Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 49
Found at i:5814534 original size:22 final size:22
Alignment explanation
Indices: 5814504--5814545 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5814494 TCAGCTGTTA
* *
5814504 TAACTCCTGAAATTATATCATG
1 TAACCCCTGAAATTAAATCATG
*
5814526 TAACCCCTGGAATTAAATCA
1 TAACCCCTGAAATTAAATCA
5814546 AATAACTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (22 bp):
TAACCCCTGAAATTAAATCATG
Found at i:5814551 original size:22 final size:22
Alignment explanation
Indices: 5814503--5814551 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
5814493 TTCAGCTGTT
* * *
5814503 ATAACTCCTGAAATTATATCAT
1 ATAACCCCTGAAATTAAATCAA
* *
5814525 GTAACCCCTGGAATTAAATCAA
1 ATAACCCCTGAAATTAAATCAA
5814547 ATAAC
1 ATAAC
5814552 TCATGTAACT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (22 bp):
ATAACCCCTGAAATTAAATCAA
Found at i:5814842 original size:6 final size:6
Alignment explanation
Indices: 5814831--5814869 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
5814821 GACACGTATT
*
5814831 ACCACG ACCACG ACCATG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
5814870 CGAGCCGAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.33, C:0.49, G:0.15, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:5819577 original size:20 final size:20
Alignment explanation
Indices: 5819510--5819804 Score: 192
Period size: 20 Copynumber: 14.5 Consensus size: 20
5819500 TGCGAAATGA
* *
5819510 AAATCGCAACGCG-ATTCTT
1 AAATCGCAACGCGTATCCGT
* *
5819529 ACTATCGCAACGAGTATCCGT
1 A-AATCGCAACGCGTATCCGT
5819550 AAAAATCGCAACGCGTATCCGT
1 --AAATCGCAACGCGTATCCGT
* *
5819572 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGTATCCGT
5819592 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
* *
5819613 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGTATCCGT
5819633 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
* *
5819654 AAATCGCAACGGCAATAT--TT
1 AAATCGCAAC-GC-GTATCCGT
* * *
5819674 AAAATCGCAACGAGAATCTGT
1 -AAATCGCAACGCGTATCCGT
* * *
5819695 AAATCACAACG-ATAATCAGT
1 AAATCGCAACGCGT-ATCCGT
* * **
5819715 AAATCGCAACGAGAATCTAT
1 AAATCGCAACGCGTATCCGT
*
5819735 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
5819755 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
5819775 AAATCGCAACGGGAATCTGT
1 AAATCGCAACGCGTATCCGT
5819795 AAATCGCAAC
1 AAATCGCAAC
5819805 ACTGAAATTT
Statistics
Matches: 221, Mismatches: 36, Indels: 37
0.75 0.12 0.13
Matches are distributed among these distances:
19 3 0.01
20 146 0.66
21 51 0.23
22 20 0.09
23 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:5819608 original size:41 final size:41
Alignment explanation
Indices: 5819509--5819785 Score: 294
Period size: 41 Copynumber: 6.8 Consensus size: 41
5819499 ATGCGAAATG
* * * ** *
5819509 AAAATCGCAACGCG-ATTCTTACTATCGCAACGAGTATCCGT
1 AAAATCGCAACGCGTATCCGTA-AATCGCAACGACAATACGT
5819550 AAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT
1 -AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT
5819592 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT
* **
5819633 AAAATCGCAACGCGTATCCGTAAATCGCAACGGCAATATTT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT
* * * * *
5819674 AAAATCGCAACGAGAATCTGTAAATCACAACGATAAT-CAGT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATAC-GT
* * ** * *
5819715 -AAATCGCAACGAGAATCTATAAATCGCAACGATAATCCGT
1 AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT
*
5819755 -AAATCGCAACG-ATAATCCGTAAATCGCAACG
1 AAAATCGCAACGCGT-ATCCGTAAATCGCAACG
5819786 GGAATCTGTA
Statistics
Matches: 208, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
40 62 0.30
41 112 0.54
42 29 0.14
43 5 0.02
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT
Found at i:5820465 original size:12 final size:12
Alignment explanation
Indices: 5820444--5820477 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5820434 ACCGCATTTC
*
5820444 CAATACCAAACA
1 CAATATCAAACA
5820456 CAATATCAAACA
1 CAATATCAAACA
*
5820468 CAATCTCAAA
1 CAATATCAAA
5820478 ACTACAACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:5820630 original size:24 final size:24
Alignment explanation
Indices: 5820603--5820652 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
5820593 TCGAAATTTC
5820603 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGTCAATACCCGGACTTTG
* *
5820627 ATCTTGGTCAATACTCGGATTTTG
1 ATCTTGGTCAATACCCGGACTTTG
5820651 AT
1 AT
5820653 GATGTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
ATCTTGGTCAATACCCGGACTTTG
Found at i:5822883 original size:14 final size:14
Alignment explanation
Indices: 5822864--5822918 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5822854 CGGAAATTAC
5822864 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5822878 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5822897 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5822911 AATCGCAA
1 AATCGCAA
5822919 TGCGAAATGA
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:5822901 original size:33 final size:33
Alignment explanation
Indices: 5822845--5822937 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5822835 CTTAATGACT
* * *
5822845 ATCGCAACGCGGAAATTACAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
5822879 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
5822912 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
5822938 TGCGAAATGA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 47 0.84
34 9 0.16
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5822902 original size:19 final size:19
Alignment explanation
Indices: 5822878--5822988 Score: 125
Period size: 19 Copynumber: 6.4 Consensus size: 19
5822868 GCAACGAGAG
5822878 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5822897 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5822911 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5822930 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5822949 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
5822963 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
5822982 AATCGCA
1 AATCGCA
5822989 TCGAGAGAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 20
0.75 0.06 0.20
Matches are distributed among these distances:
14 19 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 45 0.59
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5822943 original size:52 final size:52
Alignment explanation
Indices: 5822878--5822988 Score: 213
Period size: 52 Copynumber: 2.1 Consensus size: 52
5822868 GCAACGAGAG
5822878 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
5822930 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
5822982 AATCGCA
1 AATCGCA
5822989 TCGAGAGAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:5822967 original size:33 final size:33
Alignment explanation
Indices: 5822930--5823010 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
5822920 GCGAAATGAA
5822930 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
5822963 AATCGTAATGCGAAATGAAAATCGCATCGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
5822996 AATCGCAATGCGAAA
1 AATCGCAATGCGAAA
5823011 CTAATTCGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:5822982 original size:85 final size:86
Alignment explanation
Indices: 5822845--5823010 Score: 280
Period size: 85 Copynumber: 1.9 Consensus size: 86
5822835 CTTAATGACT
* *
5822845 ATCGCAACGCGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
5822910 GAATCGCAATGCGAAATGAAA
66 GAATCGCAATGCGAAATGAAA
* * *
5822931 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGTAATGCGAAATGAAAATCGCATCGAGA
1 ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
5822995 GAATCGCAATGCGAAA
66 GAATCGCAATGCGAAA
5823011 CTAATTCGCA
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
85 66 0.88
86 9 0.12
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (86 bp):
ATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
GAATCGCAATGCGAAATGAAA
Found at i:5823063 original size:33 final size:33
Alignment explanation
Indices: 5823021--5823282 Score: 350
Period size: 33 Copynumber: 7.8 Consensus size: 33
5823011 CTAATTCGCA
5823021 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
5823054 TTGCGATTTTCATTTCGCATTGCGGTTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
5823087 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
5823123 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
5823158 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
5823191 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
5823224 TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
5823257 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
5823283 AGTCATTTTT
Statistics
Matches: 201, Mismatches: 17, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 157 0.78
35 5 0.02
36 4 0.02
37 2 0.01
38 8 0.04
39 2 0.01
40 9 0.04
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:5823077 original size:52 final size:50
Alignment explanation
Indices: 5823015--5823282 Score: 219
Period size: 52 Copynumber: 5.3 Consensus size: 50
5823005 GCGAAACTAA
*
5823015 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCATTTCG-ATTGCGATT-TCTCATTGCGATTTTCAT
* * * * * *
5823067 TTCGCATTGCGGTTCTCTCGTTGCGATTTTC-ATTTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATT-T-TCATTTCGA-TTGCGATTTCTCATTGCGATTTTCAT
* * * *
5823119 TTCGCATTGCGATTCTCTCGTTGCGATTTTC-ATTTCGCATTGCGATTTTCAT
1 TTCGCATTGCGATT-T-TCATTTCGA-TTGCGATTTCTCATTGCGATTTTCAT
* * *
5823171 TTCGCATTGCGA--TTC-TCTCG-TTGCGATTT-TCATTTCGCA-TTGCGAT
1 TTCGCATTGCGATTTTCATTTCGATTGCGATTTCTCATTGCG-ATTTTC-AT
* *
5823217 TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTTTCAT
1 T-TCGCATTGCGATTTTCATTTCG-ATTGCGATT-TCTCATTGCGATTTTCAT
5823270 TTCGCATTGCGAT
1 TTCGCATTGCGAT
5823283 AGTCATTTTT
Statistics
Matches: 181, Mismatches: 20, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
45 12 0.07
46 8 0.04
47 12 0.07
48 2 0.01
49 4 0.02
50 4 0.02
52 110 0.61
53 10 0.06
54 19 0.10
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.46
Consensus pattern (50 bp):
TTCGCATTGCGATTTTCATTTCGATTGCGATTTCTCATTGCGATTTTCAT
Found at i:5823196 original size:14 final size:14
Alignment explanation
Indices: 5823177--5823264 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
5823167 TCATTTCGCA
5823177 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
5823191 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
5823208 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
5823224 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
5823241 CATTGCGATTCTCTCA
1 --TTGCGATTCTCTCG
5823257 TTGCGATT
1 TTGCGATT
5823265 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 20 0.34
16 13 0.22
17 14 0.24
19 12 0.20
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:5823290 original size:85 final size:85
Alignment explanation
Indices: 5823015--5823282 Score: 425
Period size: 85 Copynumber: 3.2 Consensus size: 85
5823005 GCGAAACTAA
*
5823015 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGGT
1 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
*
5823080 TCTCTCGTTGCGATTTTCAT
66 TCTCTCATTGCGATTTTCAT
*
5823100 TTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
* *
5823165 T-T-TCATTTCGCA-TTGCGAT
66 TCTCTCATTGCG-ATTTTC-AT
* *
5823184 TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
1 T-TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
5823249 TTCTCTCATTGCGATTTTCAT
65 TTCTCTCATTGCGATTTTCAT
5823270 TTCGCATTGCGAT
1 TTCGCATTGCGAT
5823283 AGTCATTTTT
Statistics
Matches: 167, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
83 9 0.05
84 5 0.03
85 138 0.83
86 5 0.03
87 10 0.06
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.46
Consensus pattern (85 bp):
TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
TCTCTCATTGCGATTTTCAT
Found at i:5823408 original size:14 final size:14
Alignment explanation
Indices: 5823389--5823425 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5823379 TATCAATTAA
5823389 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5823403 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5823417 ACAAATCAA
1 ACAAATCAA
5823426 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:5824845 original size:42 final size:42
Alignment explanation
Indices: 5824760--5824853 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
5824750 GTGAATCGGG
* * *
5824760 CTCTTGAATGGTGGGAGGGACCTCTTCAATGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAAGGATGACAGGGGC
* *
5824802 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTCAAGG-ATGACAGGGGC
*
5824844 CTCTTCAACG
1 CTCTTGAACG
5824854 ATAGAAGTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 36 0.82
43 4 0.09
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAAGGATGACAGGGGC
Found at i:5825315 original size:19 final size:18
Alignment explanation
Indices: 5825291--5825442 Score: 94
Period size: 19 Copynumber: 8.8 Consensus size: 18
5825281 CACGAAACTT
5825291 AAAATCGCAACGCGAAATG
1 AAAATCGCAA-GCGAAATG
5825310 AAAATCGCAA-CG--A-G
1 AAAATCGCAAGCGAAATG
* **
5825324 AGAATCGCAACGCGAAACC
1 AAAATCGCAA-GCGAAATG
5825343 AAAATCGCAACGCGAAATG
1 AAAATCGCAA-GCGAAATG
*
5825362 AAAATCGCTA-CG--A-G
1 AAAATCGCAAGCGAAATG
* *
5825376 AGAATCGCAATGTGAAATG
1 AAAATCGCAA-GCGAAATG
5825395 AAAATCGCAA-CG--A-G
1 AAAATCGCAAGCGAAATG
* *
5825409 AGAATCACAATGCGAAATG
1 AAAATCGCAA-GCGAAATG
5825428 AAAATCGCAATGCGA
1 AAAATCGCAA-GCGA
5825443 TTTTGGTTTC
Statistics
Matches: 103, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
14 28 0.27
15 3 0.03
16 5 0.05
17 5 0.05
18 3 0.03
19 59 0.57
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (18 bp):
AAAATCGCAAGCGAAATG
Found at i:5825362 original size:52 final size:52
Alignment explanation
Indices: 5825291--5825406 Score: 187
Period size: 52 Copynumber: 2.2 Consensus size: 52
5825281 CACGAAACTT
5825291 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAACC
* * * **
5825343 AAAATCGCAACGCGAAATGAAAATCGCTACGAGAGAATCGCAATGTGAAATG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAACC
5825395 AAAATCGCAACG
1 AAAATCGCAACG
5825407 AGAGAATCAC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (52 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:5825382 original size:33 final size:33
Alignment explanation
Indices: 5825345--5825437 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
5825335 GCGAAACCAA
* *
5825345 AATCGCAACGCGAAATGAAAATCGCTACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
5825378 AATCGCAATGTGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
5825411 AATCACAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
5825438 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:5825491 original size:19 final size:19
Alignment explanation
Indices: 5825467--5825531 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
5825457 TGCGATTTTG
5825467 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
5825486 TCGTTGCGA--TTC---TC
1 TCGTTGCGATTTTCATTTC
5825500 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTTTCATTTC
*
5825519 GCGTTGCGATTTT
1 TCGTTGCGATTTT
5825532 AAGTTTCGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 11 0.28
16 3 0.08
17 3 0.08
19 23 0.57
ACGTcount: A:0.09, C:0.22, G:0.20, T:0.49
Consensus pattern (19 bp):
TCGTTGCGATTTTCATTTC
Found at i:5825491 original size:33 final size:33
Alignment explanation
Indices: 5825438--5825531 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
5825428 AAAATCGCAA
** *
5825438 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTTTCTCGT
* *
5825471 TGCGATTTTCATTTCTCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTTTCTCGT
5825504 TGCGATTTTCATTTCGCGTTGCGATTTT
1 TGCGATTTTCATTTCGCGTTGCGATTTT
5825532 AAGTTTCGTG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.09, C:0.19, G:0.23, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTTTCTCGT
Found at i:5825503 original size:14 final size:14
Alignment explanation
Indices: 5825484--5825510 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5825474 GATTTTCATT
5825484 TCTCGTTGCGATTC
1 TCTCGTTGCGATTC
5825498 TCTCGTTGCGATT
1 TCTCGTTGCGATT
5825511 TTCATTTCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.26, G:0.22, T:0.44
Consensus pattern (14 bp):
TCTCGTTGCGATTC
Found at i:5825544 original size:20 final size:19
Alignment explanation
Indices: 5825501--5825547 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
5825491 GCGATTCTCT
*
5825501 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTAATTTCG
5825520 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTAA-TTTCG
*
5825540 TGTTGCGA
1 CGTTGCGA
5825548 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.13, C:0.17, G:0.26, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAATTTCG
Found at i:5825711 original size:83 final size:85
Alignment explanation
Indices: 5825595--5825867 Score: 275
Period size: 92 Copynumber: 3.1 Consensus size: 85
5825585 ATGGATTGCA
* **
5825595 TTACTTCAACCAATAGACAAAACAAAGACAAATACTAACTTCAGGGTATT-AG-T-TTAGCAGAA
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAGATATTAGCAGAA
5825657 TTGGCAGCAACCGAACAAAT
66 TTGGCAGCAACCGAACAAAT
* *
5825677 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ATTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATT-AAG-AT----A-T
*
5825741 TAGCAGAATTGGCAGCAACCGAATAAAT
58 TAGCAGAATTGGCAGCAACCGAACAAAT
* *
5825769 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCATAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTATT-AAG-AT----A--
* *
5825834 TTAGCAGTATTGGCAGCAACCGAATAAAT
57 TTAGCAGAATTGGCAGCAACCGAACAAAT
5825863 TTACT
1 TTACT
5825868 AAGCAATCTA
Statistics
Matches: 166, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
82 13 0.08
83 31 0.19
84 2 0.01
86 1 0.01
91 19 0.11
92 45 0.27
93 22 0.13
94 33 0.20
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (85 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAGATATTAGCAGAA
TTGGCAGCAACCGAACAAAT
Found at i:5825805 original size:92 final size:93
Alignment explanation
Indices: 5825645--5825867 Score: 369
Period size: 92 Copynumber: 2.4 Consensus size: 93
5825635 TCAGGGTATT
*
5825645 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAGACAAA
* *
5825710 TACT-ATTTCACAGTGTTAAAGAATACAC
65 TACTAACTTCACAGTGTTAAAGAATAAAC
5825738 AG-TTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAAC-AAAGACAAA
*
5825802 TACTAACTTCATAGTGTTAAAGAATAAAC
65 TACTAACTTCACAGTGTTAAAGAATAAAC
*
5825831 AGTTTAGCAGTATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
5825868 AAGCAATCTA
Statistics
Matches: 122, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
91 19 0.16
92 45 0.37
93 25 0.20
94 33 0.27
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAGACAAAT
ACTAACTTCACAGTGTTAAAGAATAAAC
Found at i:5827607 original size:40 final size:36
Alignment explanation
Indices: 5827558--5827657 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 36
5827548 TCTTTTGGTT
*
5827558 GAAAAGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACG-GAGAATGA--ATCGCAACGC
5827597 GGAAATGAAAATCGCAAC-GAG-A-GAATCGCAACGC
1 -GAAATGAAAATCGCAACGGAGAATGAATCGCAACGC
5827631 GAAATGAAAATCGCAACGCGA-AATGAA
1 GAAATGAAAATCGCAACG-GAGAATGAA
5827658 AATCGCAATG
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
33 17 0.31
34 10 0.18
35 3 0.05
36 5 0.09
37 1 0.02
38 3 0.05
40 16 0.29
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.10
Consensus pattern (36 bp):
GAAATGAAAATCGCAACGGAGAATGAATCGCAACGC
Found at i:5827644 original size:19 final size:19
Alignment explanation
Indices: 5827558--5827670 Score: 119
Period size: 19 Copynumber: 6.1 Consensus size: 19
5827548 TCTTTTGGTT
* *
5827558 GAAAAGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
5827577 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
5827597 GGAAATGAAAATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
5827615 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
5827631 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
5827650 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
5827669 GA
1 GA
5827671 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 35 0.45
20 25 0.32
21 2 0.03
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:5827731 original size:41 final size:41
Alignment explanation
Indices: 5827682--5827813 Score: 255
Period size: 41 Copynumber: 3.2 Consensus size: 41
5827672 TTTGGTTTCG
5827682 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCTCT
1 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCTCT
5827723 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCTCT
1 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCTCT
*
5827764 CGTTGCGATAGTCATTTTCGCGTTGCGATTTTCATTTCTCT
1 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCTCT
5827805 CGTTGCGAT
1 CGTTGCGAT
5827814 TCTTTTGCAA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 90 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (41 bp):
CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCTCT
Found at i:5827798 original size:20 final size:20
Alignment explanation
Indices: 5827677--5827814 Score: 150
Period size: 20 Copynumber: 6.8 Consensus size: 20
5827667 GCGATTTTGG
*
5827677 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTGTCAT
* *
5827697 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTGTCAT
* *
5827717 TTCTCTCGTTGCGATAGTCAT
1 TT-TCGCGTTGCGATTGTCAT
* *
5827738 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTGTCAT
* *
5827758 TTCTCTCGTTGCGATAGTCAT
1 TT-TCGCGTTGCGATTGTCAT
*
5827779 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTGTCAT
*
5827799 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
5827815 CTTTTGCAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
20 52 0.54
21 44 0.46
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCGATTGTCAT
Found at i:5828425 original size:22 final size:21
Alignment explanation
Indices: 5828348--5828502 Score: 108
Period size: 20 Copynumber: 7.6 Consensus size: 21
5828338 CTTTAAAAAT
5828348 CGCGTTGCGA-TTTACGGATA
1 CGCGTTGCGATTTTACGGATA
*
5828368 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTTACGGATA
* *
5828388 TGTCATTGCGA-TTTACGGATA
1 CG-CGTTGCGATTTTACGGATA
*
5828409 CGCGTTGTGATTTTTACGGATA
1 CGCGTTGCGA-TTTTACGGATA
* ** * *
5828431 CTCGTTGCGATAGTAAGAAT-
1 CGCGTTGCGATTTTACGGATA
* *
5828451 CGCGTTGCGATTTATA-TG-TT
1 CGCGTTGCGATTT-TACGGATA
** *
5828471 CGCGTTGCGATTTT-CATATT
1 CGCGTTGCGATTTTACGGATA
5828491 CGCGTTGCGATT
1 CGCGTTGCGATT
5828503 CTGGAAACTG
Statistics
Matches: 106, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.02
20 62 0.58
21 24 0.23
22 18 0.17
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (21 bp):
CGCGTTGCGATTTTACGGATA
Found at i:5828918 original size:6 final size:6
Alignment explanation
Indices: 5828907--5828962 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
5828897 ACGCGAGAGG
* * ** *
5828907 GACCGA GACCGA GACCGA GACCGT GACCGC GATAGA GAACGCA GA-CGA
1 GACCGA GACCGA GACCGA GACCGA GACCGA GACCGA GACCG-A GACCGA
5828955 GACCGA GA
1 GACCGA GA
5828963 TATTCGCGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 3 0.07
6 35 0.85
7 3 0.07
ACGTcount: A:0.34, C:0.29, G:0.34, T:0.04
Consensus pattern (6 bp):
GACCGA
Found at i:5831144 original size:2 final size:2
Alignment explanation
Indices: 5831137--5831161 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5831127 GTTACTTTGT
5831137 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5831162 GGAGATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5831772 original size:98 final size:98
Alignment explanation
Indices: 5831654--5831872 Score: 420
Period size: 98 Copynumber: 2.2 Consensus size: 98
5831644 TAAATTAAAA
*
5831654 TTACAAGCAATCTTATCAAATATAAAATTACTATGATGTAATGCAAAGGAATATGATTACATGAT
1 TTACAAGCAATCTTATCAAATATAAAATTACTATGATGTAATGCAAAGGAATATGATTAAATGAT
5831719 AGTGCGTGTCTACTTTCAAATATGTAACCATTT
66 AGTGCGTGTCTACTTTCAAATATGTAACCATTT
5831752 TTACAAGCAATCTTATCAAATATAAAATTACTATGATGTAATGCAAAGGAATATGATTAAATGAT
1 TTACAAGCAATCTTATCAAATATAAAATTACTATGATGTAATGCAAAGGAATATGATTAAATGAT
5831817 AGTGCGTGTCTACTTTCAAATATGTAACCATTT
66 AGTGCGTGTCTACTTTCAAATATGTAACCATTT
*
5831850 TTACAAGCAACCTTATCAAATAT
1 TTACAAGCAATCTTATCAAATAT
5831873 GATCACGTAC
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 119 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (98 bp):
TTACAAGCAATCTTATCAAATATAAAATTACTATGATGTAATGCAAAGGAATATGATTAAATGAT
AGTGCGTGTCTACTTTCAAATATGTAACCATTT
Found at i:5834599 original size:12 final size:12
Alignment explanation
Indices: 5834574--5834643 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
5834564 ACGGAGATAT
* *
5834574 CAGAAATCAAAA
1 CAGAATTCAGAA
5834586 CAGAATTCAGAA
1 CAGAATTCAGAA
* *
5834598 CA-TATATCATAA
1 CAGAAT-TCAGAA
* *
5834610 CAGAATCCAGAT
1 CAGAATTCAGAA
* *
5834622 CAGAAATCATAA
1 CAGAATTCAGAA
5834634 CAGAATTCAG
1 CAGAATTCAG
5834644 GTAATGTATC
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:5834606 original size:24 final size:24
Alignment explanation
Indices: 5834579--5834666 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 24
5834569 GATATCAGAA
*
5834579 ATCAAAACAGAATTCAGAACATAT
1 ATCATAACAGAATTCAGAACATAT
* * * *
5834603 ATCATAACAGAATCCAGATCAGAA
1 ATCATAACAGAATTCAGAACATAT
* *
5834627 ATCATAACAGAATTCAGGTA-ATGT
1 ATCATAACAGAATTCA-GAACATAT
*
5834651 ATCAGAACAGAATTCA
1 ATCATAACAGAATTCA
5834667 AGTCAGAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 50 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCATAACAGAATTCAGAACATAT
Found at i:5834628 original size:48 final size:47
Alignment explanation
Indices: 5834572--5834678 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
5834562 AAACGGAGAT
*
5834572 ATCAGAAATCAAAACAGAATTCA-GAACATATATCATAACAGAATCCA
1 ATCAGAAATCAAAACAGAATTCAGGAA-ATATATCAGAACAGAATCCA
* * * *
5834619 GATCAGAAATCATAACAGAATTCAGGTAATGTATCAGAACAGAATTCA
1 -ATCAGAAATCAAAACAGAATTCAGGAAATATATCAGAACAGAATCCA
5834667 AGTCAGAAATCA
1 A-TCAGAAATCA
5834679 GATAAAATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
47 1 0.02
48 49 0.94
49 2 0.04
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (47 bp):
ATCAGAAATCAAAACAGAATTCAGGAAATATATCAGAACAGAATCCA
Found at i:5834678 original size:24 final size:25
Alignment explanation
Indices: 5834572--5834680 Score: 84
Period size: 24 Copynumber: 4.5 Consensus size: 25
5834562 AAACGGAGAT
*
5834572 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * * * *
5834596 AACATATATCATAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
5834620 ATCAGAAATCATAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
5834644 GTAATG-TATCAGAACAGAATTCAAG
1 ATCA-GAAATCAGAACAGAATTCAAG
5834669 -TCAGAAATCAGA
1 ATCAGAAATCAGA
5834681 TAAAATATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
23 3 0.04
24 59 0.88
25 5 0.07
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.20
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:5837700 original size:3 final size:3
Alignment explanation
Indices: 5837694--5837806 Score: 190
Period size: 3 Copynumber: 37.7 Consensus size: 3
5837684 TTTTTATCCA
* *
5837694 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
5837742 TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5837790 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
5837807 AATATATATT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 102 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:5850602 original size:1 final size:1
Alignment explanation
Indices: 5850596--5850682 Score: 111
Period size: 1 Copynumber: 87.0 Consensus size: 1
5850586 ATGCTTGAAG
* * **
5850596 AAAAAAAAAGAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** *
5850661 AAAAAAAAGGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
5850683 GGGGGTCAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:5850621 original size:19 final size:18
Alignment explanation
Indices: 5850596--5850682 Score: 124
Period size: 17 Copynumber: 4.8 Consensus size: 18
5850586 ATGCTTGAAG
5850596 AAAAAAAAAGAAAAAAAA
1 AAAAAAAAAGAAAAAAAA
5850614 AGAAAAAAAA-AAAAAAAA
1 A-AAAAAAAAGAAAAAAAA
5850632 AAAAAAAAA-AAAAAAAA
1 AAAAAAAAAGAAAAAAAA
*
5850649 AAAAAAAAGGAAAAAAAA
1 AAAAAAAAAGAAAAAAAA
*
5850667 AAGGAAAAAAGAAAAA
1 AA-AAAAAAAGAAAAA
5850683 GGGGGTCAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
17 24 0.38
18 20 0.32
19 19 0.30
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAAA
Found at i:5850684 original size:26 final size:22
Alignment explanation
Indices: 5850596--5850683 Score: 124
Period size: 22 Copynumber: 3.9 Consensus size: 22
5850586 ATGCTTGAAG
*
5850596 AAAAAAAAAGAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAGAA
5850618 AAAAAAAAAAAAAAAAAAA-AA
1 AAAAAAAAAAAAAAAAAAAGAA
*
5850639 AAAAAAAAAAAAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAGAA
5850661 AAAAAAAAGGAAAAAAGAAAAAG
1 AAAAAAAA--AAAAAA-AAAAAG
5850684 GGGGTCAAGG
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
21 20 0.34
22 28 0.47
24 6 0.10
25 5 0.08
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAAAGAA
Found at i:5851021 original size:16 final size:16
Alignment explanation
Indices: 5850995--5851039 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5850985 TTTGAATACA
*
5850995 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
5851012 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
5851027 ATTCAATTTATTT
1 ATTCAATTTATTT
5851040 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:5851961 original size:83 final size:83
Alignment explanation
Indices: 5851822--5852199 Score: 674
Period size: 83 Copynumber: 4.6 Consensus size: 83
5851812 CATTAACTGA
5851822 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGA
5851887 ATCAAGCATTGAGTTTAG
66 ATCAAGCATTGAGTTTAG
5851905 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGA
*
5851970 ATCAAACATTGAGTTTAG
66 ATCAAGCATTGAGTTTAG
5851988 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGA
* *
5852053 ATCAAGCATTGAATTTGG
66 ATCAAGCATTGAGTTTAG
* *
5852071 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGATAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGA
*
5852136 A-CAATCA-TGAGTTTA-
66 ATCAAGCATTGAGTTTAG
5852151 AAGATGAA-TTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
5852200 GTTGGTATAA
Statistics
Matches: 286, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
79 41 0.14
80 8 0.03
81 6 0.02
82 5 0.02
83 226 0.79
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.35
Consensus pattern (83 bp):
AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGA
ATCAAGCATTGAGTTTAG
Found at i:5853198 original size:110 final size:111
Alignment explanation
Indices: 5853002--5853378 Score: 544
Period size: 110 Copynumber: 3.5 Consensus size: 111
5852992 CAAAGATTCA
** * *
5853002 AATCTATCATTTGAAAGATTAGCTTTTCC--AGAAAGTTCA-AATGAGAATAACTCATCTGAAGA
1 AATC-ATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
5853064 AGGAAGAAGAAGTTCATAATGAGAAG-TTTGTTCAACCTTTTACCTG
65 AGGAAGAAGAAGTTCATAATGAGAAGATTTGTTCAACCTTTTACCTG
* *
5853110 AATCCATCATTTGATGGATCAGTTTTTCCAGAGAAAG-TCATAATAAGAAGAACTCATCTGAAGA
1 AAT-CATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
5853174 AGGAAGAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTACCTG
65 AGGAAGAAGAAGTTCATAATGAGAAGATTTGTTCAACCTTTTACCTG
5853221 AATCATCATTTG--GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 AATCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
5853284 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 GGAAGAAGAAGTTCATAATGAGAAG-ATTTGTTCAACCTTTTACCTG
* * *
5853331 AATTCATCA--TGATGGATTATCTTTT-C-G-GAGAGTTCATAATGAGAAGAA
1 AA-TCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
5853379 GAGAAGAATT
Statistics
Matches: 246, Mismatches: 13, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
108 64 0.26
109 59 0.24
110 85 0.35
111 38 0.15
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (111 bp):
AATCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
GGAAGAAGAAGTTCATAATGAGAAGATTTGTTCAACCTTTTACCTG
Found at i:5853531 original size:3 final size:3
Alignment explanation
Indices: 5853523--5853606 Score: 111
Period size: 3 Copynumber: 28.7 Consensus size: 3
5853513 TTTTTATCCA
* *
5853523 TAT TAT TAT TA- TAA TAT TAT TAT TAT TAT CTAT TAT TAT TA- TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
*
5853567 TAT TAT TAT TAT TAT TAT TAT CAT TAT TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5853607 AATATATAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
2 6 0.08
3 64 0.88
4 3 0.04
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5856674 original size:21 final size:21
Alignment explanation
Indices: 5856649--5856689 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5856639 CTAGTGTGAG
* *
5856649 TATTTCAAAATAATTTGATCC
1 TATTTAAAAAAAATTTGATCC
5856670 TATTTAAAAAAAATTTGATC
1 TATTTAAAAAAAATTTGATC
5856690 AGACTAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (21 bp):
TATTTAAAAAAAATTTGATCC
Found at i:5863417 original size:27 final size:28
Alignment explanation
Indices: 5863365--5863417 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
5863355 ATTTGTATTG
*
5863365 ATGTATTTCTTATACATTACCCTTTTCC
1 ATGTATTTCTTATACATTACACTTTTCC
* *
5863393 ATGT-TTTTTTATACATTACATTTTT
1 ATGTATTTCTTATACATTACACTTTT
5863418 AAGTAGCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.23, C:0.17, G:0.04, T:0.57
Consensus pattern (28 bp):
ATGTATTTCTTATACATTACACTTTTCC
Found at i:5864518 original size:26 final size:27
Alignment explanation
Indices: 5864482--5864535 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
5864472 ATGTTTGAAA
5864482 AGAAAATTATTTTCTAAAAACAAAAAT
1 AGAAAATTATTTTCTAAAAACAAAAAT
* *
5864509 AGAAAA-TATTTTTTAAAAATAAAAAT
1 AGAAAATTATTTTCTAAAAACAAAAAT
5864535 A
1 A
5864536 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (27 bp):
AGAAAATTATTTTCTAAAAACAAAAAT
Found at i:5864533 original size:19 final size:19
Alignment explanation
Indices: 5864503--5864558 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
5864493 TTCTAAAAAC
5864503 AAAAATAGAAAATATTTTTT
1 AAAAATA-AAAATATTTTTT
5864523 AAAAATAAAAATATTTTTT
1 AAAAATAAAAATATTTTTT
5864542 AAAAATAAAAATATTTT
1 AAAAATAAAAATATTTT
5864559 CTAATGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 29 0.81
20 7 0.19
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAAATAAAAATATTTTTT
Found at i:5871898 original size:37 final size:38
Alignment explanation
Indices: 5871857--5871928 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 38
5871847 AAAATTTTAC
* * *
5871857 ATCCTTCACCCGACCTAATCTGACCCGAAA-AATATAT
1 ATCCTCCACCCGACCCAACCTGACCCGAAATAATATAT
* *
5871894 ATCCTCCACCTGACCCGACCTGACCCGAAATAATA
1 ATCCTCCACCCGACCCAACCTGACCCGAAATAATA
5871929 AAAATATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 25 0.86
38 4 0.14
ACGTcount: A:0.33, C:0.36, G:0.10, T:0.21
Consensus pattern (38 bp):
ATCCTCCACCCGACCCAACCTGACCCGAAATAATATAT
Found at i:5875552 original size:256 final size:256
Alignment explanation
Indices: 5875097--5875607 Score: 995
Period size: 256 Copynumber: 2.0 Consensus size: 256
5875087 GCAAAAGTTT
*
5875097 CGTTAAAATTTTAACGGAAGGGTAATAAGATGAAATAAAAACTAAACATTAGATATAAATTTAAA
1 CGTTAAAATTTTAACGAAAGGGTAATAAGATGAAATAAAAACTAAACATTAGATATAAATTTAAA
*
5875162 AAAATTAGAAATTTAAATATTAGAATGGATAAAACTGATAGTTTAGATGCTAAATATGTAGTTTA
66 AAAAATAGAAATTTAAATATTAGAATGGATAAAACTGATAGTTTAGATGCTAAATATGTAGTTTA
5875227 CCCTTAATTATATGTATTTCTCTTTCTTATCATGTTTTTGGATGGACTTAATATATGTGAAACTA
131 CCCTTAATTATATGTATTTCTCTTTCTTATCATGTTTTTGGATGGACTTAATATATGTGAAACTA
5875292 GAAAGAAAAACCAAGAAGCACATCTAAGCCCATTTTCAGTGGGATTTTGAAATGTTCTCTC
196 GAAAGAAAAACCAAGAAGCACATCTAAGCCCATTTTCAGTGGGATTTTGAAATGTTCTCTC
5875353 CGTTAAAATTTTAACGAAAGGGTAATAAGATGAAATAAAAACTAAACATTAGATATAAATTTAAA
1 CGTTAAAATTTTAACGAAAGGGTAATAAGATGAAATAAAAACTAAACATTAGATATAAATTTAAA
*
5875418 AAAAATAGAAATTTAAATATTAGAATGGATAAAACTGATAGTTTTGATGCTAAATATGTAGTTTA
66 AAAAATAGAAATTTAAATATTAGAATGGATAAAACTGATAGTTTAGATGCTAAATATGTAGTTTA
5875483 CCCTTAATTATATGTATTTCTCTTTCTTATCATGTTTTTGGATGGACTTAATATATGTGAAACTA
131 CCCTTAATTATATGTATTTCTCTTTCTTATCATGTTTTTGGATGGACTTAATATATGTGAAACTA
5875548 GAAAGAAAAACCAAGAAGCACATCTAAGCCCATTTTCAGTGGGATTTTGAAATGTTCTCT
196 GAAAGAAAAACCAAGAAGCACATCTAAGCCCATTTTCAGTGGGATTTTGAAATGTTCTCT
5875608 TATCTCCGGC
Statistics
Matches: 252, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
256 252 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (256 bp):
CGTTAAAATTTTAACGAAAGGGTAATAAGATGAAATAAAAACTAAACATTAGATATAAATTTAAA
AAAAATAGAAATTTAAATATTAGAATGGATAAAACTGATAGTTTAGATGCTAAATATGTAGTTTA
CCCTTAATTATATGTATTTCTCTTTCTTATCATGTTTTTGGATGGACTTAATATATGTGAAACTA
GAAAGAAAAACCAAGAAGCACATCTAAGCCCATTTTCAGTGGGATTTTGAAATGTTCTCTC
Found at i:5876131 original size:25 final size:25
Alignment explanation
Indices: 5876068--5876131 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
5876058 ATTGTCGAAT
5876068 TTTTTTATTCAATTCAATTTAAAATA
1 TTTTTTA-TCAATTCAATTTAAAATA
** *
5876094 AATTTTCTCAATTCAATTTAAGAA-A
1 TTTTTTATCAATTCAATTTAA-AATA
*
5876119 TTTTTTATAAATT
1 TTTTTTATCAATT
5876132 TAAAATAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 24 0.80
26 6 0.20
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTTTTATCAATTCAATTTAAAATA
Found at i:5876407 original size:20 final size:21
Alignment explanation
Indices: 5876382--5876433 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5876372 TTTTCCCAAT
*
5876382 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
5876402 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
5876423 TCGCAATGCGA
1 TCGCAATGCGA
5876434 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:5876447 original size:20 final size:20
Alignment explanation
Indices: 5876422--5876535 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
5876412 AATTGGGAAA
*
5876422 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
5876442 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
5876462 ATCGTAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
5876483 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
5876503 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
5876523 TTCGCAACGCGAT
1 ATCGCAACGCGAT
5876536 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:5876535 original size:61 final size:61
Alignment explanation
Indices: 5876419--5876535 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
5876409 GCGAATTGGG
* * * * * *
5876419 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGTAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
5876480 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
5876536 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:5877112 original size:19 final size:19
Alignment explanation
Indices: 5877052--5877132 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
5877042 TTCGAGAATG
5877052 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
5877072 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
5877088 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
5877105 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
5877124 AAAATCGCA
1 AAAATCGCA
5877133 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:5877179 original size:33 final size:33
Alignment explanation
Indices: 5877142--5877229 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
5877132 ATTGCGATTT
* *
5877142 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
5877175 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
5877208 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
5877230 ATTATCTCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:5877231 original size:20 final size:20
Alignment explanation
Indices: 5877197--5877254 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
5877187 GCGATTCTCT
**
5877197 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
5877217 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
* *
5877237 CATTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
5877255 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:5879315 original size:42 final size:42
Alignment explanation
Indices: 5879255--5879377 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
5879245 GCCTGACTCG
* * *
5879255 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
5879297 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
5879339 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
5879378 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:5879335 original size:21 final size:21
Alignment explanation
Indices: 5879311--5879377 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5879301 TCATTCCTCG
5879311 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
5879332 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
5879353 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
5879374 AGAG
1 AGAG
5879378 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:5880755 original size:14 final size:14
Alignment explanation
Indices: 5880736--5880771 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5880726 ATTGTTTAAT
5880736 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
5880750 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
5880764 TGATTTGT
1 TGATTTGT
5880772 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:5880972 original size:19 final size:19
Alignment explanation
Indices: 5880950--5881100 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
5880940 TGAAATTAAA
5880950 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5880969 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
5880984 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
5881002 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
5881016 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5881035 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
5881050 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
5881068 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
5881087 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
5881101 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:5880996 original size:33 final size:32
Alignment explanation
Indices: 5880954--5881080 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
5880944 ATTAAATTCG
5880954 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
5880987 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
5881020 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
5881053 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
5881081 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:5881043 original size:66 final size:66
Alignment explanation
Indices: 5880947--5881079 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
5880937 ACGTGAAATT
*
5880947 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
5881012 G
66 G
*
5881013 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
5881078 G
66 G
5881079 A
1 A
5881080 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:5883606 original size:24 final size:24
Alignment explanation
Indices: 5883572--5883625 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5883562 CTGAAACATC
* *
5883572 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
5883596 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
5883620 ATCAAA
1 ATCAAA
5883626 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:5884710 original size:20 final size:20
Alignment explanation
Indices: 5884685--5884742 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
5884675 ATTCATTTGA
5884685 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
5884705 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
5884725 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
5884743 CGCAATGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:5884802 original size:19 final size:19
Alignment explanation
Indices: 5884761--5884847 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
5884751 AAAATGAAAA
5884761 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
5884777 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5884794 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5884813 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5884832 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
5884848 TCGTTGCGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 49 0.74
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5884831 original size:38 final size:33
Alignment explanation
Indices: 5884761--5884876 Score: 151
Period size: 33 Copynumber: 3.4 Consensus size: 33
5884751 AAAATGAAAA
5884761 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
5884794 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
***
5884832 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
5884865 TCGCGTTGCGAT
1 TCGCATTGCGAT
5884877 AGTCTGTTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
33 38 0.51
35 3 0.04
36 3 0.04
38 30 0.41
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:5884983 original size:14 final size:14
Alignment explanation
Indices: 5884964--5885000 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5884954 CTTCAATTAA
5884964 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5884978 ACAAATCATCTTTT
1 ACAAATCAACATTT
5884992 ACAAATCAA
1 ACAAATCAA
5885001 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5886904 original size:20 final size:19
Alignment explanation
Indices: 5886869--5886935 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
5886859 GAAACTTAAA
5886869 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
5886888 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
** * **
5886908 ATATCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
5886927 ATCGCAACG
1 ATCGCAACG
5886936 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 22 0.59
20 15 0.41
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:5886943 original size:14 final size:14
Alignment explanation
Indices: 5886924--5886981 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
5886914 ATGCGAAATG
5886924 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
5886938 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
5886954 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
5886970 AAAATCGCAACG
1 AAAATCGCAACG
5886982 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5886966 original size:32 final size:33
Alignment explanation
Indices: 5886916--5886986 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 33
5886906 CTATATCAAT
5886916 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
5886949 GCGAAATG-AAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCGCAAC
5886981 GCGAAA
1 GCGAAA
5886987 CACAAATCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 30 0.79
33 8 0.21
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.08
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGACAAAATCGCAAC
Found at i:5887015 original size:19 final size:19
Alignment explanation
Indices: 5886993--5887056 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
5886983 GAAACACAAA
5886993 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
5887012 TCGCGTTTCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
5887028 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
5887045 TCGCATTTCGAT
1 TCGCATTGCGAT
5887057 AGCCATTTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
14 5 0.15
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 15 0.44
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5887063 original size:19 final size:20
Alignment explanation
Indices: 5887041--5887084 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5887031 TTGCGATTTT
*
5887041 CATTTC-GCATTTCGATAGC
1 CATTTCTGCATTGCGATAGC
* *
5887060 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCATTGCGATAGC
5887080 CATTT
1 CATTT
5887085 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTTCTGCATTGCGATAGC
Found at i:5887603 original size:18 final size:18
Alignment explanation
Indices: 5887577--5887621 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
5887567 GTCGATCAGA
*
5887577 TGATGGCTCTGGATGAGG
1 TGATGGCTCTGGACGAGG
* *
5887595 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGACGAGG
5887613 TGATGGCTC
1 TGATGGCTC
5887622 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGACGAGG
Found at i:5888966 original size:20 final size:20
Alignment explanation
Indices: 5888941--5888994 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
5888931 AATAGTTTCT
5888941 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
5888961 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
5888981 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
5888995 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:5889246 original size:20 final size:21
Alignment explanation
Indices: 5889221--5889269 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
5889211 TCTGAGAGAT
5889221 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
5889241 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
*
5889263 GAAGATG
1 GGAGATG
5889270 GGCGGGTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:5889255 original size:22 final size:22
Alignment explanation
Indices: 5889228--5889271 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5889218 GATGGAGATA
*
5889228 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGAAGATGGG
*
5889250 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCGCCGAAGATGGG
5889272 CGGGTAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATGGG
Found at i:5889859 original size:20 final size:20
Alignment explanation
Indices: 5889811--5889869 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
5889801 AATAGTTTCT
** *
5889811 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
5889831 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
5889851 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
5889870 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:5890158 original size:22 final size:22
Alignment explanation
Indices: 5890132--5890175 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5890122 GATAGAGATA
5890132 GATGGATTTCGCCGGAGATGGG
1 GATGGATTTCGCCGGAGATGGG
*
5890154 GATGGATTTCGTCGGAGATGGG
1 GATGGATTTCGCCGGAGATGGG
5890176 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.11, G:0.45, T:0.25
Consensus pattern (22 bp):
GATGGATTTCGCCGGAGATGGG
Found at i:5890388 original size:20 final size:20
Alignment explanation
Indices: 5890363--5890415 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
5890353 GATTATGTAT
*
5890363 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
5890383 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
5890403 TATCTCGTTGCGA
1 TATCGCGTTGCGA
5890416 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:5890452 original size:20 final size:20
Alignment explanation
Indices: 5890343--5890457 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
5890333 CGCTTTGAAA
*
5890343 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
5890364 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
5890384 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
5890404 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
5890425 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
5890445 ATCTCATTGCGAT
1 ATCGCATTGCGAT
5890458 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.06
20 47 0.61
21 23 0.30
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:5890476 original size:41 final size:41
Alignment explanation
Indices: 5890385--5890519 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
5890375 AAAGTCAGTA
* * ** *
5890385 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCTCATTGCGATTTTCCCAAT
* *
5890425 ATCGCATTGCGATAGTCAGTATCTCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCTCATTGCGATTTTCCCAAT
* ** *
5890467 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCTCATTGCGATTTTCCCAAT
5890508 TCGCGTTGCGAT
1 TCGCGTTGCGAT
5890520 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCTCATTGCGATTTTCCCAAT
Found at i:5890477 original size:21 final size:21
Alignment explanation
Indices: 5890451--5890521 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
5890441 CAGTATCTCA
5890451 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
5890472 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
5890492 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
5890513 TTGCGATTT
1 TTGCGATTT
5890522 ACTTATTCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:5890490 original size:20 final size:20
Alignment explanation
Indices: 5890465--5890538 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
5890455 GATTTTCCCA
*
5890465 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
5890485 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
5890506 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
5890526 ATTCGCATTGCGA
1 ATTCGCATTGCGA
5890539 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:5890520 original size:41 final size:41
Alignment explanation
Indices: 5890449--5890538 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
5890439 GTCAGTATCT
5890449 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
5890490 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
5890531 CATTGCGA
1 CATTGCGA
5890539 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
Found at i:5891120 original size:19 final size:21
Alignment explanation
Indices: 5891092--5891136 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
5891082 AATGACCAAC
*
5891092 AATAATAAAA-TGGTAGAAA-
1 AATAACAAAACTGGTAGAAAT
5891111 AATAACAAAACTGGTAGAAAT
1 AATAACAAAACTGGTAGAAAT
5891132 AATAA
1 AATAA
5891137 TGTATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 9 0.39
21 5 0.22
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.20
Consensus pattern (21 bp):
AATAACAAAACTGGTAGAAAT
Found at i:5891919 original size:100 final size:99
Alignment explanation
Indices: 5891747--5891929 Score: 269
Period size: 100 Copynumber: 1.8 Consensus size: 99
5891737 TTTAATTGGA
* * * * *
5891747 TAAATTATATTTTAGTATCTAAATTATCAGTTTTAGTTCATTTTAGTACTTAAACTTTTAGTTTT
1 TAAATTATATTTTAATATCTAAACTATCAGTTCTAGTTCATTTTAGTACCTAAACTTTTAATTTT
5891812 TTCAAAATCATACCTAAAAAAGTTTAGTTGTGGG
66 TTCAAAATCATACCTAAAAAAGTTTAGTTGTGGG
* *
5891846 TAAATTATTTGTTTAATATCTAAACTATCAGTTCTAGTAT-GTTTTAGTACCTAAACTTTTAATT
1 TAAATTATAT-TTTAATATCTAAACTATCAGTTCTAGT-TCATTTTAGTACCTAAACTTTTAATT
*
5891910 TTTTTAAAATCATACCTAAA
64 TTTTCAAAATCATACCTAAA
5891930 GTTTAGTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
99 9 0.12
100 64 0.86
101 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.46
Consensus pattern (99 bp):
TAAATTATATTTTAATATCTAAACTATCAGTTCTAGTTCATTTTAGTACCTAAACTTTTAATTTT
TTCAAAATCATACCTAAAAAAGTTTAGTTGTGGG
Found at i:5892577 original size:20 final size:20
Alignment explanation
Indices: 5892552--5892591 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5892542 AACGAGATAC
*
5892552 TGACTTTCACAATGCGATTT
1 TGACTTTCACAACGCGATTT
*
5892572 TGACTTTCGCAACGCGATTT
1 TGACTTTCACAACGCGATTT
5892592 ACATAGCGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (20 bp):
TGACTTTCACAACGCGATTT
Found at i:5893169 original size:19 final size:19
Alignment explanation
Indices: 5893145--5893189 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
5893135 GCAACGAGAG
*
5893145 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
* *
5893164 AATCGCAATGCGAAACCAA
1 AATCGCAACGCGAAACAAA
5893183 AATCGCA
1 AATCGCA
5893190 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:5893250 original size:52 final size:52
Alignment explanation
Indices: 5893185--5893301 Score: 180
Period size: 52 Copynumber: 2.2 Consensus size: 52
5893175 GAAACCAAAA
* **
5893185 TCGCATTGCGATTTTCATTTCGCGTTGTGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
* *
5893237 TCGCAATGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTTCGATAGTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
*
5893289 TCGCGTTGCGATT
1 TCGCATTGCGATT
5893302 CTCTCGTTGC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:5893293 original size:33 final size:33
Alignment explanation
Indices: 5893251--5893338 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
5893241 AATGCGATTT
*
5893251 TCATTTCGCGTTGCGATTCTCTCGTTTCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
5893284 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
5893317 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
5893339 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
Found at i:5893340 original size:20 final size:19
Alignment explanation
Indices: 5893185--5893362 Score: 107
Period size: 19 Copynumber: 10.1 Consensus size: 19
5893175 GAAACCAAAA
* *
5893185 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
*
5893204 TCGCGTTGTGATTCTC---
1 TCGCGTTGCGATTCTCATT
*
5893220 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
** *
5893237 TCGCAATGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
5893256 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
* **
5893272 T--CGTTTCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
5893289 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
5893305 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
5893322 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
5893342 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
5893362 T
1 T
5893363 TAACCAAAAA
Statistics
Matches: 120, Mismatches: 22, Indels: 34
0.68 0.12 0.19
Matches are distributed among these distances:
14 32 0.27
16 3 0.03
17 3 0.03
19 51 0.43
20 30 0.25
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:5895526 original size:42 final size:42
Alignment explanation
Indices: 5895457--5895620 Score: 193
Period size: 42 Copynumber: 3.9 Consensus size: 42
5895447 GACTCGCCTG
* * * *
5895457 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGACCCCTA
1 TCATTCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
* * * * *
5895499 ACATTCCTCGAGAGTCCCCTCCCATCGTTCAAGAGGCCACTG
1 TCATTCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
* * *
5895541 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
* * *
5895583 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATTCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCC
5895621 ACTGTCATCG
Statistics
Matches: 99, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 99 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATTCCTCAAGAGTCCACTCCCATCGTTCAAGAGGCCCCTA
Found at i:5895533 original size:21 final size:21
Alignment explanation
Indices: 5895464--5895659 Score: 74
Period size: 21 Copynumber: 9.3 Consensus size: 21
5895454 CTGTCATCCC
* *
5895464 TCAAGAGTCCACTCCTATCGT
1 TCAAGAGTCCCCTCCCATCGT
* * ** *
5895485 TGAAGAGACCCCTAACATTC-C
1 TCAAGAGTCCCCTCCCA-TCGT
*
5895506 TCGAGAGTCCCCTCCCATCGT
1 TCAAGAGTCCCCTCCCATCGT
* * ** **
5895527 TCAAGAGGCCACTGTCATCCC
1 TCAAGAGTCCCCTCCCATCGT
* *
5895548 TCAAGAGTCCACTCCTATCGT
1 TCAAGAGTCCCCTCCCATCGT
* * ** *
5895569 TGAAGAGGCCCCTATCATTC-C
1 TCAAGAGTCCCCTCCCA-TCGT
* *
5895590 TCGAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCATCGT
* * **
5895611 TCAAGAGGCCACTGTCATCGT
1 TCAAGAGTCCCCTCCCATCGT
* * *
5895632 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCATCGT
5895653 TCAAGAG
1 TCAAGAG
5895660 CCCGATTCAT
Statistics
Matches: 116, Mismatches: 54, Indels: 11
0.64 0.30 0.06
Matches are distributed among these distances:
20 4 0.03
21 107 0.92
22 5 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.22
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCATCGT
Found at i:5895638 original size:84 final size:84
Alignment explanation
Indices: 5895454--5895629 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
5895444 CCCGACTCGC
5895454 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGACCCCTAACATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGACCCCTAACATTCCTCGAGAGTCCCCT
*
5895519 CCCATCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* *
5895538 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGACCCCTAACATTCCTCGAGAGTCCCCT
5895603 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
5895622 CTGTCATC
1 CTGTCATC
5895630 GTTGAAGAGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGACCCCTAACATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:5895645 original size:42 final size:41
Alignment explanation
Indices: 5895509--5895659 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 41
5895499 ACATTCCTCG
* * *
5895509 AGAGTCCCCTCCCATCGTTCAAGAGGCCACTGTCATCCCTCA
1 AGAGT-CCCTCCCACCGTTCAAGAGGCCACTGTCATCCTTGA
* * * * * *
5895551 AGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCG-
1 AGAGTCC-CTCCCACCGTTCAAGAGGCCACTGTCA-TCCTTGA
*
5895593 AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCGTTGA
1 AGAGT-CCCTCCCACCGTTCAAGAGGCCACTGTCATCCTTGA
*
5895635 AGAGGTCCCTCCCACCATTCAAGAG
1 AGA-GTCCCTCCCACCGTTCAAGAG
5895660 CCCGATTCAT
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
41 6 0.07
42 76 0.85
43 7 0.08
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.22
Consensus pattern (41 bp):
AGAGTCCCTCCCACCGTTCAAGAGGCCACTGTCATCCTTGA
Found at i:5895659 original size:84 final size:84
Alignment explanation
Indices: 5895454--5895659 Score: 270
Period size: 84 Copynumber: 2.5 Consensus size: 84
5895444 CCCGACTCGC
* * * *
5895454 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGACCCCTAACATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGACCCCTAACATTCCTCGAGAGTCCCCT
*
5895519 CCCATCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * * * *
5895538 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGACCCCTAACATTCCTCGAGAGTCCCCT
5895603 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
5895622 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
5895660 CCCGATTCAT
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 107 0.96
85 4 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGACCCCTAACATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:5897920 original size:12 final size:12
Alignment explanation
Indices: 5897903--5897927 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5897893 TCATCGGGGA
5897903 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5897915 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5897927 C
1 C
5897928 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:5898137 original size:24 final size:24
Alignment explanation
Indices: 5898103--5898156 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5898093 CTGAAATATC
*
5898103 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
5898127 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
5898151 ATCAAA
1 ATCAAA
5898157 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:5898924 original size:20 final size:20
Alignment explanation
Indices: 5898899--5898951 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
5898889 GATTCTGTAT
5898899 TATCTCGTTGCGAAAGTAAG
1 TATCTCGTTGCGAAAGTAAG
5898919 TATCTCGTTGCGAAAGTAAG
1 TATCTCGTTGCGAAAGTAAG
*
5898939 TATCGCGTTGCGA
1 TATCTCGTTGCGA
5898952 TTTTCCTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCTCGTTGCGAAAGTAAG
Found at i:5899035 original size:20 final size:20
Alignment explanation
Indices: 5899012--5899080 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
5899002 ATCGTAATGC
5899012 GATACTGACTATCGCAACGA
1 GATACTGACTATCGCAACGA
* *
5899032 GATAAT-ACAAAATCGCAACGA
1 GATACTGAC--TATCGCAACGA
* *
5899053 GATTCTGACTTTCGCAACGA
1 GATACTGACTATCGCAACGA
*
5899073 GATTCTGA
1 GATACTGA
5899081 AAATCGCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 22 0.55
21 14 0.35
22 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (20 bp):
GATACTGACTATCGCAACGA
Found at i:5899087 original size:20 final size:20
Alignment explanation
Indices: 5899040--5899089 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5899030 GAGATAATAC
5899040 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
5899060 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
5899080 AAAATCGCAA
1 AAAATCGCAA
5899090 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:5899378 original size:20 final size:20
Alignment explanation
Indices: 5899303--5899370 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
5899293 TAACGGGGAA
5899303 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
5899323 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
5899343 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
5899363 ATCGCAAC
1 ATCGCAAC
5899371 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:5899601 original size:14 final size:14
Alignment explanation
Indices: 5899582--5899618 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5899572 CATCAATTAA
5899582 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5899596 ACAAATCATCTTTT
1 ACAAATCAACATTT
5899610 ACAAATCAA
1 ACAAATCAA
5899619 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5900861 original size:15 final size:15
Alignment explanation
Indices: 5900843--5900871 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5900833 TCTTAGCCCA
5900843 AAGGGTACTAGCCGG
1 AAGGGTACTAGCCGG
5900858 AAGGGTACTAGCCG
1 AAGGGTACTAGCCG
5900872 ATAACTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.38, T:0.14
Consensus pattern (15 bp):
AAGGGTACTAGCCGG
Found at i:5901467 original size:20 final size:19
Alignment explanation
Indices: 5901444--5901581 Score: 82
Period size: 20 Copynumber: 7.7 Consensus size: 19
5901434 GAAACTTAAA
*
5901444 ATCGCAACGCGAAAATGATT
1 ATCGCAACGCG-AAATGAAT
* **
5901464 ATCGCAATGCGGAAATGGCT
1 ATCGCAACGC-GAAATGAAT
* *
5901484 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
*
5901503 ATCGCAA--CGACA--AA-
1 ATCGCAACGCGAAATGAAT
* *
5901517 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
*
5901536 ATCGCAA--CGACA--AA-
1 ATCGCAACGCGAAATGAAT
*
5901550 ATCACAACGCGAAATGAA-
1 ATCGCAACGCGAAATGAAT
5901568 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
5901582 CACAAATCAC
Statistics
Matches: 96, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
14 13 0.14
15 4 0.04
16 8 0.08
17 8 0.08
18 17 0.18
19 20 0.21
20 25 0.26
21 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAT
Found at i:5901506 original size:19 final size:19
Alignment explanation
Indices: 5901441--5901542 Score: 88
Period size: 20 Copynumber: 5.5 Consensus size: 19
5901431 CACGAAACTT
*
5901441 AAAATCGCAACGCGAAAATG
1 AAAATCGCAATGCG-AAATG
**
5901461 ATTATCGCAATGCGGAAATG
1 AAAATCGCAATGC-GAAATG
***
5901481 GCTATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
5901500 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
5901514 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
5901533 AAAATCGCAA
1 AAAATCGCAA
5901543 CGACAAAATC
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 23 0.35
20 26 0.39
21 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.16
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:5901519 original size:14 final size:14
Alignment explanation
Indices: 5901500--5901558 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
5901490 ATGCGAAATG
5901500 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
5901514 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
5901533 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
5901547 AAAATCACAACG
1 AAAATCGCAACG
5901559 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5901526 original size:33 final size:33
Alignment explanation
Indices: 5901484--5901576 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
5901474 GGAAATGGCT
5901484 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
5901517 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
5901550 ATCACAACGCGAAATG-AAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
5901577 CGAAACACAA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 11 0.19
33 47 0.81
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:5901631 original size:14 final size:14
Alignment explanation
Indices: 5901612--5901667 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
5901602 TCATTTCGCA
5901612 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
5901626 TTGCGATTTCATTTCG
1 TTGCGATTT--TGTCG
5901642 CCTTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
5901658 TTGCGATTTT
1 TTGCGATTTT
5901668 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.09, C:0.18, G:0.23, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:5901674 original size:33 final size:33
Alignment explanation
Indices: 5901593--5901683 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
5901583 ACAAATCACA
5901593 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
5901626 TTGCGA-TTTCATTTCGCCTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
5901658 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
5901684 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:5901720 original size:20 final size:20
Alignment explanation
Indices: 5901668--5901711 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5901658 TTGCGATTTT
*
5901668 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
5901687 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
5901707 CATTT
1 CATTT
5901712 TCGTGTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:5902230 original size:18 final size:18
Alignment explanation
Indices: 5902204--5902248 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5902194 GTCGATCAGA
*
5902204 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
5902222 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
5902240 TGATGGCTC
1 TGATGGCTC
5902249 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:5903890 original size:22 final size:22
Alignment explanation
Indices: 5903864--5903907 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5903854 GAGATAGATA
*
5903864 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
5903886 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
5903908 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:5904181 original size:20 final size:19
Alignment explanation
Indices: 5904075--5904209 Score: 99
Period size: 20 Copynumber: 6.7 Consensus size: 19
5904065 CACTTTGAAA
*
5904075 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
5904096 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGT-AGT
* *
5904116 ATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATAG-TAGT
* * * *
5904136 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
5904157 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGT-AGT
*
5904177 ATCGCATTGCGATAGTCATT
1 ATCGCATTGCGATAGT-AGT
5904197 ATCGCATTGCGAT
1 ATCGCATTGCGAT
5904210 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 15, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
19 5 0.05
20 63 0.67
21 25 0.27
22 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:5904181 original size:61 final size:61
Alignment explanation
Indices: 5904075--5904212 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
5904065 CACTTTGAAA
* * * * *
5904075 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTTAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
5904136 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCATT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
5904197 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
5904213 CCCAATTCGC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Done.