Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 42
Found at i:5663547 original size:94 final size:93
Alignment explanation
Indices: 5663364--5663547 Score: 250
Period size: 94 Copynumber: 2.0 Consensus size: 93
5663354 AATCAATCCA
5663364 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAA
1 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAA
5663429 TCCATACTAATAAATTATTAAAAATAAAT
66 TCCATA-TAATAAATTATTAAAAATAAAT
* *
5663458 TATTTTAAAATAAATCAATCTATATTTTAAAATAAATTATTTTAAAATAAATTATTTTAAAATAA
1 TATTTTAAAATAAATCAATCCATA--CT--AATAAATTA-TTTAAAATAAATTATTTTAAAATAA
* *
5663523 AT-AA-CC-T-TATTAAATTATTTAAAAT
61 ATCAATCCATATAATAAATTATTAAAAAT
5663548 TATTTTAATA
Statistics
Matches: 81, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
94 39 0.48
96 2 0.02
97 2 0.02
98 11 0.14
99 27 0.33
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (93 bp):
TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATTATTTTAAAATAAATCAA
TCCATATAATAAATTATTAAAAATAAAT
Found at i:5663863 original size:6 final size:6
Alignment explanation
Indices: 5663846--5663874 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5663836 TAGTTAAGAA
5663846 CTCGAG -TCGAG CTCGAG CTCGAG CTCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG
5663875 TCCATTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.31, G:0.34, T:0.17
Consensus pattern (6 bp):
CTCGAG
Found at i:5673168 original size:66 final size:66
Alignment explanation
Indices: 5673038--5673168 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
5673028 ATCAGCATGC
* * *
5673038 TCTACTTCTCTGTTACTCTCAACAGCAGAGACGGATAATGTGCCGGAATTCTTTTCACCGATATG
1 TCTACATCTCTGTTACTCTCAACAGCAGAGACAGATAATGTGCCGGAATTCTTTTCACCAATATG
5673103 A
66 A
* * * *
5673104 TCTACATCTCTGTTAGTCTCAACAGGAGAGGA-AGATAATGTGCTGGAATTCTTTTCATCAATAT
1 TCTACATCTCTGTTACTCTCAACAGCAGA-GACAGATAATGTGCCGGAATTCTTTTCACCAATAT
5673168 G
65 G
5673169 CTCCAAATCT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 55 0.96
67 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (66 bp):
TCTACATCTCTGTTACTCTCAACAGCAGAGACAGATAATGTGCCGGAATTCTTTTCACCAATATG
A
Found at i:5683279 original size:28 final size:27
Alignment explanation
Indices: 5683248--5683310 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
5683238 AGTTGATACA
*
5683248 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
5683276 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
5683304 ATATTTT
1 ATATTTT
5683311 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:5683407 original size:16 final size:18
Alignment explanation
Indices: 5683386--5683419 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5683376 TAATTTTTTT
5683386 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
5683402 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
5683420 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:5683563 original size:21 final size:21
Alignment explanation
Indices: 5683539--5683581 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5683529 TATTACCTTA
5683539 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
5683560 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
5683581 A
1 A
5683582 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:5683599 original size:35 final size:35
Alignment explanation
Indices: 5683550--5683635 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
5683540 ATTGAAGTAT
** * *
5683550 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
5683585 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
5683620 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
5683636 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:5683818 original size:29 final size:29
Alignment explanation
Indices: 5683766--5683823 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5683756 GCAAACGGAA
* *
5683766 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGTTT
5683795 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT
5683824 CAGAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGTTT
Found at i:5684412 original size:195 final size:194
Alignment explanation
Indices: 5683877--5684540 Score: 649
Period size: 195 Copynumber: 3.4 Consensus size: 194
5683867 AACATGTCCT
* * * *
5683877 GAAAAGGGTAATAAAAAGTGAAGATGAGTATCGTAATTCGATCGAGAAGATCATACTATGGAGA-
1 GAAAAGGGTAATATAAAGTG-AGATGATTATCGTAATTCGATCGAGAAGATCATATTAGGGAGAG
* * * *
5683941 ACAGATGACGAGACTGTATCAATGTATCTCAAAGGTCCTCGTTTATAAGATAAAAACACAAATTT
65 A-AGATGCCGAAACAGTATCAATGTATCTCAAAGG-CCTCATTTATAAGATAAAAACAC-AATTT
** * * * * *
5684006 TGTAATCTGTTCTAGGCCTCAGAAAAATACCA-TCTGGGACATCATTATACTG-TTTTGAAC--A
127 TGTAATCTGTTCTAGGCCTCAGAAAGGTACCATTC-CGAACATCATTGTACTGAGTTAGAACATA
5684067 T---
191 TCAA
** ** * * *
5684068 GCCAAGGGTAATCA-AAAGTGATGATGATTGCCGAAATTCGATGGGGAAGATCATACTGT-GGG-
1 GAAAAGGGTAAT-ATAAAGTGA-GATGATTATCGTAATTCGATCGAGAAGATCATA-T-TAGGGA
* * * * *
5684130 GAGCAGATGCCGAAACAG--TCGATGTAACTCAAAGGCCCTCACTTATAAGATAAAAAACGCAAT
62 GAGAAGATGCCGAAACAGTATCAATGTATCTCAAAGG-CCTCATTTATAAGAT-AAAAACACAAT
* *
5684193 TTAGTAATCTGTTCTAGTCCTCAGAAAGGTACCATTCCGAACATCATTGTACTGAGTTAGAACAT
125 TTTGTAATCTGTTCTAGGCCTCAGAAAGGTACCATTCCGAACATCATTGTACTGAGTTAGAACAT
5684258 ATCAA
190 ATCAA
* * * **
5684263 GGAAAGGGTAGTATAAAGTGAGATGATTATCGTAATTCGATCAAGAAGATTGTATTAGGGAGAGA
1 GAAAAGGGTAATATAAAGTGAGATGATTATCGTAATTCGATCGAGAAGATCATATTAGGGAGAGA
* *
5684328 AGATGCCGAAACCGTATCAATGTATCTCAAAGGCACTCATTTATAAGATAAAAACACAGTTTTGT
66 AGATGCCGAAACAGTATCAATGTATCTCAAAGGC-CTCATTTATAAGATAAAAACACAATTTTGT
* *
5684393 AATCTGTTCAAGGCCTCAGAAAGGTACCATTCC-AGACATCATTGCACTGAGTTTA-AACATATC
130 AATCTGTTCTAGGCCTCAGAAAGGTACCATTCCGA-ACATCATTGTACTGAG-TTAGAACATATC
5684456 AA
193 AA
* * * * * *
5684458 GAAAAGGGTAAT-CAAAGTTGGAGATGGTTATCGTATTTCGATCGAGAAGACCATACTATGGAGA
1 GAAAAGGGTAATATAAAG-T-GAGATGATTATCGTAATTCGATCGAGAAGATCATATTAGGGAGA
* * *
5684522 GCAGATGTCGGAACAGTAT
64 GAAGATGCCGAAACAGTAT
5684541 TTCCCTCACA
Statistics
Matches: 384, Mismatches: 66, Indels: 41
0.78 0.13 0.08
Matches are distributed among these distances:
189 75 0.20
190 16 0.04
191 56 0.15
192 6 0.02
193 5 0.01
194 47 0.12
195 97 0.25
196 82 0.21
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (194 bp):
GAAAAGGGTAATATAAAGTGAGATGATTATCGTAATTCGATCGAGAAGATCATATTAGGGAGAGA
AGATGCCGAAACAGTATCAATGTATCTCAAAGGCCTCATTTATAAGATAAAAACACAATTTTGTA
ATCTGTTCTAGGCCTCAGAAAGGTACCATTCCGAACATCATTGTACTGAGTTAGAACATATCAA
Found at i:5692961 original size:2 final size:2
Alignment explanation
Indices: 5692954--5692995 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
5692944 ATATAAAGAA
5692954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5692994 AT
1 AT
5692996 GGTTAGAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5696679 original size:40 final size:40
Alignment explanation
Indices: 5696635--5696712 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
5696625 TCGACCACTG
5696635 TGTTTGACTTTTTACTTAAATCTATGGGTAGTGTCATTTA
1 TGTTTGACTTTTTACTTAAATCTATGGGTAGTGTCATTTA
5696675 TGTTTGACTTTTTACTTAAATCTATGGGTAGTGTCATT
1 TGTTTGACTTTTTACTTAAATCTATGGGTAGTGTCATT
5696713 CTTGAACCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.50
Consensus pattern (40 bp):
TGTTTGACTTTTTACTTAAATCTATGGGTAGTGTCATTTA
Found at i:5696857 original size:102 final size:102
Alignment explanation
Indices: 5696681--5696885 Score: 410
Period size: 102 Copynumber: 2.0 Consensus size: 102
5696671 TTTATGTTTG
5696681 ACTTTTTACTTAAATCTATGGGTAGTGTCATTCTTGAACCCCCCCCCCCAAAAAAAATAATAAAG
1 ACTTTTTACTTAAATCTATGGGTAGTGTCATTCTTGAACCCCCCCCCCCAAAAAAAATAATAAAG
5696746 CAGAACTAGGCGAATTTCTTTAACCATTGAGATATGA
66 CAGAACTAGGCGAATTTCTTTAACCATTGAGATATGA
5696783 ACTTTTTACTTAAATCTATGGGTAGTGTCATTCTTGAACCCCCCCCCCCAAAAAAAATAATAAAG
1 ACTTTTTACTTAAATCTATGGGTAGTGTCATTCTTGAACCCCCCCCCCCAAAAAAAATAATAAAG
5696848 CAGAACTAGGCGAATTTCTTTAACCATTGAGATATGA
66 CAGAACTAGGCGAATTTCTTTAACCATTGAGATATGA
5696885 A
1 A
5696886 TCATTACTGC
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (102 bp):
ACTTTTTACTTAAATCTATGGGTAGTGTCATTCTTGAACCCCCCCCCCCAAAAAAAATAATAAAG
CAGAACTAGGCGAATTTCTTTAACCATTGAGATATGA
Found at i:5699999 original size:56 final size:59
Alignment explanation
Indices: 5699928--5700065 Score: 183
Period size: 62 Copynumber: 2.3 Consensus size: 59
5699918 CTGTGATTAT
*
5699928 CAAGAACAGACACATACGCAA-ACGAATAACTGCATACTT-AAA-AAAGGAAAAAAAAA
1 CAAGAACAGACACATACGCAATACGAATAACTGCATACTTAAAAGAAAAGAAAAAAAAA
* * *
5699984 CAAGAACAGATACATACGAAATTACGAATAACTGTATACTTAGAAAAGAAAAGAAAAAAAAA
1 CAAGAACAGACACATACGCAA-TACGAATAACTGCATACTT--AAAAGAAAAGAAAAAAAAA
*
5700046 CAAGAACAAACACATACGCA
1 CAAGAACAGACACATACGCA
5700066 CGAATTGTGG
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
56 19 0.28
58 17 0.25
61 3 0.04
62 30 0.43
ACGTcount: A:0.59, C:0.17, G:0.12, T:0.12
Consensus pattern (59 bp):
CAAGAACAGACACATACGCAATACGAATAACTGCATACTTAAAAGAAAAGAAAAAAAAA
Found at i:5700554 original size:21 final size:21
Alignment explanation
Indices: 5700528--5700567 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5700518 TATAATGTAA
* *
5700528 ATTTCAGAATAATTAAATTAG
1 ATTTCAAAATAAATAAATTAG
5700549 ATTTCAAAATAAATAAATT
1 ATTTCAAAATAAATAAATT
5700568 TAATTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTTCAAAATAAATAAATTAG
Found at i:5700587 original size:19 final size:20
Alignment explanation
Indices: 5700563--5700601 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5700553 CAAAATAAAT
* *
5700563 AAATTT-AATTATTTTAGTA
1 AAATTTGAATAATTTAAGTA
5700582 AAATTTGAATAATTTAAGTA
1 AAATTTGAATAATTTAAGTA
5700602 TATATACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
AAATTTGAATAATTTAAGTA
Found at i:5707171 original size:36 final size:36
Alignment explanation
Indices: 5707124--5707192 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
5707114 TAGTTAAAGA
5707124 AATCTTTGTTGTTCTTAGAAGTCACGAGTTCGAGCG
1 AATCTTTGTTGTTCTTAGAAGTCACGAGTTCGAGCG
5707160 AATCTTTGTTGTTCTTAGAAGTCACGAGTTCGA
1 AATCTTTGTTGTTCTTAGAAGTCACGAGTTCGA
5707193 ACAAATGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (36 bp):
AATCTTTGTTGTTCTTAGAAGTCACGAGTTCGAGCG
Found at i:5709369 original size:15 final size:15
Alignment explanation
Indices: 5709349--5709405 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
5709339 AACCGGATAT
5709349 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
* **
5709364 CGGGTACCCACAAAATC
1 CGGGTACCC-GATTA-C
*
5709381 CGGGTACCCGATTAT
1 CGGGTACCCGATTAC
*
5709396 CGGATACCCG
1 CGGGTACCCG
5709406 TAACATCCGG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 18 0.56
16 4 0.12
17 10 0.31
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:5714582 original size:36 final size:35
Alignment explanation
Indices: 5714542--5714611 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
5714532 CAAATTAAAC
* * *
5714542 GGGGACGGGGAAAAATTGTTTATGTTAAACGGGGAT
1 GGGGACAGGG-AAAATCGTTTATGCTAAACGGGGAT
*
5714578 GGGGATAGGGAAAATCGTTTATGCTAAACGGGGA
1 GGGGACAGGGAAAATCGTTTATGCTAAACGGGGA
5714612 CTGGACGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 22 0.73
36 8 0.27
ACGTcount: A:0.31, C:0.07, G:0.39, T:0.23
Consensus pattern (35 bp):
GGGGACAGGGAAAATCGTTTATGCTAAACGGGGAT
Found at i:5715482 original size:64 final size:61
Alignment explanation
Indices: 5715397--5715617 Score: 230
Period size: 64 Copynumber: 3.5 Consensus size: 61
5715387 TGTTTGAATG
* *
5715397 TGCACCGATGCATTGGTAGTGCATCGATGCACTCTTTTAA-AATAAAGACATCGAATGCAATTCA
1 TGCACCGATGCA-TAGTAGTGCATCGATGCA-TCTATTAATAATAAA-ACATCGAATGCAATT-A
* * * *
5715461 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTG
1 TGCACCGATGCAT-AGTAGTGCATCGATGCAT-CTATTAATAATAAAACATCGAATGCAATTA
* * ** * * *
5715524 TGCATCGATGCATAGGAGTGC-TCGATGCATCTCAGCAATAATACAACATCGAATACATTTTA
1 TGCACCGATGCATAGTAGTGCATCGATGCATCT-ATTAATAATAAAACATCGAATGCA-ATTA
5715586 TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCACCGATGCAT-AGTAGTGCATCGATGCAT
5715618 ACCTTCATTA
Statistics
Matches: 133, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
60 1 0.01
61 28 0.21
62 21 0.16
63 22 0.17
64 56 0.42
65 5 0.04
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (61 bp):
TGCACCGATGCATAGTAGTGCATCGATGCATCTATTAATAATAAAACATCGAATGCAATTA
Found at i:5715988 original size:67 final size:67
Alignment explanation
Indices: 5715905--5716057 Score: 272
Period size: 67 Copynumber: 2.3 Consensus size: 67
5715895 TGATCAATGT
5715905 TATGATTTGTGTGATTATGAGATATATATGTTATATGGAAAGTATATGTGAAATAAGATATGAGC
1 TATGA-TTGTGTGATTATGAGATATATATGTTATATGGAAAGTATATGTGAAATAAGATATGAGC
5715970 TTA
65 TTA
5715973 TATGATTGTGTGATTATGAGATATATATGTTATATGGAAAGTATATGTGAAATAAGATATGAGCT
1 TATGATTGTGTGATTATGAGATATATATGTTATATGGAAAGTATATGTGAAATAAGATATGAGCT
5716038 TA
66 TA
* *
5716040 TATGAATATGTGA-TATGA
1 TATGATTGTGTGATTATGA
5716058 ATAAAGCTAT
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
66 5 0.06
67 73 0.88
68 5 0.06
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (67 bp):
TATGATTGTGTGATTATGAGATATATATGTTATATGGAAAGTATATGTGAAATAAGATATGAGCT
TA
Found at i:5716446 original size:31 final size:30
Alignment explanation
Indices: 5716330--5716479 Score: 243
Period size: 29 Copynumber: 5.0 Consensus size: 30
5716320 AGGGTCGAGG
5716330 GTTTACCTATGTTCTTCGGGAC-ATGGACT
1 GTTTACCTATGTTCTTCGGGACTATGGACT
5716359 GTTTACCTATGTTCTTCGGGACTATGGACT
1 GTTTACCTATGTTCTTCGGGACTATGGACT
*
5716389 GTTTACCTAT-TTCTTTGGGA-TATGGACT
1 GTTTACCTATGTTCTTCGGGACTATGGACT
5716417 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGAC-TATGGACT
*
5716448 GTTTACCTAGGTTCTTCGGGATCTATGGACT
1 GTTTACCTATGTTCTTCGGGA-CTATGGACT
5716479 G
1 G
5716480 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 3, Indels: 8
0.91 0.02 0.06
Matches are distributed among these distances:
28 18 0.16
29 40 0.35
30 17 0.15
31 37 0.33
32 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (30 bp):
GTTTACCTATGTTCTTCGGGACTATGGACT
Found at i:5719605 original size:64 final size:63
Alignment explanation
Indices: 5719520--5719743 Score: 243
Period size: 64 Copynumber: 3.5 Consensus size: 63
5719510 TGTTTGAATG
** *
5719520 TGCACCGATGCATTGGTAGTGCATCGATGCACTCTTTTAA-AATAAAGACATCGAATGCAATTCA
1 TGCACCGATGCATAAGTAGTGCATCGATGCA-TCTATTAATAATAAA-ACATCGAATGCAATTCA
* * * **
5719584 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCACCGATGCATAAGTAGTGCATCGATGCAT-CTATTAATAATAAAACATCGAATGCAATTCA
* * ** * * * *
5719648 TGCATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAATACAACATCGAATACATTTTA
1 TGCACCGATGCATAAGTAGTGCATCGATGCATCT-ATTAATAATAAAACATCGAATGCAATTCA
* *
5719712 TTCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCACCGATGCATAAGTAGTGCATCGATGCAT
5719744 ATCTTCATTA
Statistics
Matches: 135, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
63 2 0.01
64 128 0.95
65 5 0.04
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (63 bp):
TGCACCGATGCATAAGTAGTGCATCGATGCATCTATTAATAATAAAACATCGAATGCAATTCA
Found at i:5720419 original size:31 final size:31
Alignment explanation
Indices: 5720381--5720532 Score: 267
Period size: 31 Copynumber: 5.0 Consensus size: 31
5720371 AGGGTCGAGG
5720381 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5720412 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
5720443 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5720474 GTTTACCTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5720504 GTTTACCTA-GTTCTTCGGG--ATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
5720532 G
1 G
5720533 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
28 10 0.08
29 7 0.06
30 24 0.20
31 77 0.65
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:5723703 original size:60 final size:61
Alignment explanation
Indices: 5723622--5723841 Score: 176
Period size: 64 Copynumber: 3.5 Consensus size: 61
5723612 TGTTTGAATG
* ** **
5723622 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATC-GCAATTCA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCAGCAATTCA
* **
5723682 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATC--A-GCAATTCA
* * ** * * * *
5723746 TGCATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAATACAACATCGAATACATTTTA
1 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATC--A-GCAATTCA
* * *
5723810 TTCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAGTAGTGCATCGATGCAT
5723842 ATCTTCATTA
Statistics
Matches: 132, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
60 38 0.29
61 6 0.05
64 88 0.67
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (61 bp):
TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAGCAATTCA
Found at i:5723761 original size:64 final size:64
Alignment explanation
Indices: 5723675--5723841 Score: 210
Period size: 64 Copynumber: 2.6 Consensus size: 64
5723665 AAAGACATCG
* ** *
5723675 CAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGA-AACATCGAATG
1 CAATTGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAAT-ACAACATCGAATA
* * *
5723739 CAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAATACAACATCGAATA
1 CAATTGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACAACATCGAATA
* * * * *
5723803 CATTTTATTCACCGATGCATCAGTAGTGCATCGATGCAT
1 CAATTGATGCATCGATGCATAAGTAGTGCATCGATGCAT
5723842 ATCTTCATTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
63 1 0.01
64 87 0.99
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
CAATTGATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACAACATCGAATA
Found at i:5724536 original size:31 final size:31
Alignment explanation
Indices: 5724498--5724591 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
5724488 AGGGTCGAGG
*
5724498 GTTTACCTATGTTCTTCAGGACATATGGTCT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
*
5724529 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* *
5724560 GTTTACCTAGGTTCTTCGGGATC-TATGGACT
1 GTTTACCTATGTTCTTCAGGA-CATATGGACT
5724591 G
1 G
5724592 GTCATTCGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCAGGACATATGGACT
Found at i:5729190 original size:20 final size:20
Alignment explanation
Indices: 5729153--5729191 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5729143 ATTTTTTTAA
**
5729153 AAATAAAAAATATTATAAAC
1 AAATAAAAAATAAAATAAAC
5729173 AAATAAAAAATAAAATAAA
1 AAATAAAAAATAAAATAAA
5729192 TTTAGGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAAAAAATAAAATAAAC
Found at i:5731472 original size:17 final size:18
Alignment explanation
Indices: 5731438--5731479 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5731428 TTTTAGTATT
5731438 TTTATTATATATATTTAA
1 TTTATTATATATATTTAA
*
5731456 TTTATTTTATA-ATTTAA
1 TTTATTATATATATTTAA
5731473 TTT-TTAT
1 TTTATTAT
5731480 TTTTAGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
18 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTATATATATTTAA
Found at i:5731490 original size:20 final size:19
Alignment explanation
Indices: 5731435--5731490 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
5731425 CATTTTTAGT
*
5731435 ATTTTTATTATATATATTTA
1 ATTTTTATT-TTTATATTTA
5731455 A--TTTA-TTTTATAATTTA
1 ATTTTTATTTTTAT-ATTTA
5731472 ATTTTTATTTTTAGTATTT
1 ATTTTTATTTTTA-TATTT
5731491 GTATATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
16 4 0.13
17 7 0.23
18 4 0.13
19 4 0.13
20 10 0.33
21 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTTTATTTTTATATTTA
Found at i:5734392 original size:33 final size:33
Alignment explanation
Indices: 5734334--5734396 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
5734324 GATCTGACTG
*
5734334 AAATAATATTATAATTATTTATTATATATTTAA
1 AAATAATATAATAATTATTTATTATATATTTAA
5734367 AAATAATTATAATAA-TACTTT-TTATATATT
1 AAATAA-TATAATAATTA-TTTATTATATATT
5734397 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 17 0.63
34 10 0.37
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (33 bp):
AAATAATATAATAATTATTTATTATATATTTAA
Found at i:5734441 original size:2 final size:2
Alignment explanation
Indices: 5734434--5734482 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
5734424 CTAACAAAAT
5734434 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5734476 TG TA TA T
1 TA TA TA T
5734483 GGATCAAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5735061 original size:29 final size:29
Alignment explanation
Indices: 5735019--5735081 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
5735009 ATTCTACAGT
5735019 GACCTCGTAGGTCGCCATGGCATCCGGGC
1 GACCTCGTAGGTCGCCATGGCATCCGGGC
*
5735048 GACCTTGTAGGTCGCCATGGCATCCGGGC
1 GACCTCGTAGGTCGCCATGGCATCCGGGC
5735077 GACCT
1 GACCT
5735082 GTGTGGTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.14, C:0.33, G:0.33, T:0.19
Consensus pattern (29 bp):
GACCTCGTAGGTCGCCATGGCATCCGGGC
Found at i:5735170 original size:20 final size:20
Alignment explanation
Indices: 5735145--5735182 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5735135 TGGGGGAGTT
*
5735145 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
5735165 GTGGGAACTGTGCATGGG
1 GTGGGAACTGTGCATGGG
5735183 GCATGGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.50, T:0.21
Consensus pattern (20 bp):
GTGGGAACTGTGCATGGGAC
Found at i:5735189 original size:20 final size:20
Alignment explanation
Indices: 5735146--5735189 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5735136 GGGGGAGTTG
* *
5735146 TGGGAGCTGTGCATGGGACG
1 TGGGAACTGTGCATGGGACA
*
5735166 TGGGAACTGTGCATGGGGCA
1 TGGGAACTGTGCATGGGACA
5735186 TGGG
1 TGGG
5735190 GGAGTTGTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.50, T:0.20
Consensus pattern (20 bp):
TGGGAACTGTGCATGGGACA
Found at i:5735201 original size:51 final size:51
Alignment explanation
Indices: 5735132--5735233 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
5735122 ATTGGAGCAT
5735132 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
1 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
5735183 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
1 GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
5735234 ACGTGCACGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.16, C:0.12, G:0.51, T:0.22
Consensus pattern (51 bp):
GCATGGGGGAGTTGTGGGAGCTGTGCATGGGACGTGGGAACTGTGCATGGG
Found at i:5735221 original size:20 final size:20
Alignment explanation
Indices: 5735196--5735238 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
5735186 TGGGGGAGTT
*
5735196 GTGGGAGCTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
5735216 GTGGGAACTGTGCATGGGAC
1 GTGGGAACTGTGCATGGGAC
5735236 GTG
1 GTG
5735239 CACGTCGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.49, T:0.21
Consensus pattern (20 bp):
GTGGGAACTGTGCATGGGAC
Found at i:5735377 original size:43 final size:40
Alignment explanation
Indices: 5735301--5735383 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 40
5735291 CGACCAAGCT
5735301 CTGGGAGATTCCTGTGTAACTGCATGCGTTGCAT-CATAG
1 CTGGGAGATTCCTGTGTAACTGCATGCGTTGCATCCATAG
* *
5735340 CTGGGAGATTCCTGCATCCGTAGCTGCATGTGTTGCATCCATAG
1 CTGGGAGATTCCTG--T--GTAACTGCATGCGTTGCATCCATAG
5735384 TTGCGTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
39 14 0.38
41 1 0.03
43 17 0.46
44 5 0.14
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (40 bp):
CTGGGAGATTCCTGTGTAACTGCATGCGTTGCATCCATAG
Found at i:5735768 original size:21 final size:21
Alignment explanation
Indices: 5735743--5735786 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5735733 AATCTAGTTA
5735743 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
5735764 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
5735785 AT
1 AT
5735787 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:5735796 original size:28 final size:30
Alignment explanation
Indices: 5735763--5735825 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
5735753 TAGTATAAAT
*
5735763 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
5735791 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
5735821 TATTA
1 TATTA
5735826 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:5736557 original size:26 final size:25
Alignment explanation
Indices: 5736528--5736586 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
5736518 AAATCATATT
*
5736528 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
5736554 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
5736580 ATTATTA
1 ATTATTA
5736587 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:5738415 original size:45 final size:44
Alignment explanation
Indices: 5738347--5738470 Score: 125
Period size: 45 Copynumber: 2.8 Consensus size: 44
5738337 ATAGTTTACT
* *
5738347 TAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTA-TATAA
1 TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTTAACTAT-A
*
5738393 CTAACTATTAACAAAACAAACTAATT-AATTATTTTTTAACTATA
1 -TAACTATTAACAAAACAAACTAATTAAATAATTTTTTAACTATA
5738437 TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 TAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
5738471 AATTTATGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.10
42 10 0.14
43 6 0.09
44 12 0.17
45 16 0.23
46 5 0.07
47 6 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (44 bp):
TAACTATTAACAAAACAAACTAATTAAATAATTTTTTAACTATA
Found at i:5738498 original size:41 final size:40
Alignment explanation
Indices: 5738410--5738498 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
5738400 TTAACAAAAC
* *
5738410 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
5738451 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
5738492 AAACTAA
1 AAACTAA
5738499 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:5738936 original size:29 final size:29
Alignment explanation
Indices: 5738877--5739007 Score: 212
Period size: 29 Copynumber: 4.6 Consensus size: 29
5738867 TCGTGAGCTA
5738877 GGACTACATGGCGACCT--AAGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
5738904 GGACTACATGGCGACCTACAAGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
*
5738933 GGACTACATGGCGACCTACAAGGTCGTCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
*
5738962 GGACTACATGGCGACCTACAAGGTCGCCC
1 GGACTACATGGCGACCTACAAGGTCGCCG
* *
5738991 AGACTGCATGGCGACCT
1 GGACTACATGGCGACCT
5739008 CTCGATCTCT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 17 0.18
29 80 0.82
ACGTcount: A:0.24, C:0.31, G:0.31, T:0.15
Consensus pattern (29 bp):
GGACTACATGGCGACCTACAAGGTCGCCG
Found at i:5739074 original size:21 final size:21
Alignment explanation
Indices: 5739048--5739094 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
5739038 TATATGCCTT
5739048 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
5739069 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
5739090 GTATG
1 GTATG
5739095 TCGCCTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.30
Consensus pattern (21 bp):
GTATGGCTCGTATGTCACCCC
Found at i:5739137 original size:29 final size:29
Alignment explanation
Indices: 5739095--5739154 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
5739085 ACCCCGTATG
5739095 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
*
5739124 TCGCCTGGATTGCATGGCGTCCTACGAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
5739153 TC
1 TC
5739155 ACTGTAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (29 bp):
TCGCCTGGATTGCATGGCGTCCTACAAGA
Found at i:5744303 original size:14 final size:13
Alignment explanation
Indices: 5744284--5744322 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
5744274 TATATGGATA
5744284 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
5744298 TTTTATTATTTAT
1 TTTTATTATTTAT
5744311 GTTATTATTATT
1 -TT-TTATTATT
5744323 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:5744321 original size:18 final size:17
Alignment explanation
Indices: 5744282--5744324 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5744272 ATTATATGGA
5744282 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
5744298 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
5744316 TATTATTAT
1 TATTATTAT
5744325 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:5744335 original size:2 final size:2
Alignment explanation
Indices: 5744322--5744364 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5744312 TTATTATTAT
*
5744322 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5744364 T
1 T
5744365 TTCTTTAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5744757 original size:2 final size:2
Alignment explanation
Indices: 5744752--5744776 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5744742 TACTTTGATG
5744752 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5744777 TTCCTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5744850 original size:9 final size:9
Alignment explanation
Indices: 5744829--5744862 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
5744819 TTTTTTTTCC
5744829 TTTATCTTA-
1 TTTAT-TTAT
5744838 TTTATTTAT
1 TTTATTTAT
5744847 TTTATTTAT
1 TTTATTTAT
5744856 TTTATTT
1 TTTATTT
5744863 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:5744851 original size:13 final size:14
Alignment explanation
Indices: 5744829--5744863 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5744819 TTTTTTTTCC
*
5744829 TTTATCTTATTTA-
1 TTTATTTTATTTAT
5744842 TTTATTTTATTTAT
1 TTTATTTTATTTAT
5744856 TTTATTTT
1 TTTATTTT
5744864 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:5747911 original size:22 final size:22
Alignment explanation
Indices: 5747888--5747949 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
5747878 CAAAAAGGGC
5747888 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
5747911 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
5747932 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
5747950 TAAAAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:5747940 original size:20 final size:20
Alignment explanation
Indices: 5747888--5747956 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
5747878 CAAAAAGGGC
*
5747888 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
5747911 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
5747932 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
5747952 AAAAA
1 AAAAA
5747957 AAGGGACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
22 6 0.15
23 10 0.24
24 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:5748594 original size:22 final size:22
Alignment explanation
Indices: 5748566--5748616 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5748556 CCCCATCAAT
5748566 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
5748588 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
5748610 CCTTTGA
1 CCTTTGA
5748617 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:5749541 original size:36 final size:36
Alignment explanation
Indices: 5749494--5749598 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
5749484 GTGCTCACCA
5749494 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
5749530 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
5749567 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
5749599 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:5749588 original size:37 final size:37
Alignment explanation
Indices: 5749494--5749603 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
5749484 GTGCTCACCA
5749494 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
5749530 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
5749567 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
5749604 ATTGAAAACA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 31 0.46
37 33 0.49
38 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:5749688 original size:102 final size:102
Alignment explanation
Indices: 5749512--5749903 Score: 660
Period size: 102 Copynumber: 3.9 Consensus size: 102
5749502 CTTGAGACAG
** * * *
5749512 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
5749577 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
5749614 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
5749679 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
5749716 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
5749781 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
5749818 TTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
5749882 TGAGACAGCTTCTCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
5749904 CAAAACCTTT
Statistics
Matches: 275, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
101 35 0.13
102 240 0.87
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:5749689 original size:37 final size:37
Alignment explanation
Indices: 5749630--5749700 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
5749620 TTGAAATGAG
* *
5749630 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
* *
5749667 TTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
5749701 TAAACATTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:5749783 original size:37 final size:37
Alignment explanation
Indices: 5749716--5749802 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
5749706 ATTGGAAACA
** * *
5749716 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
5749752 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
5749789 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
5749803 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:5749862 original size:204 final size:203
Alignment explanation
Indices: 5749512--5749970 Score: 684
Period size: 204 Copynumber: 2.2 Consensus size: 203
5749502 CTTGAGACAG
*
5749512 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * * *
5749577 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAGTTTTGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
* * *
5749642 TGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
131 TGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACATAAACA
5749707 TTGGAAACA
195 TTGGAAACA
** * *
5749716 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
5749781 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
* *
5749846 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACACAAAACC
131 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACA-TAAACA
* ***
5749911 TTTGAGATTG
195 TTGGA-AACA
* * * * *
5749921 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
5749971 CAAAATCTTT
Statistics
Matches: 228, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
203 35 0.15
204 149 0.65
205 44 0.19
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (203 bp):
TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACATAAACAT
TGGAAACA
Found at i:5749872 original size:36 final size:36
Alignment explanation
Indices: 5749817--5749886 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
5749807 CATTGAAAAC
** *
5749817 ATTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGATA
* *
5749853 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGA
5749887 CAGCTTCTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGATA
Found at i:5749899 original size:36 final size:36
Alignment explanation
Indices: 5749832--5749903 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
5749822 CCTAGAAATG
* * *
5749832 AATTTCGTCTCTCTTGAGATAATTTCCCTTGAAACA
1 AATTTCGTCTCCCTTGAGACAACTTCCCTTGAAACA
* * *
5749868 AATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACA
1 AATTTCGTCTCCCTTGAGACAACTTCCCTTGAAACA
5749904 CAAAACCTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (36 bp):
AATTTCGTCTCCCTTGAGACAACTTCCCTTGAAACA
Found at i:5749994 original size:67 final size:67
Alignment explanation
Indices: 5749845--5750003 Score: 223
Period size: 67 Copynumber: 2.4 Consensus size: 67
5749835 TTCGTCTCTC
** *
5749845 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAAC
5749910 CT
66 CT
* * *
5749912 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAAC
5749977 CT
66 CT
*
5749979 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
5750004 ATTGTGTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 77 0.94
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAAC
CT
Found at i:5751084 original size:105 final size:105
Alignment explanation
Indices: 5750837--5751497 Score: 958
Period size: 105 Copynumber: 6.3 Consensus size: 105
5750827 GCCATCCGCG
* * * * * *
5750837 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
5750902 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGGTTGTCAAC-AACAACTTCCCAATCTCAGAGCCA
* *
5750946 ATTTCAACTCCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
5751011 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
5751051 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
5751116 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
5751156 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
5751221 ACCGCTGCTTGTCAACAACAACTTTCCATTCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
5751261 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
5751326 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGATTCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
5751361 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
5751426 A-CGACTGGTTGTCAACAAATAATTTCCCGGT-TCCAGAGCCA
66 ACCG-CTGGTTGTCAAC-AACAACTTCCCAATCT-CAGAGCCA
* *
5751467 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
5751498 TGGAACAATG
Statistics
Matches: 514, Mismatches: 31, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
99 2 0.00
100 82 0.16
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 308 0.60
106 83 0.16
107 3 0.01
109 23 0.04
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:5752516 original size:14 final size:13
Alignment explanation
Indices: 5752497--5752543 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
5752487 TATATGGATA
5752497 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
5752511 TTTTATTATTTA-
1 TTTTATTATTTAT
*
5752523 TGTTATTA-TTAT
1 TTTTATTATTTAT
*
5752535 TATTATTAT
1 TTTTATTAT
5752544 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 3 0.10
12 14 0.48
13 5 0.17
14 7 0.24
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:5752522 original size:21 final size:21
Alignment explanation
Indices: 5752498--5752541 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5752488 ATATGGATAT
*
5752498 TTTAT-TCATTTATTTTTATTA
1 TTTATGTCA-TTATTATTATTA
*
5752519 TTTATGTTATTATTATTATTA
1 TTTATGTCATTATTATTATTA
5752540 TT
1 TT
5752542 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTATGTCATTATTATTATTA
Found at i:5752534 original size:18 final size:17
Alignment explanation
Indices: 5752495--5752538 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
5752485 ATTATATGGA
5752495 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
5752511 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
5752529 TATTATTATT
1 TATTATTATT
5752539 ATTATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 3 0.13
17 7 0.30
18 13 0.57
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:5752548 original size:2 final size:2
Alignment explanation
Indices: 5752541--5752575 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5752531 TTATTATTAT
5752541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5752576 TTCTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5752756 original size:2 final size:2
Alignment explanation
Indices: 5752751--5752777 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5752741 CTTATAACTT
5752751 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5752778 TATTTTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5752974 original size:2 final size:2
Alignment explanation
Indices: 5752969--5753033 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
5752959 TACTTTGATG
5752969 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5753011 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
5753034 TTCCTTTTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5753126 original size:31 final size:31
Alignment explanation
Indices: 5753078--5753137 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
5753068 CTTTACTATT
* *
5753078 TTTTTTCCTTTATCTTATTT-ATTTATTTTA
1 TTTTTCCCTTTACCTTATTTGATTTATTTTA
*
5753108 TTTTTCCCTTTTACCTTATTTGTTTTATTT
1 TTTTTCCC-TTTACCTTATTTGATTTATTT
5753138 ACCTTGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 11 0.44
32 7 0.28
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (31 bp):
TTTTTCCCTTTACCTTATTTGATTTATTTTA
Found at i:5757584 original size:15 final size:14
Alignment explanation
Indices: 5757559--5757606 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
5757549 TATAATAAAA
5757559 ATTATAAATATATT
1 ATTATAAATATATT
5757573 ATTATAAAATATATT
1 ATTAT-AAATATATT
5757588 ATGT-TAAAT-TATT
1 AT-TATAAATATATT
*
5757601 AATATA
1 ATTATA
5757607 TTCAATTCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 1 0.03
13 7 0.23
14 9 0.30
15 12 0.40
16 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:5760548 original size:24 final size:24
Alignment explanation
Indices: 5760521--5760569 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5760511 AGTCTCTATA
5760521 AATTTCTTCTATGGTTTAATCTTG
1 AATTTCTTCTATGGTTTAATCTTG
5760545 AATTTCTTCTATGGTTTAATCTTG
1 AATTTCTTCTATGGTTTAATCTTG
5760569 A
1 A
5760570 GTCCCTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (24 bp):
AATTTCTTCTATGGTTTAATCTTG
Found at i:5767013 original size:97 final size:98
Alignment explanation
Indices: 5766875--5767057 Score: 298
Period size: 97 Copynumber: 1.9 Consensus size: 98
5766865 TAATTATTAT
* * *
5766875 AATATCACCTCTTTATTTAAAAATATTCTTTCTAATATTAATTTTAAAAAATATTAAATAAATAT
1 AATATCAACTCTTTATTTAAAAATATTCTTTATAATATTAATTTTAAAAAATATAAAATAAATAT
*
5766940 TAA-ATTCTAATGAAAAATAATGTAAAGCTAAAA
66 TAATAAT-TAATGAAAAATAATGTAAAGCTAAAA
5766973 AATATCAACTCTTTATTT-AAAATATTCTTTATAATATTAATTTTAAAAAATATAAAATAAATAT
1 AATATCAACTCTTTATTTAAAAATATTCTTTATAATATTAATTTTAAAAAATATAAAATAAATAT
*
5767037 TAATAATTAATGAATAATAAT
66 TAATAATTAATGAAAAATAAT
5767058 TCATTTTATC
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
97 60 0.76
98 19 0.24
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (98 bp):
AATATCAACTCTTTATTTAAAAATATTCTTTATAATATTAATTTTAAAAAATATAAAATAAATAT
TAATAATTAATGAAAAATAATGTAAAGCTAAAA
Found at i:5768016 original size:43 final size:43
Alignment explanation
Indices: 5767932--5768025 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 43
5767922 TAAATTTTAT
*
5767932 ATTTTAAAAACATTATTATAATACTTTAAACTAAAACATCATAA
1 ATTTTAAAAACATAATTATAATACTTTAAACTAAAACATCAT-A
* * *
5767976 ATTTTAAAAACATAATTTTGATA-TTTAAACTAAAATATCATA
1 ATTTTAAAAACATAATTATAATACTTTAAACTAAAACATCATA
5768018 A-TTTAAAA
1 ATTTTAAAA
5768026 CATGTCACGA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
41 7 0.15
42 2 0.04
43 17 0.37
44 20 0.43
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (43 bp):
ATTTTAAAAACATAATTATAATACTTTAAACTAAAACATCATA
Found at i:5773565 original size:2 final size:2
Alignment explanation
Indices: 5773558--5773596 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5773548 TTATTAAATA
5773558 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5773597 ATTCTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5774239 original size:19 final size:20
Alignment explanation
Indices: 5774211--5774253 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
5774201 TAATTAAAAA
5774211 TAAAAATATA-TCCAAA-CC
1 TAAAAATATACTCCAAACCC
*
5774229 TAAAAATTATACTTCAAACCC
1 TAAAAA-TATACTCCAAACCC
5774250 TAAA
1 TAAA
5774254 TCACAAACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 4 0.19
20 5 0.24
21 6 0.29
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAATATACTCCAAACCC
Found at i:5776137 original size:20 final size:19
Alignment explanation
Indices: 5776102--5776141 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5776092 TTTTAAAAAA
5776102 AAATTTAAAATAATAATTT
1 AAATTTAAAATAATAATTT
5776121 AAATATTAAACAT-ATAATTT
1 AAAT-TTAAA-ATAATAATTT
5776141 A
1 A
5776142 TCCATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 13 0.68
21 2 0.11
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTTAAAATAATAATTT
Found at i:5790225 original size:20 final size:20
Alignment explanation
Indices: 5790202--5790253 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5790192 AACGCGATCC
5790202 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
5790222 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
5790242 CCAAAATCGCAA
1 CCAGAATCGCAA
5790254 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:5790334 original size:20 final size:20
Alignment explanation
Indices: 5790309--5790502 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
5790299 GATTTTCCAT
* *
5790309 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
5790329 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
5790349 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
5790369 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
5790389 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
5790409 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
5790429 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
5790449 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
5790470 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
5790490 AATCGCAACGCGA
1 AATCGCAACGCGA
5790503 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:5790354 original size:40 final size:39
Alignment explanation
Indices: 5790305--5790502 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
5790295 TTGCGATTTT
* ** *
5790305 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
5790343 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
5790384 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
5790424 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
5790463 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
5790503 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:5790392 original size:60 final size:60
Alignment explanation
Indices: 5790309--5790501 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
5790299 GATTTTCCAT
* ** * *
5790309 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
5790369 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
5790429 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
5790490 AATCGCAACGCG
1 AATCGCAACGCG
5790502 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:5790918 original size:33 final size:33
Alignment explanation
Indices: 5790879--5790949 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
5790869 TTCACTTAGA
*
5790879 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
5790912 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
5790945 TTTCA
1 TTTCA
5790950 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:5791089 original size:14 final size:14
Alignment explanation
Indices: 5791070--5791124 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5791060 AGAATGACTG
5791070 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
5791084 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
5791103 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
5791117 TCGCAACG
1 TCGCAACG
5791125 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:5791107 original size:33 final size:33
Alignment explanation
Indices: 5791070--5791140 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
5791060 AGAATGACTG
**
5791070 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
5791103 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
5791136 TCGCA
1 TCGCA
5791141 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:5791158 original size:19 final size:19
Alignment explanation
Indices: 5791136--5791233 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
5791126 GAAACCAAAA
*
5791136 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5791155 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5791169 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5791188 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
5791202 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
5791221 TCGCGTTGCGATT
1 TCGCGTTGCGATT
5791234 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5791177 original size:14 final size:14
Alignment explanation
Indices: 5791158--5791247 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5791148 TTTCATTTCG
5791158 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5791172 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5791191 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5791205 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
5791222 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
5791238 CGTTGCGATT
1 CGTTGCGATT
5791248 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5791183 original size:33 final size:33
Alignment explanation
Indices: 5791141--5791255 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
5791131 CAAAATCGCA
5791141 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5791174 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
5791207 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
5791240 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
5791256 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:5793184 original size:185 final size:185
Alignment explanation
Indices: 5792954--5793425 Score: 919
Period size: 185 Copynumber: 2.6 Consensus size: 185
5792944 TAGATTGCTT
*
5792954 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5793019 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
5793084 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG-TTTGTCTTTTGGTTGAA
5793139 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5793204 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
5793269 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGAA
5793324 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5793389 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
5793426 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
185 273 0.96
186 12 0.04
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGAA
Found at i:5793268 original size:93 final size:93
Alignment explanation
Indices: 5792954--5793425 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
5792944 TAGATTGCTT
*
5792954 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5793019 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5793047 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5793111 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5793139 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5793204 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5793232 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5793297 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5793324 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5793389 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5793417 AGTAAATTT
1 AGTAAATTT
5793426 ATCCATTCAA
Statistics
Matches: 376, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.49
93 192 0.51
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:5793534 original size:19 final size:19
Alignment explanation
Indices: 5793469--5793603 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
5793459 TAGTTTACTT
* *
5793469 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
5793489 TCGCAACACGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
5793508 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5793527 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
5793541 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
5793560 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
5793574 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
5793593 TCGCAATGCGA
1 TCGCAACGCGA
5793604 TTTTCATTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 46 0.47
20 13 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:5793544 original size:14 final size:14
Alignment explanation
Indices: 5793525--5793581 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5793515 GCGAAATGAA
*
5793525 AATCGCAACGACAG
1 AATCGCAACGAAAG
5793539 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
5793556 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
5793572 AATCGCAACG
1 AATCGCAACG
5793582 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:5793552 original size:33 final size:33
Alignment explanation
Indices: 5793506--5793598 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
5793496 ACGAAACCAA
*
5793506 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
5793539 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
5793572 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
5793599 TGCGATTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:5793615 original size:19 final size:19
Alignment explanation
Indices: 5793599--5793727 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
5793589 AAAATCGCAA
5793599 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
5793618 TGCGA--TTC-TTT--CGT
1 TGCGATTTTCATTTCGCGT
*
5793632 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
*
5793651 TGCGA--TTC-TGT--CGT
1 TGCGATTTTCATTTCGCGT
5793665 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
5793684 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
5793703 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
5793723 TGCGA
1 TGCGA
5793728 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.17
16 11 0.12
17 11 0.12
19 41 0.46
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:5793634 original size:14 final size:14
Alignment explanation
Indices: 5793615--5793671 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
5793605 TTTCATTTCG
5793615 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
5793629 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
5793646 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
5793662 CGTTGCGATT
1 CGTTGCGATT
5793672 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:5793641 original size:33 final size:33
Alignment explanation
Indices: 5793599--5793690 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
5793589 AAAATCGCAA
*
5793599 TGCGATTTTCATTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
5793632 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
5793665 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
5793691 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:5795670 original size:14 final size:14
Alignment explanation
Indices: 5795651--5795686 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5795641 ATTGTTTAAT
5795651 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5795665 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5795679 TGATTTGT
1 TGATTTGT
5795687 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5795809 original size:19 final size:19
Alignment explanation
Indices: 5795793--5795894 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
5795783 AAAAATGACT
5795793 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5795812 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5795831 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5795845 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5795864 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
5795884 ATCGCAATGCG
1 ATCGCAATGCG
5795895 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5795943 original size:33 final size:33
Alignment explanation
Indices: 5795901--5796224 Score: 181
Period size: 33 Copynumber: 9.5 Consensus size: 33
5795891 TGCGTTTATA
5795901 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
5795934 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
5795970 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
5796003 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
5796038 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
5796071 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
5796111 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
5796142 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
5796175 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
5796209 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
5796225 GTATTTTCCG
Statistics
Matches: 247, Mismatches: 21, Indels: 46
0.79 0.07 0.15
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 133 0.54
34 29 0.12
35 18 0.07
36 19 0.08
37 2 0.01
38 20 0.08
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:5795963 original size:52 final size:52
Alignment explanation
Indices: 5795901--5796196 Score: 255
Period size: 52 Copynumber: 5.6 Consensus size: 52
5795891 TGCGTTTATA
5795901 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
1 ATTTCG-ATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* *
5795953 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTTTC
1 ATTTCG-ATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * * * * * *
5796007 GTTGCGATTTTC-ATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * * * *
5796059 GTTGCGATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * * * *
5796111 GTTGCGATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGA-TTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
* * *
5796163 GTTGCGATTTTC-ATTTC-CGCATTGCGATTTTCAT
1 ATTTCGA-TTGCGATTTCTCG--TTGCGATTTTCAT
5796197 GTTGGGATTT
Statistics
Matches: 226, Mismatches: 13, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
51 1 0.00
52 198 0.88
53 18 0.08
54 9 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGATTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:5796009 original size:85 final size:85
Alignment explanation
Indices: 5795901--5796138 Score: 351
Period size: 85 Copynumber: 2.8 Consensus size: 85
5795891 TGCGTTTATA
* *
5795901 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
*
5795966 ATTCTTTCGTTGCGATTTTC
66 ATTCTGTCGTTGCGATTTTC
*
5795986 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCG
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
5796051 ATTCTGTCGTTGCGATTTTC
66 ATTCTGTCGTTGCGATTTTC
*
5796071 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
5796131 TTGCGATT
61 TTGCGATT
5796139 TTCATTTCGC
Statistics
Matches: 142, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
85 121 0.85
87 7 0.05
88 8 0.06
90 6 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (85 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTGTCGTTGCGATTTTC
Found at i:5798524 original size:12 final size:12
Alignment explanation
Indices: 5798507--5798531 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5798497 TCTTCGGGGA
5798507 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5798519 CTTTTTCTTCTT
1 CTTTTTCTTCTT
5798531 C
1 C
5798532 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:5798740 original size:24 final size:24
Alignment explanation
Indices: 5798706--5798752 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5798696 CTGAAACATC
5798706 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
5798730 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5798753 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:5799463 original size:20 final size:20
Alignment explanation
Indices: 5799435--5799803 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
5799425 AAATTTCAGT
* * * *
5799435 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5799455 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
5799475 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5799495 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
5799515 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5799535 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
5799555 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
5799575 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5799595 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5799615 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
5799635 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
5799655 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5799675 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
5799695 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
5799715 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
5799735 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
5799755 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
5799775 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
5799795 GTTGCGATT
1 GTTGCGATT
5799804 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:5802610 original size:24 final size:23
Alignment explanation
Indices: 5802571--5802619 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
5802561 TATATATAAG
5802571 CTGTTAACCTTAACAGATTCTAA
1 CTGTTAACCTTAACAGATTCTAA
*
5802594 CTGTTAACCCTTAACAGGTTCTAA
1 CTGTTAA-CCTTAACAGATTCTAA
5802618 CT
1 CT
5802620 AACTTAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (23 bp):
CTGTTAACCTTAACAGATTCTAA
Found at i:5803063 original size:21 final size:21
Alignment explanation
Indices: 5803039--5803112 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
5803029 TATCGCAAAT
*
5803039 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
5803060 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
5803080 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
5803101 TCGCGTTGCGAT
1 TCGCGTTGCGAT
5803113 TTTCCATTTC
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:5803085 original size:20 final size:20
Alignment explanation
Indices: 5803060--5803138 Score: 104
Period size: 20 Copynumber: 3.9 Consensus size: 20
5803050 TAGTTGGAAA
5803060 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
5803080 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
5803101 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
5803121 TCGCGTTGCGATTTTCCA
1 TCGCGTTGCGATTTTCCA
5803139 AATTCGTTGC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 33 0.69
21 15 0.31
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:5803095 original size:41 final size:41
Alignment explanation
Indices: 5803038--5803132 Score: 181
Period size: 41 Copynumber: 2.3 Consensus size: 41
5803028 CTATCGCAAA
*
5803038 TTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
5803079 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
5803120 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
5803133 TTTCCAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:5803148 original size:19 final size:19
Alignment explanation
Indices: 5803063--5803151 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 19
5803053 TTGGAAATCG
*
5803063 CGTTGCGATTTTCCATTTC
1 CGTTGCGATTTTCCAATTC
* ** *
5803082 GCGTTGCGATAGTTGAAAATC
1 -CGTTGCGAT-TTTCCAATTC
*
5803103 GCGTTGCGATTTTCCATTTC
1 -CGTTGCGATTTTCCAATTC
5803123 GCGTTGCGATTTTCCAAATT-
1 -CGTTGCGATTTTCC-AATTC
5803143 CGTTGCGAT
1 CGTTGCGAT
5803152 AGTGTACAGT
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
19 9 0.16
20 29 0.52
21 18 0.32
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.39
Consensus pattern (19 bp):
CGTTGCGATTTTCCAATTC
Found at i:5803171 original size:22 final size:22
Alignment explanation
Indices: 5803142--5803195 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
5803132 TTTTCCAAAT
*
5803142 TCGTTGCGATAGTGTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
* *
5803164 TTGTTGCGAAAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
5803186 TCGTTGCGAT
1 TCGTTGCGAT
5803196 TTTCCAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.37
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:5803303 original size:6 final size:6
Alignment explanation
Indices: 5803292--5803347 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
5803282 GACACGTATT
5803292 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
5803340 ACC-CG ACC
1 ACCACG ACC
5803348 CGAGACGGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5803849 original size:5 final size:5
Alignment explanation
Indices: 5803845--5803985 Score: 187
Period size: 5 Copynumber: 27.2 Consensus size: 5
5803835 CTCGTCTCGG
* *
5803845 GTCGG GTCGG GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT
1 GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT
5803895 GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTC-- GTCGT GTCGT
1 GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT
5803943 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
1 -GTCGT -GTCGT -GTCGT -GTCGT -GTCGT -GTCGT -GTCGT G
5803986 GTAATACGTG
Statistics
Matches: 132, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
3 3 0.02
5 88 0.67
6 41 0.31
ACGTcount: A:0.00, C:0.19, G:0.45, T:0.36
Consensus pattern (5 bp):
GTCGT
Found at i:5804105 original size:19 final size:19
Alignment explanation
Indices: 5804081--5804146 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
5804071 CAACGACTTT
5804081 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * **
5804100 TCGCAACGATAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
5804122 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
5804141 TCGCAA
1 TCGCAA
5804147 TGACAACTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:5804138 original size:41 final size:41
Alignment explanation
Indices: 5804081--5804170 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
5804071 CAACGACTTT
*
5804081 TCGCAACGAATTTGGAAAATCGCAACGATAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
* *
5804122 TCGCAACGAATTTGGAAAATCGCAATGACAACTGTAGATTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
5804163 TCGCAACG
1 TCGCAACG
5804171 CGATTTTCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:5804187 original size:21 final size:21
Alignment explanation
Indices: 5804161--5804235 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
5804151 AACTGTAGAT
5804161 TATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGATTTTCAAC
* ** * *
5804182 TATCGCAACCCGA-AATGAAA
1 TATCGCAACGCGATTTTCAAC
*
5804202 AATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGATTTTCAAC
*
5804223 TATCCCAACGCGA
1 TATCGCAACGCGA
5804236 ACTGGAAAAT
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (21 bp):
TATCGCAACGCGATTTTCAAC
Found at i:5804207 original size:41 final size:41
Alignment explanation
Indices: 5804162--5804438 Score: 264
Period size: 41 Copynumber: 6.8 Consensus size: 41
5804152 ACTGTAGATT
* *
5804162 ATCGCAACGCGATTTTCAACTATCGCAACCCGAAATGAAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
* *
5804203 ATCGCAACGCGATTTTCAACTATCCCAACGCGAACTGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
** ** * *
5804244 ATCGCAACGCGAAATGGAA-AATCG-AA--CGAATTTGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAA-ATGGAAA
* * * *
5804282 ATCGCAACGACAACTGT-AGACTATCGCAA--CGAATTTGGAAA
1 ATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAA-ATGGAAA
* * * * * *
5804323 ATCGCAACGACAACTGT-AGACTATCACAACGTGAACTGGAAA
1 ATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAATGGAAA
5804365 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
5804406 ATCGCAACGCGATTTTCAACTATCGCAACGCGA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGA
5804439 TTTTCAATTA
Statistics
Matches: 202, Mismatches: 26, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
37 4 0.02
38 16 0.08
39 5 0.02
40 7 0.03
41 151 0.75
42 16 0.08
43 3 0.01
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:5804253 original size:20 final size:20
Alignment explanation
Indices: 5804228--5804417 Score: 115
Period size: 20 Copynumber: 9.4 Consensus size: 20
5804218 TCAACTATCC
5804228 CAACGCGAACTGGAAAATCG
1 CAACGCGAACTGGAAAATCG
*
5804248 CAACGCGAAATGGAAAATCG
1 CAACGCGAACTGGAAAATCG
*
5804268 -AA--CGAATTTGGAAAATCG
1 CAACGCGAA-CTGGAAAATCG
**
5804286 CAACGAC-AACTGTAGACTATCG
1 CAACG-CGAACTG--GAAAATCG
*
5804308 CAA--CGAATTTGGAAAATCG
1 CAACGCGAA-CTGGAAAATCG
** *
5804327 CAACGAC-AACTGTAGACTATCA
1 CAACG-CGAACTG--GAAAATCG
*
5804349 CAACGTGAACTGGAAAATCG
1 CAACGCGAACTGGAAAATCG
** ** *
5804369 CAACGCGATTTTCAACTATCG
1 CAACGCGAACTGGAA-AATCG
*
5804390 CAACGCGAAATGGAAAATCG
1 CAACGCGAACTGGAAAATCG
5804410 CAACGCGA
1 CAACGCGA
5804418 TTTTCAACTA
Statistics
Matches: 127, Mismatches: 27, Indels: 32
0.68 0.15 0.17
Matches are distributed among these distances:
17 4 0.03
18 10 0.08
19 14 0.11
20 52 0.41
21 21 0.17
22 26 0.20
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (20 bp):
CAACGCGAACTGGAAAATCG
Found at i:5804290 original size:19 final size:19
Alignment explanation
Indices: 5804238--5804332 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 19
5804228 CAACGCGAAC
*
5804238 TGGAAAATCGCAACGCGAA-A
1 TGGAAAATCGCAA--CGAATT
5804258 TGGAAAATCG-AACGAATT
1 TGGAAAATCGCAACGAATT
*
5804276 TGGAAAATCGCAACGACAACTG
1 TGGAAAATCGCAACG--AA-TT
* **
5804298 TAGACTATCGCAACGAATT
1 TGGAAAATCGCAACGAATT
5804317 TGGAAAATCGCAACGA
1 TGGAAAATCGCAACGA
5804333 CAACTGTAGA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
17 4 0.07
18 10 0.16
19 20 0.33
20 12 0.20
21 2 0.03
22 13 0.21
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (19 bp):
TGGAAAATCGCAACGAATT
Found at i:5804308 original size:22 final size:22
Alignment explanation
Indices: 5804282--5804353 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
5804272 AATTTGGAAA
5804282 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
5804304 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
5804323 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
5804345 ATCACAACG
1 ATCGCAACG
5804354 TGAACTGGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.34
20 2 0.05
21 2 0.05
22 21 0.55
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:5804391 original size:21 final size:21
Alignment explanation
Indices: 5804365--5804459 Score: 129
Period size: 21 Copynumber: 4.6 Consensus size: 21
5804355 GAACTGGAAA
5804365 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
5804386 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
5804406 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
5804427 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
5804448 ATCGCAACGCGA
1 ATCGCAACGCGA
5804460 AATGCAACGC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 15 0.24
21 47 0.76
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Done.