Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 25
Found at i:3496339 original size:44 final size:45
Alignment explanation
Indices: 3496216--3496341 Score: 191
Period size: 46 Copynumber: 2.8 Consensus size: 45
3496206 GATAAAATCT
* *
3496216 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3496261 CTTACCATTTAATCTCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTC-CATAAGCTCGTAAGCTTATTTTACCAATATA
**
3496307 CTTGTCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
3496342 CCAGTTTATC
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 22 0.30
45 17 0.23
46 35 0.47
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:3496344 original size:23 final size:23
Alignment explanation
Indices: 3496276--3496344 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 23
3496266 CATTTAATCT
3496276 CATAAGCTCGTAAGCTTATTTTAC
1 CATAAGCTCGTAAGCTTATTTT-C
* *
3496300 CAATATA-CTTGTCA--TTA--TTC
1 C-ATA-AGCTCGTAAGCTTATTTTC
3496320 CATAAGCTCGTAAGCTTATTTTC
1 CATAAGCTCGTAAGCTTATTTTC
3496343 CA
1 CA
3496345 GTTTATCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 15
0.64 0.08 0.28
Matches are distributed among these distances:
18 1 0.03
19 8 0.24
20 2 0.06
21 5 0.15
23 8 0.24
24 1 0.03
25 8 0.24
26 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (23 bp):
CATAAGCTCGTAAGCTTATTTTC
Found at i:3501688 original size:21 final size:22
Alignment explanation
Indices: 3501664--3501704 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3501654 CTGATTTTTG
3501664 TATATGA-TGTTATCATGAACA
1 TATATGATTGTTATCATGAACA
*
3501685 TATATGATTTTTATCATGAA
1 TATATGATTGTTATCATGAA
3501705 TAATACTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (22 bp):
TATATGATTGTTATCATGAACA
Found at i:3507944 original size:21 final size:20
Alignment explanation
Indices: 3507858--3508015 Score: 95
Period size: 21 Copynumber: 7.8 Consensus size: 20
3507848 AAATGACCAA
**
3507858 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3507877 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
** *
3507897 CAAAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3507917 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
3507938 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3507959 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3507979 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3508000 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3508016 ACACATAAAT
Statistics
Matches: 106, Mismatches: 27, Indels: 11
0.74 0.19 0.08
Matches are distributed among these distances:
19 16 0.15
20 43 0.41
21 47 0.44
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3508047 original size:20 final size:20
Alignment explanation
Indices: 3507982--3508211 Score: 246
Period size: 20 Copynumber: 11.5 Consensus size: 20
3507972 CGATTTTCCA
** *
3507982 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
3508002 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
3508022 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3508042 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3508062 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3508082 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
3508102 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3508122 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
3508142 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
*
3508162 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3508182 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
3508202 AAATCACAAC
1 AAATCGCAAC
3508212 ACTGAAATTT
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:3508928 original size:24 final size:24
Alignment explanation
Indices: 3508889--3508935 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3508879 AAATTTGGTC
3508889 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3508913 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3508936 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3509125 original size:12 final size:12
Alignment explanation
Indices: 3509108--3509132 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3509098 TCATAATCCT
3509108 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3509120 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3509132 G
1 G
3509133 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3511491 original size:20 final size:19
Alignment explanation
Indices: 3511466--3511597 Score: 158
Period size: 20 Copynumber: 7.4 Consensus size: 19
3511456 GATTCTCTCG
3511466 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3511486 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3511505 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3511519 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3511539 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3511558 TTGCGA--TTC-TATCG--
1 TTGCGATTTTCATTTCGCA
3511572 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3511591 TTGCGAT
1 TTGCGAT
3511598 AGTCAATTTT
Statistics
Matches: 97, Mismatches: 4, Indels: 23
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.12
16 14 0.14
17 12 0.12
18 2 0.02
19 27 0.28
20 30 0.31
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3511514 original size:53 final size:53
Alignment explanation
Indices: 3511447--3511597 Score: 286
Period size: 53 Copynumber: 2.9 Consensus size: 53
3511437 GAAATGAAAA
3511447 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
3511500 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
3511553 TCGCATTGCGATTCTATCGTTGCGATTTTCATTT-CGCATTGCGAT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGAT
3511598 AGTCAATTTT
Statistics
Matches: 97, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 11 0.11
53 86 0.89
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:3511581 original size:33 final size:32
Alignment explanation
Indices: 3511447--3511597 Score: 126
Period size: 33 Copynumber: 4.4 Consensus size: 32
3511437 GAAATGAAAA
3511447 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCT-TCGTTGCGATTTTCATT
* * *
3511480 TCCGCATTGCGATT-TTCATTTCGCA-TTGCGATT
1 T-CGCATTGCGATTCTTCGTTGCG-ATTTTC-ATT
* *
3511513 CTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 -TCGCATTGCGA--TTC--TT-CG--TTGCGATTTTCATT
3511553 TCGCATTGCGATTCTATCGTTGCGATTTTCATT
1 TCGCATTGCGATTCT-TCGTTGCGATTTTCATT
3511586 TCGCATTGCGAT
1 TCGCATTGCGAT
3511598 AGTCAATTTT
Statistics
Matches: 94, Mismatches: 10, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
32 9 0.10
33 40 0.43
34 13 0.14
35 5 0.05
36 1 0.01
37 3 0.03
38 2 0.02
39 10 0.11
40 4 0.04
41 7 0.07
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (32 bp):
TCGCATTGCGATTCTTCGTTGCGATTTTCATT
Found at i:3511735 original size:52 final size:53
Alignment explanation
Indices: 3511656--3511766 Score: 215
Period size: 52 Copynumber: 2.1 Consensus size: 53
3511646 CCATTACATT
3511656 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
3511709 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
3511761 TCGCAA
1 TCGCAA
3511767 CGAGAGAATC
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 49 0.84
53 9 0.16
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:3511744 original size:33 final size:33
Alignment explanation
Indices: 3511707--3511798 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
3511697 GCGAAATGAA
3511707 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
3511740 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
3511773 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
3511799 TTGCGATTCT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:3511745 original size:14 final size:14
Alignment explanation
Indices: 3511726--3511780 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3511716 GCGAAATGAA
3511726 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3511740 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3511759 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3511773 AATCGCAA
1 AATCGCAA
3511781 TGCGAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3511853 original size:19 final size:19
Alignment explanation
Indices: 3511811--3511910 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
3511801 GCGATTCTCC
3511811 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
3511831 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
3511850 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
3511866 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
3511883 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
3511902 CATTGCGAT
1 CATTGCGAT
3511911 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:3511907 original size:52 final size:53
Alignment explanation
Indices: 3511794--3511910 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
3511784 GAAATTAAAA
3511794 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
3511847 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
3511899 TCGCATTGCGAT
1 TCGCATTGCGAT
3511911 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:3512036 original size:14 final size:14
Alignment explanation
Indices: 3512017--3512053 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3512007 CATCAATTAC
3512017 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3512031 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3512045 ACAAATCAA
1 ACAAATCAA
3512054 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3514050 original size:14 final size:14
Alignment explanation
Indices: 3514031--3514087 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3514021 GCGAAATGAA
*
3514031 AATCGCAACGACAG
1 AATCGCAACGAAAG
3514045 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
3514062 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3514078 AATCGCAACG
1 AATCGCAACG
3514088 CAAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3514058 original size:33 final size:33
Alignment explanation
Indices: 3514012--3514104 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
3514002 GCGAAACCAA
*
3514012 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3514045 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3514078 AATCGCAACGCAAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3514105 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3514069 original size:19 final size:19
Alignment explanation
Indices: 3513975--3514109 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
3513965 TAGTTTACTT
* *
3513975 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3513995 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3514014 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3514033 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3514047 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3514066 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3514080 TCGCAACGCAAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3514099 TCGCAATGCGA
1 TCGCAACGCGA
3514110 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.17
16 10 0.11
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3514127 original size:19 final size:18
Alignment explanation
Indices: 3514105--3514214 Score: 83
Period size: 19 Copynumber: 6.3 Consensus size: 18
3514095 AAAATCGCAA
3514105 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3514124 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
3514138 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3514157 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
3514171 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
3514190 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
3514210 TGCGA
1 TGCGA
3514215 AAGTAAACTA
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
14 22 0.31
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 31 0.43
20 12 0.17
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.45
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:3514147 original size:33 final size:33
Alignment explanation
Indices: 3514105--3514196 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3514095 AAAATCGCAA
3514105 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3514138 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3514171 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3514197 TTAAGTTTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3514417 original size:93 final size:93
Alignment explanation
Indices: 3514258--3514731 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
3514248 TTGAATGGAT
3514258 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3514323 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
3514351 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3514416 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
3514444 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3514509 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3514537 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3514602 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3514630 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3514695 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3514723 AAATTTACT
1 AAATTTACT
3514732 AAGCAATCTA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3516474 original size:33 final size:33
Alignment explanation
Indices: 3516429--3516542 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
3516419 TCTTTTGGTT
3516429 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3516462 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3516495 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3516528 GAAAT-AAAATCGCAA
1 GAAATGAAAATCGCAA
3516543 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 10 0.13
33 67 0.87
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3516475 original size:19 final size:18
Alignment explanation
Indices: 3516436--3516547 Score: 86
Period size: 14 Copynumber: 6.8 Consensus size: 18
3516426 GTTGAAATGA
3516436 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
3516451 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
3516468 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
3516484 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
3516501 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
* *
3516517 -AATCGCAACGCGAAATA
1 AAATCGCAACGCGAGATG
*
3516534 AAATCGCAATGCGA
1 AAATCGCAACGCGA
3516548 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 5, Indels: 25
0.72 0.05 0.23
Matches are distributed among these distances:
14 24 0.31
16 15 0.19
17 11 0.14
18 12 0.15
19 16 0.21
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:3516578 original size:14 final size:14
Alignment explanation
Indices: 3516559--3516615 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3516549 TTTGGTTTCG
3516559 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3516573 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3516592 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3516606 CGTTGCGATT
1 CGTTGCGATT
3516616 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3516591 original size:33 final size:33
Alignment explanation
Indices: 3516543--3516623 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
3516533 AAAATCGCAA
**
3516543 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3516576 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3516609 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
3516624 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3516626 original size:21 final size:21
Alignment explanation
Indices: 3516600--3516675 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
3516590 CGCGTTGCGA
3516600 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
3516621 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3516641 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
3516662 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
3516676 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3516656 original size:41 final size:41
Alignment explanation
Indices: 3516599--3516676 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
3516589 TCGCGTTGCG
*
3516599 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
3516640 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
3516677 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:3516802 original size:33 final size:33
Alignment explanation
Indices: 3516755--3516825 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
3516745 AATACTAACT
* *
3516755 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3516788 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3516821 TGAAA
1 TGAAA
3516826 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3517057 original size:22 final size:22
Alignment explanation
Indices: 3517005--3517059 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3516995 TGGTTGTGAG
**
3517005 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3517027 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3517049 GGATTTCTTCG
1 GGATTTCTTCG
3517060 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3517234 original size:20 final size:20
Alignment explanation
Indices: 3517209--3517398 Score: 213
Period size: 20 Copynumber: 9.4 Consensus size: 20
3517199 AAATATCGCA
3517209 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* * *
3517229 TTGCGATTTTATGTATTA-TCG
1 TTGCGA-TTTACGGA-TACGCG
3517250 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
3517270 TTGCGATATACGGATACGCA
1 TTGCGATTTACGGATACGCG
**
3517290 TTGCGATTTACCCATACGCG
1 TTGCGATTTACGGATACGCG
*
3517310 TTGCGATTTACGGATACACG
1 TTGCGATTTACGGATACGCG
3517330 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
3517350 TTGCGATTTATGTG-TTCGCG
1 TTGCGATTTACG-GATACGCG
* ** *
3517370 TTGCGATTTTCATATTCGCG
1 TTGCGATTTACGGATACGCG
3517390 TTGCGATTT
1 TTGCGATTT
3517399 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:3517392 original size:60 final size:60
Alignment explanation
Indices: 3517209--3517398 Score: 245
Period size: 60 Copynumber: 3.1 Consensus size: 60
3517199 AAATATCGCA
**
3517209 TTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACGCG
* * *** * *
3517270 TTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACACG
1 TTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACGCG
* * ** *
3517330 TTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATTCGCG
1 TTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACGCG
3517390 TTGCGATTT
1 TTGCGATTT
3517399 TGGAAAATCG
Statistics
Matches: 108, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 84 0.78
61 24 0.22
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACGCG
Found at i:3517415 original size:21 final size:21
Alignment explanation
Indices: 3517385--3517467 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3517375 ATTTTCATAT
*
3517385 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3517406 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3517427 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3517448 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3517468 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3517458 original size:42 final size:43
Alignment explanation
Indices: 3517365--3517463 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3517355 ATTTATGTGT
* *
3517365 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
3517406 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
3517448 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3517464 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:3532190 original size:236 final size:240
Alignment explanation
Indices: 3531877--3532353 Score: 926
Period size: 236 Copynumber: 2.0 Consensus size: 240
3531867 ATGATTGTCC
3531877 TGAATATATTTCAAATGTTGTTTTAAATGATGCATTTTATGATTAATGCAATCTATGTACTTATC
1 TGAATATATTTCAAATGTTGTTTTAAATGATGCATTTTATGATTAATGCAATCTATGTACTTATC
3531942 TCACAAAAACAATTGCAGTGTCCTTTGCCTCAATTATTTGGTCAAGATCCATCTTTACTCTTGA-
66 TCACAAAAACAATTGCAGTGTCCTTTGCCTCAATTATTTGGTCAAGATCCATCTTTACTCTTGAT
3532006 TTGTTTTAGA-TTGATAAATTATTAGTCTAATCTTAATCTTAGTTAGATCAGAGGAAAAGACGGA
131 TTGTTTTAGATTTGATAAATTATTAGTCTAATCTTAATCTTAGTTAGATCAGAGGAAAAGACGGA
3532070 CTCT-AGGGAAGAACGAGGAGTG-TCCTAGTGGGTCTAGAACCTA
196 CTCTAAGGGAAGAACGAGGAGTGTTCCTAGTGGGTCTAGAACCTA
3532113 TGAATATATTTCAAATGTTGTTTTAAATGATGCATTTTATGATTAATGCAATCTATGTACTTATC
1 TGAATATATTTCAAATGTTGTTTTAAATGATGCATTTTATGATTAATGCAATCTATGTACTTATC
3532178 TCACAAAAACAATTGCAGTGTCCTTTGCCTCAATTATTTGGTCAAGATCCATCTTTACTCTTGAT
66 TCACAAAAACAATTGCAGTGTCCTTTGCCTCAATTATTTGGTCAAGATCCATCTTTACTCTTGAT
3532243 TTGTTTTAGATTTGATAAATTATTAGTCTAATCTTAATCTTAGTTAGATCAGAGGAAAAGACGGA
131 TTGTTTTAGATTTGATAAATTATTAGTCTAATCTTAATCTTAGTTAGATCAGAGGAAAAGACGGA
3532308 CTCTAAGGGAAGAACGAGGAGTGTTCCTAGTGGGTCTAGAACCTA
196 CTCTAAGGGAAGAACGAGGAGTGTTCCTAGTGGGTCTAGAACCTA
3532353 T
1 T
3532354 AACCTAAGGG
Statistics
Matches: 237, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
236 129 0.54
237 10 0.04
238 58 0.24
239 18 0.08
240 22 0.09
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (240 bp):
TGAATATATTTCAAATGTTGTTTTAAATGATGCATTTTATGATTAATGCAATCTATGTACTTATC
TCACAAAAACAATTGCAGTGTCCTTTGCCTCAATTATTTGGTCAAGATCCATCTTTACTCTTGAT
TTGTTTTAGATTTGATAAATTATTAGTCTAATCTTAATCTTAGTTAGATCAGAGGAAAAGACGGA
CTCTAAGGGAAGAACGAGGAGTGTTCCTAGTGGGTCTAGAACCTA
Found at i:3537320 original size:13 final size:13
Alignment explanation
Indices: 3537302--3537336 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
3537292 AATGAATTTT
3537302 AAGATTTTCCAAA
1 AAGATTTTCCAAA
3537315 AAGATTTTCCAAA
1 AAGATTTTCCAAA
3537328 AAGATTTTC
1 AAGATTTTC
3537337 TAAGTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (13 bp):
AAGATTTTCCAAA
Found at i:3539766 original size:11 final size:12
Alignment explanation
Indices: 3539744--3539768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3539734 TTCATCATTG
3539744 CTTCAATAAAAA
1 CTTCAATAAAAA
3539756 CTTCAATAAAAA
1 CTTCAATAAAAA
3539768 C
1 C
3539769 GAAGGACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (12 bp):
CTTCAATAAAAA
Found at i:3540334 original size:42 final size:42
Alignment explanation
Indices: 3540170--3540343 Score: 224
Period size: 42 Copynumber: 4.1 Consensus size: 42
3540160 TACTACGACA
* * *
3540170 TTTATTACGAAAACGCCACTAACGGATAAAACAATTGCAGTG
1 TTTATTACGAAAACGCCACTAACGGAGAAAACAATTGCGGCG
* *** *
3540212 TTTATTACGAAAACACCACTAACGGAGAAAACAATTATTGTG
1 TTTATTACGAAAACGCCACTAACGGAGAAAACAATTGCGGCG
* * *
3540254 TTTATTTCAAAAACGCCACTAACGGAGAAAATAATTGCGGCG
1 TTTATTACGAAAACGCCACTAACGGAGAAAACAATTGCGGCG
*
3540296 TTTATTACGAAAACGCCACTATA-GGAGAAAACAATTGCGGCA
1 TTTATTACGAAAACGCCACTA-ACGGAGAAAACAATTGCGGCG
3540338 TTTATT
1 TTTATT
3540344 TAAAAAATAT
Statistics
Matches: 114, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
42 113 0.99
43 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.26
Consensus pattern (42 bp):
TTTATTACGAAAACGCCACTAACGGAGAAAACAATTGCGGCG
Found at i:3541920 original size:28 final size:30
Alignment explanation
Indices: 3541864--3541924 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
3541854 TCACATGTTT
3541864 TTGTGACGTTTATACAAAAAAAAGCCACTA
1 TTGTGACGTTTATACAAAAAAAAGCCACTA
* * *
3541894 TTGTGGCGTTTGT-CAAAAAACA-CCACTA
1 TTGTGACGTTTATACAAAAAAAAGCCACTA
3541922 TTG
1 TTG
3541925 ATTAGCACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 9 0.32
29 8 0.29
30 11 0.39
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (30 bp):
TTGTGACGTTTATACAAAAAAAAGCCACTA
Found at i:3542005 original size:42 final size:40
Alignment explanation
Indices: 3541932--3542070 Score: 118
Period size: 42 Copynumber: 3.4 Consensus size: 40
3541922 TTGATTAGCA
* * * * *
3541932 CTATTGCGGCGTTTGAGGAATAAATGTCGCTATATGTATACT
1 CTATTGCGGAGTTTG-GGTATAAAAGCCGCTA-ATTTATACT
* * *
3541974 CTATTGCAGTGTTTGTGGTATAAAAGCCGCTAATTTACCACT
1 CTATTGCGGAGTTTG-GGTATAAAAGCCGCTAATTTA-TACT
*
3542016 CTATTGCGGAGTTTGGGCTA-AAAAGCCGCAAAATTTATACT
1 CTATTGCGGAGTTTGGG-TATAAAAGCCGC-TAATTTATACT
* *
3542057 CTATTACGGCGTTT
1 CTATTGCGGAGTTT
3542071 TTACAATAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
41 30 0.38
42 50 0.62
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (40 bp):
CTATTGCGGAGTTTGGGTATAAAAGCCGCTAATTTATACT
Found at i:3544565 original size:19 final size:19
Alignment explanation
Indices: 3544538--3544574 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3544528 ATGACCAACA
* *
3544538 AAATTGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
3544557 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
3544575 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:3544704 original size:20 final size:20
Alignment explanation
Indices: 3544681--3544730 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
3544671 GAATATGTAA
3544681 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
3544701 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
3544721 GTCGCAACGC
1 ATCGCAACGC
3544731 TGAATTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:3545568 original size:24 final size:24
Alignment explanation
Indices: 3545541--3545618 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
3545531 GTATTCGAAA
3545541 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
3545565 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3545589 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3545613 TTTGAT
1 TTTGAT
3545619 GATGTTTCGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3547028 original size:29 final size:29
Alignment explanation
Indices: 3546988--3547043 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
3546978 TTTAGACGTG
3546988 TTTGCCTCAGTGTGCTAAAACACTAGAGT
1 TTTGCCTCAGTGTGCTAAAACACTAGAGT
3547017 TTTGCCTCAGTGTGCTAAAACACTAGA
1 TTTGCCTCAGTGTGCTAAAACACTAGA
3547044 AGATGTCGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (29 bp):
TTTGCCTCAGTGTGCTAAAACACTAGAGT
Found at i:3547896 original size:18 final size:18
Alignment explanation
Indices: 3547875--3547917 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3547865 CAAGAAAAAG
*
3547875 GCAATCAAAATCAAAATC
1 GCAATCAAAATAAAAATC
3547893 GCAATCAAAATAAAAATC
1 GCAATCAAAATAAAAATC
*
3547911 CCAATCA
1 GCAATCA
3547918 CAACCGGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.23, G:0.05, T:0.16
Consensus pattern (18 bp):
GCAATCAAAATAAAAATC
Found at i:3548227 original size:140 final size:140
Alignment explanation
Indices: 3547975--3548257 Score: 530
Period size: 140 Copynumber: 2.0 Consensus size: 140
3547965 GCAAACGTTG
* *
3547975 TATTATGTGTATTTTATATGTAAACTTTTAACATTTTTAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATATATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
3548040 TTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3548105 CGAATTTGAC
131 CGAATTTGAC
*
3548115 TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATATATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
3548180 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3548245 CGAATTTGAC
131 CGAATTTGAC
3548255 TAT
1 TAT
3548258 CGCAACGCGA
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATATATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:3548253 original size:20 final size:20
Alignment explanation
Indices: 3548228--3548304 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
3548218 TTACACATTC
*
3548228 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
3548248 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3548268 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
3548288 ATTTGATTATCGCAACG
1 ATTTGACTATCGCAACG
3548305 GGAAAATCAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:3549972 original size:21 final size:21
Alignment explanation
Indices: 3549948--3550049 Score: 89
Period size: 21 Copynumber: 4.9 Consensus size: 21
3549938 GTGGGAGGGA
*
3549948 CCTCTTCAACGATGACAGAGG
1 CCTCTTGAACGATGACAGAGG
* ** *
3549969 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGAGG
* ** * *
3549990 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGACAGAGG
*
3550011 CCTCTTGAACGAT-AGGAGAGG
1 CCTCTTGAACGATGA-CAGAGG
3550032 CCTCTTGAACGATGACAG
1 CCTCTTGAACGATGACAG
3550050 GTGAGTCGGG
Statistics
Matches: 62, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 60 0.97
22 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.34, T:0.21
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGAGG
Found at i:3549987 original size:42 final size:42
Alignment explanation
Indices: 3549928--3550049 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
3549918 ATGAATCGGG
* *
3549928 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGAGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGAGGC
** * *
3549970 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTGAACGATGACAGAGGC
* *
3550012 CTCTTGAACGATAGGAGAGG-CCTCTTGAACGATGACAG
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACAG
3550050 GTGAGTCGGG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.02
42 61 0.92
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGAGGC
Found at i:3550550 original size:19 final size:20
Alignment explanation
Indices: 3550518--3550559 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
3550508 AATAGTTTCT
3550518 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
3550538 GAAACTT-AAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
3550557 GAA
1 GAA
3550560 TTTGACTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:3550604 original size:19 final size:20
Alignment explanation
Indices: 3550580--3550618 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3550570 GCAACGGGAT
*
3550580 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
3550599 AATCGCAACGCGAAACTAAA
1 AATCGCAACGCGAAACTAAA
3550619 TTCGCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:3550665 original size:19 final size:19
Alignment explanation
Indices: 3550619--3550667 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
3550609 CGAAACTAAA
* *
3550619 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCAATTTTCAT
*
3550638 TTCCGCATTGCAATTTTTAT
1 TT-CGCATTGCAATTTTCAT
3550658 TTCGCATTGC
1 TTCGCATTGC
3550668 GATTATCTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TTCGCATTGCAATTTTCAT
Found at i:3550722 original size:20 final size:20
Alignment explanation
Indices: 3550676--3550724 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3550666 GCGATTATCT
*
3550676 CGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
3550696 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
3550716 CGTTGCGAT
1 CGTTGCGAT
3550725 TTTTAAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3552682 original size:20 final size:20
Alignment explanation
Indices: 3552639--3552775 Score: 90
Period size: 20 Copynumber: 7.2 Consensus size: 20
3552629 GAAACTTAAA
**
3552639 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
3552659 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
*** **
3552679 ATCGCAATGTGAATTTGACT
1 ATCGCAACACGAAAATGACT
*
3552699 ATCGC-A-ACG-AGAT-A--
1 ATCGCAACACGAAAATGACT
** **
3552713 ATCGCAATGCG-AAATGAAA
1 ATCGCAACACGAAAATGACT
3552732 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
3552752 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
3552772 ATCG
1 ATCG
3552776 TTGCGATTTT
Statistics
Matches: 91, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
14 5 0.05
15 1 0.01
16 6 0.07
17 3 0.03
18 1 0.01
19 10 0.11
20 65 0.71
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:3553176 original size:22 final size:22
Alignment explanation
Indices: 3553150--3553206 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
3553140 GATGGAGATA
3553150 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
3553172 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
3553194 GACGGATGTCGCC
1 GACGGATTTCGCC
3553207 GTAGAGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:3553396 original size:20 final size:20
Alignment explanation
Indices: 3553371--3553441 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
3553361 TTGTATTATT
3553371 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
** *
3553391 GCGTTGCGATTATGT-ATTATT
1 GCGTTGCGA-TA-GTCAGAATC
*
3553412 GCGTTGCAATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
3553432 GCGTTGCGAT
1 GCGTTGCGAT
3553442 TATGTATTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.05
20 23 0.57
21 13 0.32
22 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:3553407 original size:41 final size:41
Alignment explanation
Indices: 3553357--3553461 Score: 183
Period size: 41 Copynumber: 2.6 Consensus size: 41
3553347 ATCGTATTGT
*
3553357 GATTTTGTATTATTGCGTTGCGATAGTCAGAATCGCGTTGC
1 GATTATGTATTATTGCGTTGCGATAGTCAGAATCGCGTTGC
*
3553398 GATTATGTATTATTGCGTTGCAATAGTCAGAATCGCGTTGC
1 GATTATGTATTATTGCGTTGCGATAGTCAGAATCGCGTTGC
*
3553439 GATTATGTATTATCGCGTTGCGA
1 GATTATGTATTATTGCGTTGCGA
3553462 ATCTGGAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (41 bp):
GATTATGTATTATTGCGTTGCGATAGTCAGAATCGCGTTGC
Found at i:3553417 original size:21 final size:21
Alignment explanation
Indices: 3553357--3553461 Score: 92
Period size: 21 Copynumber: 5.1 Consensus size: 21
3553347 ATCGTATTGT
* *
3553357 GATTTTGTATTATTGCGTTGC
1 GATTATGTATTATCGCGTTGC
**
3553378 GA-TA-GTCAGAATCGCGTTGC
1 GATTATGT-ATTATCGCGTTGC
*
3553398 GATTATGTATTATTGCGTTGC
1 GATTATGTATTATCGCGTTGC
* **
3553419 -AATA-GTCAGAATCGCGTTGC
1 GATTATGT-ATTATCGCGTTGC
3553439 GATTATGTATTATCGCGTTGC
1 GATTATGTATTATCGCGTTGC
3553460 GA
1 GA
3553462 ATCTGGAAAC
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
19 4 0.06
20 26 0.41
21 30 0.47
22 4 0.06
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (21 bp):
GATTATGTATTATCGCGTTGC
Found at i:3553511 original size:19 final size:19
Alignment explanation
Indices: 3553487--3553523 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3553477 TGCAATACTG
*
3553487 GAGATCACGTTGCGATTTA
1 GAGATCACATTGCGATTTA
*
3553506 GAGATCGCATTGCGATTT
1 GAGATCACATTGCGATTT
3553524 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCACATTGCGATTTA
Found at i:3555060 original size:27 final size:25
Alignment explanation
Indices: 3555005--3555067 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
3554995 CTCAAACCCG
3555005 AAAATATTATATATATAATTAATAT
1 AAAATATTATATATATAATTAATAT
3555030 AAAATATTATATATATAATTAATAT
1 AAAATATTATATATATAATTAATAT
* *
3555055 AAAAAAATATATA
1 AAAATATTATATA
3555068 AAATATTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAATATTATATATATAATTAATAT
Found at i:3555409 original size:29 final size:30
Alignment explanation
Indices: 3555353--3555410 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3555343 AAAACGGTCG
3555353 AGTGAACAAAATGATTCAATTGTAAAGTTC
1 AGTGAACAAAATGATTCAATTGTAAAGTTC
* *
3555383 AGTGAGCAAATTGA-TCGAATTG-AAAGTT
1 AGTGAACAAAATGATTC-AATTGTAAAGTT
3555411 ATGTGAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (30 bp):
AGTGAACAAAATGATTCAATTGTAAAGTTC
Found at i:3556589 original size:43 final size:43
Alignment explanation
Indices: 3556541--3557066 Score: 250
Period size: 43 Copynumber: 12.0 Consensus size: 43
3556531 TATAGTCTCC
* *
3556541 ATTTTTTCATCTTAATAATT-AGGTCCCTAATTTTTTAAATCTT
1 ATTTTTT-ATCTTTATAATTGAGGTCCCTAATTTTTTCAATCTT
* *
3556584 ATTTTTTATCTTTATAATTGAGGT-TCTAATTTTATTCAATCTC
1 ATTTTTTATCTTTATAATTGAGGTCCCTAATTTT-TTCAATCTT
* *
3556627 ATCTTTTATCTTTATAATTG-GCGTCTCTAATTTTTTTTCAAT-TT
1 ATTTTTTATCTTTATAATTGAG-GTCCCTAA--TTTTTTCAATCTT
* * *
3556671 CTTTTTTACCTTTATAATTGAGG-CCCATAATTTTTT-AATCTC
1 ATTTTTTATCTTTATAATTGAGGTCCC-TAATTTTTTCAATCTT
* * *
3556713 ACTTTTTAACTTTATAATTGAGG-CCCTTAAGTTTTTCAATCTT
1 ATTTTTTATCTTTATAATTGAGGTCCC-TAATTTTTTCAATCTT
** * * *
3556756 ATTTTCGACCTTTATATTTGAGG-CCTCTAATTTTTT-AATCTC
1 ATTTTTTATCTTTATAATTGAGGTCC-CTAATTTTTTCAATCTT
* * * * * * * *
3556798 ACTTTTAAACTTTTTAATTAAGATCCTTAAATTTTTTCAATCTC
1 ATTTTTTATCTTTATAATTGAGGTCCCT-AATTTTTTCAATCTT
* * * *
3556842 ACTTTCTACCTTTTCTACCTTCACAATTGAGGCCCCTATATTTTTTCAATCTC
1 A-TTT-T---TTATCT---TT-ATAATTGAGGTCCCTA-ATTTTTTCAATCTT
* * *** *
3556895 AATTTCTA-CTTTTATAATTGAAACCCCTAATTTTTT-AATCTC
1 ATTTTTTATC-TTTATAATTGAGGTCCCTAATTTTTTCAATCTT
* * * * *
3556937 ACTTTTTTAACTTTATTATTAAGG-CGCTTAAATTTTTTCAATCTC
1 A-TTTTTTATCTTTATAATTGAGGTC-CCT-AATTTTTTCAATCTT
* * * * *** * * *
3556982 ACTTTCTACCTTTATAATTAAAACCCCTAAGTTTTTCAATATC
1 ATTTTTTATCTTTATAATTGAGGTCCCTAATTTTTTCAATCTT
* * * * *
3557025 AATTTCTACCTTTATAATTGATG-CCCCAAGTTTTTTCAATCT
1 ATTTTTTATCTTTATAATTGAGGTCCCTAA-TTTTTTCAATCT
3557067 CGATTATACC
Statistics
Matches: 379, Mismatches: 72, Indels: 64
0.74 0.14 0.12
Matches are distributed among these distances:
41 3 0.01
42 92 0.24
43 149 0.39
44 75 0.20
45 19 0.05
46 5 0.01
47 1 0.00
48 2 0.01
49 3 0.01
51 1 0.00
52 5 0.01
53 24 0.06
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (43 bp):
ATTTTTTATCTTTATAATTGAGGTCCCTAATTTTTTCAATCTT
Found at i:3556678 original size:44 final size:42
Alignment explanation
Indices: 3556542--3556732 Score: 149
Period size: 42 Copynumber: 4.5 Consensus size: 42
3556532 ATAGTCTCCA
* * * * *
3556542 TTTTTTCATCTTAATAATTAGGTCCCTAA-TTTTTTAAATCTTA
1 TTTTTT-ATCTTTATAATTGGGTCTCTAATTTTTTTCAAT-TTC
* *
3556585 TTTTTTATCTTTATAATTGAGGT-TCTAATTTTATTCAATCTC
1 TTTTTTATCTTTATAATTG-GGTCTCTAATTTTTTTCAATTTC
*
3556627 ATCTTTTATCTTTATAATTGGCGTCTCTAATTTTTTTTCAATTTC
1 -TTTTTTATCTTTATAATTGG-GTCTCTAA-TTTTTTTCAATTTC
* * *
3556672 TTTTTTACCTTTATAATTGAGG-CCCATAA-TTTTTT-AATCTC
1 TTTTTTATCTTTATAATTG-GGTCTC-TAATTTTTTTCAATTTC
* *
3556713 ACTTTTTAACTTTATAATTG
1 -TTTTTTATCTTTATAATTG
3556733 AGGCCCTTAA
Statistics
Matches: 123, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
41 5 0.04
42 40 0.33
43 39 0.32
44 26 0.21
45 13 0.11
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.55
Consensus pattern (42 bp):
TTTTTTATCTTTATAATTGGGTCTCTAATTTTTTTCAATTTC
Found at i:3556748 original size:87 final size:85
Alignment explanation
Indices: 3556568--3557067 Score: 352
Period size: 87 Copynumber: 5.7 Consensus size: 85
3556558 ATTAGGTCCC
* * * **
3556568 TAATTTTTTAAATCTTATTTTTTATCTTTATAATTGAGGTTCTAATTTTATTCAATCTCA-TCTT
1 TAATTTTTTCAATCTTCTTTTTTACCTTTATAATTGAGGCCCTAATTTT-TTCAATCTCACT-TT
* *
3556632 TTATCTTTATAATTG-G-CGTCT
64 TTAACTTTATAATTGAGAC-CCT
3556653 CTAATTTTTTTTCAAT-TTCTTTTTTACCTTTATAATTGAGGCCCATAATTTTTT-AATCTCACT
1 -TAA--TTTTTTCAATCTTCTTTTTTACCTTTATAATTGAGGCCC-TAATTTTTTCAATCTCACT
*
3556716 TTTTAACTTTATAATTGAGGCCCT
62 TTTTAACTTTATAATTGAGACCCT
* * ** *
3556740 TAAGTTTTTCAATCTTATTTTCGACCTTTATATTTGAGGCCTCTAATTTTTT-AATCTCACTTTT
1 TAATTTTTTCAATCTTCTTTTTTACCTTTATAATTGAGGCC-CTAATTTTTTCAATCTCACTTTT
* * * *
3556804 AAACTTTTTAATTAAGATCCT
65 TAACTTTATAATTGAGACCCT
* *
3556825 TAAATTTTTTCAATCTCACTTTCTACCTTTTCTACCTTCACAATTGAGGCCCCTATATTTTTTCA
1 T-AATTTTTTCAA--T--C-TTCT---TTTT-TACCTTTATAATTGAGG-CCCTA-ATTTTTTCA
* * * *
3556890 ATCTCAATTTCT-ACTTTTATAATTGAAACCCC
54 ATCTCACTTTTTAAC-TTTATAATTGAGACCCT
* * * * *
3556922 TAATTTTTT-AATCTCACTTTTTTAACTTTATTATTAAGGCGCTTAAATTTTTTCAATCTCACTT
1 TAATTTTTTCAATCT-TCTTTTTTACCTTTATAATTGAGGC-CCT-AATTTTTTCAATCTCACTT
* * * * *
3556986 TCTACCTTTATAATTAAAACCCC
63 TTTAACTTTATAATTGAGACCCT
* * * * * *
3557009 TAAGTTTTTCAAT-ATCAATTTCTACCTTTATAATTGATGCCCCAAGTTTTTTCAATCTC
1 TAATTTTTTCAATCTTC-TTTTTTACCTTTATAATTGAGGCCCTAA-TTTTTTCAATCTC
3557068 GATTATACCT
Statistics
Matches: 332, Mismatches: 53, Indels: 58
0.75 0.12 0.13
Matches are distributed among these distances:
84 9 0.03
85 63 0.19
86 56 0.17
87 105 0.32
88 27 0.08
90 2 0.01
91 6 0.02
93 1 0.00
94 3 0.01
95 18 0.05
96 19 0.06
97 23 0.07
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.50
Consensus pattern (85 bp):
TAATTTTTTCAATCTTCTTTTTTACCTTTATAATTGAGGCCCTAATTTTTTCAATCTCACTTTTT
AACTTTATAATTGAGACCCT
Found at i:3556784 original size:129 final size:129
Alignment explanation
Indices: 3556555--3556791 Score: 295
Period size: 129 Copynumber: 1.8 Consensus size: 129
3556545 TTTCATCTTA
* * * ** *
3556555 ATAATTAGGTCCCTAATTTTTTAAATCTTATTTTTTATCTTTATAATTGAGGTTCTAATTTTATT
1 ATAATTAGGTCCCTAATTTTTTAAATCTCACTTTTTAACTTTATAATTGAGGCCCTAAGTTTATT
* * *
3556620 CAATCTCATCTTTTATCTTTATAATTGGCGTCTCTAATTTTTTTTCAATTTCTTTTTTACCTTT
66 CAATCTCATCTTTGACCTTTATAATTGGCGCCTCTAATTTTTTTTCAATTTCTTTTTTACCTTT
3556684 ATAATTGAGG-CCCATAATTTTTT-AATCTCACTTTTTAACTTTATAATTGAGGCCCTTAAGTTT
1 ATAATT-AGGTCCC-TAATTTTTTAAATCTCACTTTTTAACTTTATAATTGAGGCCC-TAAGTTT
* *
3556747 -TTCAATCTTAT-TTTCGACCTTTATATTTGAG-GCCTCTAATTTTTT
63 ATTCAATCTCATCTTT-GACCTTTATAATTG-GCGCCTCTAATTTTTT
3556792 AATCTCACTT
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
128 3 0.03
129 70 0.76
130 19 0.21
ACGTcount: A:0.24, C:0.15, G:0.08, T:0.53
Consensus pattern (129 bp):
ATAATTAGGTCCCTAATTTTTTAAATCTCACTTTTTAACTTTATAATTGAGGCCCTAAGTTTATT
CAATCTCATCTTTGACCTTTATAATTGGCGCCTCTAATTTTTTTTCAATTTCTTTTTTACCTTT
Found at i:3556893 original size:139 final size:139
Alignment explanation
Indices: 3556728--3557067 Score: 382
Period size: 139 Copynumber: 2.5 Consensus size: 139
3556718 TTAACTTTAT
* * * * ** *
3556728 AATTGAGGCCCTTAAGTTTTTCAATCTTATTTTCGACCTTTATATTTGAGGCCTCTAATTTTTTA
1 AATTGAGGCCCCTAAGTTTTTCAATCTCAATTTCGACCTTTATAATTGAAACCCCTAATTTTTTA
*
3556793 ATCTCAC-TTTTAAACTTT-TTAATTAAGATC-CTTAAATTTTTTCAATCTCACTTTCTACCTTT
66 ATCTCACTTTTTAAACTTTATT-ATTAAG-GCGCTTAAATTTTTTCAATCTCACTTTCTACCTTT
3556855 TCTACCTTCAC
129 TCTACCTTCAC
* * *
3556866 AATTGAGGCCCCTATATTTTTTCAATCTCAATTTCTACTTTTATAATTGAAACCCCTAATTTTTT
1 AATTGAGGCCCCTA-AGTTTTTCAATCTCAATTTCGACCTTTATAATTGAAACCCCTAATTTTTT
*
3556931 AATCTCACTTTTTTAACTTTATTATTAAGGCGCTTAAATTTTTTCAATCTCACTTTCTACC-TTT
65 AATCTCACTTTTTAAACTTTATTATTAAGGCGCTTAAATTTTTTCAATCTCACTTTCTACCTTTT
* *
3556995 ATA-ATT-A-
130 CTACCTTCAC
* * **
3557002 AA---A--CCCCTAAGTTTTTCAATATCAATTTCTACCTTTATAATTGATGCCCC-AAGTTTTTT
1 AATTGAGGCCCCTAAGTTTTTCAATCTCAATTTCGACCTTTATAATTGAAACCCCTAA-TTTTTT
3557061 CAATCTC
65 -AATCTC
3557068 GATTATACCT
Statistics
Matches: 177, Mismatches: 19, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
129 2 0.01
130 42 0.24
131 12 0.07
133 1 0.01
136 2 0.01
137 1 0.01
138 15 0.08
139 55 0.31
140 45 0.25
141 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (139 bp):
AATTGAGGCCCCTAAGTTTTTCAATCTCAATTTCGACCTTTATAATTGAAACCCCTAATTTTTTA
ATCTCACTTTTTAAACTTTATTATTAAGGCGCTTAAATTTTTTCAATCTCACTTTCTACCTTTTC
TACCTTCAC
Found at i:3557077 original size:42 final size:43
Alignment explanation
Indices: 3556874--3557133 Score: 217
Period size: 43 Copynumber: 6.0 Consensus size: 43
3556864 ACAATTGAGG
* *
3556874 CCCCTATA-TTTTTTCAATCTCAATTTCTACTTTTATAATTGAAA
1 CCCCTA-AGTTTTTTCAATCTC-ATTTCTACCTTTATAATTAAAA
* * * **
3556918 CCCCTAA-TTTTTT-AATCTCACTTTTTTAACTTTATTATTAAGG
1 CCCCTAAGTTTTTTCAATCTCA--TTTCTACCTTTATAATTAAAA
* * *
3556961 CGCTTAAATTTTTTCAATCTCACTTTCTACCTTTATAATTAAAA
1 CCCCTAAGTTTTTTCAATCTCA-TTTCTACCTTTATAATTAAAA
* * **
3557005 CCCCTAAG-TTTTTCAATATCAATTTCTACCTTTATAATTGATG
1 CCCCTAAGTTTTTTCAATCTC-ATTTCTACCTTTATAATTAAAA
*
3557048 CCCC-AAGTTTTTTCAATCTCGA-TTATACCTTTATAATTAAAAA
1 CCCCTAAGTTTTTTCAATCTC-ATTTCTACCTTTATAATT-AAAA
** * *
3557091 AACCTAATTTTTTTTCAATCTCAATTTCTACATTTATAATTAA
1 CCCCTAA-GTTTTTTCAATCTC-ATTTCTACCTTTATAATTAA
3557134 GGGTTCTGAG
Statistics
Matches: 172, Mismatches: 34, Indels: 19
0.76 0.15 0.08
Matches are distributed among these distances:
41 1 0.01
42 24 0.14
43 74 0.43
44 36 0.21
45 23 0.13
46 14 0.08
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.46
Consensus pattern (43 bp):
CCCCTAAGTTTTTTCAATCTCATTTCTACCTTTATAATTAAAA
Found at i:3557127 original size:88 final size:85
Alignment explanation
Indices: 3556969--3557131 Score: 220
Period size: 88 Copynumber: 1.9 Consensus size: 85
3556959 GGCGCTTAAA
* **
3556969 TTTTTTCAATCTCACTTTCTACCTTTATAATTAAAACCCCTAAGTTTTTCAATATCAATTTCTAC
1 TTTTTTCAATCTCAC-TTATACCTTTATAATTAAAAAACCTAAGTTTTTCAATATCAATTTCTAC
*
3557034 CTTTATAATTGATGCCCCAAG
65 ATTTATAATTGATGCCCCAAG
* *
3557055 TTTTTTCAATCTCGA-TTATACCTTTATAATTAAAAAAACCTAATTTTTTTTCAATCTCAATTTC
1 TTTTTTCAATCTC-ACTTATACCTTTATAATT-AAAAAACCTAA--GTTTTTCAATATCAATTTC
3557119 TACATTTATAATT
62 TACATTTATAATT
3557132 AAGGGTTCTG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
85 15 0.22
86 22 0.33
87 1 0.01
88 29 0.43
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.46
Consensus pattern (85 bp):
TTTTTTCAATCTCACTTATACCTTTATAATTAAAAAACCTAAGTTTTTCAATATCAATTTCTACA
TTTATAATTGATGCCCCAAG
Found at i:3559253 original size:43 final size:43
Alignment explanation
Indices: 3559190--3559271 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
3559180 TACATGTGCT
*
3559190 GATTCCAACATTAAGATATCAAATA-TATTTTTTAAAGATACGAA
1 GATTCAAACATTAAGATATCAAATAGTA--TTTTAAAGATACGAA
3559234 GATTCAAACA-TAAGATATCAAATAGTATTTTAAAGATA
1 GATTCAAACATTAAGATATCAAATAGTATTTTAAAGATA
3559272 AACTTAAGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 11 0.31
43 14 0.39
44 11 0.31
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (43 bp):
GATTCAAACATTAAGATATCAAATAGTATTTTAAAGATACGAA
Found at i:3559624 original size:25 final size:24
Alignment explanation
Indices: 3559553--3559644 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 24
3559543 AGGACCAATT
3559553 TTATAGTATATTTATTATTGTAT-TA
1 TTATA-TATATTTATTATT-TATATA
3559578 -TAGTATCATA-TT-TTATGTTATATA
1 TTA-TAT-ATATTTATTAT-TTATATA
*
3559602 TTATATATATTTATTATATTATAAA
1 TTATATATATTTATTAT-TTATATA
*
3559627 TTATATAT-TTTTTTATTT
1 TTATATATATTTATTATTT
3559645 TTTTTATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
23 12 0.21
24 20 0.35
25 25 0.44
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (24 bp):
TTATATATATTTATTATTTATATA
Found at i:3561485 original size:17 final size:18
Alignment explanation
Indices: 3561455--3561488 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3561445 TCATTACAAA
3561455 TAAAATTAAGATATATTT
1 TAAAATTAAGATATATTT
*
3561473 TAAATTTAA-ATATATT
1 TAAAATTAAGATATATT
3561489 AAATTAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TAAAATTAAGATATATTT
Found at i:3561751 original size:20 final size:20
Alignment explanation
Indices: 3561723--3561760 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3561713 TAGTTGAAAA
3561723 TCGCATTGCGATTTTCCATT
1 TCGCATTGCGATTTTCCATT
*
3561743 TCGCGTTGCGATTTTCCA
1 TCGCATTGCGATTTTCCA
3561761 AATTCGTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTTCCATT
Found at i:3561862 original size:6 final size:6
Alignment explanation
Indices: 3561852--3561967 Score: 193
Period size: 6 Copynumber: 19.8 Consensus size: 6
3561842 GACACGTATT
* *
3561852 ACCACT ACCACT ACCACG ACCACG ACCACG ACCACG ACCACG A-C-C-
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3561897 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3561945 ACCACG ACCACG ACCACG ACCAC
1 ACCACG ACCACG ACCACG ACCAC
3561968 ACGACGAGAC
Statistics
Matches: 106, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
3 1 0.01
4 2 0.02
5 2 0.02
6 101 0.95
ACGTcount: A:0.34, C:0.51, G:0.14, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:3562078 original size:6 final size:6
Alignment explanation
Indices: 3562067--3562123 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
3562057 CTTAAATACC
3562067 CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA
1 CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA CGACCA
3562115 CGACCA CGA
1 CGACCA CGA
3562124 GACGGGACGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.49, G:0.18, T:0.00
Consensus pattern (6 bp):
CGACCA
Found at i:3562121 original size:154 final size:152
Alignment explanation
Indices: 3561919--3562218 Score: 545
Period size: 152 Copynumber: 2.0 Consensus size: 152
3561909 ACCACGACCA
*
3561919 CGACCACGACCACGACCACGACCACGACCACGACCACGACCACGACCAC-ACGACGAGACG-GAC
1 CGACCACGACCACGACCACGACCACGACCACGACCACGACCACGACCACGACCACGAGACGAGAC
*
3561982 GGAC-GCGACGGCGGCGTCGGCGCGCG-GAGTCCCCCTTGTTCTCTATCACTCTACAAGGAAGTG
66 GGACGGCGACGGCGGCGGCGGCGCGCGAGAGTCCCCCTTGTTCTCTATCACTCTACAAGGAAGTG
3562045 GGAAAGCCAAGCCTTAAATACC
131 GGAAAGCCAAGCCTTAAATACC
*
3562067 CGACCACGACCACGACCACGACCACGACCACGACCACGACCACGACCACGACCACGAGACGGGAC
1 CGACCACGACCACGACCACGACCACGACCACGACCACGACCACGACCACGACCACGAGACGAGAC
3562132 GGACGGCGACGGCGGCGGCGGCGCGCGAGAGTCCCCCTTGTTCTCTATCACTCTACAAGGAAGTG
66 GGACGGCGACGGCGGCGGCGGCGCGCGAGAGTCCCCCTTGTTCTCTATCACTCTACAAGGAAGTG
3562197 GGAAAGCCAAGCCTTAAATACC
131 GGAAAGCCAAGCCTTAAATACC
3562219 ATTCCCAATA
Statistics
Matches: 146, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
148 49 0.34
149 10 0.07
150 7 0.05
151 21 0.14
152 59 0.40
ACGTcount: A:0.27, C:0.37, G:0.26, T:0.10
Consensus pattern (152 bp):
CGACCACGACCACGACCACGACCACGACCACGACCACGACCACGACCACGACCACGAGACGAGAC
GGACGGCGACGGCGGCGGCGGCGCGCGAGAGTCCCCCTTGTTCTCTATCACTCTACAAGGAAGTG
GGAAAGCCAAGCCTTAAATACC
Found at i:3567165 original size:14 final size:13
Alignment explanation
Indices: 3567135--3567185 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
3567125 TAAAACATAT
*
3567135 TAAATATTAAATAA
1 TAAATA-TAATTAA
3567149 TAAATATAATTATA
1 TAAATATAATTA-A
*
3567163 TAACTATAATTAA
1 TAAATATAATTAA
*
3567176 AAAATA-AATT
1 TAAATATAATT
3567186 TGGGGCTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 4 0.12
13 10 0.31
14 18 0.56
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAATATAATTAA
Found at i:3577456 original size:75 final size:76
Alignment explanation
Indices: 3577316--3577466 Score: 184
Period size: 75 Copynumber: 2.0 Consensus size: 76
3577306 GGGTGAGAAC
* * *
3577316 AAATAAAATTTTAGGGTAAACACCATCAATAAAATAAAGAATTAAGTGAAGGAAAATTTAGTTTC
1 AAATAAAATTTCAAGGTAAACACCATCAATAAAATAAAGAATTAAGTGAAGGAAAATTTAATTTC
3577381 ATG-GTAGGCAT
66 A-GAGTAGGCAT
* * * *
3577392 AAATAAAA-TTCAAGGTGAACACTATCAATAAAATAAGGAATTAA-TCGGA-GAAAATTTAAATT
1 AAATAAAATTTCAAGGTAAACACCATCAATAAAATAAAGAATTAAGT-GAAGGAAAATTT-AATT
3577454 TCAGAGTAGGCAT
64 TCAGAGTAGGCAT
3577467 GTATCATACG
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
74 10 0.15
75 47 0.72
76 8 0.12
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (76 bp):
AAATAAAATTTCAAGGTAAACACCATCAATAAAATAAAGAATTAAGTGAAGGAAAATTTAATTTC
AGAGTAGGCAT
Found at i:3586607 original size:110 final size:111
Alignment explanation
Indices: 3586484--3586684 Score: 280
Period size: 112 Copynumber: 1.8 Consensus size: 111
3586474 TTGGGGCAAC
* * * * * *
3586484 AATAGTGATG-TTTTTTGAAAATATGTCGCAATAGGTCCATCTATAGTGGTGTTTATTGGAAAAA
1 AATAGTGACGTTTTTTTCAAAAAATGTCGCAATAGATCCATCTATAGTGGCGTTTATTAGAAAAA
* *
3586548 CGCTACTATATATATA-TATTTTTGGCATTTTTTAGGGCTGCACAAT
66 CACCACTATATATATACT-TTTTTGGCATTTTTTAGGGCTGCACAAT
* *
3586594 AATAGTGACGTTTTTTTTCAAAAAATGTTGCAATAGATCCATCTATAGTGGCGTTTATTAGATAA
1 AATAGTGACG-TTTTTTTCAAAAAATGTCGCAATAGATCCATCTATAGTGGCGTTTATTAGAAAA
3586659 ACACCACTATATATATACTTTTTTGG
65 ACACCACTATATATATACTTTTTTGG
3586685 GATCTATTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
110 9 0.12
112 68 0.87
113 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (111 bp):
AATAGTGACGTTTTTTTCAAAAAATGTCGCAATAGATCCATCTATAGTGGCGTTTATTAGAAAAA
CACCACTATATATATACTTTTTTGGCATTTTTTAGGGCTGCACAAT
Found at i:3588008 original size:33 final size:33
Alignment explanation
Indices: 3587957--3588020 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
3587947 AACTTAATTT
* *
3587957 AAAAATATTTATTATTATTTTAATTTAAAAAAA
1 AAAAATATTTATTATTATTGTAACTTAAAAAAA
*
3587990 AAAAAT-TTATATTCTTATTGTAACTTAAAAA
1 AAAAATATT-TATTATTATTGTAACTTAAAAA
3588021 TACATTCCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (33 bp):
AAAAATATTTATTATTATTGTAACTTAAAAAAA
Found at i:3588115 original size:27 final size:28
Alignment explanation
Indices: 3588072--3588144 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 28
3588062 AATTTAAAAA
*
3588072 TAAAACATATTTCATTATTAACTTAATT
1 TAAAACATATTTTATTATTAACTTAATT
**
3588100 TAAAA-ATATTTTATTATTATTTTAATT
1 TAAAACATATTTTATTATTAACTTAATT
* *
3588127 TAAAATATATATT-TTATT
1 TAAAACATATTTTATTATT
3588145 CCTATCTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 29 0.73
28 11 0.28
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (28 bp):
TAAAACATATTTTATTATTAACTTAATT
Found at i:3588169 original size:31 final size:30
Alignment explanation
Indices: 3588105--3588197 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
3588095 TAATTTAAAA
** * *
3588105 ATATTTTATTATTATTTTAATTTAAAATAT
1 ATATTTTATTCCTATCTTAACTTAAAATAT
*
3588135 ATATTTTATTCCTATCTTAACTTAAGTATAT
1 ATATTTTATTCCTATCTTAACTTAA-AATAT
* * * *
3588166 ATATTTTATTCTTGTTTTAAATTAAAATAT
1 ATATTTTATTCCTATCTTAACTTAAAATAT
3588196 AT
1 AT
3588198 TTTATAAGTT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 27 0.52
31 25 0.48
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (30 bp):
ATATTTTATTCCTATCTTAACTTAAAATAT
Found at i:3589041 original size:39 final size:39
Alignment explanation
Indices: 3588998--3589089 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
3588988 CAGGTCAATC
* *
3588998 AGGAAGACTCCAGGAGTGCAC-GACGTCTTCAGAAAAAAT
1 AGGAAGACTCCAAGAGTAC-CTGACGTCTTCAGAAAAAAT
** * *
3589037 AGGAAGACTCCAAGCTTACCTGGCGTCTTCAGGAAAAAT
1 AGGAAGACTCCAAGAGTACCTGACGTCTTCAGAAAAAAT
*
3589076 AGGAAGACTTCAAG
1 AGGAAGACTCCAAG
3589090 CTTATATGGC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 1 0.02
39 44 0.98
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.17
Consensus pattern (39 bp):
AGGAAGACTCCAAGAGTACCTGACGTCTTCAGAAAAAAT
Found at i:3589090 original size:39 final size:39
Alignment explanation
Indices: 3589021--3589107 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
3589011 GAGTGCACGA
*
3589021 CGTCTTCAGAAAAAATAGGAAGACTCCAAGCTTACCTGG
1 CGTCTTCAGAAAAAATAGGAAGACTCCAAGCTTACATGG
* * *
3589060 CGTCTTCAGGAAAAATAGGAAGACTTCAAGCTTATATGG
1 CGTCTTCAGAAAAAATAGGAAGACTCCAAGCTTACATGG
3589099 CGTCTTCAG
1 CGTCTTCAG
3589108 TCTAGGGTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (39 bp):
CGTCTTCAGAAAAAATAGGAAGACTCCAAGCTTACATGG
Found at i:3589785 original size:22 final size:24
Alignment explanation
Indices: 3589760--3589814 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
3589750 TATAAATGTT
*
3589760 AAAAAATA-TAATTATAATGACAA
1 AAAAAATATTAATTATAATAACAA
* *
3589783 AAAATAATATTTATTATAATAACGA
1 AAAA-AATATTAATTATAATAACAA
3589808 AAAAAAT
1 AAAAAAT
3589815 GACACCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 7 0.26
25 16 0.59
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAAAATATTAATTATAATAACAA
Found at i:3590300 original size:24 final size:23
Alignment explanation
Indices: 3590268--3590313 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
3590258 TTTTGAAACT
*
3590268 TTAATAATATTTATTATAATTAAA
1 TTAATAATATTT-TAATAATTAAA
3590292 TTAATAATATTTTAATAATTAA
1 TTAATAATATTTTAATAATTAA
3590314 TTTATTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATAATATTTTAATAATTAAA
Found at i:3590466 original size:13 final size:13
Alignment explanation
Indices: 3590448--3590473 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3590438 TACAATGGAC
3590448 ATATTATGGAAAA
1 ATATTATGGAAAA
3590461 ATATTATGGAAAA
1 ATATTATGGAAAA
3590474 TGAGGTCGGA
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:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
ATATTATGGAAAA
Found at i:3593238 original size:27 final size:27
Alignment explanation
Indices: 3593206--3593267 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
3593196 AATGAAAATG
3593206 ATTAATATCAATAGTTGACTTAATGTA
1 ATTAATATCAATAGTTGACTTAATGTA
*
3593233 ATTAATATCAATAGTTGACTTAATGTG
1 ATTAATATCAATAGTTGACTTAATGTA
*
3593260 ATGAATAT
1 ATTAATAT
3593268 TAATCTTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40
Consensus pattern (27 bp):
ATTAATATCAATAGTTGACTTAATGTA
Found at i:3595841 original size:323 final size:313
Alignment explanation
Indices: 3595375--3596070 Score: 939
Period size: 322 Copynumber: 2.2 Consensus size: 313
3595365 AAAATATGTT
* * *
3595375 AAATCGAAATAAATAGTCTAATTAATTTATATTTACAATAAAAAACAAATAATAAAATAATAAAA
1 AAATCAAAATAAATAGTCTAATTAATTTATATTTACAAT-AAAAAC--A-AATAAAACAACAAAA
* * *
3595440 TTTAAACTAAACTTACCAAACCACTCAAATACGATTTAATCTGTAAAATCAAAATAAATAGTCCA
62 TTTAAAATAAACTTACCAAACCACTCAAATACGATTTAATCTCTAAAATAAAAATAAATAGTCCA
* *
3595505 ACAATGTATATTACTCAATAAAAAATTAAAAATATAATTTAAACTAAACTTACGAAACTACTCAA
127 ACAATGTATATTACTCAATAAAAAAATAAAAA-ATAATTTAAACTAAACTTACCAAACTACTCAA
* *
3595570 ATACAACTTAATATGTAAAATCAAAATAAATAGTTTAATAATTATAATTTAAATTAAAAACAAAA
191 ATACAACTTAATATGTAAAATCAAAATAAATAGTCTAATAATTATAATTTAAAAT-AAAA-AAAA
* * *
3595635 AAATATTGAAAATTACAAGAAAATGTAAATTAAACTTACCAAACCACTCGAATACAATTTAATTT
254 AAA-ATT----A-CAC-A-AAAATGTAAATTAAACTTACCAAACCACGCGAATACAATTTAATCT
*
3595700 GTA
311 ATA
** *
3595703 AAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAAC-CCT-AAACAACAAATTTTA
1 AAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAACAAATAAAACAACAAAATTT-
* * * * *
3595766 AAAATAAACTTACCAAACTACTTAAATACGATTTAATCTCTAAAATAAAAAT-AGTAAGTCTAAT
65 AAAATAAACTTACCAAACCACTCAAATACGATTTAATCTCTAAAATAAAAATAAAT-AGTCCAAC
* *
3595830 AATTTATATTACTCAATAAAAAAATAAAAAATAATTTAAATTAAACTTACCAAACTACTCAAATA
129 AATGTATATTACTCAATAAAAAAATAAAAAATAATTTAAACTAAACTTACCAAACTACTCAAATA
* *
3595895 CAACTTAATATGTAAAATCAAAATAAATAGTCTAATAATTATTATTTAAAATAAAAATAAAAAAT
194 CAACTTAATATGTAAAATCAAAATAAATAGTCTAATAATTATAATTTAAAATAAAAAAAAAAAAT
* *
3595960 TACACAACAATTTAAATTAAACTTACCAAACCACGCGAATACAATTTAATCTATA
259 TACACAAAAATGTAAATTAAACTTACCAAACCACGCGAATACAATTTAATCTATA
* * *
3596015 AAATCAAAATAAATAATCTAATTAATTTATATTTAAAATAAAAACAAAAAAAACAA
1 AAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAACAAATAAAACAA
3596071 AACAATAAAA
Statistics
Matches: 331, Mismatches: 33, Indels: 22
0.86 0.09 0.06
Matches are distributed among these distances:
312 87 0.26
313 1 0.00
314 8 0.02
315 1 0.00
319 3 0.01
320 6 0.02
321 4 0.01
322 95 0.29
323 82 0.25
327 6 0.02
328 38 0.11
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (313 bp):
AAATCAAAATAAATAGTCTAATTAATTTATATTTACAATAAAAACAAATAAAACAACAAAATTTA
AAATAAACTTACCAAACCACTCAAATACGATTTAATCTCTAAAATAAAAATAAATAGTCCAACAA
TGTATATTACTCAATAAAAAAATAAAAAATAATTTAAACTAAACTTACCAAACTACTCAAATACA
ACTTAATATGTAAAATCAAAATAAATAGTCTAATAATTATAATTTAAAATAAAAAAAAAAAATTA
CACAAAAATGTAAATTAAACTTACCAAACCACGCGAATACAATTTAATCTATA
Found at i:3595903 original size:101 final size:101
Alignment explanation
Indices: 3595422--3596067 Score: 351
Period size: 102 Copynumber: 6.2 Consensus size: 101
3595412 ATAAAAAACA
* * * *
3595422 AATAATAAAAT-AATAAAATTTAAACTAAACTTACCAAACCACTCAAATACGATTTAATCTGTAA
1 AATAAAAAAATAAAAAAAATTTAAATTAAACTTACCAAACCACTCAAATACAATTTAATCTGTAA
* * *
3595486 AATCAAAATAAATAGTCCAA-CAATGTATATTACT-C
66 AATCAAAATAAATAGTCTAATTAATTTATATTA-TAC
* * * * * *
3595521 AATAAAAAATTAAAAATATAATTTAAACTAAACTTACGAAACTACTCAAATACAACTTAATATGT
1 AATAAAAAAATAAAAA-A-AATTTAAATTAAACTTACCAAACCACTCAAATACAATTTAATCTGT
*
3595586 AAAATCAAAATAAATAGTTTAA-TAA-TTATAATT-TA-
64 AAAATCAAAATAAATAGTCTAATTAATTTAT-ATTATAC
* * * * ** * *
3595621 AATTAAAAACAAAAAAATATTGAAAATTACAA-GAAAATGTAAATTAAACTTAC-CAAACCACTC
1 AA-TAAAAA-AATAAAA-A---AAATTTA-AATTAAACT-T--ACCAAAC-CACTCAAA-TA--C
** ** *
3595684 GAATACAAT-T-TAATTTGTAAAATCAAAATAAATAGTCTAATTAATTTATATT-TAC
52 -AATTTAATCTGTAA--AAT-CAA----AATAAATAGTCTAATTAATTTATATTATAC
** * * * *
3595739 AATAAAAACCCTAAACAACAAATTTTAAAAATAAACTTACCAAACTACTTAAATACGATTTAATC
1 AATAAAAA-AATAAA-AA-AAA-TTT-AAATTAAACTTACCAAACCACTCAAATACAATTTAATC
* * *
3595804 TCTAAAATAAAAAT-AGTAAGTCTAA-TAATTTATATTACT-C
61 TGTAAAATCAAAATAAAT-AGTCTAATTAATTTATATTA-TAC
* * *
3595844 AATAAAAAAATAAAAAATAATTTAAATTAAACTTACCAAACTACTCAAATACAACTTAATATGTA
1 AATAAAAAAATAAAAAA-AATTTAAATTAAACTTACCAAACCACTCAAATACAATTTAATCTGTA
*
3595909 AAATCAAAATAAATAGTCTAA-TAA-TTATTATT-TAA
65 AAATCAAAATAAATAGTCTAATTAATTTA-TATTATAC
* * *
3595944 AATAAAAATAAAAAATTACACAACAATTTAAATTAAACTTACCAAACCACGCGAATACAATTTAA
1 AAT-AAAA-AAATAA--A-A-AA-AATTTAAATTAAACTTACCAAACCACTCAAATACAATTTAA
* * *
3596009 TCTATAAAATCAAAATAAATAATCTAATTAATTTATATT-TAA
59 TCTGTAAAATCAAAATAAATAGTCTAATTAATTTATATTATAC
*
3596051 AATAAAAACA-AAAAAAA
1 AATAAAAAAATAAAAAAA
3596068 CAAAACAATA
Statistics
Matches: 430, Mismatches: 66, Indels: 102
0.72 0.11 0.17
Matches are distributed among these distances:
99 11 0.03
100 14 0.03
101 74 0.17
102 83 0.19
103 5 0.01
104 29 0.07
105 26 0.06
106 68 0.16
107 22 0.05
108 7 0.02
109 6 0.01
110 8 0.02
111 8 0.02
112 5 0.01
113 4 0.01
114 8 0.02
115 3 0.01
116 18 0.04
117 24 0.06
118 7 0.02
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (101 bp):
AATAAAAAAATAAAAAAAATTTAAATTAAACTTACCAAACCACTCAAATACAATTTAATCTGTAA
AATCAAAATAAATAGTCTAATTAATTTATATTATAC
Found at i:3596839 original size:42 final size:42
Alignment explanation
Indices: 3596792--3596898 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
3596782 AAAGTTAATG
3596792 GTTAGTGTTGGAAGAAAGATTAATGTTTATGCTGATGTTTTT
1 GTTAGTGTTGGAAGAAAGATTAATGTTTATGCTGATGTTTTT
3596834 GTTAGTGTTGGAAGAAAGATTAATGTTTATGCTGATGTTTTT
1 GTTAGTGTTGGAAGAAAGATTAATGTTTATGCTGATGTTTTT
3596876 GTTAGTGTTGGAAGCCAAAGATT
1 GTTAGTGTTGGAAG--AAAGATT
3596899 CTGCTTTTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
42 56 0.89
44 7 0.11
ACGTcount: A:0.27, C:0.04, G:0.27, T:0.42
Consensus pattern (42 bp):
GTTAGTGTTGGAAGAAAGATTAATGTTTATGCTGATGTTTTT
Found at i:3601060 original size:38 final size:38
Alignment explanation
Indices: 3601009--3601083 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
3600999 ATATTAGATT
* *
3601009 TTTTTTTTTATTAATTTGGATAGACACAAGGCAATATC
1 TTTTTTTTTATTAATCTGGATAGACACAAGACAATATC
*
3601047 TTTTTTTTTATTAATCTGGGTAGACACAAGACAATAT
1 TTTTTTTTTATTAATCTGGATAGACACAAGACAATAT
3601084 ATGTTCAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (38 bp):
TTTTTTTTTATTAATCTGGATAGACACAAGACAATATC
Found at i:3603031 original size:31 final size:30
Alignment explanation
Indices: 3602974--3603043 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
3602964 TTTTTAAACA
* * *
3602974 TTAAATAAATATTAATTTACTTTTTAAATT
1 TTAAATAAACATCAATTTACTCTTTAAATT
*
3603004 TTAAATAGAACATCAATTTAGTCTTTAAATT
1 TTAAATA-AACATCAATTTACTCTTTAAATT
*
3603035 TCAAATAAA
1 TTAAATAAA
3603044 ATATCATATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 9 0.26
31 25 0.74
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (30 bp):
TTAAATAAACATCAATTTACTCTTTAAATT
Found at i:3612487 original size:15 final size:15
Alignment explanation
Indices: 3612467--3612502 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
3612457 GAGGACTCTT
3612467 TAAGGAATCAATTTC
1 TAAGGAATCAATTTC
3612482 TAAGGAATCAATTTC
1 TAAGGAATCAATTTC
3612497 TAAGGA
1 TAAGGA
3612503 TTTATGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (15 bp):
TAAGGAATCAATTTC
Found at i:3622907 original size:30 final size:30
Alignment explanation
Indices: 3622836--3622895 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3622826 ACAGTTTAAG
3622836 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
3622866 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
3622896 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:3623106 original size:21 final size:20
Alignment explanation
Indices: 3623076--3623142 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 20
3623066 ATGCAATTAG
*
3623076 TGCATCGATGCATCCTTGCCA
1 TGCATTGATGCATCCTT-CCA
3623097 TGCATTGATGCATCCTTTCCA
1 TGCATTGATGCATCC-TTCCA
*
3623118 TGC-TTCCATGCATCCTTCCA
1 TGCATT-GATGCATCCTTCCA
3623138 TGCAT
1 TGCAT
3623143 CAAGGCTGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.24
21 29 0.71
22 2 0.05
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.34
Consensus pattern (20 bp):
TGCATTGATGCATCCTTCCA
Found at i:3626439 original size:30 final size:30
Alignment explanation
Indices: 3626368--3626427 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3626358 ACAATTTAAC
3626368 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
3626398 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
3626428 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:3626535 original size:21 final size:21
Alignment explanation
Indices: 3626509--3626587 Score: 149
Period size: 21 Copynumber: 3.8 Consensus size: 21
3626499 AGGGTGTCAA
3626509 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
3626530 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
3626551 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCATCCCTGC
3626572 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
3626588 TGCACTAATA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:3626691 original size:20 final size:21
Alignment explanation
Indices: 3626650--3626696 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
3626640 ATGCAATTAG
3626650 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
3626671 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
3626691 TGCATC
1 TGCATC
3626697 CTGCCATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.19, C:0.34, G:0.19, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:3626695 original size:12 final size:12
Alignment explanation
Indices: 3626657--3626709 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
3626647 TAGTGCATCG
3626657 ATGCATCCTTGCC
1 ATGCATCC-TGCC
3626670 ATGCAT-C-G--
1 ATGCATCCTGCC
3626678 ATGCATCCTGCC
1 ATGCATCCTGCC
3626690 ATGCATCCTGCC
1 ATGCATCCTGCC
3626702 ATGCATCC
1 ATGCATCC
3626710 ATGCATCAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 6 0.17
9 1 0.03
10 2 0.06
12 21 0.58
13 6 0.17
ACGTcount: A:0.19, C:0.38, G:0.17, T:0.26
Consensus pattern (12 bp):
ATGCATCCTGCC
Found at i:3634742 original size:18 final size:18
Alignment explanation
Indices: 3634719--3634767 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
3634709 TAACACATAA
3634719 GTCCCGAAGGACCACTAT
1 GTCCCGAAGGACCACTAT
*
3634737 GTCCCGAATGACCACTAT
1 GTCCCGAAGGACCACTAT
3634755 GTCCCGAAGGACC
1 GTCCCGAAGGACC
3634768 GCGTAGACCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.35, G:0.22, T:0.16
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:3642678 original size:22 final size:22
Alignment explanation
Indices: 3642652--3642694 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3642642 TAATAAATTA
*
3642652 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATACATAT
3642674 TTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATACATA
3642695 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:3642703 original size:22 final size:22
Alignment explanation
Indices: 3642654--3642702 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3642644 ATAAATTATT
* **
3642654 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATACATATAA
3642676 TAAAATAAATCAATACATACTAA
1 TAAAATAAATCAATACATA-TAA
3642699 TAAA
1 TAAA
3642703 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATACATATAA
Found at i:3642741 original size:80 final size:80
Alignment explanation
Indices: 3642657--3642972 Score: 454
Period size: 80 Copynumber: 3.9 Consensus size: 80
3642647 AATTATTTAA
* *
3642657 AATAAATCAATTCATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
3642722 CCATACAACTACAAT
66 CCATACAACTACAAT
*
3642737 AATAAATCAATCCATATTTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *** *
3642802 TCATA-TTTTAAAAT
66 CCATACAACTACAAT
* * *
3642816 AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
1 -AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
*
3642881 AATCAATCCATGCAACTACAAT
59 AATCAATCCATACAACTACAAT
3642903 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
3642968 CCATA
66 CCATA
3642973 TTTTAAAATA
Statistics
Matches: 206, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
79 5 0.02
80 127 0.62
81 2 0.01
82 3 0.01
84 3 0.01
85 2 0.01
86 59 0.29
87 5 0.02
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:3642783 original size:22 final size:22
Alignment explanation
Indices: 3642704--3642782 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 22
3642694 ACTAATAAAT
3642704 TATT-TAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
* *
3642725 TACAACTACAATAATAAATCAATCCA
1 T---ATTATAA-AATAAATCAATCCA
*
3642751 TATTTTAAAATAAATCAATCCA
1 TATTATAAAATAAATCAATCCA
3642773 TATTAATAAA
1 TATT-ATAAA
3642783 TTATTTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
21 1 0.02
22 18 0.39
23 8 0.17
24 2 0.04
25 2 0.04
26 15 0.33
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (22 bp):
TATTATAAAATAAATCAATCCA
Found at i:3642793 original size:32 final size:31
Alignment explanation
Indices: 3642754--3643151 Score: 253
Period size: 32 Copynumber: 14.4 Consensus size: 31
3642744 CAATCCATAT
*
3642754 TTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
3642786 TTTAAAATAAATCAAT---T-C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
3642808 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
3642840 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
3642872 TTTAAAATAAATCAATCCATGC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
3642902 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
3642920 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
3642952 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
3642974 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
3643006 TTTAAAATAAATCAATTCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
3643036 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
3643054 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
3643086 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
3643108 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
3643140 TTTTAAATAAAT
1 TTTAAAATAAAT
3643152 TATTTTAAAA
Statistics
Matches: 294, Mismatches: 10, Indels: 124
0.69 0.02 0.29
Matches are distributed among these distances:
20 2 0.01
22 75 0.26
23 7 0.02
24 6 0.02
25 3 0.01
26 38 0.13
28 10 0.03
29 1 0.00
30 5 0.02
31 8 0.03
32 139 0.47
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:3642801 original size:54 final size:54
Alignment explanation
Indices: 3642737--3643026 Score: 387
Period size: 54 Copynumber: 5.3 Consensus size: 54
3642727 CAACTACAAT
*
3642737 AATAAATCAATCCATATTTTAAAATAAATCAATCCATATTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
3642791 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
3642845 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATGC-AACTACA--A--T--
1 AATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAA
3642903 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
3642957 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
3643011 AATAAATCAATTCATA
1 AATAAATCAATCCATA
3643027 CAACTACAAT
Statistics
Matches: 210, Mismatches: 8, Indels: 36
0.83 0.03 0.14
Matches are distributed among these distances:
48 24 0.11
49 3 0.01
50 2 0.01
52 3 0.01
54 133 0.63
57 1 0.00
58 12 0.06
60 3 0.01
62 2 0.01
63 3 0.01
64 24 0.11
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:3642812 original size:22 final size:22
Alignment explanation
Indices: 3642786--3642828 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3642776 TAATAAATTA
*
3642786 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
3642808 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
3642829 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3642834 original size:18 final size:18
Alignment explanation
Indices: 3642813--3642869 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
3642803 CATATTTTAA
3642813 AATAAATCAATCCATACT
1 AATAAATCAATCCATACT
* * *
3642831 AATAAAT-TAT--TTA-A
1 AATAAATCAATCCATACT
3642845 AATAAATCAATCCATACT
1 AATAAATCAATCCATACT
3642863 AATAAAT
1 AATAAAT
3642870 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 7 0.24
15 4 0.14
17 4 0.14
18 14 0.48
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATCAATCCATACT
Found at i:3642837 original size:22 final size:22
Alignment explanation
Indices: 3642788--3642836 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3642778 ATAAATTATT
* **
3642788 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
3642810 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
3642833 TAAA
1 TAAA
3642837 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:3642924 original size:134 final size:134
Alignment explanation
Indices: 3642652--3643151 Score: 476
Period size: 134 Copynumber: 3.7 Consensus size: 134
3642642 TAATAAATTA
*
3642652 TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATACATACTAATAAATTA-TTTAAAATAA
1 TTTAAAATAAATCAATTCATATATTAAAATAAATCAATACATACTAATAAATTATTTTAAAATAA
* ** * *
3642716 ATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCAT-ATTTTAAAATAAATCAATCCA
66 ATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATCA-ACTACAAT-AATAAAT-CA
**
3642773 TATTAATAAATT
127 -ATCCAT--A-T
* *
3642785 ATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTAAAATA
1 -TTTAAAATAAATCAATTCATATATTAAAATAAATCAATACATACTAATAAATTATTTTAAAATA
3642849 AATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATGCAACTACAATAATAAATCAAT
65 AATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT-CAACTACAATAATAAATCAAT
3642914 CCATAT
129 CCATAT
* * * ** * * **
3642920 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCA-TATTTTAAAAT
1 TTTAAAATAAATCAATTCATA-TATTAAAATAAAT-CAATACATACTAATAAATTATTTTAAAAT
*
3642982 AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAA
64 AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT-CAACTACAATAATAAATCAA
3643047 TCCATAT
128 TCCATAT
* * ** * * **
3643054 TTTAAAATAAATCAA-TCTATACTAATAAATTATTTAAAATAAAT-C-AATCCA-TATTTTAAAA
1 TTTAAAATAAATCAATTC-ATA-TATTAAAATAAAT-CAATACATACTAATAAATTATTTTAAAA
*
3643115 TAAATCAATCCATACTAATAAATTATTTTAAATAAAT
63 TAAATCAATCCATACTAATAAATTATTTAAAATAAAT
3643152 TATTTTAAAA
Statistics
Matches: 330, Mismatches: 23, Indels: 26
0.87 0.06 0.07
Matches are distributed among these distances:
133 3 0.01
134 274 0.83
135 12 0.04
136 7 0.02
138 5 0.02
139 2 0.01
140 21 0.06
141 5 0.02
142 1 0.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (134 bp):
TTTAAAATAAATCAATTCATATATTAAAATAAATCAATACATACTAATAAATTATTTTAAAATAA
ATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATCAACTACAATAATAAATCAATCC
ATAT
Found at i:3642948 original size:166 final size:166
Alignment explanation
Indices: 3642674--3643027 Score: 663
Period size: 166 Copynumber: 2.1 Consensus size: 166
3642664 CAATTCATAT
3642674 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
* *
3642739 TAAATCAATCCATATTTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAATTC
66 TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
3642804 ATATTTTAAAATAAATCAATCCATACTAATAAATTA
131 ATATTTTAAAATAAATCAATCCATACTAATAAATTA
* *
3642840 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATGCAACTACAATAA
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
3642905 TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
66 TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
3642970 ATATTTTAAAATAAATCAATCCATACTAATAAATTA
131 ATATTTTAAAATAAATCAATCCATACTAATAAATTA
*
3643006 TTTAAAATAAATCAATTCATAC
1 TTTAAAATAAATCAATACATAC
3643028 AACTACAATA
Statistics
Matches: 183, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
166 183 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (166 bp):
TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAA
TAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC
ATATTTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:3642949 original size:22 final size:22
Alignment explanation
Indices: 3642876--3642949 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
3642866 AAATTATTTA
3642876 AAATAAATCAATCCATGCAACTACA-
1 AAATAAATCAATCCAT---ACTA-AT
**
3642901 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACTAAT
3642923 AAAATAAATCAATCCATACTAAT
1 -AAATAAATCAATCCATACTAAT
3642946 AAAT
1 AAAT
3642950 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
22 21 0.51
23 4 0.10
25 1 0.02
26 15 0.37
ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28
Consensus pattern (22 bp):
AAATAAATCAATCCATACTAAT
Found at i:3642978 original size:22 final size:22
Alignment explanation
Indices: 3642952--3642994 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3642942 TAATAAATTA
3642952 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
3642974 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
3642995 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3643003 original size:22 final size:22
Alignment explanation
Indices: 3642954--3643002 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3642944 ATAAATTATT
**
3642954 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
3642976 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
3642999 TAAA
1 TAAA
3643003 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:3643041 original size:80 final size:83
Alignment explanation
Indices: 3642754--3643106 Score: 415
Period size: 80 Copynumber: 4.3 Consensus size: 83
3642744 CAATCCATAT
* *
3642754 TTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAA
3642819 TCAATCCATACTAATAAATTA
63 TCAATCCATACTAATAAATTA
** *
3642840 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATGCA-ACTACAAT-
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCAT--ATTTTAAAATA
* * *
3642903 AATAAATCAAT-C-CAT--A-T-
61 AATCAATCCATACTAATAAATTA
3642920 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAA
3642985 TCAATCCATACTAATAAATTA
63 TCAATCCATACTAATAAATTA
* *
3643006 TTTAAAATAAATCAATTCATAC-AACTACA-A-T-AATAAATCAATCCATATTTTAAAATAAATC
1 TTTAAAATAAATCAATCCATACTAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATC
*
3643067 AATCTATACTAATAAATTA
65 AATCCATACTAATAAATTA
3643086 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
3643107 TTTTAAAATA
Statistics
Matches: 238, Mismatches: 18, Indels: 28
0.84 0.06 0.10
Matches are distributed among these distances:
78 1 0.00
79 5 0.02
80 129 0.54
81 2 0.01
82 4 0.02
84 4 0.02
85 4 0.02
86 83 0.35
87 5 0.02
88 1 0.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (83 bp):
TTTAAAATAAATCAATCCATACTAATAAATATTAAATAAATCAATCCATATTTTAAAATAAATCA
ATCCATACTAATAAATTA
Found at i:3643106 original size:54 final size:54
Alignment explanation
Indices: 3643037--3643151 Score: 212
Period size: 54 Copynumber: 2.1 Consensus size: 54
3643027 CAACTACAAT
*
3643037 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
3643091 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTTA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
3643145 AATAAAT
1 AATAAAT
3643152 TATTTTAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:3643112 original size:22 final size:22
Alignment explanation
Indices: 3643086--3643186 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
3643076 TAATAAATTA
3643086 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
3643108 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
3643131 AATAAATTATTTTAAATAAATTAT
1 TTTAAAATA-AATCAATCCA-TAT
3643155 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
3643177 TTTATAATAA
1 TTTAAAATAA
3643187 TTTATTTTAA
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
22 33 0.56
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3643164 original size:15 final size:15
Alignment explanation
Indices: 3643131--3643233 Score: 100
Period size: 15 Copynumber: 6.5 Consensus size: 15
3643121 AATCCATACT
3643131 AATAAATTATTTT-A
1 AATAAATTATTTTAA
3643145 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
3643160 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
3643182 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
3643197 AATAATTTATTTTAT
1 AATAAATTATTTTAA
3643212 AATAAATTATTTTAA
1 AATAAATTATTTTAA
3643227 AATAAAT
1 AATAAAT
3643234 AACCGTATTA
Statistics
Matches: 75, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
14 13 0.17
15 45 0.60
17 1 0.01
18 2 0.03
19 3 0.04
20 1 0.01
22 10 0.13
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:3643173 original size:69 final size:67
Alignment explanation
Indices: 3643076--3643233 Score: 212
Period size: 69 Copynumber: 2.3 Consensus size: 67
3643066 CAATCTATAC
*
3643076 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
1 TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAAAT-AATCAAT-CATA-AAATAAATTA
3643140 TTTTA
63 TTTTA
* ** ** *
3643145 -AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAATTTATTT
1 TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATCATAAAATAAATTATTT
3643209 TA
66 TA
3643211 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTATTTTAAAATAAAT
3643234 AACCGTATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
66 13 0.16
67 24 0.30
68 14 0.17
69 29 0.36
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (67 bp):
TAATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATCATAAAATAAATTATTT
TA
Found at i:3643263 original size:26 final size:27
Alignment explanation
Indices: 3643214--3643268 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
3643204 TATTTTATAA
*
3643214 TAAATTATTTTAAAATAAATAACCGTAT
1 TAAATTATTTT-AAATAAATAACCATAT
3643242 TAAATTATTTT-AATAAATAACCATAT
1 TAAATTATTTTAAATAAATAACCATAT
3643268 T
1 T
3643269 TTATAATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 15 0.58
28 11 0.42
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (27 bp):
TAAATTATTTTAAATAAATAACCATAT
Done.