Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 19
Found at i:3539083 original size:15 final size:15
Alignment explanation
Indices: 3539063--3539091 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3539053 ACTGCAAATA
3539063 GTAATATTAGATAAT
1 GTAATATTAGATAAT
3539078 GTAATATTAGATAA
1 GTAATATTAGATAA
3539092 AACAACCACA
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:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (15 bp):
GTAATATTAGATAAT
Found at i:3540575 original size:18 final size:18
Alignment explanation
Indices: 3540554--3540588 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3540544 AATTAAAATT
3540554 TATA-ATAT-TATATAAA
1 TATATATATATATATAAA
3540570 TATATATATATATATAAA
1 TATATATATATATATAAA
3540588 T
1 T
3540589 TAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 4 0.24
18 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATATATATATATAAA
Found at i:3540977 original size:37 final size:35
Alignment explanation
Indices: 3540903--3540977 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 35
3540893 TTTTTTTTAA
* * *
3540903 AAAAATTAAAATTTATTATTATATTAAATATATTT
1 AAAAATTAAAATGTATTATTATATAAAATATAATT
3540938 AAAAATATAAAATGTATATATTATA-AAAATATTAATT
1 AAAAAT-TAAAATGTAT-TATTATATAAAATA-TAATT
3540975 AAA
1 AAA
3540978 TTTGCTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 6 0.18
36 14 0.41
37 14 0.41
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (35 bp):
AAAAATTAAAATGTATTATTATATAAAATATAATT
Found at i:3541895 original size:15 final size:15
Alignment explanation
Indices: 3541875--3541915 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
3541865 ACCTAATTGG
3541875 ATTAAAATAAAAT-AA
1 ATTAAAA-AAAATAAA
3541890 ATT-AAAAAAATAAA
1 ATTAAAAAAAATAAA
3541904 ATTAAAAAAAAT
1 ATTAAAAAAAAT
3541916 TCATCCAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.21
14 8 0.33
15 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
ATTAAAAAAAATAAA
Found at i:3541901 original size:13 final size:14
Alignment explanation
Indices: 3541883--3541913 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3541873 GGATTAAAAT
3541883 AAAAT-AAATTAAA
1 AAAATAAAATTAAA
3541896 AAAATAAAATTAAA
1 AAAATAAAATTAAA
3541910 AAAA
1 AAAA
3541914 ATTCATCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAAAATTAAA
Found at i:3543845 original size:23 final size:23
Alignment explanation
Indices: 3543815--3543860 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3543805 TAAGTGTGAC
*
3543815 TTGAAGGCTTGCAGGTTGGCAAG
1 TTGAAGGCTTGCAAGTTGGCAAG
3543838 TTGAAGGCTTGCAAGTTGGCAAG
1 TTGAAGGCTTGCAAGTTGGCAAG
3543861 ATTGGCAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.26
Consensus pattern (23 bp):
TTGAAGGCTTGCAAGTTGGCAAG
Found at i:3546899 original size:21 final size:21
Alignment explanation
Indices: 3546873--3546916 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3546863 ATTCTGGGCT
* *
3546873 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
3546894 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
3546915 AG
1 AG
3546917 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:3546985 original size:22 final size:22
Alignment explanation
Indices: 3546942--3546985 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3546932 AATGTCATGG
*
3546942 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
3546964 GGGAACCGATTCCCCTAAAGGA
1 GGGAACCGATACCCCCAAAGGA
3546986 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:3548532 original size:103 final size:103
Alignment explanation
Indices: 3548353--3548562 Score: 420
Period size: 103 Copynumber: 2.0 Consensus size: 103
3548343 GTCGAGGGTC
3548353 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
3548418 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
3548456 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
3548521 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
3548559 TATG
1 TATG
3548563 AGATCCTTAT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:3548634 original size:46 final size:46
Alignment explanation
Indices: 3548582--3548692 Score: 204
Period size: 46 Copynumber: 2.4 Consensus size: 46
3548572 TGGACATTAT
3548582 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
*
3548628 TATATGGCACTACGGTGTAACTCTACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
*
3548674 TATATGGCACTTCGGTGCA
1 TATATGGCACTACGGTGCA
3548693 TTTATATGAG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (46 bp):
TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
Found at i:3548682 original size:23 final size:23
Alignment explanation
Indices: 3548582--3548700 Score: 134
Period size: 23 Copynumber: 5.3 Consensus size: 23
3548572 TGGACATTAT
*
3548582 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
***
3548605 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
* *
3548628 TATATGGCACTACGGTGTAACTC
1 TATATGGCACTACGGTGCAATTC
***
3548651 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
3548674 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
3548695 TATATG
1 TATATG
3548701 AGCTGTGGTG
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
21 6 0.08
22 3 0.04
23 69 0.88
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:3552470 original size:21 final size:21
Alignment explanation
Indices: 3552444--3552487 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3552434 ATTCTGGGCT
* *
3552444 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
3552465 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
3552486 AG
1 AG
3552488 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:3552557 original size:23 final size:22
Alignment explanation
Indices: 3552513--3552557 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3552503 AATGTCATGG
*
3552513 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
3552535 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
3552558 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:3554150 original size:103 final size:103
Alignment explanation
Indices: 3553925--3554142 Score: 436
Period size: 103 Copynumber: 2.1 Consensus size: 103
3553915 GTCGAGGGTC
3553925 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
3553990 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
3554028 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
3554093 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
3554131 TATGTGGTCCTT
1 TATGTGGTCCTT
3554143 ATGGACATTA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:3554210 original size:23 final size:23
Alignment explanation
Indices: 3554154--3554226 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
3554144 TGGACATTAT
*
3554154 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
*** *
3554177 TACGCGACACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
3554200 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
3554221 TATATG
1 TATATG
3554227 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 6 0.15
22 3 0.08
23 31 0.77
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:3555419 original size:21 final size:21
Alignment explanation
Indices: 3555393--3555432 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3555383 AAACAAGTAG
*
3555393 TACTCCACAACAGGTGGAGCA
1 TACTCCAAAACAGGTGGAGCA
3555414 TACTCCAAAACAGGTGGAG
1 TACTCCAAAACAGGTGGAG
3555433 TTTCAGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGCA
Found at i:3567500 original size:13 final size:14
Alignment explanation
Indices: 3567477--3567509 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3567467 AGATGATTAT
3567477 TATTATTATAAATA
1 TATTATTATAAATA
*
3567491 TATT-TTATAAATT
1 TATTATTATAAATA
3567504 TATTAT
1 TATTAT
3567510 ACACTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTATTATAAATA
Found at i:3568059 original size:37 final size:39
Alignment explanation
Indices: 3568018--3568094 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
3568008 ATTTAACGTT
3568018 AAATTTTGAACG-AGG-TACTAAAATAAAACAAAAATAA
1 AAATTTTGAACGTAGGATACTAAAATAAAACAAAAATAA
* * *
3568055 AAATTTTGAAGGTGGGATACTAAAATAAAACAAAACTAA
1 AAATTTTGAACGTAGGATACTAAAATAAAACAAAAATAA
3568094 A
1 A
3568095 CTTTTAGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 11 0.31
38 2 0.06
39 22 0.63
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.22
Consensus pattern (39 bp):
AAATTTTGAACGTAGGATACTAAAATAAAACAAAAATAA
Found at i:3571051 original size:42 final size:42
Alignment explanation
Indices: 3571004--3571099 Score: 183
Period size: 42 Copynumber: 2.3 Consensus size: 42
3570994 ACGTTTCAAC
*
3571004 TCCACCGCCTCCAACTCAAAGAACATCACCAAATACGCATCT
1 TCCACCGCCACCAACTCAAAGAACATCACCAAATACGCATCT
3571046 TCCACCGCCACCAACTCAAAGAACATCACCAAATACGCATCT
1 TCCACCGCCACCAACTCAAAGAACATCACCAAATACGCATCT
3571088 TCCACCGCCACC
1 TCCACCGCCACC
3571100 CCCGCCTGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.34, C:0.44, G:0.07, T:0.15
Consensus pattern (42 bp):
TCCACCGCCACCAACTCAAAGAACATCACCAAATACGCATCT
Found at i:3571235 original size:27 final size:27
Alignment explanation
Indices: 3571192--3571252 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
3571182 AACACTCCAC
3571192 CACCACCACCTAACCATTACTC-CAATA
1 CACCACCACCTAACCATTAC-CACAATA
*
3571219 CTCCACCACC-AAGCCATTACCACAATA
1 CACCACCACCTAA-CCATTACCACAATA
3571246 CACCACC
1 CACCACC
3571253 CTCACCACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 27 0.90
ACGTcount: A:0.36, C:0.48, G:0.02, T:0.15
Consensus pattern (27 bp):
CACCACCACCTAACCATTACCACAATA
Found at i:3571308 original size:3 final size:3
Alignment explanation
Indices: 3571302--3571327 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3571292 CTATAATAAT
3571302 CCA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CC
3571328 GGCATCCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:3571627 original size:45 final size:45
Alignment explanation
Indices: 3571563--3571707 Score: 137
Period size: 45 Copynumber: 3.0 Consensus size: 45
3571553 TCAGTCTCCA
*
3571563 CCTCCACCAATAGAATACCATCCACCACCACCATCTTTTGAGCAT
1 CCTCCACCAATAGAATACCATCCACCACCACCATCTTATGAGCAT
* * **
3571608 CCTCCACCAGTTGAATACCATCCACCACCGTCATCTTATGAGCAT
1 CCTCCACCAATAGAATACCATCCACCACCACCATCTTATGAGCAT
* **
3571653 CAGTCGCCACCTCCATCAGTAGAATACCATCCACCACCGTCATCTTATGAGCAT
1 C---CTCCA---CCA--A-TAGAATACCATCCACCACCACCATCTTATGAGCAT
3571707 C
1 C
3571708 AGTCTCCTCC
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
45 41 0.49
48 4 0.05
51 3 0.04
54 35 0.42
ACGTcount: A:0.28, C:0.39, G:0.10, T:0.23
Consensus pattern (45 bp):
CCTCCACCAATAGAATACCATCCACCACCACCATCTTATGAGCAT
Found at i:3571647 original size:99 final size:99
Alignment explanation
Indices: 3571529--3571707 Score: 286
Period size: 99 Copynumber: 1.8 Consensus size: 99
3571519 CAAGCCCCCC
* *
3571529 TCCACCTCCGTCAACTTATGAGCATCAGTCTCCACCTCCACCAATAGAATACCATCCACCACCAC
1 TCCACCACCGTCAACTTATGAGCATCAGTCGCCACCTCCACCAATAGAATACCATCCACCACCAC
*
3571594 CATCTTTTGAGCATCCTCCACCAGTTGAATACCA
66 CATCTTATGAGCATCCTCCACCAGTTGAATACCA
* * * **
3571628 TCCACCACCGTCATCTTATGAGCATCAGTCGCCACCTCCATCAGTAGAATACCATCCACCACCGT
1 TCCACCACCGTCAACTTATGAGCATCAGTCGCCACCTCCACCAATAGAATACCATCCACCACCAC
3571693 CATCTTATGAGCATC
66 CATCTTATGAGCATC
3571708 AGTCTCCTCC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 72 1.00
ACGTcount: A:0.27, C:0.39, G:0.11, T:0.23
Consensus pattern (99 bp):
TCCACCACCGTCAACTTATGAGCATCAGTCGCCACCTCCACCAATAGAATACCATCCACCACCAC
CATCTTATGAGCATCCTCCACCAGTTGAATACCA
Found at i:3571662 original size:27 final size:27
Alignment explanation
Indices: 3571630--3571711 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 27
3571620 GAATACCATC
3571630 CACCACCGTCATCTTATGAGCATCAGT
1 CACCACCGTCATCTTATGAGCATCAGT
* * ** *
3571657 CGCCACC-TCCATCAGTA-GAATACCA-T
1 CACCACCGT-CATC-TTATGAGCATCAGT
3571683 CCACCACCGTCATCTTATGAGCATCAGT
1 -CACCACCGTCATCTTATGAGCATCAGT
3571711 C
1 C
3571712 TCCTCCACCA
Statistics
Matches: 39, Mismatches: 10, Indels: 12
0.64 0.16 0.20
Matches are distributed among these distances:
26 4 0.10
27 31 0.79
28 4 0.10
ACGTcount: A:0.27, C:0.37, G:0.13, T:0.23
Consensus pattern (27 bp):
CACCACCGTCATCTTATGAGCATCAGT
Found at i:3571690 original size:54 final size:54
Alignment explanation
Indices: 3571608--3571711 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
3571598 TTTTGAGCAT
*
3571608 CCTCCACCAGTTGAATACCATCCACCACCGTCATCTTATGAGCATCAGTCGCCA
1 CCTCCACCAGTAGAATACCATCCACCACCGTCATCTTATGAGCATCAGTCGCCA
*
3571662 CCTCCATCAGTAGAATACCATCCACCACCGTCATCTTATGAGCATCAGTC
1 CCTCCACCAGTAGAATACCATCCACCACCGTCATCTTATGAGCATCAGTC
3571712 TCCTCCACCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.27, C:0.38, G:0.12, T:0.23
Consensus pattern (54 bp):
CCTCCACCAGTAGAATACCATCCACCACCGTCATCTTATGAGCATCAGTCGCCA
Found at i:3573319 original size:14 final size:15
Alignment explanation
Indices: 3573300--3573328 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3573290 ATTCACTAAT
3573300 TAATTT-TTAAAATA
1 TAATTTGTTAAAATA
3573314 TAATTTGTTAAAATA
1 TAATTTGTTAAAATA
3573329 ATATTCATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TAATTTGTTAAAATA
Found at i:3573872 original size:25 final size:25
Alignment explanation
Indices: 3573844--3573894 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3573834 ATTTACTATC
3573844 AGTAACAGATAACACTTTTAGTGCT
1 AGTAACAGATAACACTTTTAGTGCT
* * * *
3573869 AGTATCATATACCACTTTTGGTGCT
1 AGTAACAGATAACACTTTTAGTGCT
3573894 A
1 A
3573895 AACAGAAGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (25 bp):
AGTAACAGATAACACTTTTAGTGCT
Found at i:3582435 original size:15 final size:16
Alignment explanation
Indices: 3582404--3582436 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3582394 ATTGAGAATG
3582404 TAAGATTACCAGGGAA
1 TAAGATTACCAGGGAA
3582420 TAAGATTACC-GGGAA
1 TAAGATTACCAGGGAA
3582435 TA
1 TA
3582437 TTGTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.21
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Found at i:3582644 original size:37 final size:37
Alignment explanation
Indices: 3582571--3582645 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
3582561 GTTGAAAAAT
*
3582571 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
3582608 ATTTATATAATTTT-TTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
3582645 A
1 A
3582646 ATGTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:3584739 original size:31 final size:32
Alignment explanation
Indices: 3584704--3584768 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
3584694 CAGGGGACCA
*
3584704 TTTATGTACTTTA-CCCATATAATGTAAACAT
1 TTTATGCACTTTACCCCATATAATGTAAACAT
3584735 TTTATGCACTTTACCCCATATAATGTAAACAT
1 TTTATGCACTTTACCCCATATAATGTAAACAT
3584767 TT
1 TT
3584769 ACTATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (32 bp):
TTTATGCACTTTACCCCATATAATGTAAACAT
Found at i:3585748 original size:18 final size:19
Alignment explanation
Indices: 3585713--3585750 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
3585703 CACGGAATGT
3585713 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
3585733 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
3585751 GATTACTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:3586257 original size:4 final size:4
Alignment explanation
Indices: 3586250--3586280 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
3586240 ATATACAATA
3586250 ATTT ATTT ATTT ATTT ATTT ATTAT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATT-T ATTT AT
3586281 ACTTAATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:3586279 original size:9 final size:9
Alignment explanation
Indices: 3586222--3586280 Score: 54
Period size: 8 Copynumber: 6.9 Consensus size: 9
3586212 TTAAGATATA
3586222 ATATTTATT
1 ATATTTATT
3586231 ATATCTTA-T
1 ATAT-TTATT
** *
3586240 ATATACAAT
1 ATATTTATT
3586249 A-ATTTATT
1 ATATTTATT
3586257 -TATTTATT
1 ATATTTATT
3586265 -TATTTATT
1 ATATTTATT
3586273 ATATTTAT
1 ATATTTAT
3586281 ACTTAATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 20 0.49
9 18 0.44
10 3 0.07
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (9 bp):
ATATTTATT
Found at i:3587659 original size:118 final size:117
Alignment explanation
Indices: 3587447--3587662 Score: 360
Period size: 118 Copynumber: 1.8 Consensus size: 117
3587437 ATTATGTTGA
* * * *
3587447 TCAACAAATTTCAGCAAAAACAACGAATTCCTTTCAAAATAATACTCGCATGGAATTATGAAAAT
1 TCAACAAATTTCAACAAAAACAACAAATTCCTTTCAAAATAATACTCGCATAGAACTATGAAAAT
*
3587512 TCTATCACAAATCCAGGAAAATAAGTGAAAATTTTACCTTATGGATGAAATT
66 TCTATCACAAATCCAGGAAAAGAAGTGAAAATTTTACCTTATGGATGAAATT
* *
3587564 TCAATAAATTTCAACAAAAACAACAAATTCCCTTTCAAAATAATACTCGCATAGAACTATTAAAA
1 TCAACAAATTTCAACAAAAACAACAAATT-CCTTTCAAAATAATACTCGCATAGAACTATGAAAA
3587629 TTCTATCACAAATCCAGGAAAAGAAGTGAAAATT
65 TTCTATCACAAATCCAGGAAAAGAAGTGAAAATT
3587663 CTATCACAAA
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 26 0.29
118 65 0.71
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.27
Consensus pattern (117 bp):
TCAACAAATTTCAACAAAAACAACAAATTCCTTTCAAAATAATACTCGCATAGAACTATGAAAAT
TCTATCACAAATCCAGGAAAAGAAGTGAAAATTTTACCTTATGGATGAAATT
Found at i:3593220 original size:15 final size:15
Alignment explanation
Indices: 3593200--3593243 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
3593190 TTTCGCACCT
*
3593200 CTGAATGATTCAGTG
1 CTGAATGATTCAGCG
*
3593215 CTGAATGATTCAACG
1 CTGAATGATTCAGCG
*
3593230 CTGATTGATTCAGC
1 CTGAATGATTCAGC
3593244 AAAACAATGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (15 bp):
CTGAATGATTCAGCG
Found at i:3593283 original size:27 final size:27
Alignment explanation
Indices: 3593253--3593318 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
3593243 CAAAACAATG
3593253 CTGAATGATTCAACACAGAAGTACATT
1 CTGAATGATTCAACACAGAAGTACATT
3593280 CTGAATGATTCAACACAGAAGTACATT
1 CTGAATGATTCAACACAGAAGTACATT
3593307 CTGAATGATTCA
1 CTGAATGATTCA
3593319 GAGCCAGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (27 bp):
CTGAATGATTCAACACAGAAGTACATT
Found at i:3593393 original size:16 final size:16
Alignment explanation
Indices: 3593372--3593412 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3593362 CCAGAGCCTC
*
3593372 TGAATCATTCAACATT
1 TGAATCATTCAACACT
*
3593388 TGAATCAATCAACACT
1 TGAATCATTCAACACT
3593404 T-AATCATTC
1 TGAATCATTC
3593413 TGAAATAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:3600991 original size:37 final size:36
Alignment explanation
Indices: 3600936--3601020 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 36
3600926 TGGTAACCAA
* *
3600936 CTTTGAAAAACTGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TGGTTTTCAAAATTTGATAAATGTTT
* *
3600973 CTTTGAAAAATAGTTTTTCAAAATTTGATAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAATTTGATAAATGTTT
*
3601010 -GTTGAAAAATG
1 CTTTGAAAAATG
3601021 ATAATGGGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 1 0.02
36 10 0.24
37 31 0.74
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAATTTGATAAATGTTT
Found at i:3605581 original size:37 final size:36
Alignment explanation
Indices: 3605499--3605610 Score: 115
Period size: 37 Copynumber: 3.2 Consensus size: 36
3605489 TGAAATTATT
** *
3605499 AAAATGGTTTTC-AAGTTTGGTAACCA--ACTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTGA
3605532 AAAACTGGTTTTCAAAGTTTGGTAAATATTTCTTTGA
1 AAAA-TGGTTTTCAAAGTTTGGTAAATATTTCTTTGA
* * * *
3605569 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATATTTCTTTGA
3605605 AAAATG
1 AAAATG
3605611 ATAATGTAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
33 4 0.06
34 8 0.12
35 13 0.19
36 10 0.15
37 32 0.48
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (36 bp):
AAAATGGTTTTCAAAGTTTGGTAAATATTTCTTTGA
Found at i:3607849 original size:27 final size:27
Alignment explanation
Indices: 3607798--3607849 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3607788 CCACGGCCCC
* * * *
3607798 TCGACGAACTACCTTGAGTAGCACCGA
1 TCGACAAACCACCTTGAGCACCACCGA
3607825 TCGACAAACCACCTTGAGCACCACC
1 TCGACAAACCACCTTGAGCACCACC
3607850 ACCACCACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.31, C:0.37, G:0.17, T:0.15
Consensus pattern (27 bp):
TCGACAAACCACCTTGAGCACCACCGA
Found at i:3609781 original size:19 final size:20
Alignment explanation
Indices: 3609757--3609797 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
3609747 GACTTCAGTC
3609757 TGCAGAACAAAG-AATCATG
1 TGCAGAACAAAGCAATCATG
*
3609776 TGCAGACCAAAGCCAATCATG
1 TGCAGAACAAAG-CAATCATG
3609797 T
1 T
3609798 TCTATCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (20 bp):
TGCAGAACAAAGCAATCATG
Found at i:3623830 original size:31 final size:31
Alignment explanation
Indices: 3623790--3623854 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
3623780 AAAAACATAT
*
3623790 GATATGATCACTTTCGTTTTTATTTAATTAA
1 GATACGATCACTTTCGTTTTTATTTAATTAA
3623821 GATACGATCACTTTCGTTTTTATTTAATTAA
1 GATACGATCACTTTCGTTTTTATTTAATTAA
3623852 GAT
1 GAT
3623855 GTGGTCATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (31 bp):
GATACGATCACTTTCGTTTTTATTTAATTAA
Found at i:3624055 original size:27 final size:26
Alignment explanation
Indices: 3624014--3624102 Score: 96
Period size: 23 Copynumber: 3.5 Consensus size: 26
3624004 GAAAATAAAA
* *
3624014 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAAAATATTT-AATTAAGTTAAT
3624041 AATAAAAAATATTTAA-TAAGTTAAT
1 AATAAAAAATATTTAATTAAGTTAAT
*
3624066 -AT-AAAAATATTT-TTTAAGTTAAT
1 AATAAAAAATATTTAATTAAGTTAAT
*
3624089 ATATATAAAATATT
1 A-ATAAAAAATATT
3624103 ATGGATTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
23 19 0.35
24 2 0.04
25 11 0.20
26 10 0.19
27 12 0.22
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
AATAAAAAATATTTAATTAAGTTAAT
Found at i:3625552 original size:13 final size:14
Alignment explanation
Indices: 3625534--3625564 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3625524 AATCGAAAGC
3625534 AAAAACAC-GAGAA
1 AAAAACACAGAGAA
3625547 AAAAACACAGAGAA
1 AAAAACACAGAGAA
3625561 AAAA
1 AAAA
3625565 GGGCTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAACACAGAGAA
Found at i:3629040 original size:2 final size:2
Alignment explanation
Indices: 3629033--3629076 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3629023 TAGTTTACCC
3629033 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3629075 AT
1 AT
3629077 GAGTTGTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3633681 original size:15 final size:15
Alignment explanation
Indices: 3633661--3633717 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
3633651 TTAGTTTAGT
3633661 TTAATATATAAAATA
1 TTAATATATAAAATA
**
3633676 TTAATA-ATTGAATA
1 TTAATATATAAAATA
*
3633690 TGTAATATTATAATATA
1 T-TAATA-TATAAAATA
3633707 TTATATATATA
1 TTA-ATATATA
3633718 TAATTGGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
14 7 0.21
15 11 0.33
16 6 0.18
17 9 0.27
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (15 bp):
TTAATATATAAAATA
Found at i:3636309 original size:21 final size:18
Alignment explanation
Indices: 3636269--3636303 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3636259 AGGCGATGGC
*
3636269 GGCATCATATATGGCTGT
1 GGCATCATAAATGGCTGT
3636287 GGCATCATAAATGGCTG
1 GGCATCATAAATGGCTG
3636304 CGGTGGCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (18 bp):
GGCATCATAAATGGCTGT
Found at i:3641994 original size:17 final size:18
Alignment explanation
Indices: 3641972--3642006 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
3641962 TTAAATTGTA
3641972 TTTAAATG-TATATTAAT
1 TTTAAATGATATATTAAT
3641989 TTTAAATGAATATATTAA
1 TTTAAATG-ATATATTAA
3642007 GGAAAATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
TTTAAATGATATATTAAT
Found at i:3642275 original size:14 final size:14
Alignment explanation
Indices: 3642258--3642288 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3642248 TGGAAAACAT
*
3642258 ATTCCGAAAAATGA
1 ATTCCAAAAAATGA
3642272 ATTCCAAAAAATGA
1 ATTCCAAAAAATGA
3642286 ATT
1 ATT
3642289 ATATTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (14 bp):
ATTCCAAAAAATGA
Found at i:3642436 original size:24 final size:22
Alignment explanation
Indices: 3642400--3642444 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
3642390 TATCAAATAC
3642400 AAAAAATAATATTATTTATTAAT
1 AAAAAATAATATTATTT-TTAAT
*
3642423 AAAATAATATTATTATTTTTAA
1 AAAA-AATAATATTATTTTTAA
3642445 AATATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAAAATAATATTATTTTTAAT
Found at i:3642445 original size:20 final size:21
Alignment explanation
Indices: 3642402--3642467 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 21
3642392 TCAAATACAA
3642402 AAAATAATATTATTTATTAAT
1 AAAATAATATTATTTATTAAT
**
3642423 AAAATAATATTA-TTATTTTT
1 AAAATAATATTATTTATTAAT
*
3642443 AAAATATTATAATATTTACTTAAT
1 AAAATA--ATATTATTTA-TTAAT
3642467 A
1 A
3642468 CTATTTATGC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.33
21 12 0.33
22 5 0.14
23 3 0.08
24 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AAAATAATATTATTTATTAAT
Found at i:3642567 original size:34 final size:36
Alignment explanation
Indices: 3642508--3642637 Score: 95
Period size: 42 Copynumber: 3.5 Consensus size: 36
3642498 TATATCTATA
3642508 ATTATAAATAAAAATATTTAAA-T-TATTAAAT-TTT
1 ATTA-AAATAAAAATATTTAAATTATATTAAATATTT
* * *
3642542 ATTAAAATAAAATTCTTATAAATTATATTAATTATTT
1 ATTAAAATAAAAATATT-TAAATTATATTAAATATTT
* * *
3642579 ATTAAAATGAGAATAATATATTACTACTTATATTAATTACTT
1 ATTAAAAT-A-AA-AATAT-TTA--AATTATATTAAATATTT
* *
3642621 ATTAAGATAATAATATT
1 ATTAAAATAAAAATATT
3642638 ATTAAAATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
33 11 0.14
34 8 0.10
35 1 0.01
36 7 0.09
37 11 0.14
38 2 0.03
39 7 0.09
40 6 0.08
41 2 0.03
42 22 0.29
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (36 bp):
ATTAAAATAAAAATATTTAAATTATATTAAATATTT
Found at i:3642784 original size:8 final size:8
Alignment explanation
Indices: 3642771--3642801 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3642761 TTAAAACAAA
3642771 ATTATAAT
1 ATTATAAT
3642779 ATTAT-AT
1 ATTATAAT
3642786 ATTATAAT
1 ATTATAAT
3642794 ATTATAAT
1 ATTATAAT
3642802 TATAACAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTATAAT
Found at i:3642791 original size:15 final size:14
Alignment explanation
Indices: 3642770--3642806 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
3642760 ATTAAAACAA
3642770 AATTATAATATTAT
1 AATTATAATATTAT
3642784 ATATTATAATATTAT
1 A-ATTATAATATTAT
3642799 AATTATAA
1 AATTATAA
3642807 CAATAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTATAATATTAT
Found at i:3644735 original size:13 final size:13
Alignment explanation
Indices: 3644717--3644741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3644707 TAATTACATT
3644717 ATTTTTAATAATC
1 ATTTTTAATAATC
3644730 ATTTTTAATAAT
1 ATTTTTAATAAT
3644742 ACTTGGATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTTAATAATC
Found at i:3645183 original size:19 final size:20
Alignment explanation
Indices: 3645143--3645186 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3645133 ATTGAGTAAT
*
3645143 CTAATCCCTAAATTAGAACC
1 CTAATCCCAAAATTAGAACC
3645163 CTAATCCCAAAATTA-AACC
1 CTAATCCCAAAATTAGAACC
3645182 CTAAT
1 CTAAT
3645187 TTTTATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.25
Consensus pattern (20 bp):
CTAATCCCAAAATTAGAACC
Found at i:3645934 original size:9 final size:9
Alignment explanation
Indices: 3645920--3645948 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
3645910 ACATAATTCT
3645920 ATAAACATA
1 ATAAACATA
3645929 ATAAACATA
1 ATAAACATA
3645938 ATAAACATA
1 ATAAACATA
3645947 AT
1 AT
3645949 TCTATAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAAACATA
Found at i:3646832 original size:25 final size:23
Alignment explanation
Indices: 3646768--3646840 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 23
3646758 ACAAAAAGAA
3646768 AAATAT-ATATAAATAAATAAAT
1 AAATATAATATAAATAAATAAAT
* * *
3646790 AGATAGAATATAAGAATAAGTAATAT
1 AAATATAATAT-A-AATAAATAA-AT
3646816 ATAATATAATATAAATAGAA-AAAT
1 A-AATATAATATAAATA-AATAAAT
3646840 A
1 A
3646841 GTAATAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
22 4 0.10
23 4 0.10
24 4 0.10
25 14 0.36
26 5 0.13
27 8 0.21
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (23 bp):
AAATATAATATAAATAAATAAAT
Found at i:3648795 original size:28 final size:29
Alignment explanation
Indices: 3648756--3648825 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
3648746 TCCCTAATTT
*
3648756 TTTTTTGGATTTTTA-GGAATTT-AGGAG
1 TTTTTTGAATTTTTATGGAATTTAAGGAG
* **
3648783 TTTTTTGAAATTTTATGGAATTTAAGGTT
1 TTTTTTGAATTTTTATGGAATTTAAGGAG
3648812 TTTTTTGGAATTTT
1 TTTTTT-GAATTTT
3648826 AATAATTTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 13 0.37
28 7 0.20
29 9 0.26
30 6 0.17
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (29 bp):
TTTTTTGAATTTTTATGGAATTTAAGGAG
Found at i:3648815 original size:29 final size:29
Alignment explanation
Indices: 3648754--3648851 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
3648744 TATCCCTAAT
* *
3648754 TTTTTTTTGGATTTTTA-GGAATTT-AGG
1 TTTTTTTTGAAATTTTATGGAATTTAAGG
**
3648781 AGTTTTTTGAAATTTTATGGAATTTAAGG
1 TTTTTTTTGAAATTTTATGGAATTTAAGG
*
3648810 TTTTTTTTGGAATTTTAAT--AATTTCATAGG
1 TTTTTTTTGAAATTTT-ATGGAATTT-A-AGG
*
3648840 TTTTTTATGAAA
1 TTTTTTTTGAAA
3648852 ATAACTTTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
27 13 0.23
28 12 0.21
29 17 0.30
30 15 0.26
ACGTcount: A:0.27, C:0.01, G:0.17, T:0.55
Consensus pattern (29 bp):
TTTTTTTTGAAATTTTATGGAATTTAAGG
Found at i:3649472 original size:21 final size:21
Alignment explanation
Indices: 3649443--3649494 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3649433 GAAATTTGCT
*
3649443 AAAA-TAAATGATCGATTCAA
1 AAAATTAAATGATCAATTCAA
* **
3649463 AAAATTAAATGGTCAATTTGA
1 AAAATTAAATGATCAATTCAA
3649484 AAAATTAAATG
1 AAAATTAAATG
3649495 GCCAATTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAATTAAATGATCAATTCAA
Found at i:3649495 original size:21 final size:21
Alignment explanation
Indices: 3649462--3649511 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3649452 GATCGATTCA
*
3649462 AAAAATTAAATGGTCAATTTG
1 AAAAATTAAATGGCCAATTTG
3649483 AAAAATTAAATGGCCAATTTG
1 AAAAATTAAATGGCCAATTTG
3649504 AAAAATTA
1 AAAAATTA
3649512 GTGACCAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (21 bp):
AAAAATTAAATGGCCAATTTG
Found at i:3649522 original size:21 final size:21
Alignment explanation
Indices: 3649462--3649519 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3649452 GATCGATTCA
**
3649462 AAAAATTAAATGGTCAATTTG
1 AAAAATTAAATGACCAATTTG
*
3649483 AAAAATTAAATGGCCAATTTG
1 AAAAATTAAATGACCAATTTG
*
3649504 AAAAATT-AGTGACCAA
1 AAAAATTAAATGACCAA
3649520 ATTAACACCG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 7 0.21
21 27 0.79
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.28
Consensus pattern (21 bp):
AAAAATTAAATGACCAATTTG
Found at i:3651615 original size:22 final size:22
Alignment explanation
Indices: 3651585--3651666 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
3651575 ATCAGATAAC
3651585 AAAGTGCCTTAACACTAATACT
1 AAAGTGCCTTAACACTAATACT
* * * * **
3651607 AAAGAGCCTCAGCACTAGTAAA
1 AAAGTGCCTTAACACTAATACT
* * *
3651629 AAAGTGCATTCACACTGATACT
1 AAAGTGCCTTAACACTAATACT
* *
3651651 AATGGGCCTTAACACT
1 AAAGTGCCTTAACACT
3651667 GATAGGAGAA
Statistics
Matches: 41, Mismatches: 19, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (22 bp):
AAAGTGCCTTAACACTAATACT
Found at i:3655280 original size:31 final size:30
Alignment explanation
Indices: 3655238--3655304 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 30
3655228 CTTAAAAAAA
3655238 CCGACCGACCAAAATAAAGTTTCACCCGAC
1 CCGACCGACCAAAATAAAGTTTCACCCGAC
3655268 CCGACCTGACCAAAATAAAGTTTCACCCGAC
1 CCGACC-GACCAAAATAAAGTTTCACCCGAC
3655299 CCGACC
1 CCGACC
3655305 CAAATATATG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.17
31 30 0.83
ACGTcount: A:0.34, C:0.39, G:0.13, T:0.13
Consensus pattern (30 bp):
CCGACCGACCAAAATAAAGTTTCACCCGAC
Found at i:3655742 original size:29 final size:31
Alignment explanation
Indices: 3655703--3655764 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
3655693 CAATACTTTA
3655703 AAAATTTATTT-GAAAACTTAGCTCTTTTTC
1 AAAATTTATTTGGAAAACTTAGCTCTTTTTC
**
3655733 AAAA-TTATTTGGAGTACTTAGCTCTTTTTC
1 AAAATTTATTTGGAAAACTTAGCTCTTTTTC
3655763 AA
1 AA
3655765 CTTTTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (31 bp):
AAAATTTATTTGGAAAACTTAGCTCTTTTTC
Found at i:3657521 original size:41 final size:39
Alignment explanation
Indices: 3657476--3657598 Score: 131
Period size: 41 Copynumber: 3.0 Consensus size: 39
3657466 ATTAGATGCA
*
3657476 AAAACCTAAAA-ACAAAATATAATATTCAAATAAATTAAACT
1 AAAACCTAAAAGACAAAAGAT-AT-TT-AAATAAATTAAACT
* *
3657517 AAAACCTAAAATGGACAAACGATATTTGAATAAATTAAACT
1 AAAACCTAAAA--GACAAAAGATATTTAAATAAATTAAACT
* *
3657558 AAAACCTAAAATGGACAAACGATATTTGAATAAATTAAACT
1 AAAACCTAAAA--GACAAAAGATATTTAAATAAATTAAACT
3657599 TTGTATGTAA
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
41 65 0.86
42 2 0.03
43 2 0.03
44 7 0.09
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (39 bp):
AAAACCTAAAAGACAAAAGATATTTAAATAAATTAAACT
Found at i:3658009 original size:20 final size:20
Alignment explanation
Indices: 3657984--3658022 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3657974 CAAATTTCGC
3657984 AACGCGAATCTGTAAATCGT
1 AACGCGAATCTGTAAATCGT
*
3658004 AACGCGAATTTGTAAATCG
1 AACGCGAATCTGTAAATCG
3658023 CAACACAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AACGCGAATCTGTAAATCGT
Found at i:3658045 original size:20 final size:19
Alignment explanation
Indices: 3658020--3658245 Score: 158
Period size: 20 Copynumber: 11.4 Consensus size: 19
3658010 AATTTGTAAA
3658020 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
3658040 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
3658060 TCGCAACACTGAAGTCAACT
1 TCGCAACAC-GAAGTCAAAT
*
3658080 TCGCAACACAAAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
3658100 TCGCAACGCGAATATGT-AAA-
1 TCGCAACACG-A-A-GTCAAAT
*
3658120 TCGCAACGCGAATTTGT-AAA-
1 TCGCAACACGAA---GTCAAAT
3658140 TCGCAACACAGAAGTCAAAT
1 TCGCAACAC-GAAGTCAAAT
*
3658160 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGA-AGTCAAAT
*
3658180 TCGCAACACTGAATTTCAAAT
1 TCGCAACAC-GAA-GTCAAAT
* * *
3658201 TCGCAGC-TGAATTTCAAAT
1 TCGCAACACGAA-GTCAAAT
* *
3658220 TCGCAAC-TGAATTTCAAAT
1 TCGCAACACGAA-GTCAAAT
3658239 TCGCAAC
1 TCGCAAC
3658246 TCGATTTTCG
Statistics
Matches: 178, Mismatches: 15, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
18 3 0.02
19 44 0.25
20 106 0.60
21 23 0.13
22 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.22
Consensus pattern (19 bp):
TCGCAACACGAAGTCAAAT
Found at i:3658048 original size:40 final size:41
Alignment explanation
Indices: 3658004--3658226 Score: 202
Period size: 40 Copynumber: 5.6 Consensus size: 41
3657994 TGTAAATCGT
*
3658004 AACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAATTCGC
1 AACGCGAA-TAGTCAAATTCGCAACACAGAAGTCAAATTCGC
* *
3658044 AACGCG-ATAGTCAAATTCGCAACACTGAAGTCAACTTCGC
1 AACGCGAATAGTCAAATTCGCAACACAGAAGTCAAATTCGC
* * *
3658084 AACAC-AAAAGTCAAATTCGCAACGC-GAATATGT-AAA-TCGC
1 AACGCGAATAGTCAAATTCGCAACACAG-A-A-GTCAAATTCGC
*
3658124 AACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAATTCGC
1 AACGCGAA-TAGTCAAATTCGCAACACAGAAGTCAAATTCGC
* *
3658164 AACGCG-ATAGTCAAATTCGCAACACTGAATTTCAAATTCGC
1 AACGCGAATAGTCAAATTCGCAACACAGAA-GTCAAATTCGC
*
3658205 -A-GCTGAAT-TTCAAATTCGCAAC
1 AACGC-GAATAGTCAAATTCGCAAC
3658227 TGAATTTCAA
Statistics
Matches: 152, Mismatches: 15, Indels: 32
0.76 0.08 0.16
Matches are distributed among these distances:
38 8 0.05
39 15 0.10
40 104 0.68
41 21 0.14
42 4 0.03
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (41 bp):
AACGCGAATAGTCAAATTCGCAACACAGAAGTCAAATTCGC
Found at i:3658084 original size:60 final size:59
Alignment explanation
Indices: 3658014--3658193 Score: 251
Period size: 60 Copynumber: 3.0 Consensus size: 59
3658004 AACGCGAATT
3658014 TGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAA
1 TGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAA
* * *
3658073 -GTCAACTTCGCAACACAAAAGTCAAATTCGCAACGCGAATATGT-AAA-TCGCAACGC-GAA
1 TGT-AA-ATCGCAACACAGAAGTCAAATTCGCAACGCG-ATA-GTCAAATTCGCAACACTGAA
3658132 TTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAA
1 --TGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAA
3658193 T
1 T
3658194 TTCAAATTCG
Statistics
Matches: 105, Mismatches: 6, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
58 4 0.04
59 12 0.11
60 74 0.70
61 11 0.10
62 4 0.04
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (59 bp):
TGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAA
Found at i:3658148 original size:120 final size:121
Alignment explanation
Indices: 3657974--3658192 Score: 413
Period size: 120 Copynumber: 1.8 Consensus size: 121
3657964 ACCCAGTTTA
* *
3657974 CAAATTTCGCAACGCGAATCTGTAAATCGTAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
1 CAAATTTCGCAACGCGAATATGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
3658039 TTCGCAACGCGATAGTCAAATTCGCAACACTGAAGTCAACTTCGCAACACAAAAGT
66 TTCGCAACGCGATAGTCAAATTCGCAACACTGAAGTCAACTTCGCAACACAAAAGT
3658095 CAAA-TTCGCAACGCGAATATGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
1 CAAATTTCGCAACGCGAATATGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
3658159 TTCGCAACGCGATAGTCAAATTCGCAACACTGAA
66 TTCGCAACGCGATAGTCAAATTCGCAACACTGAA
3658193 TTTCAAATTC
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
120 92 0.96
121 4 0.04
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (121 bp):
CAAATTTCGCAACGCGAATATGTAAATCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
TTCGCAACGCGATAGTCAAATTCGCAACACTGAAGTCAACTTCGCAACACAAAAGT
Found at i:3658212 original size:19 final size:19
Alignment explanation
Indices: 3658174--3658260 Score: 120
Period size: 19 Copynumber: 4.4 Consensus size: 19
3658164 AACGCGATAG
3658174 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
*
3658195 TCAAATTCGCAGCTGAATT
1 TCAAATTCGCAACTGAATT
3658214 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
3658233 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
*
3658253 TCGAATTC
1 TCAAATTC
3658261 AACACAAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
19 39 0.64
20 12 0.20
21 10 0.16
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:3658218 original size:60 final size:59
Alignment explanation
Indices: 3658027--3658226 Score: 221
Period size: 60 Copynumber: 3.3 Consensus size: 59
3658017 AAATCGCAAC
* *
3658027 ACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAA-GTCAACTTCGCAA
1 ACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAATTTCAAATTCGC-A
* * *
3658086 CACAAAAGTCAAATTCGCAACGCGAATATGT-AAA-TCGCAACGC-GAATTTGTAAA-TCGCAA
1 -ACAGAAGTCAAATTCGCAACGCG-ATA-GTCAAATTCGCAACACTGAATTT-CAAATTCGC-A
3658146 CACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAATTTCAAATTCGCA
1 -ACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAATTTCAAATTCGCA
* * *
3658206 GCTGAATTTCAAATTCGCAAC
1 ACAGAA-GTCAAATTCGCAAC
3658227 TGAATTTCAA
Statistics
Matches: 120, Mismatches: 11, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
58 2 0.02
59 13 0.11
60 85 0.71
61 18 0.15
62 2 0.02
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (59 bp):
ACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAATTTCAAATTCGCA
Found at i:3658271 original size:38 final size:39
Alignment explanation
Indices: 3658034--3658271 Score: 116
Period size: 40 Copynumber: 6.0 Consensus size: 39
3658024 AACACAGAAG
* ** *
3658034 TCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAA-G
1 TCAAATTCGCAACTCGATTTTCAAATTC-CAACAC-GAATT
* * * *** *
3658074 TCAACTTCGCAACACAAAAGTCAAATTCGCAACGCGAATAT
1 TCAAATTCGCAACTCGATTTTCAAATTC-CAACACGAAT-T
* *
3658115 GT-AAA-TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAA-G
1 -TCAAATTCGCAACTCG-ATTT-TCAAATTC-CAACAC-GAATT
* **
3658154 TCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGAATT
1 TCAAATTCGCAACTCGATTTTCAAATTC-CAACAC-GAATT
* * *
3658195 TCAAATTCGCAGCT-GAATTTCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACTCGATTTTCAAATTC-CAACACGAATT
* *
3658233 TCAAATTCGCAACTCGATTTTCGAATT-CAACACAAATT
1 TCAAATTCGCAACTCGATTTTCAAATTCCAACACGAATT
3658271 T
1 T
3658272 AATTTCGAAA
Statistics
Matches: 156, Mismatches: 29, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
37 4 0.03
38 25 0.16
39 21 0.13
40 83 0.53
41 21 0.13
42 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (39 bp):
TCAAATTCGCAACTCGATTTTCAAATTCCAACACGAATT
Found at i:3659246 original size:24 final size:24
Alignment explanation
Indices: 3659219--3659278 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
3659209 TAGTCAGTAT
3659219 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
3659243 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* *
3659267 TCGGATTTTGAT
1 TCGAAATTTGAT
3659279 GATGTTTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:3661941 original size:66 final size:65
Alignment explanation
Indices: 3661859--3662031 Score: 258
Period size: 66 Copynumber: 2.6 Consensus size: 65
3661849 TTAAAACAAA
3661859 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTAAA
1 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATTAAA
3661924 C
65 C
* *
3661925 AAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTAAAC
1 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAAAC
*
3661989 AAATCAACTTTCAATGCAAAATTCAATTAAACAAGCAAAAAAA
1 AAATCAACTTT---TAC-AAA-TCAATTAAACAAGCAAAAAAA
3662032 GTGTACCCAG
Statistics
Matches: 98, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
64 19 0.19
65 23 0.23
66 31 0.32
67 2 0.02
68 3 0.03
69 14 0.14
70 6 0.06
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (65 bp):
AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAAAC
Found at i:3663402 original size:21 final size:21
Alignment explanation
Indices: 3663378--3663471 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
3663368 GAGGGACCCA
* *
3663378 TTGAACGACGACAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
* *
3663399 TTGAACGGTGGGAGGGG-CTC
1 TTGAACGATGAGAGGGGCCTC
* * *
3663419 TTGAACAATGAGAGGAGTCTC
1 TTGAACGATGAGAGGGGCCTC
*
3663440 TTGAACGAT-AGGAGGTGCCTC
1 TTGAACGATGA-GAGGGGCCTC
3663461 TTGAACGATGA
1 TTGAACGATGA
3663472 CAGGTGAATC
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
20 17 0.29
21 41 0.69
22 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (21 bp):
TTGAACGATGAGAGGGGCCTC
Found at i:3663776 original size:21 final size:21
Alignment explanation
Indices: 3663752--3663801 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
3663742 TGAAACAATC
* * *
3663752 TCACGTAGAGCGGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
* *
3663773 TCACATAAAGTAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
3663794 TCACGTAA
1 TCACGTAA
3663802 CGCAACATTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:3666049 original size:22 final size:22
Alignment explanation
Indices: 3666022--3666078 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
3666012 GATGGAGATA
3666022 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3666044 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3666066 GACGGATGTCGCC
1 GACGGATTTCGCC
3666079 ATAGAGAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.19, G:0.44, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3666336 original size:20 final size:19
Alignment explanation
Indices: 3666232--3666338 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 19
3666222 TAAACGCGTT
*
3666232 TTGCGAATTTGACTTTCACG
1 TTGCGAATTTGA-TTTCATG
* **
3666252 TTACGAATTTGATTATCGCG
1 TTGCGAATTTGATT-TCATG
* ** *
3666272 TTGCAAATTTGATTTTTTTA
1 TTGCGAATTTGA-TTTCATG
* *
3666292 TTGTGAATTTGAAATTCAGTG
1 TTGCGAATTTG-ATTTCA-TG
3666313 TTGCGAATTTGATTTCTATG
1 TTGCGAATTTGATTTC-ATG
3666333 TTGCGA
1 TTGCGA
3666339 TTTACAAATT
Statistics
Matches: 66, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.03
20 49 0.74
21 15 0.23
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (19 bp):
TTGCGAATTTGATTTCATG
Found at i:3666356 original size:20 final size:20
Alignment explanation
Indices: 3666333--3666378 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3666323 GATTTCTATG
*
3666333 TTGCGATTTACAAATTTGCA
1 TTGCGATTTACAAATTCGCA
* * *
3666353 TTGCTATTTACAGATTCGCG
1 TTGCGATTTACAAATTCGCA
3666373 TTGCGA
1 TTGCGA
3666379 ATTTGACTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:3666391 original size:20 final size:20
Alignment explanation
Indices: 3666368--3666543 Score: 184
Period size: 20 Copynumber: 8.8 Consensus size: 20
3666358 ATTTACAGAT
3666368 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
3666388 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
3666408 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
3666428 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* *
3666448 TCACGTTGTGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
* *
3666467 TCTGTGTTGCG-ATTT-ACAGA
1 TC-GCGTTGCGAATTTGAC-TA
*
3666487 TTCGCATTGCGAATTTG--TAA
1 -TCGCGTTGCGAATTTGACT-A
* * *
3666507 ACTGGGTTGCGAAATTTGA-GA
1 TC-GCGTTGCG-AATTTGACTA
3666528 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
3666544 TTGGTCATTT
Statistics
Matches: 131, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.02
19 13 0.10
20 102 0.78
21 14 0.11
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:3666917 original size:41 final size:41
Alignment explanation
Indices: 3666825--3666917 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 41
3666815 AGTTGAACGG
* * *
3666825 TGCTCGACTCGACTCGATACTTGATAAGCTCCATAAAATTT
1 TGCTTGACTTGACTCGATACTTGATAAGATCCATAAAATTT
* *
3666866 TACTCT-ACTTGACTCGATACTTGATATGATCCATAAAATTT
1 TGCT-TGACTTGACTCGATACTTGATAAGATCCATAAAATTT
3666907 TGCTTGACTTG
1 TGCTTGACTTG
3666918 TATTTTTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
40 1 0.02
41 43 0.98
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (41 bp):
TGCTTGACTTGACTCGATACTTGATAAGATCCATAAAATTT
Done.