size:13 final size:12
Alignment explanation
Indices: 11314881--11314910 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
11314871 ACTAAACACC
11314881 TTTCACATACCT
1 TTTCACATACCT
11314893 TTTCTACATACCT
1 TTTC-ACATACCT
11314906 TTTCA
1 TTTCA
11314911 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTCACATACCT
Found at i:11320946 original size:19 final size:20
Alignment explanation
Indices: 11320930--11320979 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
11320920 CTTTATTTCA
11320930 TTTCATT-CTTATTATTTAT
1 TTTCATTACTTATTATTTAT
11320949 TTTCATTACTTA-TA-TTAT
1 TTTCATTACTTATTATTTAT
*
11320967 TATTCATTTCTTA
1 T-TTCATTACTTA
11320980 AACCCATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.18
19 19 0.68
20 4 0.14
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTACTTATTATTTAT
Found at i:11321203 original size:12 final size:11
Alignment explanation
Indices: 11321176--11321201 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11321166 ATTGGCGTGC
11321176 AAAACAGAAGA
1 AAAACAGAAGA
11321187 AAAACAGAAGA
1 AAAACAGAAGA
11321198 AAAA
1 AAAA
11321202 ACTCCTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAACAGAAGA
Found at i:11321271 original size:16 final size:16
Alignment explanation
Indices: 11321250--11321303 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
11321240 AAGACAAAAT
**
11321250 AAAAGAAAAAAATCAG
1 AAAAGAAAAAAAGAAG
*
11321266 AAAAGAAGAAAAGAAG
1 AAAAGAAAAAAAGAAG
11321282 AAAAGAAAAGAAA-AAG
1 AAAAGAAAA-AAAGAAG
11321298 AGAAAG
1 A-AAAG
11321304 CAAGCCAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 25 0.78
17 7 0.22
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAAAAGAAG
Found at i:11325582 original size:19 final size:17
Alignment explanation
Indices: 11325560--11325609 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 17
11325550 TTTCATTTCA
11325560 TTTCATTCTTATTATTTAT
1 TTTCATTCTTA-TA-TTAT
11325579 TTTCATTACTTATATTAT
1 TTTCATT-CTTATATTAT
11325597 TATTCATTTCTTA
1 T-TTCA-TTCTTA
11325610 AACCCATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.18
19 17 0.61
20 6 0.21
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTCATTCTTATATTAT
Found at i:11327211 original size:28 final size:28
Alignment explanation
Indices: 11327179--11327234 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
11327169 TCGTGGGGTT
*
11327179 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATATTCATCATTTGTTTTG
*
11327207 CATAACAGCATATTTATCATTTGTTTTG
1 CATAACAGCATATTCATCATTTGTTTTG
11327235 TTAAATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (28 bp):
CATAACAGCATATTCATCATTTGTTTTG
Found at i:11329593 original size:16 final size:16
Alignment explanation
Indices: 11329572--11329605 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
11329562 TCACATTTCC
11329572 TTTTATTTATCTTGTT
1 TTTTATTTATCTTGTT
11329588 TTTTATTTATCTTGTT
1 TTTTATTTATCTTGTT
11329604 TT
1 TT
11329606 CTTTGCACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTATTTATCTTGTT
Found at i:11331251 original size:19 final size:19
Alignment explanation
Indices: 11331207--11331244 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
11331197 TTTTTTTTTC
11331207 ACAAAAAAAAGCCAAAAAA
1 ACAAAAAAAAGCCAAAAAA
*
11331226 ATAAAAAAAAGCCAAAAAA
1 ACAAAAAAAAGCCAAAAAA
11331245 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.79, C:0.13, G:0.05, T:0.03
Consensus pattern (19 bp):
ACAAAAAAAAGCCAAAAAA
Found at i:11345547 original size:11 final size:13
Alignment explanation
Indices: 11345515--11345544 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11345505 TGGCCAAAGA
11345515 TGAAAAGGTATGT
1 TGAAAAGGTATGT
11345528 TGAAAAGGTATG-
1 TGAAAAGGTATGT
11345540 TGAAA
1 TGAAA
11345545 GGTGCCTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:11356918 original size:28 final size:28
Alignment explanation
Indices: 11356869--11356924 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
11356859 TGATGGGGTT
*
11356869 CATAACAGCATGTTCATAATTTGTTTTG
1 CATAACAGCATATTCATAATTTGTTTTG
* * *
11356897 CATAACATCATATTTATCATTTGTTTTG
1 CATAACAGCATATTCATAATTTGTTTTG
11356925 TTAAATTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (28 bp):
CATAACAGCATATTCATAATTTGTTTTG
Found at i:11358664 original size:8 final size:8
Alignment explanation
Indices: 11358651--11358711 Score: 58
Period size: 8 Copynumber: 8.0 Consensus size: 8
11358641 TATTTTTTTT
11358651 CAAAAAAA
1 CAAAAAAA
11358659 CAAAAAAA
1 CAAAAAAA
11358667 C-AAAAAA
1 CAAAAAAA
*
11358674 CAAAAAAGG
1 CAAAAAA-A
11358683 C--AAAAA
1 CAAAAAAA
**
11358689 -AAAAAGG
1 CAAAAAAA
11358696 CAAAAAAA
1 CAAAAAAA
11358704 CAAAAAAA
1 CAAAAAAA
11358712 GAGCCAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
7 14 0.33
8 27 0.64
9 1 0.02
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:11358671 original size:6 final size:7
Alignment explanation
Indices: 11358653--11358710 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
11358643 TTTTTTTTCA
11358653 AAAAAAC
1 AAAAAAC
11358660 AAAAAAAC
1 -AAAAAAC
11358668 AAAAAAC
1 AAAAAAC
11358675 AAAAAAGGC
1 AAAAAA--C
11358684 AAAAAA-
1 AAAAAAC
**
11358690 AAAAGGC
1 AAAAAAC
11358697 AAAAAAAC
1 -AAAAAAC
11358705 AAAAAA
1 AAAAAA
11358711 AGAGCCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
6 4 0.10
7 19 0.45
8 12 0.29
9 7 0.17
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:11358694 original size:13 final size:13
Alignment explanation
Indices: 11358670--11358703 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
11358660 AAAAAAACAA
11358670 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
11358684 AAAAAAAAAAGGC
1 AAAAAAAAAAGGC
11358697 AAAAAAA
1 AAAAAAA
11358704 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:11358729 original size:20 final size:20
Alignment explanation
Indices: 11358685--11358722 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11358675 AAAAAAGGCA
*
11358685 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
11358705 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
11358723 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:11360227 original size:30 final size:30
Alignment explanation
Indices: 11360182--11360274 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
11360172 TTTGTAAACC
*
11360182 GTTTATGTCTCCCAAATGCTCCACTAAGTT
1 GTTTATGTCTTCCAAATGCTCCACTAAGTT
* * *
11360212 GTTTGTGTCTTCCAAATGCTCCACCAAGCT
1 GTTTATGTCTTCCAAATGCTCCACTAAGTT
* * *
11360242 ATATATATCTTCCAAATGCTCCACTAAGTT
1 GTTTATGTCTTCCAAATGCTCCACTAAGTT
11360272 GTT
1 GTT
11360275 CCAACGTGTA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.37
Consensus pattern (30 bp):
GTTTATGTCTTCCAAATGCTCCACTAAGTT
Found at i:11360909 original size:30 final size:30
Alignment explanation
Indices: 11360853--11360968 Score: 164
Period size: 29 Copynumber: 3.9 Consensus size: 30
11360843 GGACAGTTTA
*
11360853 GTGGAGCAATTGGAAGACAT-TACAGCTTG
1 GTGGAGCATTTGGAAGACATATACAGCTTG
* *
11360882 GTGGAGCATTTGGAAGATATATACAGCTTA
1 GTGGAGCATTTGGAAGACATATACAGCTTG
11360912 GTGGAGCA-TTGGAAGACATATACAGCTTG
1 GTGGAGCATTTGGAAGACATATACAGCTTG
* * *
11360941 ATGGAGCATTTGGGAGACATAAACAGCT
1 GTGGAGCATTTGGAAGACATATACAGCT
11360969 CACAAACAGC
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
29 44 0.57
30 33 0.43
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (30 bp):
GTGGAGCATTTGGAAGACATATACAGCTTG
Found at i:11360919 original size:59 final size:59
Alignment explanation
Indices: 11360845--11360968 Score: 187
Period size: 59 Copynumber: 2.1 Consensus size: 59
11360835 AAAAGTTGGG
* * * *
11360845 ACAGTTTAGTGGAGCAATTGGAAGACAT-TACAGCTTGGTGGAGCATTTGGAAGATATAT
1 ACAGCTTAGTGGAGC-ATTGGAAGACATATACAGCTTGATGGAGCATTTGGAAGACATAA
*
11360904 ACAGCTTAGTGGAGCATTGGAAGACATATACAGCTTGATGGAGCATTTGGGAGACATAA
1 ACAGCTTAGTGGAGCATTGGAAGACATATACAGCTTGATGGAGCATTTGGAAGACATAA
11360963 ACAGCT
1 ACAGCT
11360969 CACAAACAGC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 12 0.20
59 47 0.80
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (59 bp):
ACAGCTTAGTGGAGCATTGGAAGACATATACAGCTTGATGGAGCATTTGGAAGACATAA
Found at i:11366422 original size:16 final size:16
Alignment explanation
Indices: 11366388--11366436 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
11366378 GTAAGTTATC
* *
11366388 TTCATTTTCTTACTAT
1 TTCATTTTCTTATTCT
11366404 TTCATTTTCTTATTCT
1 TTCATTTTCTTATTCT
11366420 TTCATCTATTCTTATTC
1 TTCAT-T-TTCTTATTC
11366437 CATTACCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 19 0.66
17 1 0.03
18 9 0.31
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.63
Consensus pattern (16 bp):
TTCATTTTCTTATTCT
Found at i:11382033 original size:37 final size:37
Alignment explanation
Indices: 11381953--11382062 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
11381943 ATTTATAAGT
*
11381953 TGGTGATAATATAGGCGTGAT-ATGGTGATGGA-ATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACATA
* *
11381988 TGGTGATGATATAGGCGTAATAATGGTGATGGACTTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACATA
*
11382025 TGGTGATGATATAGGCGGGATAATGGTGATGGACATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACATA
11382062 T
1 T
11382063 TGTATCTTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 19 0.28
36 11 0.16
37 37 0.55
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACATA
Found at i:11382438 original size:19 final size:20
Alignment explanation
Indices: 11382400--11382442 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
11382390 AAACCCCCTT
*
11382400 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
11382420 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
11382439 TGAA
1 TGAA
11382443 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:11385367 original size:16 final size:16
Alignment explanation
Indices: 11385336--11385382 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
11385326 TGGTAATGAA
11385336 ATAAGAAAAGATGAAA-G
1 ATAA-AAAA-ATGAAATG
*
11385353 AATAAAGAAATGAAATG
1 -ATAAAAAAATGAAATG
11385370 ATAAAAAAATGAA
1 ATAAAAAAATGAA
11385383 GATAACTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 18 0.69
17 4 0.15
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (16 bp):
ATAAAAAAATGAAATG
Found at i:11386058 original size:35 final size:36
Alignment explanation
Indices: 11386011--11386078 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
11386001 ATTTATAAGT
*
11386011 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGGGATAATGGTGATGGAATA
*
11386046 TGGTGATGATATAGGCGGGATAATGGTGATGGA
1 TGGTGATAATATAGGCGGGATAATGGTGATGGA
11386079 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.29, C:0.03, G:0.38, T:0.29
Consensus pattern (36 bp):
TGGTGATAATATAGGCGGGATAATGGTGATGGAATA
Found at i:11386457 original size:19 final size:20
Alignment explanation
Indices: 11386419--11386461 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
11386409 GAAACCCCTT
*
11386419 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
11386439 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
11386458 TGAA
1 TGAA
11386462 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:11404511 original size:8 final size:8
Alignment explanation
Indices: 11404498--11404560 Score: 51
Period size: 8 Copynumber: 7.8 Consensus size: 8
11404488 TTTTTTTTTC
11404498 AAAAAACA
1 AAAAAACA
11404506 AAAAAA-A
1 AAAAAACA
11404513 AACAAAA-A
1 AA-AAAACA
11404521 AGGCAAAAA-A
1 A---AAAAACA
**
11404531 AAAAGGCA
1 AAAAAACA
11404539 AAAAAACA
1 AAAAAACA
11404547 AAAAAACA
1 AAAAAACA
11404555 AAAAAA
1 AAAAAA
11404561 GAGCCAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
7 6 0.13
8 33 0.72
10 6 0.13
11 1 0.02
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:11404527 original size:20 final size:20
Alignment explanation
Indices: 11404498--11404552 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
11404488 TTTTTTTTTC
11404498 AAAAAACAAAAAAAAAA-CA
1 AAAAAACAAAAAAAAAAGCA
*
11404517 AAAAAGGCAAAAAAAAAAGGCA
1 AAAAA-ACAAAAAAAAAA-GCA
11404539 AAAAAACAAAAAAA
1 AAAAAACAAAAAAA
11404553 CAAAAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.16
20 11 0.35
21 8 0.26
22 7 0.23
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (20 bp):
AAAAAACAAAAAAAAAAGCA
Found at i:11411650 original size:21 final size:21
Alignment explanation
Indices: 11411626--11411672 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
11411616 TTATATAAGT
11411626 TTAT-ATACTTAGTTTATTTTC
1 TTATGATA-TTAGTTTATTTTC
*
11411647 TTATGTTATTAGTTTATTTTC
1 TTATGATATTAGTTTATTTTC
11411668 TTATG
1 TTATG
11411673 TTATGCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.64
Consensus pattern (21 bp):
TTATGATATTAGTTTATTTTC
Found at i:11411673 original size:21 final size:21
Alignment explanation
Indices: 11411634--11411676 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
11411624 GTTTATATAC
11411634 TTAGTTTATTTTCTTATGTTA
1 TTAGTTTATTTTCTTATGTTA
11411655 TTAGTTTATTTTCTTATGTTA
1 TTAGTTTATTTTCTTATGTTA
11411676 T
1 T
11411677 GCATGTAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.05, G:0.09, T:0.67
Consensus pattern (21 bp):
TTAGTTTATTTTCTTATGTTA
Found at i:11412885 original size:19 final size:20
Alignment explanation
Indices: 11412869--11412913 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
11412859 CTTTATTTCA
11412869 TTTCATT-CTTATTATTTAT
1 TTTCATTACTTATTATTTAT
11412888 TTTCATTACTTA-TA-TTAT
1 TTTCATTACTTATTATTTAT
11412906 TATTCATT
1 T-TTCATT
11412914 TATTAAACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.21
19 15 0.62
20 4 0.17
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTACTTATTATTTAT
Found at i:11417832 original size:19 final size:20
Alignment explanation
Indices: 11417785--11417835 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11417775 GAAACCCCTT
**
11417785 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11417805 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11417824 TGAAGATACATG
1 TGAAAATACATG
11417836 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:11421063 original size:6 final size:6
Alignment explanation
Indices: 11421052--11421095 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
11421042 GATGTAGGAG
*
11421052 TCTTTT TC-TTT TCTTTT TATTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
11421096 TGTTGCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:11421934 original size:19 final size:20
Alignment explanation
Indices: 11421887--11421937 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11421877 GAAACCCCTT
**
11421887 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11421907 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11421926 TGAAGATACATG
1 TGAAAATACATG
11421938 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:11426996 original size:47 final size:45
Alignment explanation
Indices: 11426926--11427051 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
11426916 TATAAAATCT
*
11426926 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
11426971 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
11427018 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
11427052 GCATGGTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 38 0.52
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:11431413 original size:36 final size:36
Alignment explanation
Indices: 11431363--11431476 Score: 185
Period size: 36 Copynumber: 3.2 Consensus size: 36
11431353 AAATCTGTTC
*
11431363 ATCACCATCTTCCATCACCATTATCACGCCTATATA
1 ATCACCATATTCCATCACCATTATCACGCCTATATA
* *
11431399 ATCACCATAGTCCATCACCATTATCACGCCTATATC
1 ATCACCATATTCCATCACCATTATCACGCCTATATA
*
11431435 ATCACCATATTCCATCACCA-TATCACGCCTATATT
1 ATCACCATATTCCATCACCATTATCACGCCTATATA
11431470 ATCACCA
1 ATCACCA
11431477 ACTTCTAAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 21 0.29
36 52 0.71
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
ATCACCATATTCCATCACCATTATCACGCCTATATA
Found at i:11431417 original size:13 final size:11
Alignment explanation
Indices: 11431361--11431459 Score: 58
Period size: 13 Copynumber: 8.3 Consensus size: 11
11431351 TAAAATCTGT
*
11431361 TCATCACCATCT
1 TCATCACCAT-A
11431373 TCCATCACCATTA
1 T-CATCACCA-TA
*
11431386 TCA-CGCCTATA
1 TCATCACC-ATA
*
11431397 TAATCACCATA
1 TCATCACCATA
11431408 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
11431422 TCA-CGCCTATA
1 TCATCACC-ATA
11431433 TCATCACCATA
1 TCATCACCATA
11431444 TTCCATCACCATA
1 -T-CATCACCATA
11431457 TCA
1 TCA
11431460 CGCCTATATT
Statistics
Matches: 69, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
11 23 0.33
12 16 0.23
13 27 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:11431922 original size:5 final size:5
Alignment explanation
Indices: 11431907--11431948 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
11431897 ATTGGAGTAC
11431907 AAAAG -AAAG AAAAG AAAAG --AAG AAAAG AAAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAA
11431949 AGTGAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.09
4 4 0.12
5 21 0.64
6 5 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:11431926 original size:14 final size:15
Alignment explanation
Indices: 11431907--11431948 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
11431897 ATTGGAGTAC
11431907 AAAAGAAAGAAAAG-
1 AAAAGAAAGAAAAGA
11431921 AAAAG-AAGAAAAGA
1 AAAAGAAAGAAAAGA
11431935 AAAAGAAAAGAAAA
1 AAAAG-AAAGAAAA
11431949 AGTGAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.32
14 10 0.40
16 7 0.28
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:11431958 original size:11 final size:11
Alignment explanation
Indices: 11431912--11431950 Score: 60
Period size: 11 Copynumber: 3.4 Consensus size: 11
11431902 AGTACAAAAG
11431912 AAAGAAAAGAAA
1 AAAGAAAAG-AA
11431924 AGAAGAAAAGAA
1 A-AAGAAAAGAA
11431936 AAAGAAAAGAA
1 AAAGAAAAGAA
11431947 AAAG
1 AAAG
11431951 TGAAGAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 14 0.54
12 4 0.15
13 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:11435932 original size:23 final size:23
Alignment explanation
Indices: 11435905--11436025 Score: 83
Period size: 23 Copynumber: 5.1 Consensus size: 23
11435895 CACTATCTTC
*
11435905 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
11435928 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
11435951 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCACCATA-T
*
11435976 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
11436000 CATCACCA-TATTCCATCACCATAT
1 CATCACCATTA-T-CATCACCATAT
11436024 CA
1 CA
11436026 CGCCTATTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
22 9 0.11
23 29 0.37
24 17 0.22
25 17 0.22
26 2 0.03
27 5 0.06
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.28
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:11435943 original size:36 final size:36
Alignment explanation
Indices: 11435903--11436042 Score: 246
Period size: 36 Copynumber: 3.9 Consensus size: 36
11435893 ATCACTATCT
11435903 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
11435939 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
11435975 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
11436011 TCCATCACCA-TATCACGCCTATTTTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
11436043 ACTTCTAAAT
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.20
36 81 0.80
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:11435946 original size:13 final size:11
Alignment explanation
Indices: 11435905--11436025 Score: 86
Period size: 11 Copynumber: 10.2 Consensus size: 11
11435895 CACTATCTTC
11435905 CATCACCATTAT
1 CATCACCA-TAT
*
11435917 CA-CGCCTATAT
1 CATCACC-ATAT
11435928 CATCACCATAGT
1 CATCACCATA-T
11435940 CCATCACCATTAT
1 -CATCACCA-TAT
*
11435953 CA-CGCCTATAT
1 CATCACC-ATAT
11435964 CATCACCATAGT
1 CATCACCATA-T
11435976 CCATCACCATTAT
1 -CATCACCA-TAT
*
11435989 CA-CGCCTATAT
1 CATCACC-ATAT
11436000 CATCACCATATT
1 CATCACCATA-T
11436012 CCATCACCATAT
1 -CATCACCATAT
11436024 CA
1 CA
11436026 CGCCTATTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
11 35 0.39
12 22 0.25
13 28 0.31
14 4 0.04
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:11437707 original size:19 final size:21
Alignment explanation
Indices: 11437679--11437728 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
11437669 GCCAAGAGCG
*
11437679 TGTATCTTCA-TTAAAA-TCA
1 TGTATTTTCATTTAAAAGTCA
11437698 TGTATTTTCATTTAAAAGTCA
1 TGTATTTTCATTTAAAAGTCA
11437719 TGTATTTTCA
1 TGTATTTTCA
11437729 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 9 0.32
20 6 0.21
21 13 0.46
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (21 bp):
TGTATTTTCATTTAAAAGTCA
Found at i:11438480 original size:8 final size:8
Alignment explanation
Indices: 11438469--11438493 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11438459 GAGAAAAATC
11438469 AGAAAAGA
1 AGAAAAGA
11438477 AGAAAAGA
1 AGAAAAGA
11438485 AGAAAAGA
1 AGAAAAGA
11438493 A
1 A
11438494 AAGAAAAAGA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:11438503 original size:16 final size:16
Alignment explanation
Indices: 11438452--11438503 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
11438442 TTGGAGTGCA
11438452 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAAA--AG
*
11438471 AAAAGAAGAAAAGAAG
1 AAAAGAAGAAAAAAAG
11438487 AAAAGAA-AAGAAAAAG
1 AAAAGAAGAA-AAAAAG
11438503 A
1 A
11438504 GAAGTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
18 4 0.13
19 9 0.30
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:11441816 original size:19 final size:21
Alignment explanation
Indices: 11441794--11441837 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
11441784 AGCATGAATC
11441794 TTCA-TTAAAA-TCATGTATT
1 TTCATTTAAAAGTCATGTATT
11441813 TTCATTTAAAAGTCATGTATT
1 TTCATTTAAAAGTCATGTATT
11441834 TTCA
1 TTCA
11441838 AAGGGGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 6 0.26
21 13 0.57
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (21 bp):
TTCATTTAAAAGTCATGTATT
Found at i:11453047 original size:20 final size:21
Alignment explanation
Indices: 11453024--11453072 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 21
11453014 TTCTTTTCTT
11453024 TGCTTTTTTC-TTCTTTTGAG
1 TGCTTTTTTCTTTCTTTTGAG
11453044 TGCTGGATTTTTCTTTCTTTTGAG
1 TGCT---TTTTTCTTTCTTTTGAG
11453068 TGCTT
1 TGCTT
11453073 CACTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 4 0.16
21 1 0.04
23 6 0.24
24 14 0.56
ACGTcount: A:0.06, C:0.14, G:0.18, T:0.61
Consensus pattern (21 bp):
TGCTTTTTTCTTTCTTTTGAG
Found at i:11453079 original size:23 final size:24
Alignment explanation
Indices: 11453030--11453082 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
11453020 TCTTTGCTTT
* *
11453030 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
11453053 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
11453076 TTTCTTT
1 TTTCTTT
11453083 TCTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:11457219 original size:13 final size:13
Alignment explanation
Indices: 11457201--11457245 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
11457191 CATTGCCATT
*
11457201 TCATCATCATCCA
1 TCATCAACATCCA
*
11457214 TCATCAACATCCT
1 TCATCAACATCCA
*
11457227 TCATCAAGA-CCA
1 TCATCAACATCCA
11457239 TCATCAA
1 TCATCAA
11457246 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:11457595 original size:17 final size:18
Alignment explanation
Indices: 11457573--11457614 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
11457563 GCAAAAAGAA
11457573 AAGAAAAAGA-CA-AAAAG
1 AAGAAAAA-ATCAGAAAAG
11457590 AAGAAAAAATCAGAAAAG
1 AAGAAAAAATCAGAAAAG
11457608 AAGAAAA
1 AAGAAAA
11457615 GAAAGGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 10 0.43
18 12 0.52
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (18 bp):
AAGAAAAAATCAGAAAAG
Found at i:11461589 original size:5 final size:5
Alignment explanation
Indices: 11461581--11461614 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
11461571 CTTTTCTTTC
11461581 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
11461615 TCTTCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Done.