Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 128 of 216
Found at i:40524436 original size:23 final size:26
Alignment explanation
Indices: 40524410--40524458 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 26
40524400 ATTGCGAATT
40524410 AATTATTG-ATTGAAAA-GTG-GAAA
1 AATTATTGAATTGAAAATGTGAGAAA
40524433 AATTATTGAATTGAAAATGTGAGAAA
1 AATTATTGAATTGAAAATGTGAGAAA
40524459 TTGTGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.35
24 8 0.35
25 3 0.13
26 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (26 bp):
AATTATTGAATTGAAAATGTGAGAAA
Found at i:40529141 original size:41 final size:41
Alignment explanation
Indices: 40529090--40529327 Score: 140
Period size: 41 Copynumber: 5.7 Consensus size: 41
40529080 GGAGCAGGGT
*
40529090 TAGCAGCATTTTTCCCATAAACACCGCGAAAGGTAAAGAAA
1 TAGCGGCATTTTTCCCATAAACACCGCGAAAGGTAAAGAAA
* * * * * *
40529131 TAGCGACA-TTTTCCCCTAAACGCCACTAAAGGTATAACAAAAA
1 TAGCGGCATTTTTCCCATAAACACCGCGAAAGG--TAA-AGAAA
*** *
40529174 TAGCGGCATTTTTCCCATAAACGTTGCGAAAGGTAAAGCAA
1 TAGCGGCATTTTTCCCATAAACACCGCGAAAGGTAAAGAAA
* * ** * *
40529215 TAGCGGCGTTTTT-GCATAAACATAGCAAAATGTTAAA-AACGA
1 TAGCGGCATTTTTCCCATAAACACCGCGAAA-GGTAAAGAA--A
* * ** * *
40529257 TAGCGGCGTTTTTCTCATAAACATTGCTAAAGGTAAAGCAA
1 TAGCGGCATTTTTCCCATAAACACCGCGAAAGGTAAAGAAA
** * * **
40529298 TAGAAGCGTTTTACCCATAAATGCCGCGAA
1 TAGCGGCATTTTTCCCATAAACACCGCGAA
40529328 TATTTTTAAA
Statistics
Matches: 152, Mismatches: 36, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
40 34 0.22
41 48 0.32
42 25 0.16
43 26 0.17
44 19 0.12
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (41 bp):
TAGCGGCATTTTTCCCATAAACACCGCGAAAGGTAAAGAAA
Found at i:40534598 original size:27 final size:27
Alignment explanation
Indices: 40534581--40534758 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
40534571 ATATTAAGTC
40534581 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* ** *
40534608 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
* * *
40534635 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* *** ** *
40534663 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
40534690 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
40534717 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
40534744 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
40534759 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:40534720 original size:82 final size:81
Alignment explanation
Indices: 40534602--40534757 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40534592 TGCTATATAA
* *
40534602 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40534667 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40534684 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40534748 CACTTAGTGC
65 CACTTAGTGC
40534758 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40534741 original size:54 final size:54
Alignment explanation
Indices: 40534581--40534757 Score: 205
Period size: 54 Copynumber: 3.3 Consensus size: 54
40534571 ATATTAAGTC
* * * *
40534581 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
40534635 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
40534690 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
40534744 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40534758 TGTACAATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
54 57 0.55
55 45 0.43
56 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:40542697 original size:27 final size:27
Alignment explanation
Indices: 40542667--40542844 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40542657 ATATTGAGTC
* * * *
40542667 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40542694 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40542721 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40542749 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40542776 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40542803 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40542830 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40542845 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40542806 original size:82 final size:81
Alignment explanation
Indices: 40542688--40542843 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40542678 TGCTATATAA
* *
40542688 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40542753 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40542770 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40542834 CACTTAGTGC
65 CACTTAGTGC
40542844 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40547993 original size:22 final size:21
Alignment explanation
Indices: 40547968--40548008 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
40547958 TGTATGGTGT
* *
40547968 GATTTGGTTTTGGTATTATATA
1 GATTCGGTTATGGT-TTATATA
40547990 GATTCGGTTATGGTTTATA
1 GATTCGGTTATGGTTTATA
40548009 AGTAGAGAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.22, C:0.02, G:0.24, T:0.51
Consensus pattern (21 bp):
GATTCGGTTATGGTTTATATA
Found at i:40552499 original size:152 final size:152
Alignment explanation
Indices: 40552317--40552618 Score: 550
Period size: 152 Copynumber: 2.0 Consensus size: 152
40552307 ATTGCAAAAT
*
40552317 GGGCTTAGTGTGACTTGAATGTTGATTCAGAGCTTCTAGTTGATGCTGAGGATTGTTTGAGATTC
1 GGGCTTAGTGTGACTTGAATGTTGATTCAGAGCTTCTAGTTGATGCTAAGGATTGTTTGAGATTC
40552382 AGAAAACGATTATGTGTTCCGAAAAATTTAGAGTTAATTCAGATGATATTGAATGAAGCTCATAA
66 AGAAAACGATTATGTGTTCCGAAAAATTTAGAGTTAATTCAGATGATATTGAATGAAGCTCATAA
*
40552447 TAGTCAATTATCTATTTATCCG
131 TAGTCAATTATATATTTATCCG
*
40552469 GGGCTTAGTGTGACTTGAATGTTGATTCAGAGTTTCTAGTTGATGCTAAGGATTGTTTGAGATTC
1 GGGCTTAGTGTGACTTGAATGTTGATTCAGAGCTTCTAGTTGATGCTAAGGATTGTTTGAGATTC
* *
40552534 AGAAACCGATTATGTGTTTCGAAAAATTTAGAGTTAATTCAGATGATATTGAATGAAGCTCATAA
66 AGAAAACGATTATGTGTTCCGAAAAATTTAGAGTTAATTCAGATGATATTGAATGAAGCTCATAA
*
40552599 TAGTCGATTATATATTTATC
131 TAGTCAATTATATATTTATC
40552619 TGAGTAGTAG
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 144 1.00
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.37
Consensus pattern (152 bp):
GGGCTTAGTGTGACTTGAATGTTGATTCAGAGCTTCTAGTTGATGCTAAGGATTGTTTGAGATTC
AGAAAACGATTATGTGTTCCGAAAAATTTAGAGTTAATTCAGATGATATTGAATGAAGCTCATAA
TAGTCAATTATATATTTATCCG
Found at i:40571487 original size:50 final size:49
Alignment explanation
Indices: 40571378--40571561 Score: 185
Period size: 50 Copynumber: 3.7 Consensus size: 49
40571368 TAAAGAGATC
* * **
40571378 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAACT
* * * *
40571427 CCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACT
1 -CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAACT
* * * *
40571477 CTCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACACGA-AACAT
1 C-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ACATGAGAAC-T
*
40571526 CCTATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CC-ATGTAAGACCATGTCTGGGACATGGCATTGGCA
40571562 TGTTATTATC
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
48 5 0.05
49 36 0.32
50 70 0.63
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (49 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATGAGAACT
Found at i:40572874 original size:13 final size:13
Alignment explanation
Indices: 40572856--40572880 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40572846 ATACAATTGA
40572856 TAATGAATAAAGC
1 TAATGAATAAAGC
40572869 TAATGAATAAAG
1 TAATGAATAAAG
40572881 GAAATAGTGT
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:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (13 bp):
TAATGAATAAAGC
Found at i:40587934 original size:23 final size:23
Alignment explanation
Indices: 40587916--40587966 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
40587906 TTATTAGGAT
* * *
40587916 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCAAAAATTACGAC
**
40587939 TGTAATACCCCAAAAATTATTAC
1 TGTAATACCCCAAAAATTACGAC
40587962 TGTAA
1 TGTAA
40587967 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACGAC
Found at i:40591090 original size:158 final size:158
Alignment explanation
Indices: 40590802--40591120 Score: 566
Period size: 158 Copynumber: 2.0 Consensus size: 158
40590792 TCACCAATAC
* **
40590802 AAGTATAGTTAAGATTAGTGCAAGATAGGGTTAAATTTTAAAAAGATGACCATATGGCTTATGAT
1 AAGTATAGTTAAGATTAGTGCAAGATAGGGTAAAATTTTAAAAAGATGAAAATATGGCTTATGAT
*
40590867 GTAGGTAAATAGAAATAGAATAAGCTATATGGCTCAAACTAAGGTTTCAAGGGTTAAATTCATAT
66 GTAGGTAAATAGAAATAAAATAAGCTATATGGCTCAAACTAAGGTTTCAAGGGTTAAATTCATAT
40590932 GGTAGGCTTGAAAGGCTCAAACGATCCA
131 GGTAGGCTTGAAAGGCTCAAACGATCCA
*
40590960 AAGTATAGTTAAGATTAGTGCAATATAGGGTAAAATTTTAAAAAGATGAAAATATGGCTTATGAT
1 AAGTATAGTTAAGATTAGTGCAAGATAGGGTAAAATTTTAAAAAGATGAAAATATGGCTTATGAT
* *
40591025 GTAGGTAAATAGCAATAAAATAGGCTATATGGCTCAAACTAAGGTTTCAAGGGTTAAATTCATAT
66 GTAGGTAAATAGAAATAAAATAAGCTATATGGCTCAAACTAAGGTTTCAAGGGTTAAATTCATAT
*
40591090 GGTAGGCTTGAAAGGCTTAAACGATCCA
131 GGTAGGCTTGAAAGGCTCAAACGATCCA
40591118 AAG
1 AAG
40591121 AAAATGTGCT
Statistics
Matches: 153, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
158 153 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (158 bp):
AAGTATAGTTAAGATTAGTGCAAGATAGGGTAAAATTTTAAAAAGATGAAAATATGGCTTATGAT
GTAGGTAAATAGAAATAAAATAAGCTATATGGCTCAAACTAAGGTTTCAAGGGTTAAATTCATAT
GGTAGGCTTGAAAGGCTCAAACGATCCA
Found at i:40599065 original size:196 final size:196
Alignment explanation
Indices: 40598719--40599112 Score: 635
Period size: 196 Copynumber: 2.0 Consensus size: 196
40598709 TATTTGTTAC
* * * *
40598719 CTGCCAGTCGGTCCAACATCTGATGCATAAAAGGTAGCAGAAAACGATCCATTCGAGTGGCATTG
1 CTGCCAGTCGATCCAACATCTAATCCATAAAAGGCAGCAGAAAACGATCCATTCGAGTGGCATTG
* *
40598784 TTCAATTTTCTGTAGTCAATACAAATTCTTCAACCCATGACCGACCTCATTGAGATTAACTCATT
66 TTCAATTTTCTGTAGTCAATACAAATTCTCCAACCCATGACCAACCTCATTGAGATTAACTCATT
40598849 ATGTTCATCTCCACAATCATAATTCCACCCTTCTTTGGTACACACTGTACCAGACTTACCAATGA
131 ATGTTCATCTCCACAATCATAATTCCACCCTTCTTTGGTACACACTGTACCAGACTTACCAATGA
40598914 A
196 A
* * *
40598915 CTGCTAGTCGATCCAACATCTAATCCATAAAAGGCAGTAGAAAATGATCCATTCGAGTGGCATTG
1 CTGCCAGTCGATCCAACATCTAATCCATAAAAGGCAGCAGAAAACGATCCATTCGAGTGGCATTG
* * * * **
40598980 TTTAATTTTCTGTATTCTATACAAATTCTCCAACCCGTGACCAACCTCATTGAGATTAACTTGTT
66 TTCAATTTTCTGTAGTCAATACAAATTCTCCAACCCATGACCAACCTCATTGAGATTAACTCATT
* *
40599045 ATGTTCATCTCCATAATCATAATTCCACCCTTCTTTGGTACACACTGTACCGGACTTACCAATGA
131 ATGTTCATCTCCACAATCATAATTCCACCCTTCTTTGGTACACACTGTACCAGACTTACCAATGA
40599110 A
196 A
40599111 CT
1 CT
40599113 ATCTAAGATG
Statistics
Matches: 181, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
196 181 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (196 bp):
CTGCCAGTCGATCCAACATCTAATCCATAAAAGGCAGCAGAAAACGATCCATTCGAGTGGCATTG
TTCAATTTTCTGTAGTCAATACAAATTCTCCAACCCATGACCAACCTCATTGAGATTAACTCATT
ATGTTCATCTCCACAATCATAATTCCACCCTTCTTTGGTACACACTGTACCAGACTTACCAATGA
A
Found at i:40610653 original size:18 final size:18
Alignment explanation
Indices: 40610630--40610674 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
40610620 AAATCTGAGC
*
40610630 CTCAATTTTGAAATCGAT
1 CTCAATTTCGAAATCGAT
*
40610648 CTCAATTTCGAAATTGAT
1 CTCAATTTCGAAATCGAT
40610666 CTCAATTTC
1 CTCAATTTC
40610675 ATCCTTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (18 bp):
CTCAATTTCGAAATCGAT
Found at i:40617220 original size:13 final size:13
Alignment explanation
Indices: 40617202--40617226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40617192 GATTACGTGC
40617202 TTAAAATAAAATT
1 TTAAAATAAAATT
40617215 TTAAAATAAAAT
1 TTAAAATAAAAT
40617227 GTAATTAAAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAATAAAATT
Found at i:40632304 original size:28 final size:28
Alignment explanation
Indices: 40632273--40632418 Score: 118
Period size: 28 Copynumber: 5.2 Consensus size: 28
40632263 TTGAAAGATC
* *
40632273 TCCACTTATATGATAGTCCTGATAGACT
1 TCCACATATAAGATAGTCCTGATAGACT
* * *
40632301 TCCACATATAAGTTAGTCTTGATGGACT
1 TCCACATATAAGATAGTCCTGATAGACT
* * * *
40632329 TCCCCAT-TAAGAT-GTTCCTAACATACT
1 TCCACATATAAGATAG-TCCTGATAGACT
* *
40632356 TCCACATATAAGATAGTCTTGA-CGAACT
1 TCCACATATAAGATAGTCCTGATAG-ACT
* * **
40632384 TCCACATATGAGATAATCCTGACGGACT
1 TCCACATATAAGATAGTCCTGATAGACT
40632412 TCCACAT
1 TCCACAT
40632419 TTACGGTAAT
Statistics
Matches: 92, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.01
27 18 0.20
28 71 0.77
29 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (28 bp):
TCCACATATAAGATAGTCCTGATAGACT
Found at i:40641047 original size:18 final size:19
Alignment explanation
Indices: 40641003--40641068 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 19
40640993 TCTTTGTTTT
*
40641003 ATATTTA-TTT-TTAGTTTT
1 ATATTTATTTTCTTA-TTTG
40641021 ATAATTTATTTTCATTA-TTG
1 AT-ATTTATTTTC-TTATTTG
*
40641041 ATA-TTATTGTCTTATTTG
1 ATATTTATTTTCTTATTTG
40641059 ATATTTATTT
1 ATATTTATTT
40641069 ATTTATGTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
17 3 0.08
18 15 0.38
19 11 0.28
20 7 0.18
22 3 0.08
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (19 bp):
ATATTTATTTTCTTATTTG
Found at i:40645885 original size:38 final size:37
Alignment explanation
Indices: 40645835--40645911 Score: 145
Period size: 38 Copynumber: 2.1 Consensus size: 37
40645825 AATAATAAAT
40645835 ACTCTATTATAACCCAAAAAGTTGACTTATTGAAAGA
1 ACTCTATTATAACCCAAAAAGTTGACTTATTGAAAGA
40645872 ACTCTGATTATAACCCAAAAAGTTGACTTATTGAAAGA
1 ACTCT-ATTATAACCCAAAAAGTTGACTTATTGAAAGA
40645910 AC
1 AC
40645912 AAGAGATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
37 5 0.13
38 34 0.87
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.29
Consensus pattern (37 bp):
ACTCTATTATAACCCAAAAAGTTGACTTATTGAAAGA
Found at i:40646144 original size:21 final size:21
Alignment explanation
Indices: 40646120--40646160 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40646110 GTTTTAAAAG
*
40646120 TTTTATAATATTTT-AAAGAAT
1 TTTTAGAA-ATTTTCAAAGAAT
40646141 TTTTAGAAATTTTCAAAGAA
1 TTTTAGAAATTTTCAAAGAA
40646161 AAAGGAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (21 bp):
TTTTAGAAATTTTCAAAGAAT
Found at i:40650286 original size:88 final size:88
Alignment explanation
Indices: 40650132--40650303 Score: 290
Period size: 88 Copynumber: 2.0 Consensus size: 88
40650122 GACAGGTACT
* ** *
40650132 TCCTTCGAACATACTAAGTTCACATCCTTATTTAGCATACATTTTCAATATTAACTCATTAATTC
1 TCCTTCGAACATACAAAGTTCACATCCTTATCCAGCATACATTTTCAATATTAACCCATTAATTC
40650197 TCTATATCCCTTCAAAGTTCACA
66 TCTATATCCCTTCAAAGTTCACA
* *
40650220 TCCTTCGAACATACAAAGTTCACATCCTTATCCAGCATATATTTTCAATATTAACCCATTACTTC
1 TCCTTCGAACATACAAAGTTCACATCCTTATCCAGCATACATTTTCAATATTAACCCATTAATTC
40650285 TCTATATCCCTTCAAAGTT
66 TCTATATCCCTTCAAAGTT
40650304 TTAAGAGTTC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (88 bp):
TCCTTCGAACATACAAAGTTCACATCCTTATCCAGCATACATTTTCAATATTAACCCATTAATTC
TCTATATCCCTTCAAAGTTCACA
Found at i:40650380 original size:27 final size:26
Alignment explanation
Indices: 40650350--40650448 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 26
40650340 ATTGGGAGAA
40650350 TGCCATAGAGGCTATTCTTTCAGAGTT
1 TGCCATA-AGGCTATTCTTTCAGAGTT
*
40650377 TGCCATAAAGTCTATTCTTTCAGAGTT
1 TGCCAT-AAGGCTATTCTTTCAGAGTT
**
40650404 CACCACTAAGGCTATTCTTAT-AGAGTT
1 TGCCA-TAAGGCTATTCTT-TCAGAGTT
*
40650431 TGACACAAAAGGCTATTC
1 TG-C-CATAAGGCTATTC
40650449 CTTATTGACA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 44 0.73
28 14 0.23
29 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (26 bp):
TGCCATAAGGCTATTCTTTCAGAGTT
Found at i:40667995 original size:46 final size:45
Alignment explanation
Indices: 40667918--40668128 Score: 217
Period size: 46 Copynumber: 4.6 Consensus size: 45
40667908 GGCGTTACAT
* * *
40667918 GGTCACTCGTTAGGGTTGAACCTACATGAATCAAATAATAGTGCC
1 GGTCACTCATTAGGGTTGAACCTACACGAATCGAATAATAGTGCC
* * *
40667963 GGACCAC-CTATTAGGGTTGAACCTACACGAATCGGATAATAGTGCTT
1 GG-TCACTC-ATTAGGGTTGAACCTACACGAATCGAATAATAGTGC-C
* * * * *
40668010 GGTCACCCGTTAGGGTTGAACCTACACAAATCGGATAATAGTGTCT
1 GGTCACTCATTAGGGTTGAACCTACACGAATCGAATAATAGTG-CC
* * * * *
40668056 AGTCATTCATTAGGGTTGAACGTACATGAATCGAACAATAGTGCC
1 GGTCACTCATTAGGGTTGAACCTACACGAATCGAATAATAGTGCC
*
40668101 TGGTCACTCATTCGGGTTGAACCTACAC
1 -GGTCACTCATTAGGGTTGAACCTACAC
40668129 AACAAATAGC
Statistics
Matches: 136, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
45 4 0.03
46 128 0.94
47 4 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (45 bp):
GGTCACTCATTAGGGTTGAACCTACACGAATCGAATAATAGTGCC
Found at i:40668962 original size:129 final size:129
Alignment explanation
Indices: 40668815--40669063 Score: 453
Period size: 129 Copynumber: 1.9 Consensus size: 129
40668805 TAGTCTTATT
* *
40668815 TCCCATCAAAGCTTCAAACTCTACCATAAGCATTAAAAAACTTCAATTAACATCAATGGGAACTT
1 TCCCATCAAAGCTTCAAACTCTACCATAAGCATTAAAAAACTTCAATTAAAATCAATGGAAACTT
* * *
40668880 TAGAAATCTTTAATAGTTTTGAAAATAAAGATGCGAGTTAGCTAGGCCTAGTTGCAATGATCCA
66 TAGAAATCTTTAACAATTTTGAAAACAAAGATGCGAGTTAGCTAGGCCTAGTTGCAATGATCCA
40668944 TCCCATCAAAGCTTCAAACTCTACCATAAGCATTAAAAAACTTCAATTAAAATCAATGGAAACTT
1 TCCCATCAAAGCTTCAAACTCTACCATAAGCATTAAAAAACTTCAATTAAAATCAATGGAAACTT
40669009 TAGAAATCTTTAACAATTTTGAAAACAAAGATGCGAGTTAGCTAGGCCTAGTTGC
66 TAGAAATCTTTAACAATTTTGAAAACAAAGATGCGAGTTAGCTAGGCCTAGTTGC
40669064 TACGATCCCA
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
129 115 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (129 bp):
TCCCATCAAAGCTTCAAACTCTACCATAAGCATTAAAAAACTTCAATTAAAATCAATGGAAACTT
TAGAAATCTTTAACAATTTTGAAAACAAAGATGCGAGTTAGCTAGGCCTAGTTGCAATGATCCA
Found at i:40690795 original size:79 final size:81
Alignment explanation
Indices: 40690694--40690878 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
40690684 GCTACTCGTT
* *
40690694 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
40690757 AGATTTAGTAAC-TCGCA
64 AGATATAGTAACTTAGCA
* ** *
40690774 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCAG
* *
40690838 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
40690854 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40690879 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCAG
ATATAGTAACTTAGCA
Found at i:40690878 original size:40 final size:40
Alignment explanation
Indices: 40690675--40690878 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
40690665 CGGAATTTAA
** *
40690675 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40690715 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40690755 CCAGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40690794 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40690834 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40690874 CCGGA
1 CCGGA
40690879 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:40701190 original size:50 final size:48
Alignment explanation
Indices: 40701106--40701230 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 48
40701096 GAGACTCCAT
* *
40701106 GTAAGACCATGTCTAGGACATGGCATTGGTACCGAGATGAAAGGTCCCAC
1 GTAAGACCATGTCTGGGACATGGCA-TGGCACCGAGATGAAA-GTCCCAC
* * * * *
40701156 GTAAGGCCATGTCTGGGACATGGCATGGACACCGATATGAGAGTCTCAT
1 GTAAGACCATGTCTGGGACATGGCATGG-CACCGAGATGAAAGTCCCAC
** *
40701205 GTAAGACCACATCTGGGATATGGCAT
1 GTAAGACCATGTCTGGGACATGGCAT
40701231 TTGCAGTACA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 30 0.48
50 33 0.52
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (48 bp):
GTAAGACCATGTCTGGGACATGGCATGGCACCGAGATGAAAGTCCCAC
Found at i:40705785 original size:25 final size:27
Alignment explanation
Indices: 40705733--40705808 Score: 102
Period size: 26 Copynumber: 2.9 Consensus size: 27
40705723 AAACACGTTA
40705733 GAAAAGAAAGCCTTTGTGGAAAACCAT
1 GAAAAGAAAGCCTTTGTGGAAAACCAT
40705760 GAAAA-AAAGCCTTTGT-GAAAACCAT
1 GAAAAGAAAGCCTTTGTGGAAAACCAT
* **
40705785 GTAGTGAAAGCCTTTGTGGTAAAA
1 GAAAAGAAAGCCTTTGTGG-AAAA
40705809 AAAAAGGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 11 0.26
26 22 0.51
27 6 0.14
28 4 0.09
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.22
Consensus pattern (27 bp):
GAAAAGAAAGCCTTTGTGGAAAACCAT
Found at i:40705916 original size:27 final size:27
Alignment explanation
Indices: 40705886--40705952 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
40705876 CTCTATTGCA
* * * *
40705886 AACTCTAAAGGAATGGTATTCATGGTG
1 AACTCTGAAGGAACGGTATGCATGGCG
40705913 AACTCTGAAGGAACGGTATGCATGGCG
1 AACTCTGAAGGAACGGTATGCATGGCG
*
40705940 AACTATGAAGGAA
1 AACTCTGAAGGAA
40705953 ATACCCTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.22
Consensus pattern (27 bp):
AACTCTGAAGGAACGGTATGCATGGCG
Found at i:40710120 original size:16 final size:16
Alignment explanation
Indices: 40710099--40710130 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40710089 GTTTTGTTGC
*
40710099 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
40710115 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
40710131 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:40710416 original size:51 final size:51
Alignment explanation
Indices: 40710358--40710548 Score: 210
Period size: 51 Copynumber: 3.8 Consensus size: 51
40710348 CCGATTCACA
* * *
40710358 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACGCG
* * * * *
40710409 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGTTATCCGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCTGGTACGCG
* * * *
40710460 TAGTAGCCTACACATAGTACTAAACATGCGACCTATCA-T-TCTGGTACGCG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCTGGTACGCG
*
40710510 TAGTAGCCTGCACATAGTACTACACACATGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
40710549 TTCACTTTCA
Statistics
Matches: 113, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
49 4 0.04
50 39 0.35
51 67 0.59
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACGCG
Found at i:40710570 original size:101 final size:102
Alignment explanation
Indices: 40710352--40710574 Score: 251
Period size: 101 Copynumber: 2.2 Consensus size: 102
40710342 ATGATACCGA
* * *
40710352 TTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCTGATACACGTAGTAGCC
1 TTCACATAGTAGCCTACACATAGTACTAAACATGCGACCATCACTATCTGATACACGTAGTAGCC
* * *
40710417 TGCACATAGTACTACACACGTGATCGAAGTTATCCGGT
66 TGCACATAGTACTACACACATGATCCAACTTATCC-GT
* * * *
40710455 AT-GCATAGTAGCCTACACATAGTACTAAACATGCGACCTATCA-T-TCTGGTACGCGTAGTAGC
1 TTCACATAGTAGCCTACACATAGTACTAAACATGCGACC-ATCACTATCTGATACACGTAGTAGC
40710517 CTGCACATAGTACTACACACATGA-CCATCACTT-TCAC-T
65 CTGCACATAGTACTACACACATGATCCA--ACTTATC-CGT
* *
40710555 TTCACAGAGTGGCCTACACA
1 TTCACATAGTAGCCTACACA
40710575 CTGTCCATGC
Statistics
Matches: 101, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
100 4 0.04
101 55 0.54
102 37 0.37
103 5 0.05
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (102 bp):
TTCACATAGTAGCCTACACATAGTACTAAACATGCGACCATCACTATCTGATACACGTAGTAGCC
TGCACATAGTACTACACACATGATCCAACTTATCCGT
Found at i:40713057 original size:18 final size:18
Alignment explanation
Indices: 40713034--40713073 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
40713024 ATATGAGAAA
40713034 AATATTTTATAAACCTCC
1 AATATTTTATAAACCTCC
*
40713052 AATATTTTATAAATCTCC
1 AATATTTTATAAACCTCC
40713070 AATA
1 AATA
40713074 ACATTCGTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATTTTATAAACCTCC
Found at i:40722823 original size:29 final size:29
Alignment explanation
Indices: 40722781--40722944 Score: 147
Period size: 29 Copynumber: 5.7 Consensus size: 29
40722771 TATCGGGGAT
40722781 TATCGAATATGAAAAGGGATAGCTTCGGC
1 TATCGAATATGAAAAGGGATAGCTTCGGC
* * ** *
40722810 TATCGACTATGAAAAGGAATAATTTCAGC
1 TATCGAATATGAAAAGGGATAGCTTCGGC
* * *
40722839 TATCAAATATGAAAAGAGATAGCTTCAGC
1 TATCGAATATGAAAAGGGATAGCTTCGGC
* * *
40722868 TATCG-ATCATGAAAA-GGAT-GGTGACGAC
1 TATCGAAT-ATGAAAAGGGATAGCT-TCGGC
* *
40722896 TATCGAATATAAAAAGGAATAGCTTCGGC
1 TATCGAATATGAAAAGGGATAGCTTCGGC
*
40722925 TATCG-ATCATGAAAACGGAT
1 TATCGAAT-ATGAAAAGGGAT
40722945 GGTGACGACC
Statistics
Matches: 104, Mismatches: 25, Indels: 12
0.74 0.18 0.09
Matches are distributed among these distances:
27 2 0.02
28 20 0.19
29 80 0.77
30 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (29 bp):
TATCGAATATGAAAAGGGATAGCTTCGGC
Found at i:40722988 original size:58 final size:57
Alignment explanation
Indices: 40722782--40723031 Score: 177
Period size: 58 Copynumber: 4.3 Consensus size: 57
40722772 ATCGGGGATT
* * * ** ** *
40722782 ATCGAATATGAAAAGGGATAGCTTCGGCTATCGA-CTATGAAAAGGAATAATTTC-AGCT
1 ATCGAATATGAAAAGGGATAGCTACGACCATCGATC-ATGAAAAGG-ATGGTGACGA-CC
* * * * *
40722840 ATCAAATATGAAAAGAGATAGCTTC-AGCTATCGATCATGAAAAGGATGGTGACGACT
1 ATCGAATATGAAAAGGGATAGCTACGA-CCATCGATCATGAAAAGGATGGTGACGACC
* * * * *
40722897 ATCGAATATAAAAAGGAATAGCTTCGGCTATCGATCATGAAAACGGATGGTGACGACC
1 ATCGAATATGAAAAGGGATAGCTACGACCATCGATCATGAAAA-GGATGGTGACGACC
* * * **
40722955 ATC-AACTATGACAAGGGAT-GGTGACGACCATCGATTAATGAAAAGGGATGGTTTCGACC
1 ATCGAA-TATGAAAAGGGATAGCT-ACGACCATCGA-TCATGAAAA-GGATGGTGACGACC
40723014 ATCGAATATGAAAAGGGA
1 ATCGAATATGAAAAGGGA
40723032 CGGTTACAGC
Statistics
Matches: 158, Mismatches: 25, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
57 47 0.30
58 74 0.47
59 35 0.22
60 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.22
Consensus pattern (57 bp):
ATCGAATATGAAAAGGGATAGCTACGACCATCGATCATGAAAAGGATGGTGACGACC
Found at i:40723003 original size:30 final size:29
Alignment explanation
Indices: 40722876--40723031 Score: 140
Period size: 29 Copynumber: 5.4 Consensus size: 29
40722866 GCTATCGATC
*
40722876 ATGAAAA-GGATGGTGACGACTATCGAAT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
* * * * * *
40722904 ATAAAAAGGAATAGCT-TCGGCTATCG-AT
1 ATGAAAAGGGAT-GGTGACGACCATCGAAT
*
40722932 CATGAAAACGGATGGTGACGACCATC-AACT
1 -ATGAAAAGGGATGGTGACGACCATCGAA-T
* *
40722962 ATGACAAGGGATGGTGACGACCATCGATT
1 ATGAAAAGGGATGGTGACGACCATCGAAT
**
40722991 AATGAAAAGGGATGGTTTCGACCATCGAAT
1 -ATGAAAAGGGATGGTGACGACCATCGAAT
40723021 ATGAAAAGGGA
1 ATGAAAAGGGA
40723032 CGGTTACAGC
Statistics
Matches: 101, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
28 10 0.10
29 62 0.61
30 29 0.29
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.21
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGACGACCATCGAAT
Found at i:40731770 original size:20 final size:19
Alignment explanation
Indices: 40731743--40731784 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
40731733 CTTTCCAAAT
40731743 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
40731762 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
40731782 TTT
1 TTT
40731785 ACTTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:40732584 original size:24 final size:24
Alignment explanation
Indices: 40732548--40732655 Score: 76
Period size: 25 Copynumber: 4.4 Consensus size: 24
40732538 ACGAGCTCTG
* * * *
40732548 AATCAGTATGCTCTTATGAGCTGT
1 AATCGGTAAGCTCTTACGAGCTGA
* *
40732572 AATCGGTAAGCTCATGCGAGCTGA
1 AATCGGTAAGCTCTTACGAGCTGA
40732596 ATATCGGTAAGCTCTCT-CGAGCTGA
1 A-ATCGGTAAGCTCT-TACGAGCTGA
** *
40732621 ATATCATTAAGCT-TTCTCGAGCTGA
1 A-ATCGGTAAGCTCTT-ACGAGCTGA
40732646 GAATCGGTAA
1 -AATCGGTAA
40732656 CCTTAATGAC
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
23 1 0.01
24 20 0.29
25 45 0.66
26 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (24 bp):
AATCGGTAAGCTCTTACGAGCTGA
Found at i:40732607 original size:25 final size:25
Alignment explanation
Indices: 40732565--40732655 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
40732555 ATGCTCTTAT
*
40732565 GAGCTGTA-ATCGGTAAGCTCAT-GC
1 GAGCTGAATATCGGTAAGCTC-TCGC
*
40732589 GAGCTGAATATCGGTAAGCTCTCTC
1 GAGCTGAATATCGGTAAGCTCTCGC
** * *
40732614 GAGCTGAATATCATTAAGCTTTCTC
1 GAGCTGAATATCGGTAAGCTCTCGC
40732639 GAGCTGAGA-ATCGGTAA
1 GAGCTGA-ATATCGGTAA
40732656 CCTTAATGAC
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.14
25 48 0.84
26 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (25 bp):
GAGCTGAATATCGGTAAGCTCTCGC
Found at i:40740240 original size:16 final size:17
Alignment explanation
Indices: 40740213--40740246 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
40740203 TCTATTAACT
40740213 TTAAACCCAAAATTGAC
1 TTAAACCCAAAATTGAC
40740230 TTAAA-CCAAAATTGAC
1 TTAAACCCAAAATTGAC
40740246 T
1 T
40740247 AAAATACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (17 bp):
TTAAACCCAAAATTGAC
Found at i:40741580 original size:30 final size:28
Alignment explanation
Indices: 40741509--40741582 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 28
40741499 ATTGTATTTT
* *
40741509 GTTTTTTAATTCAATAAATGGATAAATTA
1 GTTTTTT-ATTAAATAAATGAATAAATTA
40741538 GTTTTGTATATTAAATAAATGAATAAATTA
1 GTTTT-T-TATTAAATAAATGAATAAATTA
40741568 GTAATTTTTATTAAA
1 GT--TTTTTATTAAA
40741583 AATTTTATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 5 0.13
30 29 0.74
31 2 0.05
32 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.46
Consensus pattern (28 bp):
GTTTTTTATTAAATAAATGAATAAATTA
Found at i:40742383 original size:16 final size:16
Alignment explanation
Indices: 40742362--40742393 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40742352 TAGTTTGCAC
40742362 TTTAAAATTTTAAAAA
1 TTTAAAATTTTAAAAA
*
40742378 TTTAAATTTTTAAAAA
1 TTTAAAATTTTAAAAA
40742394 AATTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAATTTTAAAAA
Found at i:40742461 original size:31 final size:29
Alignment explanation
Indices: 40742424--40742494 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
40742414 GTTCAAAATT
40742424 TTATACTTTTAAAGTTTTTAAAATATTTTAA
1 TTATACTTTTAAA-TTTTTAAAA-ATTTTAA
* *
40742455 TTATACTCTTTTTAATTTTTGAAAATTTTAA
1 TTATA--CTTTTAAATTTTTAAAAATTTTAA
*
40742486 TTAAACTTT
1 TTATACTTT
40742495 CTTAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 4 0.11
31 16 0.46
32 8 0.23
33 7 0.20
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (29 bp):
TTATACTTTTAAATTTTTAAAAATTTTAA
Found at i:40743926 original size:6 final size:6
Alignment explanation
Indices: 40743915--40743959 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
40743905 AAAAATGTCG
*
40743915 TCTTTT TC-TTT TC--TT TCCTTT TC-TTT TCTTTT TCTTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
40743959 T
1 T
40743960 GTTAGGCAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.11
5 10 0.28
6 22 0.61
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:40743928 original size:5 final size:5
Alignment explanation
Indices: 40743918--40743958 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
40743908 AATGTCGTCT
*
40743918 TTTTC TTTTC TTTCC TTTTC TTTTC TTTTTC TTTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC -TTTTC TTTT
40743959 TGTTAGGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 22 0.67
6 11 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:40743942 original size:11 final size:11
Alignment explanation
Indices: 40743915--40743958 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
40743905 AAAAATGTCG
*
40743915 TCTTTTTCTTT
1 TCTTTTCCTTT
40743926 TC-TTTCCTTT
1 TCTTTTCCTTT
*
40743936 TCTTTTCTTTT
1 TCTTTTCCTTT
*
40743947 TCTTTTTCTTT
1 TCTTTTCCTTT
40743958 T
1 T
40743959 TGTTAGGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTTTTCCTTT
Found at i:40744577 original size:129 final size:130
Alignment explanation
Indices: 40744420--40744670 Score: 334
Period size: 133 Copynumber: 1.9 Consensus size: 130
40744410 TTTGTTCAAT
* * *
40744420 ACCAGATTTGCCTTTATTCCCAGTGAAGC-AG-AG-A-A-ATATATAGAATACATA-TAGATATT
1 ACCAGATTTGCCTTTACTCCCAGTGAAGCAAGTAGTACACATA-ATA-AATACACATTAGATA-C
40744479 ATATATAAAAACTAATGGAACATTCATCAATATCCATGCTCACTAGTCATCATAATTGACTTAGT
63 ATATATAAAAACTAATGGAACATTCATC-A-ATCCATGCTCACTAGTCATCATAATTGACTTAGT
40744544 TTCAC
126 TTCAC
* *
40744549 ACCAGATTTGCCTTTACTCCTAGTGAAGCATAGTAGTACACATAATACATACACATTAGATACAT
1 ACCAGATTTGCCTTTACTCCCAGTGAAGCA-AGTAGTACACATAATAAATACACATTAGATACAT
* * *
40744614 ATATAAAACCTAATGGAACATTCATCAATCCGTGCTCACTAGTTATCATAATTGACT
65 ATATAAAAACTAATGGAACATTCATCAATCCATGCTCACTAGTCATCATAATTGACT
40744671 GATTAATTAA
Statistics
Matches: 107, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
129 27 0.25
131 30 0.28
132 3 0.03
133 34 0.32
134 10 0.09
135 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.31
Consensus pattern (130 bp):
ACCAGATTTGCCTTTACTCCCAGTGAAGCAAGTAGTACACATAATAAATACACATTAGATACATA
TATAAAAACTAATGGAACATTCATCAATCCATGCTCACTAGTCATCATAATTGACTTAGTTTCAC
Found at i:40746156 original size:15 final size:14
Alignment explanation
Indices: 40746123--40746166 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
40746113 ACATCAATTC
*
40746123 AAAAAGAAAAATTA
1 AAAAAGAAAAAATA
*
40746137 CAAAAGAAAATAATAA
1 AAAAAGAAAA-AAT-A
40746153 AAAAAGAAAAAATA
1 AAAAAGAAAAAATA
40746167 TGTGATGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 10 0.40
15 5 0.20
16 10 0.40
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (14 bp):
AAAAAGAAAAAATA
Found at i:40746893 original size:38 final size:38
Alignment explanation
Indices: 40746851--40746926 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
40746841 AACCCCTTCT
40746851 TAGAAGTCAAACCATTTTACTTTCCCAAAAAAAATTAA
1 TAGAAGTCAAACCATTTTACTTTCCCAAAAAAAATTAA
* * *
40746889 TAGAAGTCAAACCATTTTACTTTCTCTAAAATAATTAA
1 TAGAAGTCAAACCATTTTACTTTCCCAAAAAAAATTAA
40746927 CTTCCTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (38 bp):
TAGAAGTCAAACCATTTTACTTTCCCAAAAAAAATTAA
Found at i:40746989 original size:16 final size:18
Alignment explanation
Indices: 40746953--40746986 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40746943 ATTTTTTTTT
*
40746953 CTTTTATTTCTCTCAAAA
1 CTTTTACTTCTCTCAAAA
40746971 CTTTTACTTCTC-CAAA
1 CTTTTACTTCTCTCAAA
40746987 CTTCCAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (18 bp):
CTTTTACTTCTCTCAAAA
Found at i:40747137 original size:18 final size:17
Alignment explanation
Indices: 40747105--40747139 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40747095 CATTTTGTAC
*
40747105 TATTTATATTATTGAAT
1 TATTTATAATATTGAAT
40747122 TATTTAATAATATTGAAT
1 TATTT-ATAATATTGAAT
40747140 CTTTATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TATTTATAATATTGAAT
Found at i:40755321 original size:45 final size:45
Alignment explanation
Indices: 40755254--40755393 Score: 181
Period size: 45 Copynumber: 3.1 Consensus size: 45
40755244 TTCGTCTAAG
40755254 AATGAGTAAGACCATAGCTGAAAGATACTATGGCATCATGATAAA
1 AATGAGTAAGACCATAGCTGAAAGATACTATGGCATCATGATAAA
* * * * *
40755299 AATGAGTAAGAACATAGTTGAAAGATGCTATGGCATCATGACAGA
1 AATGAGTAAGACCATAGCTGAAAGATACTATGGCATCATGATAAA
* * * * *
40755344 AATGAGTAAGACCATGGCTGAAAAACACCATGACATCATGATAAA
1 AATGAGTAAGACCATAGCTGAAAGATACTATGGCATCATGATAAA
*
40755389 CATGA
1 AATGA
40755394 CTAATGTAAC
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (45 bp):
AATGAGTAAGACCATAGCTGAAAGATACTATGGCATCATGATAAA
Found at i:40756538 original size:28 final size:29
Alignment explanation
Indices: 40756498--40756556 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
40756488 TCTTTGAATG
* *
40756498 TTTTCTTTGGATGTTTACCACAGA-GACA
1 TTTTCTTTGGATGGTTACCACAAAGGACA
*
40756526 TTTTCTTTGGATGGTTGCCACAAAGGACA
1 TTTTCTTTGGATGGTTACCACAAAGGACA
40756555 TT
1 TT
40756557 ATTTAGAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTCTTTGGATGGTTACCACAAAGGACA
Found at i:40756599 original size:27 final size:28
Alignment explanation
Indices: 40756568--40756621 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
40756558 TTTAGAGTAC
*
40756568 ACCATAAAGG-TT-TTTTTTTCGTAGATA
1 ACCATAAAGGCTTCCTTTTTT-GTAGATA
40756595 ACCATAAAGGCTTCCTTTTTTGTAGAT
1 ACCATAAAGGCTTCCTTTTTTGTAGAT
40756622 CGCCACAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 8 0.33
29 6 0.25
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (28 bp):
ACCATAAAGGCTTCCTTTTTTGTAGATA
Found at i:40756671 original size:28 final size:28
Alignment explanation
Indices: 40756581--40756671 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 28
40756571 ATAAAGGTTT
* * *
40756581 TTTTTTCGTAGATAACCATAAAGGCTTCC
1 TTTTTTCGTAGATCACCACAAAGACTT-C
* *
40756610 TTTTTT-GTAGATCGCCACAAAGCCTT-
1 TTTTTTCGTAGATCACCACAAAGACTTC
*
40756636 TATTTTTCATAGATCACCACAAAGACTTC
1 T-TTTTTCGTAGATCACCACAAAGACTTC
40756665 TTTTTTC
1 TTTTTTC
40756672 TGGCATGTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 5 0.10
28 39 0.75
29 7 0.13
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (28 bp):
TTTTTTCGTAGATCACCACAAAGACTTC
Found at i:40769608 original size:137 final size:138
Alignment explanation
Indices: 40769356--40769629 Score: 329
Period size: 137 Copynumber: 2.0 Consensus size: 138
40769346 GGCTATAAAA
* * *
40769356 TGGGTCTGCTCACACAAGCTGTCGGTCAGAATGTAAGCTACACGATGCTATTCACACAAGTTATC
1 TGGGTCTGATCACACAAGCTGTCAGTCAGAATGTAAGCTACACGATGCTATTCACACAAGCTATC
* * *
40769421 GAGTATTCGCAACTAATGCCAGATCTCAGCCATAGGTAGGACATTCAAGACCAGCACCCAAAACA
66 AAGTATTCGCAACTAATGCCAGAACTCAGCCACAGGTAGGACATTCAAGACCAGCACCCAAAACA
*
40769486 TGGTAACT
131 TCGTAACT
* * * * * *
40769494 TGGGTCTGATCACACAAGCTGTTAGTCGGAATGT-AGCTACACGGTGTTGCTT-ACACAAGCTGT
1 TGGGTCTGATCACACAAGCTGTCAGTCAGAATGTAAGCTACACGATGCT-ATTCACACAAGCTAT
*** * * * *
40769557 CAAGTATTCGCAAC-ACATGTTGGAACTCAGCCACCGGTAGGACATTTAAGACCAGCACTCGAAA
65 CAAGTATTCGCAACTA-ATGCCAGAACTCAGCCACAGGTAGGACATTCAAGACCAGCACCCAAAA
40769621 CATCGTAAC
129 CATCGTAAC
40769630 CCTAATGACA
Statistics
Matches: 114, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
136 1 0.01
137 81 0.71
138 32 0.28
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (138 bp):
TGGGTCTGATCACACAAGCTGTCAGTCAGAATGTAAGCTACACGATGCTATTCACACAAGCTATC
AAGTATTCGCAACTAATGCCAGAACTCAGCCACAGGTAGGACATTCAAGACCAGCACCCAAAACA
TCGTAACT
Found at i:40771753 original size:16 final size:16
Alignment explanation
Indices: 40771732--40771764 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40771722 GTTCGTATAT
40771732 CATAAAACATAACTTA
1 CATAAAACATAACTTA
40771748 CATAAAACATAACTTA
1 CATAAAACATAACTTA
40771764 C
1 C
40771765 CATTTCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (16 bp):
CATAAAACATAACTTA
Found at i:40774785 original size:35 final size:36
Alignment explanation
Indices: 40774710--40774797 Score: 117
Period size: 35 Copynumber: 2.4 Consensus size: 36
40774700 GATGTTTTAA
* *
40774710 TCGCATGTTAAGCATGTTAATGTTCTGATATTTTGGC
1 TCGCATGTTAAGCATGTTAATATTCTGA-ATTTTGAC
*
40774747 TCGCATGTTAAGCATGTTATTAATT-TG-ATTTTGAC
1 TCGCATGTTAAGCATGTTAAT-ATTCTGAATTTTGAC
40774782 TCGCATGTTAAGCATG
1 TCGCATGTTAAGCATG
40774798 CCATGATTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
35 23 0.49
37 22 0.47
38 2 0.04
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (36 bp):
TCGCATGTTAAGCATGTTAATATTCTGAATTTTGAC
Found at i:40776225 original size:29 final size:29
Alignment explanation
Indices: 40776184--40776245 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
40776174 TAGATTTCTA
*
40776184 TATATTGTGAAACTTTAAATTCTGAAAAC
1 TATATTGTGAAACTCTAAATTCTGAAAAC
* *
40776213 TATATTGTGAAACTCTAGATTTTGAAAAC
1 TATATTGTGAAACTCTAAATTCTGAAAAC
40776242 TATA
1 TATA
40776246 GATATTGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TATATTGTGAAACTCTAAATTCTGAAAAC
Found at i:40778749 original size:23 final size:23
Alignment explanation
Indices: 40778723--40778776 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
40778713 TCGTGAGTAT
40778723 GATAATGGTGTGTGAACATTAGG
1 GATAATGGTGTGTGAACATTAGG
40778746 GATAATGGTGTGTGAACATTAGG
1 GATAATGGTGTGTGAACATTAGG
40778769 GA-AATGGT
1 GATAATGGT
40778777 TAGTATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.19
23 25 0.81
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (23 bp):
GATAATGGTGTGTGAACATTAGG
Found at i:40790536 original size:29 final size:29
Alignment explanation
Indices: 40790490--40790673 Score: 226
Period size: 29 Copynumber: 6.3 Consensus size: 29
40790480 TCGTCAACCA
* *
40790490 ATGAAAAGGGATAACTTCGGCTATTGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
40790519 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* *
40790548 ATGAAAAGGGATAGCTTTGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* * * * *
40790577 ATGAAAAAGGAT-GGTGACGACCATCGAAT
1 ATGAAAAGGGATAGCT-TCGGCTATCGAAT
* * *
40790606 ATGAAAAGGGATAGCTTCGACTATTGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* *
40790635 ATGAAAAGGGATAGCTTTGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
40790664 ATGAAAAGGG
1 ATGAAAAGGG
40790674 GTGGTGACGA
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
28 2 0.02
29 129 0.97
30 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAAT
Found at i:40790638 original size:87 final size:87
Alignment explanation
Indices: 40790515--40790704 Score: 308
Period size: 87 Copynumber: 2.2 Consensus size: 87
40790505 TTCGGCTATT
*
40790515 GAATATGAAAAGGGATAGCTTCGGCTATCGAATATGAAAAGGGATAGCTTTGGCTATCGATTATG
1 GAATATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTTGGCTATCGATTATG
40790580 AAAAAGGATGGTGACGACCATC
66 AAAAAGGATGGTGACGACCATC
* *
40790602 GAATATGAAAAGGGATAGCTTCGACTATTGATTATGAAAAGGGATAGCTTTGGCTATCGATTATG
1 GAATATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTTGGCTATCGATTATG
* * *
40790667 AAAAGGGGTGGTGACGACCATT
66 AAAAAGGATGGTGACGACCATC
*
40790689 GATTAATGAAAAGGGA
1 GAAT-ATGAAAAGGGA
40790705 CGATTATAAC
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
87 84 0.88
88 11 0.12
ACGTcount: A:0.36, C:0.11, G:0.28, T:0.25
Consensus pattern (87 bp):
GAATATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTTGGCTATCGATTATG
AAAAAGGATGGTGACGACCATC
Found at i:40790692 original size:29 final size:29
Alignment explanation
Indices: 40790490--40790704 Score: 146
Period size: 29 Copynumber: 7.4 Consensus size: 29
40790480 TCGTCAACCA
* * * * * *
40790490 ATGAAAAGGGATAACTTCGGCTATTGAAT
1 ATGAAAAGGGATAGCTACGACCATCGATT
* * * *
40790519 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTACGACCATCGATT
** * *
40790548 ATGAAAAGGGATAGCTTTGGCTATCGATT
1 ATGAAAAGGGATAGCTACGACCATCGATT
* * *
40790577 ATGAAAAAGGAT-GGTGACGACCATCGAAT
1 ATGAAAAGGGATAGCT-ACGACCATCGATT
* * *
40790606 ATGAAAAGGGATAGCTTCGACTATTGATT
1 ATGAAAAGGGATAGCTACGACCATCGATT
** * *
40790635 ATGAAAAGGGATAGCTTTGGCTATCGATT
1 ATGAAAAGGGATAGCTACGACCATCGATT
* * *
40790664 ATGAAAAGGGGT-GGTGACGACCATTGATT
1 ATGAAAAGGGATAGCT-ACGACCATCGATT
40790693 AATGAAAAGGGA
1 -ATGAAAAGGGA
40790705 CGATTATAAC
Statistics
Matches: 154, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
28 4 0.03
29 138 0.90
30 12 0.08
ACGTcount: A:0.36, C:0.11, G:0.28, T:0.26
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTACGACCATCGATT
Found at i:40799241 original size:48 final size:48
Alignment explanation
Indices: 40799170--40799265 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
40799160 GAAAGGTTAG
40799170 GGATTCCTATTGATTTCGAAAAAGTGTTTGAAAGAGTGTTTGTGTCTT
1 GGATTCCTATTGATTTCGAAAAAGTGTTTGAAAGAGTGTTTGTGTCTT
40799218 GGATTCCTATTGATTTCGAAAAAGTGTTTGAAAGAGTGTTTGTGTCTT
1 GGATTCCTATTGATTTCGAAAAAGTGTTTGAAAGAGTGTTTGTGTCTT
40799266 TATTTTATAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (48 bp):
GGATTCCTATTGATTTCGAAAAAGTGTTTGAAAGAGTGTTTGTGTCTT
Found at i:40809992 original size:67 final size:67
Alignment explanation
Indices: 40809884--40810014 Score: 235
Period size: 67 Copynumber: 2.0 Consensus size: 67
40809874 TTTATATTAC
* *
40809884 AGGGGATTTAGCCTGGACTGGTAATCCCATTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
1 AGGGGATTTAGCCTGGACTGGTAATCCCACTATAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
40809949 GT
66 GT
*
40809951 AGGGGATTTAGCCTGGACTGGTAATCCCACTATAAGAAATGAGGTTCGCGGGAGTGTTCTCTCT
1 AGGGGATTTAGCCTGGACTGGTAATCCCACTATAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
40810015 AAATTGAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (67 bp):
AGGGGATTTAGCCTGGACTGGTAATCCCACTATAAGAAATGAGGTTCGCGGGAGTGTGCTCTCTT
GT
Found at i:40813854 original size:17 final size:17
Alignment explanation
Indices: 40813833--40813877 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 17
40813823 GTATGTACAG
40813833 AAGTATGATTCGATTAT
1 AAGTATGATTCGATTAT
*
40813850 GAGTATTATGATTCGATTAT
1 -A--AGTATGATTCGATTAT
40813870 AAGTATGA
1 AAGTATGA
40813878 GTAAAGCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 1 0.04
20 15 0.65
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (17 bp):
AAGTATGATTCGATTAT
Found at i:40813861 original size:20 final size:20
Alignment explanation
Indices: 40813836--40813875 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40813826 TGTACAGAAG
*
40813836 TATGATTCGATTATGAGTAT
1 TATGATTCGATTATAAGTAT
40813856 TATGATTCGATTATAAGTAT
1 TATGATTCGATTATAAGTAT
40813876 GAGTAAAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (20 bp):
TATGATTCGATTATAAGTAT
Found at i:40814261 original size:23 final size:23
Alignment explanation
Indices: 40814231--40814467 Score: 246
Period size: 23 Copynumber: 10.3 Consensus size: 23
40814221 AAACAGAGCT
40814231 TTTGTGGCATATT-TCATAATGCC
1 TTTGTGGCATATTCT-ATAATGCC
* *
40814254 TTTATGGCATATTCTGTAATGCC
1 TTTGTGGCATATTCTATAATGCC
* * *
40814277 TTTGTGACATATTCTTTAATGTC
1 TTTGTGGCATATTCTATAATGCC
*
40814300 TTTGTGG-AGTATTCTATAATGTC
1 TTTGTGGCA-TATTCTATAATGCC
* *
40814323 TTTATGGCATATTTTATAATGCC
1 TTTGTGGCATATTCTATAATGCC
*
40814346 TTTGTGGCATATTCTGTAATGCC
1 TTTGTGGCATATTCTATAATGCC
* *
40814369 TTTGTGGCATATTCTGTAATGTC
1 TTTGTGGCATATTCTATAATGCC
* * *
40814392 TTTGTGACATATTCTGTAATGTC
1 TTTGTGGCATATTCTATAATGCC
* *
40814415 TTTGTGGCATATTCTGTAATGAC
1 TTTGTGGCATATTCTATAATGCC
** * *
40814438 TTTACGACATATTCTGTAATGTCC
1 TTTGTGGCATATTCTATAATG-CC
40814462 -TTGTGG
1 TTTGTGG
40814468 TAAGTTCTAT
Statistics
Matches: 185, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
22 1 0.01
23 181 0.98
24 3 0.02
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (23 bp):
TTTGTGGCATATTCTATAATGCC
Found at i:40814281 original size:46 final size:46
Alignment explanation
Indices: 40814231--40814467 Score: 273
Period size: 46 Copynumber: 5.2 Consensus size: 46
40814221 AAACAGAGCT
*
40814231 TTTGTGGCATATT-TCATAATGCCTTTATGGCATATTCTGTAATGCC
1 TTTGTGGCATATTCT-ATAATGCCTTTGTGGCATATTCTGTAATGCC
* * * * *
40814277 TTTGTGACATATTCTTTAATGTCTTTGTGG-AGTATTCTATAATGTC
1 TTTGTGGCATATTCTATAATGCCTTTGTGGCA-TATTCTGTAATGCC
* *
40814323 TTTATGGCATATTTTATAATGCCTTTGTGGCATATTCTGTAATGCC
1 TTTGTGGCATATTCTATAATGCCTTTGTGGCATATTCTGTAATGCC
* * * *
40814369 TTTGTGGCATATTCTGTAATGTCTTTGTGACATATTCTGTAATGTC
1 TTTGTGGCATATTCTATAATGCCTTTGTGGCATATTCTGTAATGCC
* * ** *
40814415 TTTGTGGCATATTCTGTAATGACTTTACGACATATTCTGTAATGTCC
1 TTTGTGGCATATTCTATAATGCCTTTGTGGCATATTCTGTAATG-CC
40814462 -TTGTGG
1 TTTGTGG
40814468 TAAGTTCTAT
Statistics
Matches: 164, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
45 1 0.01
46 160 0.98
47 3 0.02
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (46 bp):
TTTGTGGCATATTCTATAATGCCTTTGTGGCATATTCTGTAATGCC
Found at i:40814343 original size:69 final size:69
Alignment explanation
Indices: 40814231--40814460 Score: 293
Period size: 69 Copynumber: 3.3 Consensus size: 69
40814221 AAACAGAGCT
* * *
40814231 TTTGTGGCATATT-TCATAATGCCTTTATGGCATATTCTGTAATGCCTTTGTGACATATTCTTTA
1 TTTGTGGCATATTCT-ATAATGTCTTTATGGCATATTCTGTAATGCCTTTGTGGCATATTCTGTA
*
40814295 ATGTC
65 ATGAC
* *
40814300 TTTGTGG-AGTATTCTATAATGTCTTTATGGCATATTTTATAATGCCTTTGTGGCATATTCTGTA
1 TTTGTGGCA-TATTCTATAATGTCTTTATGGCATATTCTGTAATGCCTTTGTGGCATATTCTGTA
*
40814364 ATGCC
65 ATGAC
* * * *
40814369 TTTGTGGCATATTCTGTAATGTCTTTGTGACATATTCTGTAATGTCTTTGTGGCATATTCTGTAA
1 TTTGTGGCATATTCTATAATGTCTTTATGGCATATTCTGTAATGCCTTTGTGGCATATTCTGTAA
40814434 TGAC
66 TGAC
** * *
40814438 TTTACGACATATTCTGTAATGTC
1 TTTGTGGCATATTCTATAATGTC
40814461 CTTGTGGTAA
Statistics
Matches: 142, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
68 1 0.01
69 139 0.98
70 2 0.01
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (69 bp):
TTTGTGGCATATTCTATAATGTCTTTATGGCATATTCTGTAATGCCTTTGTGGCATATTCTGTAA
TGAC
Found at i:40817717 original size:18 final size:19
Alignment explanation
Indices: 40817688--40817725 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
40817678 TACTAAGTTG
*
40817688 AAAATAAAAATAAATAAAT
1 AAAATAAAAATAAAAAAAT
40817707 AAAAT-AAAATAAAAAAAT
1 AAAATAAAAATAAAAAAAT
40817725 A
1 A
40817726 CTAGTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAATAAAAATAAAAAAAT
Found at i:40818827 original size:20 final size:20
Alignment explanation
Indices: 40818804--40818860 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
40818794 TAAAAAAAAT
40818804 TCAAAATAATTTTTAAAGAC
1 TCAAAATAATTTTTAAAGAC
40818824 TCAAAATAATTTTTAAAGAC
1 TCAAAATAATTTTTAAAGAC
40818844 TCAAAATAATTTTTAAA
1 TCAAAATAATTTTTAAA
40818861 ATTTAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (20 bp):
TCAAAATAATTTTTAAAGAC
Found at i:40818868 original size:19 final size:19
Alignment explanation
Indices: 40818799--40818879 Score: 101
Period size: 20 Copynumber: 4.2 Consensus size: 19
40818789 AATTATAAAA
40818799 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
*
40818818 AAAGACTCAAAATAATTTTT
1 AAA-ATTCAAAATAATTTTT
*
40818838 AAAGACTCAAAATAATTTTT
1 AAA-ATTCAAAATAATTTTT
* *
40818858 AAAATTTAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
40818876 AAAA
1 AAAA
40818880 ATTTAAAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
18 9 0.16
19 10 0.18
20 38 0.67
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:40818878 original size:18 final size:20
Alignment explanation
Indices: 40818798--40818888 Score: 78
Period size: 20 Copynumber: 4.7 Consensus size: 20
40818788 AAATTATAAA
* *
40818798 AAAAATTCAAAATAATTTTT
1 AAAAATTTAAAATAATTTAT
* * * *
40818818 AAAGACTCAAAATAATTTTT
1 AAAAATTTAAAATAATTTAT
* * *
40818838 AAAGACTCAAAATAATTT-T
1 AAAAATTTAAAATAATTTAT
*
40818857 TAAAATTTAAAAT-ATTTAT
1 AAAAATTTAAAATAATTTAT
40818876 AAAAATTTAAAAT
1 AAAAATTTAAAAT
40818889 TTATATTTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
18 4 0.06
19 23 0.37
20 36 0.57
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAATTTAAAATAATTTAT
Found at i:40819072 original size:16 final size:16
Alignment explanation
Indices: 40819051--40819081 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40819041 TTTGAATTTT
40819051 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
40819067 TTTCAAATTTATATG
1 TTTCAAATATATATG
40819082 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:40833696 original size:14 final size:14
Alignment explanation
Indices: 40833677--40833705 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40833667 GCAATGAATA
40833677 TAAAGAAGAACACT
1 TAAAGAAGAACACT
40833691 TAAAGAAGAACACT
1 TAAAGAAGAACACT
40833705 T
1 T
40833706 GAGCTAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (14 bp):
TAAAGAAGAACACT
Found at i:40834066 original size:20 final size:20
Alignment explanation
Indices: 40834016--40834054 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40834006 TGGAGTAGGA
*
40834016 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
40834036 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
40834055 AGTATCAATA
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:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:40834448 original size:33 final size:33
Alignment explanation
Indices: 40834411--40834477 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
40834401 TGAATAGATT
* *
40834411 GCTCCCCCT-TAATAATAGTCATTTTCAATTTAA
1 GCTCCCCCTAT-ATAAAAATCATTTTCAATTTAA
40834444 GCTCCCCCTATATAAAAATCATTTTCAATTTAA
1 GCTCCCCCTATATAAAAATCATTTTCAATTTAA
40834477 G
1 G
40834478 GCATAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (33 bp):
GCTCCCCCTATATAAAAATCATTTTCAATTTAA
Found at i:40854114 original size:28 final size:28
Alignment explanation
Indices: 40854083--40854138 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
40854073 TATAATCAAA
* *
40854083 TCATATAAACAATTTATATATTCATTTT
1 TCATATAAACAATTCATATACTCATTTT
* *
40854111 TCATATAATCGATTCATATACTCATTTT
1 TCATATAAACAATTCATATACTCATTTT
40854139 ATATATTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (28 bp):
TCATATAAACAATTCATATACTCATTTT
Found at i:40854142 original size:13 final size:13
Alignment explanation
Indices: 40854095--40854157 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
40854085 ATATAAACAA
40854095 TTTATATATTCATT
1 TTTATATATTCA-T
*
40854109 TTTCATATAATCGA-
1 TTT-ATATATTC-AT
* *
40854123 TTCATATACTCAT
1 TTTATATATTCAT
40854136 TTTATATATTCAT
1 TTTATATATTCAT
*
40854149 TTTCTATAT
1 TTTATATAT
40854158 AACTGATTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
12 1 0.03
13 26 0.65
14 5 0.12
15 7 0.17
16 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.02, T:0.56
Consensus pattern (13 bp):
TTTATATATTCAT
Found at i:40854193 original size:41 final size:42
Alignment explanation
Indices: 40854039--40854193 Score: 169
Period size: 41 Copynumber: 3.8 Consensus size: 42
40854029 TCCATATGCC
* * *
40854039 CGATTCTTAAAATCATTTTGTATA-TC-TATTTC-CATATAAT
1 CGATTCATATAATCATTTTATATATTCAT-TTTCTCATATAAT
* * * *
40854079 CAAATCATATAAACAATTTATATATTCATTTT-TCATATAAT
1 CGATTCATATAATCATTTTATATATTCATTTTCTCATATAAT
*
40854120 CGATTCATATACTCATTTTATATATTCATTTTCT-ATATAA-
1 CGATTCATATAATCATTTTATATATTCATTTTCTCATATAAT
*
40854160 CTGATTCATATAATCATTTTATAAATTCATTTTC
1 C-GATTCATATAATCATTTTATATATTCATTTTC
40854194 CACCCGATGA
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
40 18 0.19
41 76 0.79
42 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.48
Consensus pattern (42 bp):
CGATTCATATAATCATTTTATATATTCATTTTCTCATATAAT
Found at i:40855564 original size:20 final size:20
Alignment explanation
Indices: 40855539--40855577 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40855529 TTGCTTTTTC
40855539 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
40855559 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
40855578 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:40855986 original size:56 final size:50
Alignment explanation
Indices: 40855769--40856011 Score: 220
Period size: 50 Copynumber: 4.8 Consensus size: 50
40855759 TGATAATAAC
* ** *
40855769 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATATTTC--CTGTA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-TA
* * * * * ** * *
40855818 CTGCCAATGTCATATCCCAGATATGGTCTTACATTGGAGTTCTCATATTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTA
* * * **
40855868 GTGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTA
* *
40855918 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CT---TA
*
40855974 ATGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
40856012 TCTCATTCCC
Statistics
Matches: 154, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
49 35 0.23
50 79 0.51
51 1 0.01
53 2 0.01
56 37 0.24
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTA
Found at i:40858379 original size:74 final size:74
Alignment explanation
Indices: 40858258--40858403 Score: 274
Period size: 74 Copynumber: 2.0 Consensus size: 74
40858248 ATGCTCTTAA
* *
40858258 AATTTGGGCACATTATGAATAGCCCTTAGATCGGTGGCTAGAACATTACTCTGTAGTTCATTGGA
1 AATTTGGGCACATTATGAATAGCCCTTAGATCGGTGGCTAGAACATTACTCTATAGTTCATCGGA
40858323 ACCTACTTG
66 ACCTACTTG
40858332 AATTTGGGCACATTATGAATAGCCCTTAGATCGGTGGCTAGAACATTACTCTATAGTTCATCGGA
1 AATTTGGGCACATTATGAATAGCCCTTAGATCGGTGGCTAGAACATTACTCTATAGTTCATCGGA
40858397 ACCTACT
66 ACCTACT
40858404 CGATCTGATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (74 bp):
AATTTGGGCACATTATGAATAGCCCTTAGATCGGTGGCTAGAACATTACTCTATAGTTCATCGGA
ACCTACTTG
Found at i:40860109 original size:14 final size:12
Alignment explanation
Indices: 40860064--40860111 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
40860054 CATATCTATC
40860064 CATATAAACATTT
1 CATAT-AACATTT
*
40860077 CATATACACAATT
1 CATATA-ACATTT
40860090 CATATAACTATTT
1 CATATAAC-ATTT
40860103 CCATATAAC
1 -CATATAAC
40860112 GGTTTCGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 3 0.10
13 19 0.63
14 8 0.27
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (12 bp):
CATATAACATTT
Found at i:40860333 original size:25 final size:25
Alignment explanation
Indices: 40860266--40860335 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
40860256 ATACACGAGA
* * *
40860266 ATAAA-GCTCACTCATGTTGTAACT
1 ATAAATGCTCACACAAGCTGTAACT
* ** *
40860290 ATAATTGCTCACATGAGCTGTAATT
1 ATAAATGCTCACACAAGCTGTAACT
40860315 ATAAATGCTCACACAAGCTGT
1 ATAAATGCTCACACAAGCTGT
40860336 GAAATGAGTC
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
24 4 0.11
25 31 0.89
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (25 bp):
ATAAATGCTCACACAAGCTGTAACT
Found at i:40864792 original size:39 final size:39
Alignment explanation
Indices: 40864636--40864861 Score: 231
Period size: 39 Copynumber: 5.7 Consensus size: 39
40864626 AATTGTTGTA
* *
40864636 TGAATACACATACGTGCCCCTGTTGTACTTC-GTTACCTCC
1 TGAATGCACATACGTGCCCCTATTGTACTTCAG-TACC-CC
** *
40864676 -GAATGCACATACGTGCCATTACTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTA-TTGTACTTCAGTACCCC
* * * *
40864715 TAAATGCACATACATGCCCTTATTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTA-TTGTACTTCAGTACCCC
**
40864755 TGAATGCACATATATGCCCCTATTGTACTTCAGTACCCC
1 TGAATGCACATACGTGCCCCTATTGTACTTCAGTACCCC
* * * * *
40864794 TAAATGCACATATGTTCCCCTATTGTACTTGAGTACCTC
1 TGAATGCACATACGTGCCCCTATTGTACTTCAGTACCCC
* * *
40864833 TGTATGGACATACGTGCCCCTGTTGTACT
1 TGAATGCACATACGTGCCCCTATTGTACT
40864862 GCGGTACATA
Statistics
Matches: 160, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 92 0.57
40 67 0.42
41 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.32
Consensus pattern (39 bp):
TGAATGCACATACGTGCCCCTATTGTACTTCAGTACCCC
Found at i:40864859 original size:78 final size:79
Alignment explanation
Indices: 40864642--40864861 Score: 232
Period size: 79 Copynumber: 2.8 Consensus size: 79
40864632 TGTATGAATA
* * * * **
40864642 CACATACGTGCCCCT-GTTGTACTTCGTTACCTCC-GAATGCACATACGTGCCATTACTTGTACT
1 CACATACATGCCCCTATTTGTACTTCGGTACC-CCTGAATGCACATACATGCCCCTA-TTGTACT
*
40864705 TCGGTACCCCTAAATG
64 TCAGTACCCCTAAATG
* *
40864721 CACATACATGCCCTTATTTGTACTTCGGTACCCCTGAATGCACATATATGCCCCTATTGTACTTC
1 CACATACATGCCCCTATTTGTACTTCGGTACCCCTGAATGCACATACATGCCCCTATTGTACTTC
40864786 AGTACCCCTAAATG
66 AGTACCCCTAAATG
** * * * * * *
40864800 CACATATGTTCCCCTA-TTGTACTT-GAGTACCTCTGTATGGACATACGTGCCCCTGTTGTACT
1 CACATACATGCCCCTATTTGTACTTCG-GTACCCCTGAATGCACATACATGCCCCTATTGTACT
40864862 GCGGTACATA
Statistics
Matches: 119, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
77 1 0.01
78 38 0.32
79 49 0.41
80 31 0.26
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.32
Consensus pattern (79 bp):
CACATACATGCCCCTATTTGTACTTCGGTACCCCTGAATGCACATACATGCCCCTATTGTACTTC
AGTACCCCTAAATG
Found at i:40865178 original size:23 final size:22
Alignment explanation
Indices: 40865140--40865182 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
40865130 ATAGATAAAT
40865140 ATGTAGTTCTTAAATGTGGATAG
1 ATGTAGTTCTTAAATG-GGATAG
40865163 ATGTAGTTCATT-AATGGGAT
1 ATGTAGTTC-TTAAATGGGAT
40865183 GTGTGTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 13 0.68
24 2 0.11
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.40
Consensus pattern (22 bp):
ATGTAGTTCTTAAATGGGATAG
Found at i:40869119 original size:15 final size:16
Alignment explanation
Indices: 40869089--40869121 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40869079 TAGTGATGAA
40869089 TACATGTTAATGGTAT
1 TACATGTTAATGGTAT
*
40869105 TACAT-TTAGTGGTAT
1 TACATGTTAATGGTAT
40869120 TA
1 TA
40869122 GAGCTACAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (16 bp):
TACATGTTAATGGTAT
Found at i:40883182 original size:81 final size:80
Alignment explanation
Indices: 40883045--40883311 Score: 376
Period size: 81 Copynumber: 3.3 Consensus size: 80
40883035 GTTATGACGA
* *
40883045 AAATACCTCCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATAACCGAAATACCCAC-
1 AAATACCTCCATAGGGTAAAATGACCGAAATACCCTCATAGGGT-AAATGACCGAAATACCC-CT
40883109 ATAGGGTAAAATGACCG
64 ATAGGGTAAAATGACCG
* * *
40883126 AAATACC-CTCATAGGGTAGAATAACCGAAATACCCTCATAGGGTAACATGATCGAAATACCCCT
1 AAATACCTC-CATAGGGTAAAATGACCGAAATACCCTCATAGGGTAA-ATGACCGAAATACCCCT
* * *
40883190 ATAGGATAGAATGATCG
64 ATAGGGTAAAATGACCG
* *
40883207 AAATACCCCCATAGGGTAAAATGACCGAAATACCCTCATAAGGTAAATGACCGAAATACCCCTAT
1 AAATACCTCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAATGACCGAAATACCCCTAT
* *
40883272 AGAGTAAAATGACCT
66 AGGGTAAAATGACCG
40883287 AAATACCTCCATAGGGTAAAATGAC
1 AAATACCTCCATAGGGTAAAATGAC
40883312 TGTTATACCA
Statistics
Matches: 164, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
80 56 0.34
81 107 0.65
82 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (80 bp):
AAATACCTCCATAGGGTAAAATGACCGAAATACCCTCATAGGGTAAATGACCGAAATACCCCTAT
AGGGTAAAATGACCG
Found at i:40883320 original size:27 final size:26
Alignment explanation
Indices: 40883045--40883311 Score: 338
Period size: 27 Copynumber: 9.9 Consensus size: 26
40883035 GTTATGACGA
40883045 AAATACCTCCATAGGGTAAAATGACCG
1 AAATACC-CCATAGGGTAAAATGACCG
*
40883072 AAATACCCCCATAGGGTAAAATAACCG
1 AAATA-CCCCATAGGGTAAAATGACCG
40883099 AAATACCCACATAGGGTAAAATGACCG
1 AAATACCC-CATAGGGTAAAATGACCG
* *
40883126 AAATACCCTCATAGGGTAGAATAACCG
1 AAATACCC-CATAGGGTAAAATGACCG
* *
40883153 AAATACCCTCATAGGGTAACATGATCG
1 AAATACCC-CATAGGGTAAAATGACCG
* * *
40883180 AAATACCCCTATAGGATAGAATGATCG
1 AAATACCCC-ATAGGGTAAAATGACCG
40883207 AAATACCCCCATAGGGTAAAATGACCG
1 AAATA-CCCCATAGGGTAAAATGACCG
*
40883234 AAATACCCTCATAAGGT-AAATGACCG
1 AAATACCC-CATAGGGTAAAATGACCG
* *
40883260 AAATACCCCTATAGAGTAAAATGACCT
1 AAATACCCC-ATAGGGTAAAATGACCG
40883287 AAATACCTCCATAGGGTAAAATGAC
1 AAATACC-CCATAGGGTAAAATGAC
40883312 TGTTATACCA
Statistics
Matches: 212, Mismatches: 20, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
25 1 0.00
26 29 0.14
27 174 0.82
28 8 0.04
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (26 bp):
AAATACCCCATAGGGTAAAATGACCG
Found at i:40895680 original size:24 final size:21
Alignment explanation
Indices: 40895641--40895720 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 21
40895631 ATAAGACTAC
40895641 AAAAAAAATAAAAGAAAAATA
1 AAAAAAAATAAAAGAAAAATA
40895662 AAAAGAAAGATAATAAGAAAAATA
1 AAAA-AAA-ATAA-AAGAAAAATA
* * *
40895686 AACAATAACTAAATAAAATAAATA
1 AA-AAAAAATAAA-AGAA-AAATA
*
40895710 AAATAAAATAA
1 AAAAAAAATAA
40895721 TAAAAAGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
21 4 0.09
22 4 0.09
23 16 0.34
24 21 0.45
25 2 0.04
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAAAAAATAAAAGAAAAATA
Found at i:40895715 original size:14 final size:13
Alignment explanation
Indices: 40895696--40895725 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
40895686 AACAATAACT
40895696 AAATAAAATAAATA
1 AAATAAAAT-AATA
40895710 AAATAAAATAATA
1 AAATAAAATAATA
40895723 AAA
1 AAA
40895726 AGAAAAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:40897328 original size:50 final size:50
Alignment explanation
Indices: 40897256--40897426 Score: 177
Period size: 50 Copynumber: 3.4 Consensus size: 50
40897246 TATCCCGGAT
* ** *
40897256 ATGGTCTTACATGGGAGTTCTCATATTGGTTCCCATGCCATGTCTCAGAC
1 ATGGTCTTACAGGGGACCTCTCATATTGGTTCCCATGCCATGTCCCAGAC
*** * *
40897306 ATGGTCTTTTGGGGGACCTCTCA-ACTCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACAGGGGACCTCTCATA-TTGGTTCCCATGCCATGTCCCAGAC
* * *
40897356 ATGGTCTTACATGGGACCTCTTAT-TTCGGTT-CCAGCGCCATGTCCCAGAC
1 ATGGTCTTACAGGGGACCTCTCATATT-GGTTCCCA-TGCCATGTCCCAGAC
*
40897406 ATGGTCTTACATGGGACCTCT
1 ATGGTCTTACAGGGGACCTCT
40897427 TTACCCAAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
49 5 0.05
50 95 0.95
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.30
Consensus pattern (50 bp):
ATGGTCTTACAGGGGACCTCTCATATTGGTTCCCATGCCATGTCCCAGAC
Found at i:40907851 original size:72 final size:72
Alignment explanation
Indices: 40907734--40907878 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
40907724 CTAAACTGAG
40907734 TAAGTGTGAGTTTTGGTTGAAGGAGGTTATGTTTTCGGGTCATGCGGCATCTACTGAGGGTATAC
1 TAAGTGTGAGTTTTGGTTGAAGGAGGTTATGTTTTCGGGTCATGCGGCATCTACTGAGGGTATAC
40907799 GTGTAGA
66 GTGTAGA
40907806 TAAGTGTGAGTTTTGGTTGAAGGAGGTTATGTTTTCGGGTCATGCGGCATCTACTGAGGGTATAC
1 TAAGTGTGAGTTTTGGTTGAAGGAGGTTATGTTTTCGGGTCATGCGGCATCTACTGAGGGTATAC
40907871 GTGTAGA
66 GTGTAGA
40907878 T
1 T
40907879 TCAAGAAAGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.35
Consensus pattern (72 bp):
TAAGTGTGAGTTTTGGTTGAAGGAGGTTATGTTTTCGGGTCATGCGGCATCTACTGAGGGTATAC
GTGTAGA
Found at i:40934236 original size:30 final size:30
Alignment explanation
Indices: 40934201--40934260 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40934191 TAGACTTAAT
40934201 TTGGTTTAGTGTTAAAACCCACACCTGATC
1 TTGGTTTAGTGTTAAAACCCACACCTGATC
40934231 TTGGTTTAGTGTTAAAACCCACACCTGATC
1 TTGGTTTAGTGTTAAAACCCACACCTGATC
40934261 ATAGATCCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (30 bp):
TTGGTTTAGTGTTAAAACCCACACCTGATC
Found at i:40939687 original size:21 final size:21
Alignment explanation
Indices: 40939644--40939688 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
40939634 TATTTATATG
*
40939644 TATGATAATATTATTTATCTT
1 TATGATAATATTATATATCTT
*
40939665 TATGATAACT-TTATATATTTT
1 TATGATAA-TATTATATATCTT
40939686 TAT
1 TAT
40939689 TTTCTTACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (21 bp):
TATGATAATATTATATATCTT
Found at i:40940195 original size:7 final size:7
Alignment explanation
Indices: 40940183--40940213 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
40940173 TTTCAAACCT
40940183 AATTCCA
1 AATTCCA
40940190 AATTCCA
1 AATTCCA
40940197 AATTCCA
1 AATTCCA
40940204 AATTCCA
1 AATTCCA
40940211 AAT
1 AAT
40940214 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (7 bp):
AATTCCA
Found at i:40949381 original size:47 final size:47
Alignment explanation
Indices: 40949302--40950043 Score: 1205
Period size: 47 Copynumber: 15.6 Consensus size: 47
40949292 TATTTGAATA
40949302 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
40949351 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40949398 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40949445 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
40949494 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40949541 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
40949590 AATGTGAAATTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40949637 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
40949686 AATATGAAATTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40949733 AATGTGAAAGTGTATATATGTGATAAGGCTTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40949780 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
40949829 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40949876 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
40949923 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * * * *
40949970 AATGTGAAAGTGTATATATGCGACAGGGCCGAGTGGTCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40950017 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
40950044 TCCCGAAGGG
Statistics
Matches: 652, Mismatches: 33, Indels: 18
0.93 0.05 0.03
Matches are distributed among these distances:
47 461 0.71
49 191 0.29
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40949414 original size:96 final size:94
Alignment explanation
Indices: 40949302--40950043 Score: 1205
Period size: 96 Copynumber: 7.8 Consensus size: 94
40949292 TATTTGAATA
40949302 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
40949367 TATGTGATAAGGCCTAATAGCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
* *
40949398 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
40949463 TATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
40949494 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
40949559 TATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
40949590 AATGTGAAATTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
40949655 TATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
40949686 AATATGAAATTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
40949751 TGTGATAAGGCTTAATAGCCGATGTGATG
66 TGTGATAAGGCCTAATGGCCGATGTGATG
40949780 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
40949845 TATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATGTGATAAGGCCTAATGGCCGATGTGATG
40949876 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
40949941 TGTGATAAGGCCTAATGGCCGATGTGATG
66 TGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * * * * * *
40949970 AATGTGAAAGTGTATATATGCGACAGGGCCGAGTGGTCAACGTGATGGATGTGAAAGTGTATAAA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
40950035 TGTGATAAG
66 TGTGATAAG
40950044 TCCCGAAGGG
Statistics
Matches: 613, Mismatches: 29, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
94 234 0.38
96 379 0.62
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (94 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:40949463 original size:143 final size:143
Alignment explanation
Indices: 40949302--40950043 Score: 1194
Period size: 143 Copynumber: 5.2 Consensus size: 143
40949292 TATTTGAATA
40949302 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* *
40949367 TATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAT
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
*
40949432 GGCCAATGTGATG
131 GGCCGATGTGATG
40949445 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
40949510 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTA
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTA
40949575 ATGGCCGATGTGATG
129 ATGGCCGATGTGATG
* * *
40949590 AATGTGAAA-T-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TA
* *
40949653 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATATGAAATTGTATATATGTGATAAGGCCTA
64 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
*
40949718 ATAGCCGATGTGATG
129 ATGGCCGATGTGATG
* *
40949733 AATGTGAAAGTG--TATATATGTGATAAGGCTTAATAGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TA
40949796 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
64 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTA
40949861 ATGGCCGATGTGATG
129 ATGGCCGATGTGATG
40949876 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* * * * *
40949939 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGCGACAGGGCCGAGT
66 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
* * *
40950004 GGTCAACGTGATG
131 GGCCGATGTGATG
*
40950017 GATGTGAAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
40950044 TCCCGAAGGG
Statistics
Matches: 564, Mismatches: 27, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
141 95 0.17
142 1 0.00
143 379 0.67
144 2 0.00
145 87 0.15
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (143 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
GGCCGATGTGATG
Found at i:40950263 original size:37 final size:37
Alignment explanation
Indices: 40950162--40950263 Score: 150
Period size: 37 Copynumber: 2.8 Consensus size: 37
40950152 CCGAGCTCTA
* *
40950162 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCAGGT
*
40950199 AAGACTCGATGACTACGTGTGGAGATTTTGTCCAGGT
1 AAGACCCGATGACTACGTGTGGAGATTTTGTCCAGGT
* * *
40950236 AAGACCCGATAACTTCATGTGGAGATTT
1 AAGACCCGATGACTACGTGTGGAGATTT
40950264 CGTCTGAGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGAGATTTTGTCCAGGT
Found at i:40955560 original size:30 final size:30
Alignment explanation
Indices: 40955509--40955574 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
40955499 GTAATTTTCG
* *
40955509 AGCTTTGGGGCAGAAGTGTAATTATGTAAA
1 AGCTTAGGGGCAGAAATGTAATTATGTAAA
* *
40955539 AGCTTAGGGGCA-AAATCGTAATTTTGTCAA
1 AGCTTAGGGGCAGAAAT-GTAATTATGTAAA
40955569 AG-TTAG
1 AGCTTAG
40955575 AGTCGAGGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (30 bp):
AGCTTAGGGGCAGAAATGTAATTATGTAAA
Found at i:40956017 original size:50 final size:50
Alignment explanation
Indices: 40955918--40956155 Score: 278
Period size: 50 Copynumber: 4.6 Consensus size: 50
40955908 GATGAGATCT
*
40955918 CATGTAAGACCATGTCTGGGAAATGGCATTGGCACCATTGAGATTATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACC---GAG---ATGAGAGGTCC
40955974 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* ** *
40956024 CAAGTAAGACCATGTCTAAGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
** * * * * ** *
40956074 CCCGTAAGACCATGTCTAGGACATGGCATGGGCACCTATATGAGAACTCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* *
40956124 CATGTAAGACCATATCTGGGATATGGCATTGG
1 CATGTAAGACCATGTCTGGGACATGGCATTGG
40956156 TAATACAAGA
Statistics
Matches: 161, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
50 123 0.76
53 3 0.02
56 35 0.22
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:40959884 original size:51 final size:49
Alignment explanation
Indices: 40959821--40959939 Score: 130
Period size: 51 Copynumber: 2.3 Consensus size: 49
40959811 GCACGGACTG
* **
40959821 TGTGTAGGCTACTATGTAAAAGTGAAAGTGATGGTCACGTGTGTAGTACTA
1 TGTGTAGGCTACTATGT-AAAG-GAAAGTAATGGTCACACGTGTAGTACTA
* ** **
40959872 TGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACACGTGTAGTACTA
1 TGTGTAGGCTACTA--TGTAAAGGAAAGTAATGGTCACACGTGTAGTACTA
40959923 TGTGTAGGCTACTATGT
1 TGTGTAGGCTACTATGT
40959940 GAACTGAACA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
49 3 0.05
51 49 0.86
52 2 0.04
53 3 0.05
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.32
Consensus pattern (49 bp):
TGTGTAGGCTACTATGTAAAGGAAAGTAATGGTCACACGTGTAGTACTA
Found at i:40960033 original size:45 final size:45
Alignment explanation
Indices: 40959942--40960033 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
40959932 TACTATGTGA
* * *
40959942 ACTGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACTGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCC
* *
40959987 ACTGGACATCATTGATTAATAAGGTGGTTGGTATGTGCTAAATCC
1 ACTGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCC
40960032 AC
1 AC
40960034 CGAGTATCTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (45 bp):
ACTGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCC
Found at i:40963434 original size:13 final size:13
Alignment explanation
Indices: 40963418--40963447 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40963408 TGATTAAATA
*
40963418 TAAATTAATTTTT
1 TAAATCAATTTTT
40963431 TAAATCAATTTTT
1 TAAATCAATTTTT
40963444 TAAA
1 TAAA
40963448 AACGATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
TAAATCAATTTTT
Found at i:40967702 original size:29 final size:29
Alignment explanation
Indices: 40967616--40967702 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
40967606 CAATTTTTAG
40967616 GGGTTCT-AAAAAATAA-TTTGTAC-AGGAT
1 GGGTTCTGAAAAAATAATTTTG-ACGA-GAT
* *
40967644 GGGTTCTGAAAAAATAATTTTGAGGTGAT
1 GGGTTCTGAAAAAATAATTTTGACGAGAT
* * *
40967673 GTGTTTTGAAGAAATAATTTTGACGAGAT
1 GGGTTCTGAAAAAATAATTTTGACGAGAT
40967702 G
1 G
40967703 CGTTGAGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 7 0.14
29 38 0.78
30 4 0.08
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (29 bp):
GGGTTCTGAAAAAATAATTTTGACGAGAT
Found at i:40969955 original size:16 final size:17
Alignment explanation
Indices: 40969928--40969963 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
40969918 AGAGAGTTGA
40969928 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
40969945 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
40969961 GAG
1 GAG
40969964 GGATGATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.53, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:40972264 original size:14 final size:14
Alignment explanation
Indices: 40972245--40972271 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40972235 GTACCAATAT
40972245 TATTTGGTTTGTAA
1 TATTTGGTTTGTAA
40972259 TATTTGGTTTGTA
1 TATTTGGTTTGTA
40972272 TTTTTATATT
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:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (14 bp):
TATTTGGTTTGTAA
Found at i:40978651 original size:9 final size:8
Alignment explanation
Indices: 40978626--40978650 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40978616 CTTACTGTAC
40978626 TATTTTTT
1 TATTTTTT
40978634 TATTTTTT
1 TATTTTTT
40978642 TATTTTTT
1 TATTTTTT
40978650 T
1 T
40978651 TGGGTATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TATTTTTT
Found at i:40991704 original size:27 final size:28
Alignment explanation
Indices: 40991620--40991717 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 28
40991610 CATGAGATTG
* * * * *
40991620 GCACTAAATGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
40991649 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40991677 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40991704 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
40991718 GACTTAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.35
29 17 0.27
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:40991731 original size:29 final size:27
Alignment explanation
Indices: 40991648--40991731 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
40991638 TAAATTGTAC
* *
40991648 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
40991676 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
40991703 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
40991732 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:40997790 original size:39 final size:39
Alignment explanation
Indices: 40997742--40997958 Score: 339
Period size: 39 Copynumber: 5.6 Consensus size: 39
40997732 CATATTCACT
* * *
40997742 TTTAGGCATATATCACATTACACATATAATTACATAAAA
1 TTTAAGCATATATCACAATACTCATATAATTACATAAAA
* *
40997781 TTTAAGCATATATTACAATACTCATATAATCACA-AAACA
1 TTTAAGCATATATCACAATACTCATATAATTACATAAA-A
40997820 TTTAAGCATATATCACAATACTCATATAATTACATAAAA
1 TTTAAGCATATATCACAATACTCATATAATTACATAAAA
* *
40997859 TTTAAGCATATATTACAATACTCATATAATCACA-AAACA
1 TTTAAGCATATATCACAATACTCATATAATTACATAAA-A
40997898 TTTAAGCATATATCACAATACTCATATAATTACATAAAA
1 TTTAAGCATATATCACAATACTCATATAATTACATAAAA
40997937 TTTAAGCATATATCACAATACT
1 TTTAAGCATATATCACAATACT
40997959 TGTAAGGCCC
Statistics
Matches: 163, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
38 6 0.04
39 151 0.93
40 6 0.04
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATTACATAAAA
Found at i:40997876 original size:78 final size:78
Alignment explanation
Indices: 40997742--40997958 Score: 398
Period size: 78 Copynumber: 2.8 Consensus size: 78
40997732 CATATTCACT
* * *
40997742 TTTAGGCATATATCACATTACACATATAATTACATAAAATTTAAGCATATATTACAATACTCATA
1 TTTAAGCATATATCACAATACTCATATAATTACATAAAATTTAAGCATATATTACAATACTCATA
40997807 TAATCACAAAACA
66 TAATCACAAAACA
40997820 TTTAAGCATATATCACAATACTCATATAATTACATAAAATTTAAGCATATATTACAATACTCATA
1 TTTAAGCATATATCACAATACTCATATAATTACATAAAATTTAAGCATATATTACAATACTCATA
40997885 TAATCACAAAACA
66 TAATCACAAAACA
*
40997898 TTTAAGCATATATCACAATACTCATATAATTACATAAAATTTAAGCATATATCACAATACT
1 TTTAAGCATATATCACAATACTCATATAATTACATAAAATTTAAGCATATATTACAATACT
40997959 TGTAAGGCCC
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 135 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (78 bp):
TTTAAGCATATATCACAATACTCATATAATTACATAAAATTTAAGCATATATTACAATACTCATA
TAATCACAAAACA
Found at i:41004163 original size:28 final size:28
Alignment explanation
Indices: 41004124--41004247 Score: 162
Period size: 28 Copynumber: 4.5 Consensus size: 28
41004114 CTATTCAGTA
*
41004124 ACAGT-ACAGTGTGGGCCTTAGCCCGAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
41004151 ACAGTAACAGTGTAGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * *
41004179 ACAGAAATAGTATGGGCCTTAG-CCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
41004206 ACAGAAATAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
*
41004234 ATAGTAACAGTGTG
1 ACAGTAACAGTGTG
41004248 ATAATGCAAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
27 31 0.36
28 54 0.64
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:41004423 original size:20 final size:20
Alignment explanation
Indices: 41004383--41004425 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
41004373 AAAACATAAA
**
41004383 CTTGTTGATAAAACTTGTTT
1 CTTGTTGATAAAACTCATTT
41004403 CTTGTTGATAAAACTCATTT
1 CTTGTTGATAAAACTCATTT
41004423 CTT
1 CTT
41004426 AAGTTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (20 bp):
CTTGTTGATAAAACTCATTT
Found at i:41005078 original size:26 final size:26
Alignment explanation
Indices: 41005042--41005092 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
41005032 ACACCAATAT
41005042 CGCAACAAAGCTTCCAGTAACAGTAA
1 CGCAACAAAGCTTCCAGTAACAGTAA
*
41005068 CGCAGCAAAGCTTCCAGTAACAGTA
1 CGCAACAAAGCTTCCAGTAACAGTA
41005093 TATGTGGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (26 bp):
CGCAACAAAGCTTCCAGTAACAGTAA
Found at i:41005275 original size:27 final size:27
Alignment explanation
Indices: 41005245--41005440 Score: 209
Period size: 27 Copynumber: 7.3 Consensus size: 27
41005235 GGGTATAACA
* *
41005245 GTCATTTTACCCATCGGGGGTATTTCG
1 GTCATTTTACCCTTCAGGGGTATTTCG
* * *
41005272 GTCA-TTTATCCTT-TGGGGTTATTTCA
1 GTCATTTTACCCTTCAGGGG-TATTTCG
* *
41005298 GACATTTTACCCTTTAGGGGTATTTCG
1 GTCATTTTACCCTTCAGGGGTATTTCG
* *
41005325 GTCATTTTATCCTTCAGTGGTATTTCG
1 GTCATTTTACCCTTCAGGGGTATTTCG
*
41005352 GTCATTTTACCCTTCAGAGGTATTTCG
1 GTCATTTTACCCTTCAGGGGTATTTCG
* * *
41005379 ATCATTTTACCCATCTA-GAGTATTTCG
1 GTCATTTTACCCTTC-AGGGGTATTTCG
* *
41005406 GTCATTTTACCCTTCGGGGGTATTTCA
1 GTCATTTTACCCTTCAGGGGTATTTCG
*
41005433 GACATTTT
1 GTCATTTT
41005441 CCCACGAATC
Statistics
Matches: 140, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
25 4 0.03
26 16 0.11
27 115 0.82
28 5 0.04
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTTCAGGGGTATTTCG
Done.