Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009084.1 Hibiscus syriacus cultivar Beakdansim tig00112528_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: 881682
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 3 of 4
Found at i:429999 original size:16 final size:16
Alignment explanation
Indices: 429978--430064 Score: 70
Period size: 16 Copynumber: 5.4 Consensus size: 16
429968 ACCTGAAAAA
*
429978 AAAAAAACAGAGACAGAA
1 AAAAAAACAGAGA-A-AG
* *
429996 AAAAAAACGGAGACAG
1 AAAAAAACAGAGAAAG
*
430012 -AAAAAA-AGAGAGAG
1 AAAAAAACAGAGAAAG
* * * *
430026 ACAGAACCGGAGAAAG
1 AAAAAAACAGAGAAAG
430042 AAAAAAACAGAGAAAG
1 AAAAAAACAGAGAAAG
430058 AAAAAAA
1 AAAAAAA
430065 AACTACTAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
14 6 0.11
15 9 0.17
16 26 0.49
18 12 0.23
ACGTcount: A:0.69, C:0.09, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAAAAACAGAGAAAG
Found at i:429999 original size:18 final size:18
Alignment explanation
Indices: 429976--430031 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
429966 CAACCTGAAA
429976 AAAAAAAAACAGAGACAG
1 AAAAAAAAACAGAGACAG
*
429994 AAAAAAAAACGGAGACAG
1 AAAAAAAAACAGAGACAG
* *
430012 AAAAAAAGAGAGAGACAG
1 AAAAAAAAACAGAGACAG
430030 AA
1 AA
430032 CCGGAGAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.70, C:0.09, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAAAAAACAGAGACAG
Found at i:438843 original size:165 final size:164
Alignment explanation
Indices: 438557--438858 Score: 561
Period size: 165 Copynumber: 1.8 Consensus size: 164
438547 CATTAACTGA
438557 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGCAGA
438622 ACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
66 ACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
438687 TGATCTGGTTGGACAGAACAATCATTGAGTTTAG
131 TGATCTGGTTGGACAGAACAATCATTGAGTTTAG
* *
438721 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGG-CAG
438785 AACCAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
65 AA-CAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
438850 TCTGATCTG
129 TCTGATCTG
438859 ATTCAGTAGG
Statistics
Matches: 134, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
163 4 0.03
164 59 0.44
165 71 0.53
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (164 bp):
AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGGCAGA
ACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTGGACAGAACAATCATTGAGTTTAG
Found at i:438844 original size:83 final size:82
Alignment explanation
Indices: 438557--438858 Score: 561
Period size: 82 Copynumber: 3.7 Consensus size: 82
438547 CATTAACTGA
* *
438557 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTTGG-CAG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
438621 AACAATCATTGAGTTTAG
65 AACAATCATTGAGTTTAG
438639 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
438704 ACAATCATTGAGTTTAG
66 ACAATCATTGAGTTTAG
438721 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
438786 ACCAATCATTGAGTTTAG
66 A-CAATCATTGAGTTTAG
438804 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
438859 ATTCAGTAGG
Statistics
Matches: 216, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
81 4 0.02
82 141 0.65
83 71 0.33
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (82 bp):
AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
ACAATCATTGAGTTTAG
Found at i:439789 original size:113 final size:113
Alignment explanation
Indices: 439591--439879 Score: 535
Period size: 113 Copynumber: 2.6 Consensus size: 113
439581 TCGAATCCAC
439591 TTGATGGATCA-TTTCTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCAGTTT-TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
439655 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
439704 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
439769 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCAT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
* *
439817 TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAA
1 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
439880 TTTGTTCAAA
Statistics
Matches: 172, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
113 169 0.98
114 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
Found at i:439958 original size:95 final size:93
Alignment explanation
Indices: 439781--439959 Score: 250
Period size: 94 Copynumber: 1.9 Consensus size: 93
439771 TTCATAATGA
* * * * * **
439781 GAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGAAGCAGCATCCCCAGAGAAAGTT
439846 CATAATGAGAAGAACTCATCTAAAGAAG
66 CATAATGAGAAGAACTCATCTAAAGAAG
* * *
439874 GAAGAATTTGTTCAAACCTTTTACATGAATCCATTACTTGATGAAGCATCATCCCCAGCGGAAAG
1 GAAGAATTTGTTC-AACCTTTTACATGAATCCATCACTTGATGAAGCAGCATCCCCAG-AGAAAG
439939 TTCATAATGAGAAGAACTCAT
64 TTCATAATGAGAAGAACTCAT
439960 ATGAAAAAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 13 0.18
94 35 0.47
95 26 0.35
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (93 bp):
GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGAAGCAGCATCCCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTAAAGAAG
Found at i:439975 original size:207 final size:207
Alignment explanation
Indices: 439668--440073 Score: 559
Period size: 208 Copynumber: 2.0 Consensus size: 207
439658 TTCATAATGA
* * * * * **
439668 GAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAGTTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGAAGCAGTATCCCCAGAGAAAGTT
* * *
439733 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
66 CATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
* * *
439798 TTTT-ACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAAC
131 TTTTGACTTGAATCCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAAC
439861 TCATCTAAAGAAG
195 TCATCTAAAGAAG
* *
439874 GAAGAATTTGTTCAAACCTTTTACATGAATCCATTACTTGATGAAGCA-TCATCCCCAGCGGAAA
1 GAAGAATTTGTTC-AACCTTTTACATGAATCCATCACTTGATGAAGCAGT-ATCCCCAG-AGAAA
439938 GTTCATAATGAGAAGAACTCATATGAA-AAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
63 GTTCATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
** ** * *
440002 ATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGA
128 ACCTTTTGACTTGAATCCATCATTTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGA
440067 ACTCATC
193 ACTCATC
440074 ATCTGAAGAA
Statistics
Matches: 174, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
206 14 0.08
207 75 0.43
208 85 0.49
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (207 bp):
GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGAAGCAGTATCCCCAGAGAAAGTT
CATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
TTTTGACTTGAATCCATCATTTGATGGATCAACATTGCCAGGTAAAGTTCATAATGAGAAGAACT
CATCTAAAGAAG
Found at i:440298 original size:233 final size:229
Alignment explanation
Indices: 439933--440359 Score: 603
Period size: 233 Copynumber: 1.8 Consensus size: 229
439923 CATCCCCAGC
439933 GGAAAGTTCATAATGAGAAGAACTCATATGAAAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 GGAAAGTTCATAATGAGAAGAACTCATATGAAAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
** * * * * *
439998 TTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAG
66 TTCAACCTTTTGATCTGAATTCATCACTGGATGGATCAACATTGCCAGGTAAAGTTCATAATGAG
*
440063 AAGAACTCATCATCTGAAGAAGGAAA-AAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTG
131 AAGAACTCATCATATGAAGAA-GAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTG
440127 GTTTGAATTCATCATTTGATGGATCAACATTGCCA
195 GTTTGAATTCATCATTTGATGGATCAACATTGCCA
* *
440162 GGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 GGAA-AGTTCATAATGAGAAGAA--C-TCATATGAA-AAAGAAGAAGAAGTTCATAATGAGAAGA
* * *
440227 ATTTGTTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATTTC-TT-CCAGAG-AAAGTTC
61 ACTTGTTCAACCTTTTGATCTGAATTCATCACTGGATGGATCA--ACATTGCCAG-GTAAAGTTC
*
440288 ATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
123 ATAATGAGAAGAACTCATCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
*
440353 CTTTTTG
188 CCTTTTG
440360 CATAATTCTA
Statistics
Matches: 174, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
229 4 0.02
230 18 0.10
232 5 0.03
233 103 0.59
234 43 0.25
235 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (229 bp):
GGAAAGTTCATAATGAGAAGAACTCATATGAAAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGATCTGAATTCATCACTGGATGGATCAACATTGCCAGGTAAAGTTCATAATGAG
AAGAACTCATCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGG
TTTGAATTCATCATTTGATGGATCAACATTGCCA
Found at i:440323 original size:116 final size:116
Alignment explanation
Indices: 439933--440359 Score: 573
Period size: 117 Copynumber: 3.7 Consensus size: 116
439923 CATCCCCAGC
* *
439933 GGAAAGTTCATAATGAGAAGAA---CTCATATGAAAAAG-AAGAAGAAGTTCATAATGAGAAGAA
1 GGAAAGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAA
**
439994 CTTGTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCA
66 CTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCA
* * *
440045 GGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAA-AAGAAGTTCATAATAAGAAG
1 GG-AAAGTTCATAATGAGAAGAACTCCTCATATGAAGAA-GAAAGAAGAAGTTCATAATAAGAAG
440109 AACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCA
64 AACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCA
* * * *
440162 GGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 GGAA-AGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGA
* * * * * * *
440227 ATTTGTTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATTTC-TT-CCA
65 ACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCA--ACATTGCCA
440278 GAGAAAGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGA
1 G-GAAAGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGA
*
440343 ACTTGTTCAACTTTTTG
65 ACTTGTTCAACCTTTTG
440360 CATAATTCTA
Statistics
Matches: 279, Mismatches: 24, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
112 2 0.01
113 19 0.07
116 109 0.39
117 146 0.52
118 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (116 bp):
GGAAAGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAA
CTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCA
Found at i:440591 original size:3 final size:3
Alignment explanation
Indices: 440583--440650 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
440573 TTTTTATCCA
440583 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
440631 TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
440651 AATAAATATA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:440679 original size:12 final size:13
Alignment explanation
Indices: 440645--440687 Score: 63
Period size: 12 Copynumber: 3.4 Consensus size: 13
440635 ATATTATTAT
440645 TATTATAATAAATA
1 TATTA-AATAAATA
440659 TATTAAATAAATA
1 TATTAAATAAATA
440672 TA-TAAATAAATA
1 TATTAAATAAATA
440684 -ATTA
1 TATTA
440688 CAGACCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.04
12 12 0.43
13 10 0.36
14 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTAAATAAATA
Found at i:441117 original size:20 final size:21
Alignment explanation
Indices: 441092--441185 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 21
441082 CCCCAACCTG
*
441092 AAAAAAAAAGCAGAGACA-AA
1 AAAAAAAAAACAGAGACAGAA
*
441112 AAAAAAAAAACGGAGACAGAA
1 AAAAAAAAAACAGAGACAGAA
* *
441133 AAAAAGAGAGAGACAGA-ACCGGAGA
1 AAAAA-A-A-AAACAGAGA-CAGA-A
* *
441158 AAGAAAAAAACAGAGAAAGAA
1 AAAAAAAAAACAGAGACAGAA
441179 AAAAAAA
1 AAAAAAA
441186 CTACTAAACC
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
20 16 0.28
21 14 0.25
22 9 0.16
23 4 0.07
24 9 0.16
25 5 0.09
ACGTcount: A:0.71, C:0.09, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAGAGACAGAA
Found at i:441134 original size:16 final size:16
Alignment explanation
Indices: 441115--441183 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
441105 AGACAAAAAA
*
441115 AAAAAAACGGAGACAG
1 AAAAAAACGGAGAAAG
*
441131 AAAAAAA--GAGAGAG
1 AAAAAAACGGAGAAAG
* * *
441145 ACAGAACCGGAGAAAG
1 AAAAAAACGGAGAAAG
*
441161 AAAAAAACAGAGAAAG
1 AAAAAAACGGAGAAAG
441177 AAAAAAA
1 AAAAAAA
441184 AACTACTAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
14 10 0.24
16 32 0.76
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAAAACGGAGAAAG
Found at i:444640 original size:19 final size:19
Alignment explanation
Indices: 444616--444660 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
444606 GAACTCACTG
444616 GAAATAATGAGATTATTTT
1 GAAATAATGAGATTATTTT
444635 GAAATAATGAGATTATTTT
1 GAAATAATGAGATTATTTT
444654 GAAATAA
1 GAAATAA
444661 ATGTTGGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (19 bp):
GAAATAATGAGATTATTTT
Found at i:448792 original size:3 final size:3
Alignment explanation
Indices: 448784--448847 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
448774 GTTTATTTAT
* *
448784 TTA TTA TTA TTT TTA TTA TTA TT- TTA TTTA TTT TCTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA TTA TTA TTA
*
448830 ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
448848 CATGCCTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.87
4 5 0.10
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:448810 original size:31 final size:31
Alignment explanation
Indices: 448775--448843 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
448765 TTTCATTTGG
* *
448775 TTTATTTATTTAT-TATTATTTTTATTATTAT
1 TTTATTTATTT-TCTATTATTATTAATATTAT
448806 TTTATTTATTTTCTATTATTATTAATATTAT
1 TTTATTTATTTTCTATTATTATTAATATTAT
448837 TATTATT
1 T-TTATT
448844 ATTACATGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 1 0.03
31 28 0.82
32 5 0.15
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (31 bp):
TTTATTTATTTTCTATTATTATTAATATTAT
Found at i:449458 original size:23 final size:24
Alignment explanation
Indices: 449419--449463 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
449409 CTTTTTCTGA
*
449419 TATTTTTAAATAAATAA-ATATTT
1 TATTTATAAATAAATAATATATTT
449442 TATTTATAAA-AATATAATATAT
1 TATTTATAAATAA-ATAATATAT
449464 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 13 0.68
24 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTTATAAATAAATAATATATTT
Found at i:453411 original size:24 final size:26
Alignment explanation
Indices: 453356--453411 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
453346 TAATTATTAA
*
453356 ATAAAGTTAAAATTATTAATTATATT
1 ATAAAGTTAAAATTAATAATTATATT
* * *
453382 AAAAAGTT-AATTTAATGATTATA-T
1 ATAAAGTTAAAATTAATAATTATATT
453406 ATAAAG
1 ATAAAG
453412 AAATTATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 6 0.24
25 12 0.48
26 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (26 bp):
ATAAAGTTAAAATTAATAATTATATT
Found at i:454016 original size:31 final size:29
Alignment explanation
Indices: 453968--454042 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 29
453958 CAATACTTAT
*
453968 TTTAAATATTAATGACTTAATTGAAT-ATA
1 TTTAAATATTAATGACTTAATT-AATAAAA
453997 TTTAAATAGTTAAATGACTTAATTAATAAAA
1 TTTAAATA-TT-AATGACTTAATTAATAAAA
* *
454028 TTTAAAAAATAATGA
1 TTTAAATATTAATGA
454043 TCAAAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 13 0.32
30 6 0.15
31 21 0.52
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.40
Consensus pattern (29 bp):
TTTAAATATTAATGACTTAATTAATAAAA
Found at i:457982 original size:13 final size:13
Alignment explanation
Indices: 457964--457989 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
457954 TTAGTGGTGT
457964 TTAGAGAACACTA
1 TTAGAGAACACTA
457977 TTAGAGAACACTA
1 TTAGAGAACACTA
457990 AAGATAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
TTAGAGAACACTA
Found at i:463586 original size:2 final size:2
Alignment explanation
Indices: 463579--463616 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
463569 CGATCTAACC
463579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
463617 TATTTTAGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:463678 original size:30 final size:31
Alignment explanation
Indices: 463644--463714 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 31
463634 TTTATATTAT
*
463644 TAAAATATATTATTTTGATTA-TTAAAAATA
1 TAAAATATATTATTTTAATTATTTAAAAATA
*
463674 TAAAATATATTATTTTAATTATTTTAAAATA
1 TAAAATATATTATTTTAATTATTTAAAAATA
*
463705 -ATAATATATT
1 TAAAATATATT
463715 TAGATCAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 29 0.78
31 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
TAAAATATATTATTTTAATTATTTAAAAATA
Found at i:464484 original size:2 final size:2
Alignment explanation
Indices: 464477--464512 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
464467 TATTCTTGTG
464477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
464513 TGTAATACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:467491 original size:21 final size:21
Alignment explanation
Indices: 467449--467491 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
467439 TGACCTTAAC
**
467449 TTTTTTAATGATTATGCATTT
1 TTTTTTAATGATTATAAATTT
*
467470 TTTTTTAAT-ATTATAAAGTT
1 TTTTTTAATGATTATAAATTT
467490 TT
1 TT
467492 AATGCATAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTTTTAATGATTATAAATTT
Found at i:469132 original size:31 final size:31
Alignment explanation
Indices: 469034--469124 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
469024 CAATTTAAGG
*
469034 CAAAATGGTTTTTAGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
469065 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
469096 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
469125 TTCAAAATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 11 0.19
30 12 0.20
31 36 0.61
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:469297 original size:21 final size:21
Alignment explanation
Indices: 469271--469312 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
469261 ATTTGAATAT
*
469271 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
469292 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
469313 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:469374 original size:21 final size:21
Alignment explanation
Indices: 469341--469380 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
469331 TTTGAGTAGA
*
469341 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
469363 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
469381 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:471352 original size:22 final size:23
Alignment explanation
Indices: 471326--471376 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
471316 ATAGGGCATA
*
471326 GGGAATCGATAC-CTCCTTGAAG
1 GGGAACCGATACACTCCTTGAAG
* * *
471348 GGGAACCGATTCACTCTTTGAAT
1 GGGAACCGATACACTCCTTGAAG
471371 GGGAAC
1 GGGAAC
471377 TGATTCCCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (23 bp):
GGGAACCGATACACTCCTTGAAG
Found at i:475241 original size:15 final size:15
Alignment explanation
Indices: 475223--475252 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
475213 AGAGATTGAT
475223 GGGGAATAGAAGGAA
1 GGGGAATAGAAGGAA
*
475238 GGGGAATAGAGGGAA
1 GGGGAATAGAAGGAA
475253 AATTATATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.50, T:0.07
Consensus pattern (15 bp):
GGGGAATAGAAGGAA
Found at i:478321 original size:19 final size:20
Alignment explanation
Indices: 478278--478323 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
478268 TACTATGATG
* *
478278 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
478298 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
478317 GAAATTG
1 GAAATTG
478324 GATCATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:478353 original size:9 final size:9
Alignment explanation
Indices: 478330--478391 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
478320 ATTGGATCAT
478330 TTTGGAAA-
1 TTTGGAAAG
* *
478338 CTTGGTAAG
1 TTTGGAAAG
478347 TTTGGTAAGTAG
1 TTTGG-AA--AG
*
478359 TTTGGGAAG
1 TTTGGAAAG
478368 TTTGGAAAG
1 TTTGGAAAG
*
478377 TATGGAAAG
1 TTTGGAAAG
478386 TTTGGA
1 TTTGGA
478392 GGGTTTAAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
8 6 0.14
9 27 0.64
10 1 0.02
11 1 0.02
12 7 0.17
ACGTcount: A:0.29, C:0.02, G:0.34, T:0.35
Consensus pattern (9 bp):
TTTGGAAAG
Found at i:478368 original size:21 final size:21
Alignment explanation
Indices: 478339--478378 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
478329 TTTTGGAAAC
* *
478339 TTGGTAAGTTTGGTAAGTAGT
1 TTGGGAAGTTTGGAAAGTAGT
478360 TTGGGAAGTTTGGAAAGTA
1 TTGGGAAGTTTGGAAAGTA
478379 TGGAAAGTTT
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:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (21 bp):
TTGGGAAGTTTGGAAAGTAGT
Found at i:480154 original size:20 final size:19
Alignment explanation
Indices: 480129--480167 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
480119 TATACATTGG
480129 GCTATGAATATGAAAGTAAA
1 GCTATGAATATGAAA-TAAA
*
480149 GCTATGAATCTGAAATAAA
1 GCTATGAATATGAAATAAA
480168 TTGTGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (19 bp):
GCTATGAATATGAAATAAA
Found at i:484701 original size:22 final size:21
Alignment explanation
Indices: 484656--484706 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
484646 TATATAAAAT
484656 GTGTCT-ATTTTTTTAATTTA
1 GTGTCTAATTTTTTTAATTTA
* * *
484676 GTGTTTAATTTTGTTTAGTTTG
1 GTGTCTAATTTT-TTTAATTTA
484698 GTGTCTAAT
1 GTGTCTAAT
484707 GTTTCATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 5 0.20
21 5 0.20
22 15 0.60
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.61
Consensus pattern (21 bp):
GTGTCTAATTTTTTTAATTTA
Found at i:487449 original size:22 final size:23
Alignment explanation
Indices: 487419--487465 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
487409 AAAATATATT
487419 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
487442 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
487464 TA
1 TA
487466 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:487815 original size:27 final size:26
Alignment explanation
Indices: 487785--487861 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
487775 ATTATAAAAA
487785 TAATATTTAATAATAAATAAATTATTT
1 TAATATTT-ATAATAAATAAATTATTT
*
487812 TAATATTT-TAA-AAAT-AATTATAT
1 TAATATTTATAATAAATAAATTATTT
*
487835 TAAGT-TTTATGATAAATAATATTATTT
1 TAA-TATTTATAATAAATAA-ATTATTT
487862 ATTGTATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
23 13 0.31
24 7 0.17
25 7 0.17
26 1 0.02
27 14 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
TAATATTTATAATAAATAAATTATTT
Found at i:487837 original size:23 final size:26
Alignment explanation
Indices: 487785--487859 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 26
487775 ATTATAAAAA
*
487785 TAATATTTAATAATAAATAAATTATTT
1 TAATATTT-ATAATAAATAAATTATAT
487812 TAATATTT-TAA-AAAT-AATTATAT
1 TAATATTTATAATAAATAAATTATAT
*
487835 TAAGT-TTTATGATAAATAATATTAT
1 TAA-TATTTATAATAAATAA-ATTAT
487860 TTATTGTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 13 0.32
24 7 0.17
25 7 0.17
26 1 0.02
27 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
TAATATTTATAATAAATAAATTATAT
Found at i:487972 original size:14 final size:14
Alignment explanation
Indices: 487955--487981 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
487945 CAAAAAATAC
487955 AATTCAATTTTCAG
1 AATTCAATTTTCAG
487969 AATTCAATTTTCA
1 AATTCAATTTTCA
487982 AAAAATTAAT
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:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (14 bp):
AATTCAATTTTCAG
Found at i:502788 original size:29 final size:29
Alignment explanation
Indices: 502746--502804 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
502736 ATTTTCACCT
502746 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
502775 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
502804 A
1 A
502805 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:507472 original size:29 final size:29
Alignment explanation
Indices: 507430--507488 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
507420 ATTTTCACTT
507430 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
507459 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
507488 A
1 A
507489 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:508660 original size:2 final size:2
Alignment explanation
Indices: 508655--508679 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
508645 TAAAAAAACA
508655 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 A
508680 CTACCATTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:509841 original size:30 final size:31
Alignment explanation
Indices: 509794--509852 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
509784 GGTGATGATA
*
509794 TGACATGTTCAATGTCATGACTGTGGACACG
1 TGACATGTTCAATGTCATCACTGTGGACACG
*
509825 TGACAATG-TCAA-GTCATCACTTTGGACA
1 TGAC-ATGTTCAATGTCATCACTGTGGACA
509853 AATTAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 14 0.56
31 8 0.32
32 3 0.12
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (31 bp):
TGACATGTTCAATGTCATCACTGTGGACACG
Found at i:509947 original size:30 final size:30
Alignment explanation
Indices: 509913--509980 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
509903 TTTATTAAGC
509913 TTTAAATTTTTAT-TGTAATTTTAATAATTA-
1 TTTAAATTTTTATAT-T-ATTTTAATAATTAT
*
509943 TTTAACATTTTTATATTTTTTTAATAATTAT
1 TTTAA-ATTTTTATATTATTTTAATAATTAT
509974 TTTAAAT
1 TTTAAAT
509981 GTTATATACG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
30 19 0.56
31 14 0.41
32 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTAAATTTTTATATTATTTTAATAATTAT
Found at i:509995 original size:30 final size:30
Alignment explanation
Indices: 509931--509995 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
509921 TTTATTGTAA
* **
509931 TTTTAATAATTATTTAACATTTTTATATTT
1 TTTTAATAATTATTTAACATTTATATATCG
509961 TTTTAATAATTATTTTAA-ATGTTATATA-CG
1 TTTTAATAATTA-TTTAACAT-TTATATATCG
509991 TTTTA
1 TTTTA
509996 GTTCAGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (30 bp):
TTTTAATAATTATTTAACATTTATATATCG
Found at i:523511 original size:36 final size:36
Alignment explanation
Indices: 523459--523534 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
523449 GTCAACGGAG
* * *
523459 GAGAAACCTGAGGAATCGAAAGCTCTTGCGGTAGTT
1 GAGAAACCTGAAGAATCGAAAGCTCTGGCAGTAGTT
523495 GAGAAACCTGAAGAATCGAAAGCTCTGGCAGTAGTT
1 GAGAAACCTGAAGAATCGAAAGCTCTGGCAGTAGTT
523531 GAGA
1 GAGA
523535 GTAAGCTTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (36 bp):
GAGAAACCTGAAGAATCGAAAGCTCTGGCAGTAGTT
Found at i:542300 original size:39 final size:38
Alignment explanation
Indices: 542246--542358 Score: 153
Period size: 34 Copynumber: 3.1 Consensus size: 38
542236 AAGTCAAGTA
* *
542246 TTCACCAAAGAGTAGTAAAGCAAATCCATTTTGTAAGCC
1 TTCACCAAAGAGTAGTGAAGCAAATCCA-TCTGTAAGCC
542285 TTCACCAAAGAGTAGTGAAGC--AT-CATCT-TAAGCC
1 TTCACCAAAGAGTAGTGAAGCAAATCCATCTGTAAGCC
**
542319 TTCACGGAAGAGTAGTGAAGCAAATCCATCTGTAAGCC
1 TTCACCAAAGAGTAGTGAAGCAAATCCATCTGTAAGCC
542357 TT
1 TT
542359 TAGAGCAAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
34 25 0.38
35 2 0.03
36 4 0.06
37 7 0.11
38 8 0.12
39 20 0.30
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (38 bp):
TTCACCAAAGAGTAGTGAAGCAAATCCATCTGTAAGCC
Found at i:542571 original size:42 final size:41
Alignment explanation
Indices: 542505--542606 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
542495 TTCACAATTT
* * * *
542505 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * *
542546 CTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
*
542588 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
542607 CATAAAACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:543114 original size:53 final size:53
Alignment explanation
Indices: 543056--543265 Score: 242
Period size: 53 Copynumber: 3.9 Consensus size: 53
543046 AGAATCACAC
* * **
543056 CAGAAGATTGTTCGAGTTCTATTCCCTGAAGCAAGAGGGAGTGAACCCGTGGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* *
543109 CAGAAGATTGTTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGAAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * * * ***
543162 CAGAAGATTATTCGAGTTCTACTCCCTGAAGAAATAGGGAGCGAACCCATTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * * *
543215 TAGAAGATTGTTCGAGTTCCTTAATCCCTTAA-CAAGAGGGAGCGGACCCGT
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCCGT
543266 CATTTGAAGA
Statistics
Matches: 132, Mismatches: 23, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
53 107 0.81
54 16 0.12
55 9 0.07
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
Found at i:544376 original size:17 final size:17
Alignment explanation
Indices: 544354--544389 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
544344 CGTGAAGTAG
544354 ATTAGGATTAGTTTAAT
1 ATTAGGATTAGTTTAAT
*
544371 ATTAGGTTTAGTTTAAT
1 ATTAGGATTAGTTTAAT
544388 AT
1 AT
544390 ATATATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (17 bp):
ATTAGGATTAGTTTAAT
Found at i:546138 original size:15 final size:14
Alignment explanation
Indices: 546115--546155 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
546105 GATGCATAAG
546115 TTAATAAATAATAT
1 TTAATAAATAATAT
546129 TTATATAAAT-ATA-
1 TTA-ATAAATAATAT
*
546142 TTAATAAAAAATAT
1 TTAATAAATAATAT
546156 AATAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
12 5 0.22
13 6 0.26
14 6 0.26
15 6 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAATAAATAATAT
Found at i:550136 original size:22 final size:22
Alignment explanation
Indices: 550108--550160 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
550098 TCTGTGACAT
550108 GTTTATCTAGCCTTTATAGCAC
1 GTTTATCTAGCCTTTATAGCAC
* * *
550130 GTTTATCTCGTCTTTATGGCAC
1 GTTTATCTAGCCTTTATAGCAC
550152 GTTTATCTA
1 GTTTATCTA
550161 TTCCTTTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (22 bp):
GTTTATCTAGCCTTTATAGCAC
Found at i:553657 original size:57 final size:58
Alignment explanation
Indices: 553596--553709 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 58
553586 TTAATTTTTC
* *
553596 AAAAAATATACTTTAAA-T-TAAAATTTATTTAAAAGGTTCAATGTAAACTTTTATCCT
1 AAAAAATATACTTGAAATTATAAAATTTATCTAAAA-GTTCAATGTAAACTTTTATCCT
*
553653 AAAAAATATACTTGAAATTAACTAAAATTTATCTGAAAGTTCAATGTAAACTTTTAT
1 AAAAAATATACTTGAAATT-A-TAAAATTTATCTAAAAGTTCAATGTAAACTTTTAT
553710 TTCCTTGATA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
57 16 0.32
58 1 0.02
60 19 0.38
61 14 0.28
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (58 bp):
AAAAAATATACTTGAAATTATAAAATTTATCTAAAAGTTCAATGTAAACTTTTATCCT
Found at i:554207 original size:21 final size:21
Alignment explanation
Indices: 554146--554207 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
554136 CTAATTGTAT
554146 AATATACCGTAATAGTTAAC-
1 AATATACCGTAATAGTTAACA
*
554166 AA-AT--C-TTATA-TGTACACA
1 AATATACCGTAATAGT-TA-ACA
554184 AATATACCGTAATAGTTAACA
1 AATATACCGTAATAGTTAACA
554205 AAT
1 AAT
554208 TTAGTCGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 15
0.65 0.04 0.31
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 3 0.09
18 2 0.06
19 4 0.12
20 2 0.06
21 7 0.22
22 6 0.19
23 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.31
Consensus pattern (21 bp):
AATATACCGTAATAGTTAACA
Found at i:554555 original size:31 final size:31
Alignment explanation
Indices: 554500--554574 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
554490 ACTTAAAGCA
* *
554500 TTTAATACTTAAACTATTAATTTTGGTCTAC
1 TTTAATACCTAAAATATTAATTTTGGTCTAC
* * *
554531 TTTAGTACCTAAAATATTAGTTTTGGTCTAT
1 TTTAATACCTAAAATATTAATTTTGGTCTAC
554562 TTTAATACCTAAA
1 TTTAATACCTAAA
554575 TTTTCATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (31 bp):
TTTAATACCTAAAATATTAATTTTGGTCTAC
Found at i:563995 original size:3 final size:3
Alignment explanation
Indices: 563989--564018 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
563979 AGACATTTTT
563989 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
564019 CTTTCTGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:564704 original size:14 final size:14
Alignment explanation
Indices: 564687--564736 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
564677 AACACACATA
*
564687 AATGAATATAAACG
1 AATGAACATAAACG
564701 AATGAACATAAACG
1 AATGAACATAAACG
* *
564715 AACGAACATAAATG
1 AATGAACATAAACG
*
564729 AACGAACA
1 AATGAACA
564737 ATTACCGAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
AATGAACATAAACG
Found at i:564983 original size:32 final size:31
Alignment explanation
Indices: 564899--565015 Score: 121
Period size: 31 Copynumber: 3.8 Consensus size: 31
564889 GTTTATAAAA
*
564899 TTATAA-AATTTAATAAATTTAATGATTACT
1 TTATAATAATTTAATAAATTTAATGATTATT
** *
564929 TTATGTTAA-TTATTAAAATTTAATGATTATT
1 TTATAATAATTTAAT-AAATTTAATGATTATT
* * * *
564960 TTATAATAGTTTATTAAACTTTAATAATTATA
1 TTATAATAATTTAATAAA-TTTAATGATTATT
*
564992 TTCTAATAATTTAATAAATTTAAT
1 TTATAATAATTTAATAAATTTAAT
565016 CATTTTGTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
30 8 0.11
31 32 0.45
32 31 0.44
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (31 bp):
TTATAATAATTTAATAAATTTAATGATTATT
Found at i:567320 original size:36 final size:37
Alignment explanation
Indices: 567252--567323 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
567242 AAACGAAGCA
567252 AAAACAATGTCAAGCAATAAAAAAGTTCCCCAAATAT
1 AAAACAATGTCAAGCAATAAAAAAGTTCCCCAAATAT
* *
567289 AAAACAATGTCAAGCAA-ATAAAAGTTTCCCAAATA
1 AAAACAATGTCAAGCAATAAAAAAGTTCCCCAAATA
567324 GAATAAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 16 0.48
37 17 0.52
ACGTcount: A:0.54, C:0.18, G:0.08, T:0.19
Consensus pattern (37 bp):
AAAACAATGTCAAGCAATAAAAAAGTTCCCCAAATAT
Found at i:569255 original size:2 final size:2
Alignment explanation
Indices: 569250--569275 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
569240 ATATATTTTA
569250 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
569276 TAAATATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:576807 original size:22 final size:22
Alignment explanation
Indices: 576782--576823 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
576772 ATTCTTTGTA
576782 AATTCATTTC-AAACATATTTGG
1 AATT-ATTTCTAAACATATTTGG
*
576804 AATTATTTCTTAACATATTT
1 AATTATTTCTAAACATATTT
576824 ATATATTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (22 bp):
AATTATTTCTAAACATATTTGG
Found at i:577178 original size:29 final size:29
Alignment explanation
Indices: 577123--577180 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
577113 CCTTAAGGAC
* **
577123 CGATAGTCTAGTACATGTGACGGAGATGA
1 CGATAGTCTAGTACAGGTGACAAAGATGA
*
577152 CGATAGTCTGGTACAGGTGACAAAGATGA
1 CGATAGTCTAGTACAGGTGACAAAGATGA
577181 GTCATGTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.31, T:0.22
Consensus pattern (29 bp):
CGATAGTCTAGTACAGGTGACAAAGATGA
Found at i:577519 original size:22 final size:22
Alignment explanation
Indices: 577491--577534 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
577481 ACTGTTTCAT
577491 ATCTCTCGTATGATTCTCCACC
1 ATCTCTCGTATGATTCTCCACC
577513 ATCTCTCGTATGATTCTCCACC
1 ATCTCTCGTATGATTCTCCACC
577535 GTTTTGAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.36
Consensus pattern (22 bp):
ATCTCTCGTATGATTCTCCACC
Found at i:578783 original size:13 final size:13
Alignment explanation
Indices: 578765--578791 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
578755 TTGGTAGAAA
578765 TTGGTAAGTCAAG
1 TTGGTAAGTCAAG
578778 TTGGTAAGTCAAG
1 TTGGTAAGTCAAG
578791 T
1 T
578792 GCATCATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (13 bp):
TTGGTAAGTCAAG
Found at i:579863 original size:45 final size:45
Alignment explanation
Indices: 579775--579884 Score: 114
Period size: 45 Copynumber: 2.4 Consensus size: 45
579765 GTCCTAAACG
* * ** *
579775 TCCTGGTCTCTCGCAAGAGCCAGCTCCTCCTGTAAGTTCGGAACA
1 TCCTGATCTCTCGCGAGAGCCAGCTCCTCCAATAACTTCGGAACA
* *
579820 TCCTGATCTCTGGCGAGAGCCAGCTCCTCCAATAAC-TCTGGAACG
1 TCCTGATCTCTCGCGAGAGCCAGCTCCTCCAATAACTTC-GGAACA
* * *
579865 TTCTGATCTCTTGAGAGAGC
1 TCCTGATCTCTCGCGAGAGC
579885 AACTGCGTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 2 0.04
45 52 0.96
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (45 bp):
TCCTGATCTCTCGCGAGAGCCAGCTCCTCCAATAACTTCGGAACA
Found at i:580281 original size:114 final size:113
Alignment explanation
Indices: 580081--580501 Score: 416
Period size: 114 Copynumber: 3.8 Consensus size: 113
580071 CCAGATTGCC
* * * * * * *
580081 GAAGGGAATCCCCAGCCAATGGTCCCTAAACAC-CCAAAACGAAAATATCGATGCAGTCGCTGTG
1 GAAGAGAATCCCCAACCAATGATCCCTACAC-CTCCACAAGGAAAATACCGATGCAGTCG-TGTG
* *
580145 GTCAACAG-GGACACAACCGCCGCACTGTTGTTTTCTGTCAGATTACAGAA
64 GTCGAC-GTGGACACAACCGCCGCACTGTTGCTTTCTGTCAGATTACAGAA
* * * *
580195 GAAGGGAATCCCCAACCTATGATCCCTACACCTCCGCTAGGAAAATACCGATGCAGTCGTTGTGG
1 GAAGAGAATCCCCAACCAATGATCCCTACACCTCCACAAGGAAAATACCGATGCAGTCG-TGTGG
* *
580260 TCGACGTGGACACAACCGCCGCACTGTTGCTTTGTGTCTGATTACAGAA
65 TCGACGTGGACACAACCGCCGCACTGTTGCTTTCTGTCAGATTACAGAA
* ** * *
580309 GAAGAGAATCGCCAGTCAATGATTCCTATACCTCCACAAGGAAAATACC---GC--T-GTG-GG-
1 GAAGAGAATCCCCAACCAATGATCCCTACACCTCCACAAGGAAAATACCGATGCAGTCGTGTGGT
*
580366 CGACGTGGACACAACTGCCGCACTGTTGCTTTCTGTCAGATTACAGAA
66 CGACGTGGACACAACCGCCGCACTGTTGCTTTCTGTCAGATTACAGAA
* * ** * * * *
580414 GAAGAGAATCCCCAATCAATGGTCCGGA-AGCTTCCAAAAAGAAAATACCGATGCAGTAAC-TGC
1 GAAGAGAATCCCCAACCAATGATCCCTACA-CCTCCACAAGGAAAATACCGATGCAGT--CGTGT
* *
580477 GGTCAACGTGGACACAACAGCCGCA
63 GGTCGACGTGGACACAACCGCCGCA
580502 GTTGTCATTG
Statistics
Matches: 257, Mismatches: 37, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
104 1 0.00
105 83 0.32
106 2 0.01
107 2 0.01
108 3 0.01
109 1 0.00
110 1 0.00
111 2 0.01
112 2 0.01
113 4 0.02
114 156 0.61
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.20
Consensus pattern (113 bp):
GAAGAGAATCCCCAACCAATGATCCCTACACCTCCACAAGGAAAATACCGATGCAGTCGTGTGGT
CGACGTGGACACAACCGCCGCACTGTTGCTTTCTGTCAGATTACAGAA
Found at i:580458 original size:105 final size:105
Alignment explanation
Indices: 580255--580463 Score: 287
Period size: 105 Copynumber: 2.0 Consensus size: 105
580245 ATGCAGTCGT
* * * *
580255 TGTGGTCGACGTGGACACAACCGCCGCACTGTTGCTTTGTGTCTGATTACAGAAGAAGAGAATCG
1 TGTGGGCGACGTGGACACAACCGCCGCACTGTTGCTTTCTGTCAGATTACAGAAGAAGAGAATCC
* * * * *
580320 CCAGTCAATGATTCCTATACCTCCACAAGGAAAATACCGC
66 CCAATCAATGAGTCCGATACCTCCAAAAAGAAAATACCGC
*
580360 TGTGGGCGACGTGGACACAACTGCCGCACTGTTGCTTTCTGTCAGATTACAGAAGAAGAGAATCC
1 TGTGGGCGACGTGGACACAACCGCCGCACTGTTGCTTTCTGTCAGATTACAGAAGAAGAGAATCC
*
580425 CCAATCAATG-GTCCGGA-AGCTTCCAAAAAGAAAATACCG
66 CCAATCAATGAGTCC-GATA-CCTCCAAAAAGAAAATACCG
580464 ATGCAGTAAC
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
104 4 0.04
105 87 0.96
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (105 bp):
TGTGGGCGACGTGGACACAACCGCCGCACTGTTGCTTTCTGTCAGATTACAGAAGAAGAGAATCC
CCAATCAATGAGTCCGATACCTCCAAAAAGAAAATACCGC
Found at i:587029 original size:12 final size:12
Alignment explanation
Indices: 586969--587038 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
586959 ACAACTACTT
*
586969 CATCACCATCAC
1 CATCACCACCAC
* *
586981 CATCTCCACCTC
1 CATCACCACCAC
**
586993 CATCATTACCAC
1 CATCACCACCAC
* **
587005 CTTCACCTTCAC
1 CATCACCACCAC
587017 CATCACCACCAC
1 CATCACCACCAC
*
587029 CATCTCCACC
1 CATCACCACC
587039 TCGGCTAGTT
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.26, C:0.53, G:0.00, T:0.21
Consensus pattern (12 bp):
CATCACCACCAC
Found at i:587038 original size:21 final size:21
Alignment explanation
Indices: 586972--587038 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
586962 ACTACTTCAT
*
586972 CACCATCACCATCTCCACCTC
1 CACCATCACCACCTCCACCTC
* * * *
586993 CATCATTACCACCTTCACCTT
1 CACCATCACCACCTCCACCTC
* *
587014 CACCATCACCACCACCATCTC
1 CACCATCACCACCTCCACCTC
587035 CACC
1 CACC
587039 TCGGCTAGTT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.54, G:0.00, T:0.21
Consensus pattern (21 bp):
CACCATCACCACCTCCACCTC
Found at i:597109 original size:24 final size:24
Alignment explanation
Indices: 597082--597130 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
597072 AATAAAATTC
597082 TAAAA-TATAAAAATTTAATTAGAT
1 TAAAAGTATAAAAATTTAATT-GAT
* *
597106 TAAAAGTGTAAGAATTTAATTGAT
1 TAAAAGTATAAAAATTTAATTGAT
597130 T
1 T
597131 TTTTCCGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (24 bp):
TAAAAGTATAAAAATTTAATTGAT
Found at i:598003 original size:14 final size:15
Alignment explanation
Indices: 597971--598002 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
597961 GTCAAATTCT
597971 AAATATTTAAATAAA
1 AAATATTTAAATAAA
*
597986 AAATATTTATATAAA
1 AAATATTTAAATAAA
598001 AA
1 AA
598003 TTCTATTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATTTAAATAAA
Found at i:601842 original size:37 final size:37
Alignment explanation
Indices: 601766--601843 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 37
601756 CAAGTTGGAA
* *
601766 AAAATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAATTTATATATTTTCTTTAAAAAATTGAAAATCAT
* *
601803 AAAATTTATATAATTTTTTTTACAAAATTGAAAAT-AT
1 AAAATTTATAT-ATTTTCTTTAAAAAATTGAAAATCAT
601840 AAAA
1 AAAA
601844 AGATTTAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 17 0.47
38 19 0.53
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
AAAATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:602463 original size:22 final size:22
Alignment explanation
Indices: 602435--602515 Score: 61
Period size: 22 Copynumber: 3.9 Consensus size: 22
602425 TTTATTTTTT
602435 AATTTTATAAAAATATTATATA
1 AATTTTATAAAAATATTATATA
*
602457 AATTTTAT---GA-ATT-TA-A
1 AATTTTATAAAAATATTATATA
602473 AATTTT-TAAAATATA-TATATA
1 AATTTTATAAAA-ATATTATATA
*
602494 AATTAATTATAATAATATTATA
1 AATT--TTATAAAAATATTATA
602516 GTAGAATTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 20
0.66 0.04 0.29
Matches are distributed among these distances:
15 1 0.02
16 7 0.16
17 2 0.04
18 3 0.07
19 3 0.07
20 3 0.07
21 5 0.11
22 8 0.18
23 5 0.11
24 8 0.18
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
AATTTTATAAAAATATTATATA
Found at i:613787 original size:11 final size:12
Alignment explanation
Indices: 613768--613798 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
613758 CAATCCAGGC
613768 GACATACGGGGT
1 GACATACGGGGT
613780 GA-ATACGGGGT
1 GACATACGGGGT
613791 GACATACG
1 GACATACG
613799 AGCCATACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.29, C:0.16, G:0.39, T:0.16
Consensus pattern (12 bp):
GACATACGGGGT
Found at i:613904 original size:29 final size:29
Alignment explanation
Indices: 613854--613962 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
613844 AGGAATAGAG
* *
613854 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
613883 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
613912 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
613941 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
613963 CCATTCCCAT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:614170 original size:25 final size:25
Alignment explanation
Indices: 614141--614192 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
614131 TGTACAATTA
614141 TTGGTGAAAAAATTGAGGCAGCCGG
1 TTGGTGAAAAAATTGAGGCAGCCGG
* *
614166 TTGGTGAAATAATTGAGGCATCCGG
1 TTGGTGAAAAAATTGAGGCAGCCGG
614191 TT
1 TT
614193 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.27
Consensus pattern (25 bp):
TTGGTGAAAAAATTGAGGCAGCCGG
Found at i:614233 original size:23 final size:23
Alignment explanation
Indices: 614205--614250 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
614195 AAAAGAAAGA
614205 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
**
614228 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
614251 CCGAGAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.04, G:0.35, T:0.13
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:614265 original size:25 final size:23
Alignment explanation
Indices: 614205--614265 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
614195 AAAAGAAAGA
**
614205 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
614228 AAGAAAGTTAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
614251 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
614266 AGGGAGAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 21 0.68
25 10 0.32
ACGTcount: A:0.51, C:0.07, G:0.33, T:0.10
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:614279 original size:21 final size:21
Alignment explanation
Indices: 614255--614307 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
614245 TTGCAGCCGA
614255 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
614276 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
614297 GAAAGTAAGAA
1 GAAAGAAAGAA
614308 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:614301 original size:17 final size:16
Alignment explanation
Indices: 614253--614284 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
614243 GATTGCAGCC
614253 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
614269 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
614285 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:614576 original size:45 final size:47
Alignment explanation
Indices: 614511--614600 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 47
614501 TTATATAGTT
*
614511 AAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATATAA
1 AAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
*
614555 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAA-TAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
614601 TTTTTGTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 5 0.12
45 15 0.38
46 5 0.12
47 7 0.17
48 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (47 bp):
AAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:614826 original size:50 final size:47
Alignment explanation
Indices: 614751--614850 Score: 114
Period size: 50 Copynumber: 2.1 Consensus size: 47
614741 TTATATTTTA
**
614751 AAAGTTTAGTTTGTTAGTTTATTAGTTA-TTATATATAAGTTATTATATT
1 AAAGTTTAGTTTGTTAAATTATTAGTTAGTT-TATATAAG--ATTATATT
*
614800 AAAGTTTAGTGTTG-TAAATTAGTTAGTTAGTTTATATTAGATTATATT
1 AAAGTTTAGT-TTGTTAAATTA-TTAGTTAGTTTATATAAGATTATATT
614848 AAA
1 AAA
614851 TGATTTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
48 11 0.24
49 15 0.33
50 17 0.38
51 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (47 bp):
AAAGTTTAGTTTGTTAAATTATTAGTTAGTTTATATAAGATTATATT
Found at i:616974 original size:17 final size:17
Alignment explanation
Indices: 616952--616984 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
616942 CAATGATTTT
*
616952 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
616969 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
616985 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:617001 original size:24 final size:22
Alignment explanation
Indices: 616969--617037 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
616959 AAATCATTAC
616969 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
616991 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
617016 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
617038 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:617255 original size:35 final size:37
Alignment explanation
Indices: 617174--617260 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
617164 TTAGTATTCT
* * *
617174 ATAATTATTAGT-AATAATTATTAAATCATTAGTATTAA
1 ATAATTATTA-TAAATAATTACTAAATCAATAG-ACTAA
*
617212 ATCATTATTATAAATAATTACTAAAT-AATA-ACTAA
1 ATAATTATTATAAATAATTACTAAATCAATAGACTAA
617247 ATAATTATTATAAA
1 ATAATTATTATAAA
617261 ATCATTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (37 bp):
ATAATTATTATAAATAATTACTAAATCAATAGACTAA
Found at i:617281 original size:12 final size:13
Alignment explanation
Indices: 617190--617848 Score: 280
Period size: 14 Copynumber: 48.5 Consensus size: 13
617180 ATTAGTAATA
617190 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
617204 AGTATTAAATCATT
1 ATTA-TAAATCATT
617218 ATTATAAAT-A--
1 ATTATAAATCATT
617228 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
617239 ATAACTAAATAATT
1 ATTA-TAAATCATT
617253 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
617267 ATTAT-AATGATT
1 ATTATAAATCATT
617279 ATTATCAAATCATT
1 ATTAT-AAATCATT
617293 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
617312 AAATATTTAAATCATT
1 --AT-TATAAATCATT
617328 A-T-TAAATCATT
1 ATTATAAATCATT
* *
617339 TTTAT-AATGATT
1 ATTATAAATCATT
617351 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
617365 ATTAT-AATGATT
1 ATTATAAATCATT
617377 ATTATTAAATCATT
1 ATTA-TAAATCATT
* *
617391 ACTAT-AATGATT
1 ATTATAAATCATT
617403 ATTATCAAATCATT
1 ATTAT-AAATCATT
617417 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
617436 AAATATTTAAATCATT
1 --AT-TATAAATCATT
617452 A-T-TAAATCATT
1 ATTATAAATCATT
* *
617463 TTTAT-AATGATT
1 ATTATAAATCATT
617475 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
617489 ATTAT-AATGATT
1 ATTATAAATCATT
617501 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
617515 ACTAT-AATGATT
1 ATTATAAATCATT
617527 ATTATCAAATCATT
1 ATTAT-AAATCATT
617541 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
617560 AAATATTTAAATCATT
1 --AT-TATAAATCATT
*
617576 A-T-TAAATTATT
1 ATTATAAATCATT
* *
617587 TTTAT-AATAATT
1 ATTATAAATCATT
617599 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
617613 ATTAT-AATGATT
1 ATTATAAATCATT
617625 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
617639 ACTAT-AATGATT
1 ATTATAAATCATT
*
617651 ATTATCAAATTATT
1 ATTAT-AAATCATT
* *
617665 ACTAT-AATGATT
1 ATTATAAATCATT
617677 ATTATCAAATCATT
1 ATTAT-AAATCATT
617691 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
617710 AAATATTTAAATCATT
1 --AT-TATAAATCATT
617726 A-T-TAAATCATT
1 ATTATAAATCATT
* *
617737 TTTAT-AATGATT
1 ATTATAAATCATT
617749 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
617763 ATTAT-AATGATT
1 ATTATAAATCATT
617775 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
617789 ACTAT-AATGATT
1 ATTATAAATCATT
617801 ATTATCAAATCATT
1 ATTAT-AAATCATT
*
617815 AAATATTTAAATCATT
1 --AT-TATAAATCATT
617831 A-T-TAAATCATT
1 ATTATAAATCATT
*
617842 TTTATAA
1 ATTATAA
617849 TGATTAATAA
Statistics
Matches: 513, Mismatches: 58, Indels: 149
0.71 0.08 0.21
Matches are distributed among these distances:
10 4 0.01
11 59 0.12
12 152 0.30
13 23 0.04
14 159 0.31
15 4 0.01
16 42 0.08
17 6 0.01
18 12 0.02
19 44 0.09
20 4 0.01
21 4 0.01
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:617288 original size:26 final size:26
Alignment explanation
Indices: 617190--617854 Score: 455
Period size: 26 Copynumber: 26.6 Consensus size: 26
617180 ATTAGTAATA
* * *
617190 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
617215 ATTATTATAA--ATAATTA-CTAAATA
1 ATTATTATAATGATTATTATC-AAATC
* * * *
617239 ATAACTA-AATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
617264 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
617290 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
617313 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
617336 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
*
617362 ATTATTATAATGATTATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
617388 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
617414 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
617437 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
617460 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
617486 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
617512 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
617538 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * * *
617561 AATATT-TAA--ATCATTATTAAATT
1 ATTATTATAATGATTATTATCAAATC
* *
617584 ATTTTTATAATAATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
617610 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
617636 ATTACTATAATGATTATTATCAAATT
1 ATTATTATAATGATTATTATCAAATC
*
617662 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
617688 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
617711 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
617734 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
617760 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
617786 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * *
617812 ATTAAATATTTAA--ATCATTATTAAATC
1 ATT--AT-TATAATGATTATTATCAAATC
*
617839 ATTTTTATAATGATTA
1 ATTATTATAATGATTA
617855 ATAAATACAT
Statistics
Matches: 502, Mismatches: 95, Indels: 85
0.74 0.14 0.12
Matches are distributed among these distances:
21 16 0.03
22 8 0.02
23 58 0.12
24 42 0.08
25 47 0.09
26 308 0.61
27 18 0.04
28 1 0.00
29 4 0.01
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:617414 original size:124 final size:124
Alignment explanation
Indices: 617206--617854 Score: 874
Period size: 124 Copynumber: 5.2 Consensus size: 124
617196 AAATCATTAG
* * * * * * *
617206 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
617268 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
617327 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATTAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
617392 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
617451 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
617516 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* *
617575 TATTAAATTATTTTTATAATAATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
* * * * *
617640 CTATAATGATTATTATCAAATTATTACTATAATGAT--TATTATCAAATCATTACTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTA-AATCATCAAATCATTAAAT-ATT--TAAATCAT
* *
617701 CAAATCATTAAAT-A--TTTA-AATCATTA-T--TAAATCATTTTTATAATGATTATTA-CTAAA
1 ----T-ATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATC-AAA
* *
617758 TCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTAAATATTT
60 TCATTACTATAATGATTATTATCAAATCATTAC--T-A--A--ATCATCAAATCATTAAATATTT
617823 AAATCAT
118 AAATCAT
617830 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
617855 ATAAATACAT
Statistics
Matches: 477, Mismatches: 26, Indels: 43
0.87 0.05 0.08
Matches are distributed among these distances:
121 18 0.04
123 26 0.05
124 360 0.75
125 7 0.01
126 10 0.02
127 12 0.03
128 12 0.03
129 8 0.02
130 6 0.01
131 10 0.02
132 8 0.02
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (124 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:617494 original size:150 final size:146
Alignment explanation
Indices: 617325--617815 Score: 636
Period size: 150 Copynumber: 3.3 Consensus size: 146
617315 TATTTAAATC
* ** * *
617325 ATTATTAAATCATTTTTATAATGATTATTA-CTAAATCATTATTATAATGATTATTATTAAATCA
1 ATTATCAAATCATTACTATAATGATTATTATC-AAATCATTACTATAATGATTATTATCAAATCA
* * * * *
617389 TTACTATAATGAT-TATTATCAAATCATTACTAAATCATCAAATCATTAAATA-TTTA-AATCAT
65 TTACTA-AATCATAAATCATTAAAT-ATT--TAAATCAT----T-ATTAAATATTTTATAATAAT
*
617451 TA-T-TAAATCATTTTTATAATGATT
121 TATTATAAATCATTATTATAATGATT
*
617475 ATTA-CTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCA
1 ATTATC-AAATCATTACTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCA
617539 TTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATTATTTTTATAATAATTATTAC
65 TTACTAAATCAT-AAATCATTAAATATTTAAATCATTATTAAA-TA-TTTTATAATAATTATTA-
617604 TAAATCATTATTATAATGATT
126 TAAATCATTATTATAATGATT
*
617625 ATTATCAAATCATTACTATAATGATTATTATCAAATTATTACTATAATGATTATTATCAAATCAT
1 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
*
617690 TACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACT
66 TACTAAATCAT-AAATCATTAAATATTTAAATCATTATTAAAT-A-TTTTATAATAATTATTA-T
617755 AAATCATTATTATAATGATT
127 AAATCATTATTATAATGATT
617775 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTA
1 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTA
617816 AATATTTAAA
Statistics
Matches: 314, Mismatches: 14, Indels: 26
0.89 0.04 0.07
Matches are distributed among these distances:
143 6 0.02
144 3 0.01
146 4 0.01
147 7 0.02
148 9 0.03
149 6 0.02
150 269 0.86
151 10 0.03
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (146 bp):
ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
TACTAAATCATAAATCATTAAATATTTAAATCATTATTAAATATTTTATAATAATTATTATAAAT
CATTATTATAATGATT
Found at i:620750 original size:26 final size:24
Alignment explanation
Indices: 620690--620750 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
620680 TACTAATATT
*
620690 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
620714 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
620741 ATTTAATAAT
1 A-TTAATAAT
620751 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:621565 original size:21 final size:21
Alignment explanation
Indices: 621532--621580 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
621522 AATATAATAT
*
621532 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* *
621553 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
621574 ATTAACT
1 A-TAACT
621581 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:622049 original size:35 final size:35
Alignment explanation
Indices: 622009--622076 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
621999 TGGATGCAAC
622009 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
622044 GCATGCATGAGTGATACAGTTAAAGCTTGGTCG
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCG
622077 CGATGCAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (35 bp):
GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
Found at i:622133 original size:12 final size:12
Alignment explanation
Indices: 622116--622140 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
622106 TCCATGGCGA
622116 CCTACCACCTAC
1 CCTACCACCTAC
622128 CCTACCACCTAC
1 CCTACCACCTAC
622140 C
1 C
622141 ATGTCGTCGG
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:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCTACCACCTAC
Found at i:622167 original size:29 final size:29
Alignment explanation
Indices: 622134--622204 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
622124 CTACCCTACC
622134 ACCTACCATGTCGTCGGGACTCCATGGCG
1 ACCTACCATGTCGTCGGGACTCCATGGCG
622163 ACCTACCATGTCGTCGGGACTCCATGGCG
1 ACCTACCATGTCGTCGGGACTCCATGGCG
622192 ACCTACCATGTCG
1 ACCTACCATGTCG
622205 CCGGCAACCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.18, C:0.35, G:0.25, T:0.21
Consensus pattern (29 bp):
ACCTACCATGTCGTCGGGACTCCATGGCG
Found at i:622405 original size:31 final size:31
Alignment explanation
Indices: 622367--622431 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
622357 CCCATGCATA
622367 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
1 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
622398 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
1 GCACCAAAGCAGCATCAGCGAGCAACAGCGG
622429 GCA
1 GCA
622432 AAGAACCAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.32, G:0.29, T:0.03
Consensus pattern (31 bp):
GCACCAAAGCAGCATCAGCGAGCAACAGCGG
Found at i:622496 original size:29 final size:29
Alignment explanation
Indices: 622454--622567 Score: 212
Period size: 29 Copynumber: 3.9 Consensus size: 29
622444 AAATAATGAT
622454 GGACGCCGGGCGTGCATGGCGACCT-TATA
1 GGACGCCGGGCGTGCATGGCGACCTATA-A
622483 GGACGCCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
622512 GGACGCCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
622541 GGACGCCGGGCGTGCATGGCGACCTAT
1 GGACGCCGGGCGTGCATGGCGACCTAT
622568 GTTGCCACTG
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
29 82 0.98
30 2 0.02
ACGTcount: A:0.18, C:0.28, G:0.39, T:0.15
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGACCTATAA
Found at i:625085 original size:2 final size:2
Alignment explanation
Indices: 625078--625121 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
625068 TAATAAGAAC
625078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
625120 AT
1 AT
625122 TTGATTTACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:628782 original size:39 final size:39
Alignment explanation
Indices: 628739--628861 Score: 203
Period size: 39 Copynumber: 3.2 Consensus size: 39
628729 TTTGGTTGTC
**
628739 CATTCTGACCCACTTTAGTAGATGAACTTATCTGACCTG
1 CATTCTGACCCACACTAGTAGATGAACTTATCTGACCTG
*
628778 CATTCTGACCCACACAAGTAGATGAACTTATCTGACCTG
1 CATTCTGACCCACACTAGTAGATGAACTTATCTGACCTG
*
628817 CATTCTGACCCACACTAGTAGATGAACTAATCTGACCTG
1 CATTCTGACCCACACTAGTAGATGAACTTATCTGACCTG
628856 C-TTCTG
1 CATTCTG
628862 TTCCATTTCC
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
38 5 0.06
39 74 0.94
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (39 bp):
CATTCTGACCCACACTAGTAGATGAACTTATCTGACCTG
Found at i:629396 original size:21 final size:21
Alignment explanation
Indices: 629370--629441 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
629360 AAAAATCACC
629370 TTCTCATCTTGGGCGGCTGTT
1 TTCTCATCTTGGGCGGCTGTT
629391 TTCTCATCTTGGGCGGCTGTT
1 TTCTCATCTTGGGCGGCTGTT
* **
629412 TTCTCATATTGGATGGCTGTT
1 TTCTCATCTTGGGCGGCTGTT
629433 TTCTCATCT
1 TTCTCATCT
629442 CTGATTGTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.08, C:0.22, G:0.24, T:0.46
Consensus pattern (21 bp):
TTCTCATCTTGGGCGGCTGTT
Found at i:641630 original size:20 final size:20
Alignment explanation
Indices: 641607--641647 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
641597 GTTTCCAGAT
*
641607 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
641627 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
641647 T
1 T
641648 TGCGTTGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:642521 original size:24 final size:24
Alignment explanation
Indices: 642494--642547 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
642484 GTATTCGAAA
642494 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
642518 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
642542 TTTGAT
1 TTTGAT
642548 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:642755 original size:15 final size:15
Alignment explanation
Indices: 642737--642773 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
642727 AGAAAAAGAA
642737 GAAGAAAAAATCCCC
1 GAAGAAAAAATCCCC
*
642752 GAAG-AAAAGTCCCC
1 GAAGAAAAAATCCCC
642766 GAAGAAAA
1 GAAGAAAA
642774 TACCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.54, C:0.22, G:0.19, T:0.05
Consensus pattern (15 bp):
GAAGAAAAAATCCCC
Found at i:645057 original size:140 final size:140
Alignment explanation
Indices: 644800--645082 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 140
644790 TCAAACGTTT
* *
644800 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATTTATTAGTAACTTGATT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
644865 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
644930 CGAATTTGAC
131 CGAATTTGAC
644940 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* * *
645005 TTGAACATTGCTATGATCTGTTTAGTTGTTATCACTTATTACACATTTATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
645070 CGAATTTGAC
131 CGAATTTGAC
645080 TAT
1 TAT
645083 CGCAACGCAA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:645078 original size:20 final size:20
Alignment explanation
Indices: 645053--645514 Score: 326
Period size: 20 Copynumber: 23.9 Consensus size: 20
645043 TTACACATTT
*
645053 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
645073 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
645092 AATTGACTATCGCAACTCGA
1 ATTTGACTATCGCAACGCGA
645112 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
645132 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
645152 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
645172 ATTTGACTATTGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
645192 ATTTGATTATCGTAA--CG-
1 ATTTGACTATCGCAACGCGA
* * * *
645209 A---GAATATCGCAAAGTGT
1 ATTTGACTATCGCAACGCGA
* * *
645226 ATTAGACCATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* ***
645246 A-TTGACTTTCGCGTTGCG-
1 ATTTGACTATCGCAACGCGA
* * **
645264 ATTTTAGCTTTCGCATTGCGA
1 ATTTGA-CTATCGCAACGCGA
* *
645285 TTTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
645305 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
* * *
645325 ATTTTACTAACGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
645345 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
* *
645359 ATTAGACCATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* ***
645379 A-TTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCAACGCGA
* * ***
645398 TTTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCAACGCGA
* * * **
645418 TTTTGGCTTTCGCATTGCGA
1 ATTTGACTATCGCAACGCGA
* *
645438 TTTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
645458 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
* *
645478 ATTTGACTATCGCAATGGGA
1 ATTTGACTATCGCAACGCGA
645498 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
645515 AGAAAATCGC
Statistics
Matches: 357, Mismatches: 68, Indels: 34
0.78 0.15 0.07
Matches are distributed among these distances:
14 18 0.05
16 2 0.01
17 2 0.01
18 3 0.01
19 42 0.12
20 286 0.80
21 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:645294 original size:133 final size:133
Alignment explanation
Indices: 645100--645479 Score: 483
Period size: 133 Copynumber: 2.8 Consensus size: 133
645090 CAAATTGACT
* * *** * * ** *
645100 ATCGCAACTCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
1 ATCGCAACACGAA-TTGACTTTCGCGTTGCGATTTTGACTTTCGCATTGCGATTTTGACTATCGC
* * *
645165 AACGCGAATTTGACTATTGCAACGTGAATTTGATTATCGTAACGAGAATATCGCAAAGTGTATTA
65 AACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACGAGAATATCGCAAAGCGTATTA
645230 GACC
130 GACC
645234 ATCGCAACACGAATTGACTTTCGCGTTGCGATTTT-AGCTTTCGCATTGCGATTTTGACTATCGC
1 ATCGCAACACGAATTGACTTTCGCGTTGCGATTTTGA-CTTTCGCATTGCGATTTTGACTATCGC
* * * * * * *
645298 AACGTGAATTTGATTATCGCAACGGGAATTTTACTAACGCAACGAGAAAATCGCAAAGCGTATTA
65 AACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACGAGAATATCGCAAAGCGTATTA
645363 GACC
130 GACC
* * * *
645367 ATCGCAACGCGAATTGACTTTCGCGTTGCGATTTTGACTTTCGCGTTGCGATTTTGGCTTTCGCA
1 ATCGCAACACGAATTGACTTTCGCGTTGCGATTTTGACTTTCGCATTGCGATTTTGACTATCGCA
** * *
645432 TTGCGATTTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAAT
66 ACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACGAGAAT
645480 TTGACTATCG
Statistics
Matches: 209, Mismatches: 35, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
132 1 0.00
133 195 0.93
134 13 0.06
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (133 bp):
ATCGCAACACGAATTGACTTTCGCGTTGCGATTTTGACTTTCGCATTGCGATTTTGACTATCGCA
ACGCGAATTTGACTATCGCAACGTGAATTTGATTATCGCAACGAGAATATCGCAAAGCGTATTAG
ACC
Found at i:645340 original size:153 final size:153
Alignment explanation
Indices: 645128--645546 Score: 502
Period size: 153 Copynumber: 2.7 Consensus size: 153
645118 CTATCGCAAC
* * * * * *
645128 GCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATTGCAACGTGAA
1 GCGATTTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAGAA
* * *
645193 TTTGATTATCGTAACGAGAATATCGCAAAGTGTATTAGACCATCGCAACACGA-ATTGACTTTCG
66 TTTGA-TATCGTAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAACACGATATTGACTTTCG
645257 CGTTGCGATTTTAGCTTTCGCATT
130 CGTTGCGATTTTAGCTTTCGCATT
* *
645281 GCGATTTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTTACTAACGCAACGAGAA
1 GCGATTTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAG-A
* * * * ** ** * * * **** *
645346 AATCGCAAAGCGT-ATTAGACCATCGCAACGCGAATT-GACTTTCGCGTTGCGATTTTGACTTTC
65 ATTTG-ATATCGTAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAACACGATATTGACTTTC
*
645409 GCGTTGCGATTTTGGCTTTCGCATT
129 GCGTTGCGATTTTAGCTTTCGCATT
* *
645434 GCGATTTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTGACTATCGCAATGGGAA
1 GCGATTTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAGAA
*
645499 TTTGACTATCGCAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAA
66 TTTGA-TATCGTAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAA
645547 TATCTTTTGC
Statistics
Matches: 215, Mismatches: 45, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
151 1 0.00
152 17 0.08
153 180 0.84
154 16 0.07
155 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (153 bp):
GCGATTTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAGAA
TTTGATATCGTAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAACACGATATTGACTTTCGC
GTTGCGATTTTAGCTTTCGCATT
Found at i:645670 original size:14 final size:14
Alignment explanation
Indices: 645651--645687 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
645641 CATCAATTAA
645651 ACAAATCAACTTTT
1 ACAAATCAACTTTT
645665 ACAAATCAACTTTT
1 ACAAATCAACTTTT
645679 ACAAATCAA
1 ACAAATCAA
645688 TTAAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:647051 original size:21 final size:21
Alignment explanation
Indices: 646991--647105 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
646981 GTGAATCGGA
* * *
646991 CTCTAGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
647012 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
647033 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
* **
647054 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
647075 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
647096 CTCTTGAACG
1 CTCTTGAACG
647106 ATGACAGGTG
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.04
21 65 0.93
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:647067 original size:42 final size:42
Alignment explanation
Indices: 647004--647113 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 42
646994 TAGAATGGTG
* * *
647004 GGAG-GGACCTCTTCAACGATGACAGGGGCCTCTTGAACGGTG
1 GGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATA
* ** *
647046 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
*
647088 GGAGAGGCCTCTTGAACGATGACAGG
1 GGAGAGGACTCTTGAACGATGACAGG
647114 TGAGTCAGGC
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 53 0.95
43 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.38, T:0.19
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATA
Found at i:647619 original size:40 final size:40
Alignment explanation
Indices: 647563--647650 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
647553 GAAACTTAAA
*
647563 ATCGCAACACGAAAATGACTATCGCAATGCGAAAATGACT
1 ATCGCAACACGAAAATGACTATCGCAACGCGAAAATGACT
* * * **
647603 ATCGCAACACGGAAATGTCTATCGTAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACTATCGCAACGCGAAAATGACT
647643 ATCGCAAC
1 ATCGCAAC
647651 GGGATAATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (40 bp):
ATCGCAACACGAAAATGACTATCGCAACGCGAAAATGACT
Found at i:647651 original size:20 final size:20
Alignment explanation
Indices: 647563--647651 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
647553 GAAACTTAAA
*
647563 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
647583 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
647603 ATCGCAACACGGAAATGTCT
1 ATCGCAACGCGAAAATGACT
* **
647623 ATCGTAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
647643 ATCGCAACG
1 ATCGCAACG
647652 GGATAATCGC
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:647694 original size:18 final size:18
Alignment explanation
Indices: 647656--647694 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
647646 GCAACGGGAT
* *
647656 AATCGCAATGCGAAATAA
1 AATCGCAACGCGAAACAA
*
647674 AATCGCAACGCGAAACCA
1 AATCGCAACGCGAAACAA
647692 AAT
1 AAT
647695 GCGATTTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.23, G:0.15, T:0.13
Consensus pattern (18 bp):
AATCGCAACGCGAAACAA
Found at i:647770 original size:20 final size:20
Alignment explanation
Indices: 647727--647773 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
647717 GATTATCCCG
* *
647727 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCACA
**
647747 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCAAATTCACA
647767 TTGCGAT
1 TTGCGAT
647774 TTTAAGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCACA
Found at i:649708 original size:20 final size:20
Alignment explanation
Indices: 649685--649735 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
649675 TCTGAAACTT
649685 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
649705 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
649725 ACTATCGCAAC
1 AAAATCGCAAC
649736 GAGAATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.24, G:0.14, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:649746 original size:20 final size:20
Alignment explanation
Indices: 649723--649760 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
649713 AACACGAAAA
649723 TGACTATCGCAACGAGAATT
1 TGACTATCGCAACGAGAATT
*
649743 TGACTATCGGAACGAGAA
1 TGACTATCGCAACGAGAA
649761 ATGAAAATCG
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:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGAGAATT
Found at i:650207 original size:22 final size:22
Alignment explanation
Indices: 650180--650230 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
650170 GATGGAGATA
650180 GATGGATTTCGTCGGAGATGGG
1 GATGGATTTCGTCGGAGATGGG
650202 GATGGATTTCGTCGGAGATGGG
1 GATGGATTTCGTCGGAGATGGG
*
650224 GACGGAT
1 GATGGAT
650231 GTCGCCGTAG
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:0.20, C:0.10, G:0.45, T:0.25
Consensus pattern (22 bp):
GATGGATTTCGTCGGAGATGGG
Found at i:650580 original size:19 final size:19
Alignment explanation
Indices: 650556--650592 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
650546 TGTGATAATG
*
650556 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
650575 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
650593 TATTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:655694 original size:22 final size:22
Alignment explanation
Indices: 655666--655762 Score: 176
Period size: 22 Copynumber: 4.4 Consensus size: 22
655656 ATGAACAGTG
*
655666 GGGGAATCGATTCCCTGTAGTA
1 GGGGAATCGATTCCCTGTAGCA
655688 GGGGAATCGATTCCCTGTAGCA
1 GGGGAATCGATTCCCTGTAGCA
655710 GGGGAATCGATTCCCTGTAGCA
1 GGGGAATCGATTCCCTGTAGCA
*
655732 GTGGAATCGATTCCCTGTAGCA
1 GGGGAATCGATTCCCTGTAGCA
655754 GGGGAATCG
1 GGGGAATCG
655763 GTACCCCTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 72 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.24
Consensus pattern (22 bp):
GGGGAATCGATTCCCTGTAGCA
Found at i:656275 original size:47 final size:44
Alignment explanation
Indices: 656203--656328 Score: 139
Period size: 47 Copynumber: 2.8 Consensus size: 44
656193 ATAAAAATCT
656203 CTTACCATT-TATCACATAAGCTCGTAAGCTTATTTTACCA-AAATA
1 CTTACCATTAT-TC-CATAAGCTCGTAAGCTTATTTT-CCATAAATA
* * *
656248 CTTACCATTTAATTTCCATAAGATCGTAAGCTTATTTTTCATATATA
1 CTTACCA-TT-A-TTCCATAAGCTCGTAAGCTTATTTTCCATAAATA
* *
656295 CTTGCCATTATTCCATAAGCTCATAAGCTTATTT
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTT
656329 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
44 22 0.31
45 8 0.11
46 6 0.09
47 31 0.44
48 2 0.03
49 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (44 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTCCATAAATA
Found at i:656324 original size:44 final size:47
Alignment explanation
Indices: 656217--656328 Score: 142
Period size: 47 Copynumber: 2.4 Consensus size: 47
656207 CCATTTATCA
656217 CATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAATTTC
1 CATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAATTTC
* * * *
656264 CATAAGATCGTAAGCTTATTTT-TCATATATACTTGCCA-TT-A-TTC
1 CATAAGCTCGTAAGCTTATTTTACCA-AAATACTTACCATTTAATTTC
*
656308 CATAAGCTCATAAGCTTATTT
1 CATAAGCTCGTAAGCTTATTT
656329 GCATGGTTAC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
44 22 0.38
45 1 0.02
46 4 0.07
47 31 0.53
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (47 bp):
CATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAATTTC
Found at i:656477 original size:40 final size:40
Alignment explanation
Indices: 656433--656514 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
656423 ACCGTAGTGC
*
656433 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
656473 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
656513 TA
1 TA
656515 TAAACCTGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Done.