Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000935.1 Hibiscus syriacus cultivar Beakdansim tig00001869_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: 730910
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:509903 original size:15 final size:16
Alignment explanation
Indices: 509865--509905 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
509855 CTAGAGCCTC
*
509865 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
509881 TGAATCATTCAGCACT
1 TGAATCATTCAGCACT
509897 T-AATCATTC
1 TGAATCATTC
509906 TAAAGTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:510365 original size:45 final size:45
Alignment explanation
Indices: 510301--510393 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
510291 AACATGTTCA
* *
510301 ACATATTAACATAAAGTAGAGACAAATCTAGACTAATGCTATAGT
1 ACATATTAACATAAAGTAGAGACAAATCTAAACTAATGCAATAGT
*
510346 ACATATTAAGATAAAGTAGAGACAAATCTAAACTAATGCAATAGT
1 ACATATTAACATAAAGTAGAGACAAATCTAAACTAATGCAATAGT
510391 ACA
1 ACA
510394 GGTCCTCCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (45 bp):
ACATATTAACATAAAGTAGAGACAAATCTAAACTAATGCAATAGT
Found at i:519744 original size:2 final size:2
Alignment explanation
Indices: 519737--519764 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
519727 TATACAATAA
519737 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
519765 TAAGACAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:522130 original size:25 final size:25
Alignment explanation
Indices: 522101--522176 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
522091 TATTCAATTG
522101 ACTCAATAATTGGTATTAGAGCTTA
1 ACTCAATAATTGGTATTAGAGCTTA
* * * * *
522126 ACTCATTAGA-AGG--CTCGA-C-TG
1 ACTCAATA-ATTGGTATTAGAGCTTA
522147 ACTCAATAATTGGTATTAGAGCTTA
1 ACTCAATAATTGGTATTAGAGCTTA
522172 ACTCA
1 ACTCA
522177 TTAGAATGCT
Statistics
Matches: 35, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
20 1 0.03
21 10 0.29
22 1 0.03
23 6 0.17
24 1 0.03
25 15 0.43
26 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (25 bp):
ACTCAATAATTGGTATTAGAGCTTA
Found at i:523753 original size:8 final size:8
Alignment explanation
Indices: 523733--523762 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
523723 ATGATATGAT
523733 ATATAATAA
1 ATATAA-AA
523742 ATATAAAA
1 ATATAAAA
523750 ATATAAAA
1 ATATAAAA
523758 ATATA
1 ATATA
523763 TACTTATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
ATATAAAA
Found at i:524084 original size:16 final size:16
Alignment explanation
Indices: 524051--524109 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
524041 AAATAAGGTC
524051 AAAATAAAA-AGAAATA
1 AAAATAAAATA-AAATA
*
524067 AAAATAAAATAAATTA
1 AAAATAAAATAAAATA
*
524083 AATATGAAAATAAAGA-A
1 AAAAT-AAAATAAA-ATA
524100 AATAATAAAA
1 AA-AATAAAA
524110 ATAATCAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 17 0.49
17 16 0.46
18 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:524102 original size:17 final size:18
Alignment explanation
Indices: 524051--524113 Score: 51
Period size: 22 Copynumber: 3.4 Consensus size: 18
524041 AAATAAGGTC
*
524051 AAAATAAA-AAGA-AATA
1 AAAATAAAGAAAATAATA
524067 AAAATAAA-ATAAATTAAATA
1 AAAATAAAGA-AAA-T-AATA
524087 TGAAAATAAAGAAAATAATA
1 --AAAATAAAGAAAATAATA
524107 AAAATAA
1 AAAATAA
524114 TCAGTTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
16 9 0.23
17 2 0.05
18 7 0.18
20 8 0.21
21 1 0.03
22 11 0.28
23 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (18 bp):
AAAATAAAGAAAATAATA
Found at i:526055 original size:36 final size:35
Alignment explanation
Indices: 526015--526423 Score: 137
Period size: 36 Copynumber: 11.3 Consensus size: 35
526005 AAATGCCTCG
* *
526015 AGTGAGATAAAATTTGTTTTAATGGAAACTTTCACA
1 AGTGAGATAAAATTTGTTTCAA-GGAAACTTTCTCA
* * **
526051 AGTGAGATAAAAATTTTGTTTCGAGAGAAACTGTCTTG
1 AGTGAGAT-AAAA-TTTGTTTCAAG-GAAACTTTCTCA
* * *
526089 ATTAAGATGAAATTTGTTTCAAGGGAAACTTTCTCA
1 AGTGAGATAAAATTTGTTTCAA-GGAAACTTTCTCA
* * * *
526125 AGTGAGGTAAAATTTTTGTTTCGAGAGATACTGTC-CA
1 AGTGAGATAAAA--TTTGTTTCAAG-GAAACTTTCTCA
* ** * * * *
526162 TAGTGAGACAAAACCTATTTTAAGAAAAACTATCTCA
1 -AGTGAGATAAAATTTGTTTCAAG-GAAACTTTCTCA
* ** * * *
526199 AGTGAGATAAAAAATTTATTTTGAGAGAAAGTGTCTCG
1 AGTGAGAT--AAAATTTGTTTCAAG-GAAACTTTCTCA
* *
526237 AGTGAGATAAAATTTTGTTTCAACAGAAACTATCTCA
1 AGTGAGATAAAA-TTTGTTTCAA-GGAAACTTTCTCA
* * * * *
526274 AGTGA-A-ATAATAT-TTT-GAGGAAAGTTATCTCG
1 AGTGAGATAAAATTTGTTTCAAGGAAACTT-TCTCA
* * *
526306 AGTGAGATAAAATTT-TATTTAAGGAAAACTATCTAA
1 AGTGAGATAAAATTTGT-TTCAAGG-AAACTTTCTCA
*** * * * * *
526342 AACAAGATAAATTTTTGTTTTAAGAAAAACTGTCTCG
1 AGTGAGATAAA-ATTTGTTTCAAG-GAAACTTTCTCA
* * * * *
526379 AGTGATACAAAATTTGTTTTAATGAAAACTATCTCA
1 AGTGAGATAAAATTTGTTTCAA-GGAAACTTTCTCA
*
526415 AGTTAGATA
1 AGTGAGATA
526424 TTTTTTTTTG
Statistics
Matches: 272, Mismatches: 78, Indels: 46
0.69 0.20 0.12
Matches are distributed among these distances:
31 5 0.02
32 10 0.04
33 4 0.01
34 8 0.03
35 5 0.02
36 99 0.36
37 63 0.23
38 78 0.29
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (35 bp):
AGTGAGATAAAATTTGTTTCAAGGAAACTTTCTCA
Found at i:526081 original size:38 final size:38
Alignment explanation
Indices: 526015--526283 Score: 187
Period size: 38 Copynumber: 7.3 Consensus size: 38
526005 AAATGCCTCG
* * *
526015 AGTGAGAT-AAAA-TTTGTTTTAATG-GAAACTTTCACA
1 AGTGAGATAAAAATTTTGTTTCAA-GAGAAACTGTCTCA
* **
526051 AGTGAGATAAAAATTTTGTTTCGAGAGAAACTGTCTTG
1 AGTGAGATAAAAATTTTGTTTCAAGAGAAACTGTCTCA
* * * * *
526089 ATTAAGAT-GAAA-TTTGTTTCAAGGGAAACTTTCTCA
1 AGTGAGATAAAAATTTTGTTTCAAGAGAAACTGTCTCA
* * * *
526125 AGTGAGGTAAAATTTTTGTTTCGAGAGATACTGTC-CA
1 AGTGAGATAAAAATTTTGTTTCAAGAGAAACTGTCTCA
* ** * * *
526162 TAGTGAGACAAAACCTAT-TTT-AAGAAAAACTATCTCA
1 -AGTGAGATAAAAATTTTGTTTCAAGAGAAACTGTCTCA
* * ** * *
526199 AGTGAGATAAAAAATTTATTTTGAGAGAAAGTGTCTCG
1 AGTGAGATAAAAATTTTGTTTCAAGAGAAACTGTCTCA
* *
526237 AGTGAGAT-AAAATTTTGTTTCAACAGAAACTATCTCA
1 AGTGAGATAAAAATTTTGTTTCAAGAGAAACTGTCTCA
*
526274 AGTGAAATAA
1 AGTGAGATAA
526284 TATTTTGAGG
Statistics
Matches: 173, Mismatches: 50, Indels: 18
0.72 0.21 0.07
Matches are distributed among these distances:
36 54 0.31
37 48 0.28
38 71 0.41
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (38 bp):
AGTGAGATAAAAATTTTGTTTCAAGAGAAACTGTCTCA
Found at i:526145 original size:74 final size:74
Alignment explanation
Indices: 526019--526283 Score: 226
Period size: 74 Copynumber: 3.6 Consensus size: 74
526009 GCCTCGAGTG
* *
526019 AGATAAAATTTGTTTTAATGGAAACTTTCACAAGTGAGATAAAAATTTTGTTTCGAGAGAAACTG
1 AGATAAAATTTGTTTCAAGGGAAACTTTCACAAGTGAGATAAAAATTTTGTTTCGAGAGAAACTG
526084 TCTTGATTA
66 TCTTGATTA
* * * * *
526093 AGATGAAATTTGTTTCAAGGGAAACTTTCTCAAGTGAGGTAAAATTTTTGTTTCGAGAGATACTG
1 AGATAAAATTTGTTTCAAGGGAAACTTTCACAAGTGAGATAAAAATTTTGTTTCGAGAGAAACTG
* * *
526158 TCCAT-AGTG
66 T-CTTGATTA
* ** * * ** * * * * * *
526167 AGACAAAACCTATTTTAAGAAAAACTATCTCAAGTGAGATAAAAAATTTATTTTGAGAGAAAGTG
1 AGATAAAATTTGTTTCAAGGGAAACTTTCACAAGTGAGATAAAAATTTTGTTTCGAGAGAAACTG
* * *
526232 TCTCGAGTG
66 TCTTGATTA
** * * *
526241 AGATAAAATTTTGTTTCAACAGAAACTATCTCAAGTGAAATAA
1 AGATAAAA-TTTGTTTCAAGGGAAACTTTCACAAGTGAGATAA
526284 TATTTTGAGG
Statistics
Matches: 152, Mismatches: 36, Indels: 5
0.79 0.19 0.03
Matches are distributed among these distances:
73 1 0.01
74 122 0.80
75 29 0.19
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (74 bp):
AGATAAAATTTGTTTCAAGGGAAACTTTCACAAGTGAGATAAAAATTTTGTTTCGAGAGAAACTG
TCTTGATTA
Found at i:526325 original size:37 final size:36
Alignment explanation
Indices: 526192--526325 Score: 107
Period size: 37 Copynumber: 3.8 Consensus size: 36
526182 TAAGAAAAAC
*
526192 TATCTCAAGTGAGATAAAAAATTTATTTTGAGAGAAAG
1 TATCTCAAGTGAGAT-AAAATTTTATTTTGAG-GAAAG
* * * ** * *
526230 TGTCTCGAGTGAGATAAAATTTTGTTTCAACAGAAAC
1 TATCTCAAGTGAGATAAAATTTTATTTTGA-GGAAAG
*
526267 TATCTCAAGTGA-A-ATAA---TATTTTGAGGAAAG
1 TATCTCAAGTGAGATAAAATTTTATTTTGAGGAAAG
*
526298 TTATCTCGAGTGAGATAAAATTTTATTT
1 -TATCTCAAGTGAGATAAAATTTTATTT
526326 AAGGAAAACT
Statistics
Matches: 71, Mismatches: 18, Indels: 15
0.68 0.17 0.14
Matches are distributed among these distances:
31 4 0.06
32 16 0.23
33 1 0.01
34 3 0.04
35 3 0.04
36 1 0.01
37 30 0.42
38 13 0.18
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (36 bp):
TATCTCAAGTGAGATAAAATTTTATTTTGAGGAAAG
Found at i:527736 original size:21 final size:20
Alignment explanation
Indices: 527702--527741 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
527692 AGTACTTAAT
*
527702 ATTTGTACATACTAAATTAC
1 ATTTGTACAAACTAAATTAC
*
527722 ATTTGATACAAACTATATTA
1 ATTTG-TACAAACTAAATTA
527742 ATAGTTTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (20 bp):
ATTTGTACAAACTAAATTAC
Found at i:528235 original size:39 final size:40
Alignment explanation
Indices: 528180--528284 Score: 106
Period size: 39 Copynumber: 2.7 Consensus size: 40
528170 CGAGTTGAAC
* * *
528180 CGAAGTTCTTACGCATAAGGTTGCGTCAACCC-TTTGCAT
1 CGAAGTGCTTATGCATAAGGTTGCGTCAACCCTTTTGCAG
** *
528219 CGAAGTGCTTATGCATAAGGTTTTGTCGACCCTTTTGCAG
1 CGAAGTGCTTATGCATAAGGTTGCGTCAACCCTTTTGCAG
** * *
528259 ATAAGTGATTATGCATAA-TTTGCGTC
1 CGAAGTGCTTATGCATAAGGTTGCGTC
528285 GATGCTTTGC
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
39 32 0.60
40 21 0.40
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (40 bp):
CGAAGTGCTTATGCATAAGGTTGCGTCAACCCTTTTGCAG
Found at i:529658 original size:19 final size:20
Alignment explanation
Indices: 529634--529679 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
529624 AATAATATCC
529634 CAATTTC-ACATCCTAACAT
1 CAATTTCAACATCCTAACAT
529653 CAATTTCAACATCCTAACAT
1 CAATTTCAACATCCTAACAT
*
529673 TAATTTC
1 CAATTTC
529680 CAGCATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (20 bp):
CAATTTCAACATCCTAACAT
Found at i:530527 original size:14 final size:14
Alignment explanation
Indices: 530510--530540 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
530500 CCTTTACAGT
530510 TTTATTCATACAAC
1 TTTATTCATACAAC
*
530524 TTTATTCATGCAAC
1 TTTATTCATACAAC
530538 TTT
1 TTT
530541 CCAAGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.03, T:0.48
Consensus pattern (14 bp):
TTTATTCATACAAC
Found at i:534048 original size:21 final size:20
Alignment explanation
Indices: 534014--534053 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
534004 AGTACTTAAT
*
534014 ATTTGTACATACTAAATTAC
1 ATTTGTACAAACTAAATTAC
*
534034 ATTTGATACAAACTATATTA
1 ATTTG-TACAAACTAAATTA
534054 ATAGTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (20 bp):
ATTTGTACAAACTAAATTAC
Found at i:542244 original size:31 final size:32
Alignment explanation
Indices: 542183--542244 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
542173 TCTGCTCATA
*
542183 AAAAGGTAAGGGTAAGATTTTGATGTTTCAAG
1 AAAAGGTAAGGGTAAGATTGTGATGTTTCAAG
*
542215 AAAAGGTAA-TGTCAAGATTGTG-TGTTTCAA
1 AAAAGGTAAGGGT-AAGATTGTGATGTTTCAA
542245 TGTTGGTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 10 0.37
32 17 0.63
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (32 bp):
AAAAGGTAAGGGTAAGATTGTGATGTTTCAAG
Found at i:544060 original size:22 final size:23
Alignment explanation
Indices: 544015--544064 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
544005 AAAATAATCC
544015 AAAAAAAACAACAATAATAAAAT
1 AAAAAAAACAACAATAATAAAAT
544038 AAAAAAAACTAA-AATATATAATAAT
1 AAAAAAAAC-AACAATA-ATAA-AAT
544063 AA
1 AA
544065 TAACAAACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 13 0.54
24 6 0.25
25 5 0.21
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAAAAAACAACAATAATAAAAT
Found at i:546020 original size:105 final size:106
Alignment explanation
Indices: 545794--546208 Score: 467
Period size: 105 Copynumber: 4.0 Consensus size: 106
545784 AGTATTGTTC
* ** * *
545794 TGAGTCCAATATCCTCTGCTGTGAAGTTGAGATTGGTTCTGGAACCGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTCTGCTGTGAAGTTGAAATTGGCCCTGGAACTGGGAAATTGTTTGTTGACA
** * *
545859 GTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * *
545900 TGGGTCCAATATCCT-TCACTGTGAAGTTGAAACTGGCCCTGGAACTGGGAAATTG-TTGTTGAT
1 TGAGTCCAATATCCTCT-GCTGTGAAGTTGAAATTGGCCCTGGAACTGGGAAATTGTTTGTTGAC
* * * *
545963 AACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * *
546005 CGAGTCCAATATCCT-TCGTTGTGAAGTTGAGATTGG--CT----C--CGAAATTGTTTGTTGAC
1 TGAGTCCAATATCCTCT-GCTGTGAAGTTGAAATTGGCCCTGGAACTGGGAAATTGTTTGTTGAC
** *
546061 AGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 AACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* *
546103 TGGGTCCAATATCCTCTGCTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTG-TTGTTGACA
1 TGAGTCCAATATCCTCTGCTGTGAAGTTGAAATTGGCCCTGGAACTGGGAAATTGTTTGTTGACA
* * *
546167 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
546208 T
1 T
546209 AGGTAGCATG
Statistics
Matches: 255, Mismatches: 43, Indels: 23
0.79 0.13 0.07
Matches are distributed among these distances:
97 7 0.03
98 72 0.28
99 2 0.01
100 2 0.01
103 2 0.01
104 1 0.00
105 116 0.45
106 53 0.21
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (106 bp):
TGAGTCCAATATCCTCTGCTGTGAAGTTGAAATTGGCCCTGGAACTGGGAAATTGTTTGTTGACA
ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
Found at i:546152 original size:203 final size:203
Alignment explanation
Indices: 545842--546207 Score: 653
Period size: 203 Copynumber: 1.8 Consensus size: 203
545832 CTGGAACCGG
545842 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCTTGGGTCC
* *
545907 AATATCCTTCACTGTGAAGTTGAAACTGGCCCTGGAACTGGGAAATTGTTGTTGATAACCAACCG
66 AATATCCTTCACTGTGAAGTTGAAACTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAACCG
545972 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAGA
131 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAGA
546037 TTGGCTCC
196 TTGGCTCC
* *
546045 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCTTGGGTCC
* * *
546110 AATATCC-TCTGCTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAGCC
66 AATATCCTTC-ACTGTGAAGTTGAAACTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAACC
546174 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
130 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
546208 TAGGTAGCAT
Statistics
Matches: 155, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
202 2 0.01
203 153 0.99
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (203 bp):
GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCTTGGGTCC
AATATCCTTCACTGTGAAGTTGAAACTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAACCG
TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAGA
TTGGCTCC
Found at i:546269 original size:105 final size:103
Alignment explanation
Indices: 546150--546340 Score: 321
Period size: 105 Copynumber: 1.8 Consensus size: 103
546140 CCTGAAACTG
546150 GGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT-AGGTA
1 GGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGA-GTA
* *
546214 GCATGATATCCTCCGTCGTGGAAAATCAGCTTTGAAATT
65 GCACGATATCCTCCATCGTGGAAAATCAGCTTTGAAATT
546253 GGAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
1 GGAAA-TTGTT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
*
546318 GGCACGATATCCTCCATCGTGGA
64 AGCACGATATCCTCCATCGTGGA
546341 GTTGAAATCG
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
103 5 0.06
104 5 0.06
105 71 0.87
106 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (103 bp):
GGAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTAG
CACGATATCCTCCATCGTGGAAAATCAGCTTTGAAATT
Found at i:559975 original size:20 final size:19
Alignment explanation
Indices: 559950--560002 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
559940 TGATTCAATC
*
559950 AGTATCGATACCAAAGGTA
1 AGTATCGATACCAAAGGGA
*
559969 GAGTATCGATACCGAAGGGA
1 -AGTATCGATACCAAAGGGA
559989 ATGTATCGATACCA
1 A-GTATCGATACCA
560003 TTTTGAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:560077 original size:22 final size:19
Alignment explanation
Indices: 560025--560098 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
560015 ATGCAAAAAT
*
560025 GGTATCGATACCATAGGAG
1 GGTATCGATACCATAGTAG
*
560044 GGTATCGGTACCATAGTATG
1 GGTATCGATACCATAGTA-G
*
560064 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGT-AG
560086 GGTATCGATACCA
1 GGTATCGATACCA
560099 GGTAACATTG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
19 16 0.34
20 14 0.30
22 16 0.34
23 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:560680 original size:59 final size:59
Alignment explanation
Indices: 560517--560792 Score: 377
Period size: 59 Copynumber: 4.7 Consensus size: 59
560507 TGGCACTAGT
* *
560517 TGTGCTAAAATGTTAAGAAA-T--T--TAAGTGTATGTATTTCCGTATTGGACACTTTG
1 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
* *
560571 TGTGCTAAAATGTTAAAAAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTTG
1 TGTGCTAAAATGTT-AAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
* * *
560631 TATGCTAAAATGTTAAGAAATTCATACTAAGCT-TATGAATTTTCGTATTGGGTACTTTG
1 TGTGCTAAAATGTTAAGAAATTCATACTAAG-TGTATGAATTTCCGTATTGGGCACTTTG
* *
560690 TGTTCTAAAATGTAAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
1 TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
* *
560749 TGTGC-AAACATGTTAAGAAATTCATACTAGGTGTATAAATTTCC
1 TGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCC
560793 ATATGGGAAA
Statistics
Matches: 195, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
54 14 0.07
55 5 0.03
56 1 0.01
58 5 0.03
59 127 0.65
60 43 0.22
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (59 bp):
TGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTG
Found at i:566759 original size:20 final size:20
Alignment explanation
Indices: 566734--566806 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
566724 TGATTCAATC
* *
566734 AGTATCGATATCGAAGGAGG
1 AGTATCGATACCAAAGGAGG
566754 AGTATCGATACCAAAGGAGG
1 AGTATCGATACCAAAGGAGG
*
566774 AGTATCGATACCAAAGG-GA
1 AGTATCGATACCAAAGGAGG
566793 AGGTATCGATACCA
1 A-GTATCGATACCA
566807 TTTTGAACAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 2 0.04
20 47 0.96
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.18
Consensus pattern (20 bp):
AGTATCGATACCAAAGGAGG
Found at i:567380 original size:59 final size:59
Alignment explanation
Indices: 567325--567727 Score: 675
Period size: 59 Copynumber: 6.8 Consensus size: 59
567315 ATGGCACTAG
*
567325 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTAGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
* *
567384 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTTTGAATTTCCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
*
567443 ATGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
* * *
567502 GTGTGCTAAAATGTAAAGAAATTCATACTAAGTGTATAAATTTCAGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
*
567561 GTGTGCTAGAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
*
567620 CTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTAGGG-ACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATT-GGGCACTTT
* *
567679 GTGTGC-AAACATGTTAAGAAATTCATACTATGTTTATGAATTTCTGTAT
1 GTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTAT
567728 GGGAAATGCA
Statistics
Matches: 323, Mismatches: 19, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
58 3 0.01
59 317 0.98
60 3 0.01
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
Found at i:570036 original size:9 final size:8
Alignment explanation
Indices: 570022--570122 Score: 56
Period size: 7 Copynumber: 13.1 Consensus size: 8
570012 GAAAATCAAT
570022 TATTTTTAA
1 TATTTTT-A
570031 TATTTTT-
1 TATTTTTA
570038 TA-TTTT-
1 TATTTTTA
570044 TATTTTTA
1 TATTTTTA
570052 T-TTTTTA
1 TATTTTTA
*
570059 T-TCTTTA
1 TATTTTTA
* *
570066 TCTTTATTT
1 TATTT-TTA
*
570075 TATGTTTTT
1 TAT-TTTTA
*
570084 TATTTCTAA
1 TATTT-TTA
570093 TATTTTT-
1 TATTTTTA
*
570100 TATTTAT-
1 TATTTTTA
570107 TATTTTT-
1 TATTTTTA
570114 TATTTTTA
1 TATTTTTA
570122 T
1 T
570123 CTTTATTTTA
Statistics
Matches: 76, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
6 6 0.08
7 38 0.50
8 7 0.09
9 23 0.30
10 2 0.03
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (8 bp):
TATTTTTA
Found at i:570045 original size:6 final size:6
Alignment explanation
Indices: 570034--570131 Score: 79
Period size: 6 Copynumber: 14.7 Consensus size: 6
570024 TTTTTAATAT
* *
570034 TTTTTA TTTTTA TTTTTA TTTTTTA TTCTTTA TCTTTA TTTTATGT TTTTTA
1 TTTTTA TTTTTA TTTTTA -TTTTTA TT-TTTA TTTTTA TTTT-T-A TTTTTA
*
570086 TTTCTAATA TTTTTTA TTTATTA TTTTTTA TTTTTA TCTTTA TTTT
1 TTT-T--TA -TTTTTA TTT-TTA -TTTTTA TTTTTA TTTTTA TTTT
570132 ATGTTTTTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 20
0.75 0.06 0.20
Matches are distributed among these distances:
6 41 0.54
7 22 0.29
8 7 0.09
9 3 0.04
10 3 0.04
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:570113 original size:56 final size:55
Alignment explanation
Indices: 570040--570145 Score: 194
Period size: 56 Copynumber: 1.9 Consensus size: 55
570030 ATATTTTTTA
570040 TTTTTATTTTTATTTTTTATTCTTTATCTTTATTTTATGTTTTTTATTTCTAATAT
1 TTTTTATTTTTATTTTTTATT-TTTATCTTTATTTTATGTTTTTTATTTCTAATAT
570096 TTTTTATTTATTATTTTTTATTTTTATCTTTATTTTATGTTTTTTATTTC
1 TTTTTATTT-TTATTTTTTATTTTTATCTTTATTTTATGTTTTTTATTTC
570146 GTTCTCTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
56 37 0.76
57 12 0.24
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (55 bp):
TTTTTATTTTTATTTTTTATTTTTATCTTTATTTTATGTTTTTTATTTCTAATAT
Found at i:570320 original size:2 final size:2
Alignment explanation
Indices: 570309--570380 Score: 112
Period size: 2 Copynumber: 37.0 Consensus size: 2
570299 TTATGTTTTA
570309 AT AT -T 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
* *
570350 AT AT AT AT AT AT AT AA AT AT AT TT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
570381 TTTCTATAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
1 2 0.03
2 62 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:571208 original size:21 final size:21
Alignment explanation
Indices: 571182--571226 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
571172 CATTTATATT
571182 TATTATTAACATATAATTATA
1 TATTATTAACATATAATTATA
** *
571203 TATTATTATTATATTATTATA
1 TATTATTAACATATAATTATA
571224 TAT
1 TAT
571227 CATATCATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATTAACATATAATTATA
Found at i:571219 original size:5 final size:5
Alignment explanation
Indices: 571201--571260 Score: 50
Period size: 5 Copynumber: 11.2 Consensus size: 5
571191 CATATAATTA
* *
571201 TATAT TATTAT TATAT TAT-T ATATAT CATAT CATAT TATACAT TATAT
1 TATAT TA-TAT TATAT TATAT -TATAT TATAT TATAT TAT--AT TATAT
571249 TATAT TCATAT T
1 TATAT T-ATAT T
571261 TTTCATATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
4 1 0.02
5 30 0.64
6 11 0.23
7 5 0.11
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:571239 original size:17 final size:17
Alignment explanation
Indices: 571217--571259 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
571207 ATTATTATAT
571217 TATTATATATCATATCA
1 TATTATATATCATATCA
* * *
571234 TATTATACATTATATTA
1 TATTATATATCATATCA
571251 TATTCATAT
1 TATT-ATAT
571260 TTTTCATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATATATCATATCA
Found at i:571268 original size:37 final size:38
Alignment explanation
Indices: 571175--571254 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 38
571165 GATATATCAT
* *
571175 TTATATTTATTAT-TAACATAT-A-ATTATATATTATTA
1 TTATA-TTATTATATATCATATCATATTATACATTATTA
571211 TTATATTATTATATATCATATCATATTATACATTA-TA
1 TTATATTATTATATATCATATCATATTATACATTATTA
571248 TTATATT
1 TTATATT
571255 CATATTTTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
35 7 0.18
36 12 0.31
37 10 0.26
38 10 0.26
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (38 bp):
TTATATTATTATATATCATATCATATTATACATTATTA
Found at i:589724 original size:13 final size:14
Alignment explanation
Indices: 589706--589738 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
589696 AGTAAAACCC
*
589706 AAGGAAGAA-GAAG
1 AAGGAAGAAGGAAA
589719 AAGGAAGAAGGAAA
1 AAGGAAGAAGGAAA
589733 AAGGAA
1 AAGGAA
589739 AATAAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AAGGAAGAAGGAAA
Found at i:589740 original size:7 final size:7
Alignment explanation
Indices: 589706--589738 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
589696 AGTAAAACCC
589706 AAGGAAG
1 AAGGAAG
589713 AA-GAAG
1 AAGGAAG
589719 AAGGAAG
1 AAGGAAG
*
589726 AAGGAAA
1 AAGGAAG
589733 AAGGAA
1 AAGGAA
589739 AATAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (7 bp):
AAGGAAG
Found at i:591839 original size:19 final size:20
Alignment explanation
Indices: 591799--591850 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
591789 TCATATCATA
591799 TTATATTCCTTATCTTCTTT
1 TTATATTCCTTATCTTCTTT
*
591819 TTAT-TTCCTTGTCTT-TATT
1 TTATATTCCTTATCTTCT-TT
*
591838 TTATATTTCTTAT
1 TTATATTCCTTAT
591851 ATTAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 16 0.59
20 10 0.37
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATATTCCTTATCTTCTTT
Found at i:592233 original size:2 final size:2
Alignment explanation
Indices: 592228--592256 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
592218 AAAAAAACTA
592228 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 A
592257 GAAAATGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:593492 original size:19 final size:20
Alignment explanation
Indices: 593461--593500 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
593451 TGGGATTTTG
593461 ACAATATCAGTACTATTCAT
1 ACAATATCAGTACTATTCAT
593481 ACAATA-CAGTACTATTCAT
1 ACAATATCAGTACTATTCAT
593500 A
1 A
593501 AAAACATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (20 bp):
ACAATATCAGTACTATTCAT
Found at i:594836 original size:20 final size:20
Alignment explanation
Indices: 594790--594838 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
594780 AGGAATTCAA
*
594790 GACAAAAAGGTATCAGTTCC
1 GACAAAGAGGTATCAGTTCC
*
594810 GACAAAGAGGTATCAGTTTC
1 GACAAAGAGGTATCAGTTCC
594830 GACAAAGAG
1 GACAAAGAG
594839 TTATATGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.18
Consensus pattern (20 bp):
GACAAAGAGGTATCAGTTCC
Found at i:596850 original size:29 final size:29
Alignment explanation
Indices: 596818--596904 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
596808 TACAACAAAT
596818 GACAAAAT-ATTTTAGAAATTATAATGAAA
1 GACAAAATCATTTTAGAAATTATAAT-AAA
*
596847 GAC-AAATCTTTTTAGAAATTATAATAAA
1 GACAAAATCATTTTAGAAATTATAATAAA
* *
596875 GA-ACAAATCTTTTTA-AATATTACAATAAA
1 GACA-AAATCATTTTAGAA-ATTATAATAAA
596904 G
1 G
596905 TATAAAAGTA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
28 11 0.21
29 41 0.79
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (29 bp):
GACAAAATCATTTTAGAAATTATAATAAA
Found at i:596875 original size:28 final size:29
Alignment explanation
Indices: 596827--596904 Score: 115
Period size: 29 Copynumber: 2.7 Consensus size: 29
596817 TGACAAAATA
596827 TTTTAGAAATTATAATGAAAG-ACAAATCT
1 TTTTAGAAATTATAAT-AAAGAACAAATCT
596856 TTTTAGAAATTATAATAAAGAACAAATCT
1 TTTTAGAAATTATAATAAAGAACAAATCT
*
596885 TTTTA-AATATTACAATAAAG
1 TTTTAGAA-ATTATAATAAAG
596905 TATAAAAGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 6 0.13
29 40 0.87
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (29 bp):
TTTTAGAAATTATAATAAAGAACAAATCT
Found at i:596940 original size:29 final size:28
Alignment explanation
Indices: 596893--597147 Score: 199
Period size: 29 Copynumber: 8.9 Consensus size: 28
596883 CTTTTTAAAT
* * *
596893 ATTACAATAAAGTATAAAAGTATTTATAA
1 ATTACAATAAA-TACAAAACTATTTCTAA
* *
596922 ATTACAATAATATACAAAAAT-TTTATTAA
1 ATTACAATAA-ATACAAAACTATTT-CTAA
* ** *
596951 ATTACAATAAGTTACAAATGTATTTATAA
1 ATTACAATAA-ATACAAAACTATTTCTAA
* ** *
596980 ATTAAAATATGGTACATAACTATTTCTAA
1 ATTACAATA-AATACAAAACTATTTCTAA
* *
597009 ATTACAATAAAGTGCAAAATTATTTCTAA
1 ATTACAATAAA-TACAAAACTATTTCTAA
* *
597038 ATTACAATCAATTGCAAAACTATTTCT-A
1 ATTACAAT-AAATACAAAACTATTTCTAA
* *
597066 ATTAAAATAAAGTACAAAGCTATTTCTAA
1 ATTACAATAAA-TACAAAACTATTTCTAA
* *
597095 AATACAATAAAGTATAAAACTATTTCTAA
1 ATTACAATAAA-TACAAAACTATTTCTAA
* **
597124 ATTATAATAGGTACAAAACTATTT
1 ATTACAATAAATACAAAACTATTT
597148 AGAAATTATG
Statistics
Matches: 182, Mismatches: 36, Indels: 17
0.77 0.15 0.07
Matches are distributed among these distances:
27 2 0.01
28 36 0.20
29 138 0.76
30 6 0.03
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.35
Consensus pattern (28 bp):
ATTACAATAAATACAAAACTATTTCTAA
Found at i:597010 original size:58 final size:57
Alignment explanation
Indices: 596893--597155 Score: 232
Period size: 58 Copynumber: 4.6 Consensus size: 57
596883 CTTTTTAAAT
* * * *
596893 ATTACAATAAAGTATAAAAGTATTTATAAATTACAATAATATACAAAAAT-TTTATTAA
1 ATTACAATAAAGTA-CAAAGTATTTATAAATTACAATAATGTACAAAACTATTT-CTAA
* *
596951 ATTACAAT-AAGTTACAAATGTATTTATAAATTAAAAT-ATGGTACATAACTATTTCTAA
1 ATTACAATAAAG-TACAAA-GTATTTATAAATTACAATAAT-GTACAAAACTATTTCTAA
* * * *
597009 ATTACAATAAAGTGCAAAATTATTTCTAAATTACAATCAAT-TGCAAAACTATTTCT-A
1 ATTACAATAAAGTAC-AAAGTATTTATAAATTACAAT-AATGTACAAAACTATTTCTAA
* * * * *
597066 ATTAAAATAAAGTACAAAGCTATTTCTAAAATACAATAAAGTATAAAACTATTTCTAA
1 ATTACAATAAAGTACAAAG-TATTTATAAATTACAATAATGTACAAAACTATTTCTAA
* * * *
597124 ATTATAAT-AGGTACAAAACTATTTAGAAATTA
1 ATTACAATAAAGTAC-AAAGTATTTATAAATTA
597156 TGATAAATCA
Statistics
Matches: 168, Mismatches: 25, Indels: 25
0.77 0.11 0.11
Matches are distributed among these distances:
56 5 0.03
57 66 0.39
58 86 0.51
59 9 0.05
60 2 0.01
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (57 bp):
ATTACAATAAAGTACAAAGTATTTATAAATTACAATAATGTACAAAACTATTTCTAA
Found at i:597027 original size:87 final size:86
Alignment explanation
Indices: 596893--597148 Score: 256
Period size: 86 Copynumber: 3.0 Consensus size: 86
596883 CTTTTTAAAT
* * *
596893 ATTACAATAAAGTATAAAAG-TATTTATAAATTACAATAATA-TACAAAAATT-TTAT-TAAATT
1 ATTAAAATAAAGTA-CAAAGCTATTTCTAAATTACAATAA-AGTAC-AAAATTATT-TCTAAATT
**
596954 ACAAT-AAGTTACAAATGTATTTATAA
62 ACAATCAA-TTACAAAACTATTTAT-A
** *
596980 ATTAAAATATGGTACATAA-CTATTTCTAAATTACAATAAAGTGCAAAATTATTTCTAAATTACA
1 ATTAAAATAAAGTACA-AAGCTATTTCTAAATTACAATAAAGTACAAAATTATTTCTAAATTACA
* *
597044 ATCAATTGCAAAACTATTTCTA
65 ATCAATTACAAAACTATTTATA
* * * *
597066 ATTAAAATAAAGTACAAAGCTATTTCTAAAATACAATAAAGTATAAAACTATTTCTAAATTATAA
1 ATTAAAATAAAGTACAAAGCTATTTCTAAATTACAATAAAGTACAAAATTATTTCTAAATTACAA
**
597131 T-AGGTACAAAACTATTTA
66 TCAATTACAAAACTATTTA
597149 GAAATTATGA
Statistics
Matches: 141, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
85 15 0.11
86 66 0.47
87 58 0.41
88 2 0.01
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.35
Consensus pattern (86 bp):
ATTAAAATAAAGTACAAAGCTATTTCTAAATTACAATAAAGTACAAAATTATTTCTAAATTACAA
TCAATTACAAAACTATTTATA
Found at i:597162 original size:57 final size:57
Alignment explanation
Indices: 596997--597152 Score: 152
Period size: 57 Copynumber: 2.7 Consensus size: 57
596987 TATGGTACAT
* * * ** * * * **
596997 AACTATTTCTAAATTACAATAAAGTGCAAAATTATTTCTAAATTACAATCAATTGCAA
1 AACTATTTCT-AATTAAAATAAAGTACAAAACTATTTAGAAAATACAATAAAGTATAA
* **
597055 AACTATTTCTAATTAAAATAAAGTACAAAGCTATTTCTAAAATACAATAAAGTATAA
1 AACTATTTCTAATTAAAATAAAGTACAAAACTATTTAGAAAATACAATAAAGTATAA
* *
597112 AACTATTTCTAAATTATAAT-AGGTACAAAACTATTTAGAAA
1 AACTATTTCT-AATTAAAATAAAGTACAAAACTATTTAGAAA
597153 TTATGATAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
57 65 0.78
58 18 0.22
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (57 bp):
AACTATTTCTAATTAAAATAAAGTACAAAACTATTTAGAAAATACAATAAAGTATAA
Found at i:597162 original size:86 final size:86
Alignment explanation
Indices: 596893--597147 Score: 232
Period size: 87 Copynumber: 3.0 Consensus size: 86
596883 CTTTTTAAAT
* * * * * * * *
596893 ATTACAATAAAGTATAAAAGTATTTATAAATTACAATAATA-TACAAAAAT-TTTATTAAATTAC
1 ATTAAAATAAAGTACATAACTATTTCTAAAATACAATAA-AGTACAAAACTATTT-CTAAATTAC
** *
596956 AAT-AAGTTACAAATGTATTTATAA
64 AATCAAG-TACAAAACTATTT-CAA
** * * *
596980 ATTAAAATATGGTACATAACTATTTCTAAATTACAATAAAGTGCAAAATTATTTCTAAATTACAA
1 ATTAAAATAAAGTACATAACTATTTCTAAAATACAATAAAGTACAAAACTATTTCTAAATTACAA
* * *
597045 TCAATTGCAAAACTATTTCTA
66 TCAAGTACAAAACTATTTCAA
* *
597066 ATTAAAATAAAGTACA-AAGCTATTTCTAAAATACAATAAAGTATAAAACTATTTCTAAATTATA
1 ATTAAAATAAAGTACATAA-CTATTTCTAAAATACAATAAAGTACAAAACTATTTCTAAATTACA
*
597130 AT-AGGTACAAAACTATTT
65 ATCAAGTACAAAACTATTT
597148 AGAAATTATG
Statistics
Matches: 138, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
85 15 0.11
86 58 0.42
87 60 0.43
88 5 0.04
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.35
Consensus pattern (86 bp):
ATTAAAATAAAGTACATAACTATTTCTAAAATACAATAAAGTACAAAACTATTTCTAAATTACAA
TCAAGTACAAAACTATTTCAA
Found at i:597842 original size:32 final size:32
Alignment explanation
Indices: 597761--597843 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 32
597751 CCTAAGGAAA
* * *
597761 TACCTTGGGGCCTTAGAACCTACCCAAGGGAG
1 TACCTTGGGGCCTAAGAGCCTACCCAAAGGAG
*
597793 TACCTTGGGGCCTAAGAGCCTTCCCAAAGGAG
1 TACCTTGGGGCCTAAGAGCCTACCCAAAGGAG
*
597825 TACCCTGGGGCCTAAGAGC
1 TACCTTGGGGCCTAAGAGC
597844 ATAAACCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (32 bp):
TACCTTGGGGCCTAAGAGCCTACCCAAAGGAG
Found at i:597960 original size:32 final size:32
Alignment explanation
Indices: 597922--597998 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
597912 CGAGGCCACG
* *
597922 GAGCCTACCTAAGAACAT-ATCTTAGGGCTGCA
1 GAGCCTACCTAAGAA-ATGATCTCAGGGCCGCA
* **
597954 GGGCCTACCCGAG-AATGATCTCAGGGCCGCA
1 GAGCCTACCTAAGAAATGATCTCAGGGCCGCA
597985 GAGCCTACCTAAGA
1 GAGCCTACCTAAGA
597999 GTCACATTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
30 2 0.06
31 23 0.66
32 10 0.29
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (32 bp):
GAGCCTACCTAAGAAATGATCTCAGGGCCGCA
Found at i:609405 original size:22 final size:22
Alignment explanation
Indices: 609379--609439 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
609369 TTGGTGCAGA
*
609379 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
* *
609401 GGGAACCGATTTCCCCTTTGAAG
1 GGGAACCGA-TACCCCCTTGAAG
*
609424 GGGAACCGATTCCCCC
1 GGGAACCGATACCCCC
609440 CACATGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:609421 original size:23 final size:23
Alignment explanation
Indices: 609390--609440 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
609380 GGAATCGATA
*
609390 CCCCCTTGAAGGGGAACCGATTT
1 CCCCCTTGAAGGGGAACCGATTC
*
609413 CCCCTTTGAAGGGGAACCGATTC
1 CCCCCTTGAAGGGGAACCGATTC
609436 CCCCC
1 CCCCC
609441 ACATGGGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.37, G:0.24, T:0.20
Consensus pattern (23 bp):
CCCCCTTGAAGGGGAACCGATTC
Found at i:611025 original size:18 final size:19
Alignment explanation
Indices: 610999--611046 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
610989 GACGACTCCG
* *
610999 ACGATGAACCAGAAC-AGC
1 ACGAGGAACAAGAACGAGC
611017 ACGAGGAACAAGAACGAGC
1 ACGAGGAACAAGAACGAGC
611036 A-GAGGAACAAG
1 ACGAGGAACAAG
611047 CACAGCCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.48, C:0.21, G:0.29, T:0.02
Consensus pattern (19 bp):
ACGAGGAACAAGAACGAGC
Found at i:611056 original size:18 final size:18
Alignment explanation
Indices: 611004--611059 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
610994 CTCCGACGAT
*
611004 GAACCAGAAC-AGCACGAG
1 GAACAAGAACGAGCA-GAG
611022 GAACAAGAACGAGCAGAG
1 GAACAAGAACGAGCAGAG
*
611040 GAACAAGCAC-AGCCAGAG
1 GAACAAGAACGAG-CAGAG
611058 GA
1 GA
611060 TCAAATGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 2 0.06
18 28 0.82
19 4 0.12
ACGTcount: A:0.46, C:0.23, G:0.30, T:0.00
Consensus pattern (18 bp):
GAACAAGAACGAGCAGAG
Found at i:611736 original size:16 final size:16
Alignment explanation
Indices: 611715--611746 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
611705 AGGGGGAGTA
611715 ATTTCAAACTTGATTT
1 ATTTCAAACTTGATTT
611731 ATTTCAAACTTGATTT
1 ATTTCAAACTTGATTT
611747 CAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTCAAACTTGATTT
Found at i:618197 original size:21 final size:21
Alignment explanation
Indices: 618161--618219 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
618151 TATTAAGAAA
*
618161 ATATTATTTAATTTAATAT-T
1 ATATTATTTAAATTAATATAT
*
618181 TTATTATGTTAAATTAATTATAT
1 ATATTAT-TTAAATTAA-TATAT
618204 ATATTA-TTAAATTAAT
1 ATATTATTTAAATTAAT
618220 TAATTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.21
21 17 0.52
22 3 0.09
23 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATTATTTAAATTAATATAT
Found at i:619566 original size:23 final size:25
Alignment explanation
Indices: 619521--619568 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
619511 ATACATTGAC
*
619521 AAATTATATAAAATACAATAACATT
1 AAATTATATAAAATACAAAAACATT
*
619546 AAATTAT-TAGAA-ACAAAAACATT
1 AAATTATATAAAATACAAAAACATT
619569 TATTTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 4 0.19
25 7 0.33
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (25 bp):
AAATTATATAAAATACAAAAACATT
Found at i:621249 original size:3 final size:3
Alignment explanation
Indices: 621241--621276 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
621231 TTTTATTGTA
621241 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
621277 ATTGAGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:622392 original size:4 final size:4
Alignment explanation
Indices: 622378--622746 Score: 612
Period size: 4 Copynumber: 92.2 Consensus size: 4
622368 TGTACGTGTA
*
622378 TATG AATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
622426 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
622474 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
622522 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
622570 TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * * * * *
622618 CATG CATG CATG CATG CATG CATG CATG CATG CATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
622666 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
622714 TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG T
622747 CACAAATGTA
Statistics
Matches: 361, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 361 1.00
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:623757 original size:24 final size:25
Alignment explanation
Indices: 623721--623774 Score: 94
Period size: 24 Copynumber: 2.2 Consensus size: 25
623711 GAGTGTCTTG
623721 AAACC-AAAGGAGGGTTCAAGTTGA
1 AAACCTAAAGGAGGGTTCAAGTTGA
623745 AAACCTAAA-GAGGGTTCAAGTTGA
1 AAACCTAAAGGAGGGTTCAAGTTGA
623769 AAACCT
1 AAACCT
623775 GAAAAGGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.19
Consensus pattern (25 bp):
AAACCTAAAGGAGGGTTCAAGTTGA
Found at i:624866 original size:36 final size:36
Alignment explanation
Indices: 624757--624992 Score: 148
Period size: 34 Copynumber: 6.6 Consensus size: 36
624747 ACAAAAAAAT
** *
624757 ATCTCACTTGAGATAACTTTCCTTAAAACATATTTC
1 ATCTCACTTGAGATAGTTTTCCTTAAAACAAATTTC
* ** * *
624793 GTCTCACTCAAGACAG-TTTCTCTCGAAAA-AAA--TC
1 ATCTCACTTGAGATAGTTTTC-CT-TAAAACAAATTTC
* **
624827 ATCTCATTTGAGATAGTTTTCCTTAAAACACGTTTC
1 ATCTCACTTGAGATAGTTTTCCTTAAAACAAATTTC
* * *
624863 ATCTCACTTGAGATA-ATTTCTCTCGAAGCAA-AAATTTT
1 ATCTCACTTGAGATAGTTTTC-CT-TAA--AACAAATTTC
*
624901 ATCTCACTTGAGATAGTTTTCCTTAAAAC-AAGTT-
1 ATCTCACTTGAGATAGTTTTCCTTAAAACAAATTTC
* * * * * *
624935 GTCTCACTCGGGATAGTTTCCCTTGAAACAAAAATTGC
1 ATCTCACTTGAGATAGTTTTCCTT-AAA-ACAAATTTC
624973 ATCTCACTTGAGATA-TTTTC
1 ATCTCACTTGAGATAGTTTTC
624993 TCCTAAAAAT
Statistics
Matches: 149, Mismatches: 35, Indels: 31
0.69 0.16 0.14
Matches are distributed among these distances:
33 4 0.03
34 36 0.24
35 21 0.14
36 34 0.23
37 15 0.10
38 33 0.22
39 6 0.04
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (36 bp):
ATCTCACTTGAGATAGTTTTCCTTAAAACAAATTTC
Found at i:625000 original size:72 final size:72
Alignment explanation
Indices: 624744--624992 Score: 267
Period size: 70 Copynumber: 3.5 Consensus size: 72
624734 TGTCTATCTT
* ** * * *
624744 GAAACAAAAAAAT-ATCTCACTTGAGATAACTTTCCTTAAAACATATTTCGTCTCACTCAAGACA
1 GAAAC-AAAAATTCATCTCACTTGAGATAGTTTTCCTTAAAACA-AGTTCGTCTCACTCGAGATA
624808 GTTTCTCTC
64 GTTTCTCTC
* * * * *
624817 G-AA-AAAAA-TCATCTCATTTGAGATAGTTTTCCTTAAAACACGTTTCATCTCACTTGAGATAA
1 GAAACAAAAATTCATCTCACTTGAGATAGTTTTCCTTAAAACAAG-TTCGTCTCACTCGAGATAG
624879 TTTCTCTC
65 TTTCTCTC
* * *
624887 GAAGCAAAAATTTTATCTCACTTGAGATAGTTTTCCTTAAAACAAGTT-GTCTCACTCGGGATAG
1 GAAACAAAAA-TTCATCTCACTTGAGATAGTTTTCCTTAAAACAAGTTCGTCTCACTCGAGATAG
* *
624951 TTTCCCTT
65 TTTCTCTC
624959 GAAACAAAAATTGCATCTCACTTGAGATA-TTTTC
1 GAAACAAAAATT-CATCTCACTTGAGATAGTTTTC
624993 TCCTAAAAAT
Statistics
Matches: 147, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
69 1 0.01
70 55 0.37
71 8 0.05
72 49 0.33
73 3 0.02
74 31 0.21
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (72 bp):
GAAACAAAAATTCATCTCACTTGAGATAGTTTTCCTTAAAACAAGTTCGTCTCACTCGAGATAGT
TTCTCTC
Found at i:625014 original size:144 final size:144
Alignment explanation
Indices: 624756--625026 Score: 327
Period size: 144 Copynumber: 1.9 Consensus size: 144
624746 AACAAAAAAA
* *
624756 TATCTCACTTGAGATAACTTTCCTTAAAACATATTTCGTCTCACTCAAGACAGTTTCTCTCGAAA
1 TATCTCACTTGAGATAACTTTCCTTAAAACATAGTTCGTCTCACTCAAGACAGTTTCCCTCGAAA
* * *
624821 AAAATCATCTCATTTGAGATAGTTTTCCTTAAAACACGTTTCATCTCACTTGAGATAATTTCTCT
66 AAAATCATCTCACTTGAGATAGTTTTCCCTAAAACACGTTTCATATCACTTGAGATAATTTCTCT
624886 CGAAGCAAAAATTT
131 CGAAGCAAAAATTT
** ** * *
624900 TATCTCACTTGAGATAGTTTTCCTTAAAACA-AGTT-GTCTCACTCGGGATAGTTTCCCTTGAAA
1 TATCTCACTTGAGATAACTTTCCTTAAAACATAGTTCGTCTCACTCAAGACAGTTTCCCTCG-AA
* ** *
624963 CAAAAATTGCATCTCACTTGAGATA-TTTTCTCCTAAAA-A-TTTTTTTATCACTTGAGATAGTT
65 -AAAAA-T-CATCTCACTTGAGATAGTTTTC-CCTAAAACACGTTTCATATCACTTGAGATAATT
625025 TC
126 TC
625027 ATGACATGAC
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
142 20 0.19
143 5 0.05
144 54 0.50
145 7 0.07
146 21 0.20
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (144 bp):
TATCTCACTTGAGATAACTTTCCTTAAAACATAGTTCGTCTCACTCAAGACAGTTTCCCTCGAAA
AAAATCATCTCACTTGAGATAGTTTTCCCTAAAACACGTTTCATATCACTTGAGATAATTTCTCT
CGAAGCAAAAATTT
Found at i:634894 original size:2 final size:2
Alignment explanation
Indices: 634887--634911 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
634877 GGAATAAAGA
634887 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
634912 CAAATTCAGC
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:634999 original size:20 final size:19
Alignment explanation
Indices: 634967--635015 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
634957 AATTTTTTGA
634967 TTTTTTTTATTTCTATTTC
1 TTTTTTTTATTTCTATTTC
*
634986 TTTTTTCTTTTTTCTATTTCC
1 TTTTTT-TTATTTCTATTT-C
635007 TTTCTTTTT
1 TTT-TTTTT
635016 TGAGTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 6 0.23
20 11 0.42
21 6 0.23
22 3 0.12
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTTTATTTCTATTTC
Found at i:635015 original size:25 final size:26
Alignment explanation
Indices: 634967--635016 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
634957 AATTTTTTGA
*
634967 TTTTTTTTATTTCTATTTCTTTTTTC
1 TTTTTTCTATTTCTATTTCTTTTTTC
*
634993 TTTTTTCTATTTC-CTTTCTTTTTT
1 TTTTTTCTATTTCTATTTCTTTTTT
635017 GAGTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTTCTATTTCTATTTCTTTTTTC
Found at i:635023 original size:25 final size:26
Alignment explanation
Indices: 634959--635029 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
634949 TAATTTTTAA
634959 TTTTTTGATTTTTTTTATTTCTATTTC
1 TTTTTTGA-TTTTTTTATTTCTATTTC
* *
634986 TTTTTT-CTTTTTTCTATTTC-CTTTC
1 TTTTTTGATTTTTT-TATTTCTATTTC
*
635011 TTTTTTGAGTTTTTTATTT
1 TTTTTTGATTTTTTTATTT
635030 TTTTATGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
25 21 0.55
26 11 0.29
27 6 0.16
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.77
Consensus pattern (26 bp):
TTTTTTGATTTTTTTATTTCTATTTC
Found at i:644311 original size:19 final size:20
Alignment explanation
Indices: 644283--644358 Score: 75
Period size: 22 Copynumber: 3.8 Consensus size: 20
644273 ATCTAATTTT
*
644283 GGTATTGATACC-GGTAGGG
1 GGTATCGATACCAGGTAGGG
*
644302 GGTATCGATACCATAGTAGGG
1 GGTATCGATACCA-GGTAGGG
* *
644323 TAGTATCGATACCATGGTA-AG
1 -GGTATCGATACCA-GGTAGGG
644344 GGTATCGATACCAGG
1 GGTATCGATACCAGG
644359 AAACATCGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.27
20 12 0.25
21 7 0.15
22 16 0.33
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCAGGTAGGG
Found at i:644350 original size:20 final size:20
Alignment explanation
Indices: 644301--644356 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 20
644291 TACCGGTAGG
*
644301 GGGTATCGATACCATAGTAG
1 GGGTATCGATACCATAGTAA
*
644321 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
644343 GGGTATCGATACCA
1 GGGTATCGATACCA
644357 GGAAACATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
22 18 0.56
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:644380 original size:95 final size:96
Alignment explanation
Indices: 644227--644411 Score: 255
Period size: 95 Copynumber: 1.9 Consensus size: 96
644217 CTGATTCAAT
* * * ** *
644227 TAGTATCGATACCATGATTAGGGGTATCGATACCAAGAAACATCAAATCTAATTTTGGTATTGAT
1 TAGTATCGATACCATGAGTAAGGGTATCGATACCAAGAAACATCAAACCTAAAATTGGTATCGAT
***
644292 ACCGGTAGGGGGTATCGATACCATAGTAGGG
66 ACCAAAAGGGGGTATCGATACCATAGTAGGG
* *
644323 TAGTATCGATACCATG-GTAAGGGTATCGATACCAGGAAACATCGAACCTAAAATTGGTATCGAT
1 TAGTATCGATACCATGAGTAAGGGTATCGATACCAAGAAACATCAAACCTAAAATTGGTATCGAT
*
644387 ACCAAAAGGGGGTATTGATACCATA
66 ACCAAAAGGGGGTATCGATACCATA
644412 ACATAGAAGT
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
95 61 0.79
96 16 0.21
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.26
Consensus pattern (96 bp):
TAGTATCGATACCATGAGTAAGGGTATCGATACCAAGAAACATCAAACCTAAAATTGGTATCGAT
ACCAAAAGGGGGTATCGATACCATAGTAGGG
Found at i:644423 original size:95 final size:95
Alignment explanation
Indices: 644228--644436 Score: 238
Period size: 95 Copynumber: 2.2 Consensus size: 95
644218 TGATTCAATT
* * * ** *
644228 AGTATCGATACCATGATTAGGGGTATCGATACCAAGAAACATCAAATCTAATTTTGGTATTGATA
1 AGTATCGATACCATG-GTAAGGGTATCGATACCAAGAAACATCAAACCTAAAATTGGTATCGATA
*** ** * *
644293 CCGGTAGGGGGTATCGATACCATAGTAGGGT
65 CCAAAAGGGGGTATCGATACCATAACAGAGA
* *
644324 AGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAACCTAAAATTGGTATCGATAC
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAAAATTGGTATCGATAC
* *
644389 CAAAAGGGGGTATTGATACCATAACATAGA
66 CAAAAGGGGGTATCGATACCATAACAGAGA
* *
644419 AGTATCGGTACCAGGGTA
1 AGTATCGATACCATGGTA
644437 GTAGTACCGA
Statistics
Matches: 94, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
95 79 0.84
96 15 0.16
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (95 bp):
AGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAAAATTGGTATCGATAC
CAAAAGGGGGTATCGATACCATAACAGAGA
Found at i:644862 original size:59 final size:60
Alignment explanation
Indices: 644790--644938 Score: 219
Period size: 63 Copynumber: 2.5 Consensus size: 60
644780 TTTGCAAATT
644790 TAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCAC-TTTGTGTGCTAAAATGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTTTGTGTGCTAAAATGA
* ** * *
644849 TAAGAAACTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTTTTTTTTTTGCTAAAATGA
1 TAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCAC---TTTTGTGTGCTAAAATGA
644912 TAAGAAATTCATACTAAGTGTATGAAT
1 TAAGAAATTCATACTAAGTGTATGAAT
644939 ATCCGTATAG
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
59 39 0.49
63 41 0.51
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (60 bp):
TAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTTTGTGTGCTAAAATGA
Found at i:645376 original size:68 final size:68
Alignment explanation
Indices: 645291--645476 Score: 282
Period size: 68 Copynumber: 2.7 Consensus size: 68
645281 AAAAGATTAA
* * *
645291 AGGCCTAACTATGCATTTGACAGAAAAGTGTCAATTATACCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
645356 ATG
66 ATG
* * *
645359 AGGCCTAACTGTGCATTTGACATAAAGGTCTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
645424 TTG
66 ATG
* * *
645427 AGGCCTAACTGTGTATTTGACTGAAAGGTGTCAATTATGCTAGTTAGATG
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATG
645477 TGCGGTTAAG
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 105 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
ATG
Found at i:645597 original size:79 final size:79
Alignment explanation
Indices: 645497--646032 Score: 901
Period size: 79 Copynumber: 6.8 Consensus size: 79
645487 TACCTTTGAG
645497 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
645562 GTACATTGTCAGCA
66 GTACATTGTCAGCA
* * * *
645576 TAAAAGAATAATGTATATGGGTGCATTATTGGTATGAAATGATGCCATAACTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
645641 GTACATTGTCAGCA
66 GTACATTGTCAGCA
* * * * *
645655 TAAATGAATAATGCATATGAGTTCATTATTGGTATGAAAGGATTCCATAGCTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
*
645720 GTACATTGTCAGAA
66 GTACATTGTCAGCA
* *
645734 TAAAAGAATAATGCATATGGGTGCATTATTAGTATGAAAGGATGCCATAGCTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
645799 GTACATTGTCAGCA
66 GTACATTGTCAGCA
645813 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
645878 GTACATTGTCAGCA
66 GTACATTGTCAGCA
* *
645892 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTATATGT
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
*
645957 GTACATTATCAGCA
66 GTACATTGTCAGCA
* * **
645971 TAAAAGAATAATGCATATGGGTACATTATTGGCATGAAAAGATGCCATAAATGAAATGTATA
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATA
646033 ACGGTGTATA
Statistics
Matches: 429, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 429 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
GTACATTGTCAGCA
Found at i:646089 original size:45 final size:45
Alignment explanation
Indices: 646001--646090 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
645991 GTACATTATT
* * * **
646001 GGCATGAAAAGATGCCATAAATGAAATGTATAACGGTGTATAAAA
1 GGCATGAAAAGATGCCATAAATAAAATATATAACAGTAAATAAAA
* * *
646046 GGCATGAAATGATGTCATAAATAAAATATATAATAGTAAATAAAA
1 GGCATGAAAAGATGCCATAAATAAAATATATAACAGTAAATAAAA
646091 TGTATAATAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.24
Consensus pattern (45 bp):
GGCATGAAAAGATGCCATAAATAAAATATATAACAGTAAATAAAA
Found at i:646111 original size:19 final size:19
Alignment explanation
Indices: 646063--646111 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
646053 AATGATGTCA
*
646063 TAAATAAAATATATAATAG
1 TAAATAAAATGTATAATAG
646082 TAAATAAAATGTATAATAG
1 TAAATAAAATGTATAATAG
*
646101 TATATAAAATG
1 TAAATAAAATG
646112 ACATGAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (19 bp):
TAAATAAAATGTATAATAG
Found at i:657763 original size:27 final size:26
Alignment explanation
Indices: 657733--657816 Score: 64
Period size: 27 Copynumber: 3.2 Consensus size: 26
657723 TTTTGATACT
657733 TTCTACAAGTATCGATACTTTTAAACA
1 TTCTACAAGTATC-ATACTTTTAAACA
** * * * * *
657760 TTCT-GGAGT-GCCTAGTTTTGATACT
1 TTCTACAAGTATCATACTTTT-AAACA
657785 TTCTACAAGTATCAATACTTTTAAACA
1 TTCTACAAGTATC-ATACTTTTAAACA
657812 TTCTA
1 TTCTA
657817 GAGTGCCTAG
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 6 0.15
25 8 0.21
26 6 0.15
27 13 0.33
28 6 0.15
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (26 bp):
TTCTACAAGTATCATACTTTTAAACA
Found at i:657788 original size:25 final size:26
Alignment explanation
Indices: 657760--657846 Score: 72
Period size: 25 Copynumber: 3.4 Consensus size: 26
657750 CTTTTAAACA
657760 TTCT-GGAGTGCCTAGTTTTGATACT
1 TTCTAGGAGTGCCTAGTTTTGATACT
** * * * * *
657785 TTCTACAAGTATCAATACTTTT-AAACA
1 TTCTAGGAGT-GC-CTAGTTTTGATACT
657812 TTCTA-GAGTGCCTAGTTTTGATACT
1 TTCTAGGAGTGCCTAGTTTTGATACT
657837 TTCTAGGAGT
1 TTCTAGGAGT
657847 TTCAAAACTA
Statistics
Matches: 44, Mismatches: 13, Indels: 9
0.67 0.20 0.14
Matches are distributed among these distances:
24 6 0.14
25 13 0.30
26 10 0.23
27 9 0.20
28 6 0.14
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (26 bp):
TTCTAGGAGTGCCTAGTTTTGATACT
Found at i:657803 original size:52 final size:52
Alignment explanation
Indices: 657722--657841 Score: 222
Period size: 52 Copynumber: 2.3 Consensus size: 52
657712 TCCTACAATC
* *
657722 GTTTTGATACTTTCTACAAGTATCGATACTTTTAAACATTCTGGAGTGCCTA
1 GTTTTGATACTTTCTACAAGTATCAATACTTTTAAACATTCTAGAGTGCCTA
657774 GTTTTGATACTTTCTACAAGTATCAATACTTTTAAACATTCTAGAGTGCCTA
1 GTTTTGATACTTTCTACAAGTATCAATACTTTTAAACATTCTAGAGTGCCTA
657826 GTTTTGATACTTTCTA
1 GTTTTGATACTTTCTA
657842 GGAGTTTCAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (52 bp):
GTTTTGATACTTTCTACAAGTATCAATACTTTTAAACATTCTAGAGTGCCTA
Found at i:669564 original size:58 final size:58
Alignment explanation
Indices: 669487--669767 Score: 382
Period size: 58 Copynumber: 4.8 Consensus size: 58
669477 TTCCCATATG
* * * **
669487 GAAATTCTTACACTTAGTATGAATCTCTTAACTTTTTGTACACAAAGTGTGCAATACA
1 GAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACA
* * * * * * **
669545 TAAATCCATACAGTTAGTATGAATTTCTTAACCTTTTGCACAAAAAGAGCCCAATATG
1 GAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACA
* * *
669603 GAAATTCATACAATTAATATGAATTTCTTAACTTTTTGCATACAAAGTGCCCAATACA
1 GAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACA
* * *
669661 AAAATTTATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACG
1 GAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACA
*
669719 GAAATTCATACACTTAGTATGAATTTCTTAATTTTTTGCACACAAAGTG
1 GAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG
669768 TCATTTGGTA
Statistics
Matches: 191, Mismatches: 32, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 191 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (58 bp):
GAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACA
Found at i:669632 original size:116 final size:116
Alignment explanation
Indices: 669482--669769 Score: 423
Period size: 116 Copynumber: 2.5 Consensus size: 116
669472 CATATTTCCC
* * * * *
669482 ATATGGAAATTCTTACACTTAGTATGAATCTCTTAACTTTTTGTACACAAAGTGTGCAATACATA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGTCCAATACAAA
*
669547 AATCCATACAGTTAGTATGAATTTCTTAACCTTTTGCACAAAAAGAGCCCA
66 AATCCATACACTTAGTATGAATTTCTTAACCTTTTGCACAAAAAGAGCCCA
* * * *
669598 ATATGGAAATTCATACAATTAATATGAATTTCTTAACTTTTTGCATACAAAGTGCCCAATACAAA
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGTCCAATACAAA
** * * *
669663 AATTTATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCA
66 AATCCATACACTTAGTATGAATTTCTTAACCTTTTGCACAAAAAGAGCCCA
* *
669714 ATACGGAAATTCATACACTTAGTATGAATTTCTTAATTTTTTGCACACAAAGTGTC
1 ATATGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGTC
669770 ATTTGGTAAT
Statistics
Matches: 151, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
116 151 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (116 bp):
ATATGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGTCCAATACAAA
AATCCATACACTTAGTATGAATTTCTTAACCTTTTGCACAAAAAGAGCCCA
Found at i:670160 original size:19 final size:19
Alignment explanation
Indices: 670091--670162 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
670081 TGGGTCCTCA
*
670091 GTATCGATACCCCTACCATG
1 GTATCGATA-CCCTACTATG
*
670111 GTATTGATACTACCATACTATG
1 GTATCGATAC--CC-TACTATG
*
670133 GTACCGATACCCTACTATG
1 GTATCGATACCCTACTATG
*
670152 GTATAGATACC
1 GTATCGATACC
670163 ATTTTTGCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 17 0.40
20 10 0.23
21 2 0.05
22 14 0.33
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (19 bp):
GTATCGATACCCTACTATG
Found at i:676358 original size:58 final size:57
Alignment explanation
Indices: 676257--676469 Score: 286
Period size: 58 Copynumber: 3.7 Consensus size: 57
676247 CATACAGATA
* * **
676257 TCATACACTTAATATGAATCTCTTAACTTTTTGCACATTAAGTGTCCAATACGAAAAT
1 TCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG-CCAATACGAAAAT
* *
676315 TTATACACTTAGTATGAATTTCTTAACTTTTTGTACACAAAGTGCCCAATAC-AGAAAT
1 TCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTG-CCAATACGA-AAAT
*
676373 TCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCTAATACTG-AAAC
1 TCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCC-AATAC-GAAAAT
* *
676431 TCATAAACTTAGTACGAATTTCTTAACTTTTTGCACACA
1 TCATACACTTAGTATGAATTTCTTAACTTTTTGCACACA
676470 CATTTTCATT
Statistics
Matches: 139, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
57 3 0.02
58 136 0.98
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (57 bp):
TCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCAATACGAAAAT
Found at i:676866 original size:19 final size:19
Alignment explanation
Indices: 676797--676868 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
676787 TAGCTCCTTA
* *
676797 GTATCAATACCCCTACCATG
1 GTATCGATA-CCCTACTATG
*
676817 ATATCGATACTACCATACTATG
1 GTATCGATAC--CC-TACTATG
*
676839 TTAAT-GATACCCTACTATG
1 GT-ATCGATACCCTACTATG
676858 GTATCGATACC
1 GTATCGATACC
676869 ATTTTTGCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
18 2 0.05
19 15 0.36
20 9 0.21
21 2 0.05
22 12 0.29
23 2 0.05
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (19 bp):
GTATCGATACCCTACTATG
Found at i:676942 original size:20 final size:21
Alignment explanation
Indices: 676891--676942 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
676881 TGTTTTGAAT
* *
676891 GGTATCGATAC-CTTCCCTTT
1 GGTATCGATACTCTCCCCTTA
676911 GGTATCGATACTC-CCCCTTA
1 GGTATCGATACTCTCCCCTTA
676931 GGTATCGATACT
1 GGTATCGATACT
676943 GATTGAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (21 bp):
GGTATCGATACTCTCCCCTTA
Found at i:678209 original size:4 final size:4
Alignment explanation
Indices: 678200--678244 Score: 69
Period size: 4 Copynumber: 12.0 Consensus size: 4
678190 TCGAAGTTGT
678200 TTTA TTTA TTTA TTTA -TTA TTTA TTTA -TTA -TTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
678245 GTATTATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 9 0.23
4 30 0.77
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:678232 original size:14 final size:14
Alignment explanation
Indices: 678201--678242 Score: 75
Period size: 14 Copynumber: 2.9 Consensus size: 14
678191 CGAAGTTGTT
678201 TTATTTATTTATTTA
1 TTATTTATTTA-TTA
678216 TTATTTATTTATTA
1 TTATTTATTTATTA
678230 TTATTTATTTATT
1 TTATTTATTTATT
678243 TAGTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTATTTATTA
Found at i:678237 original size:18 final size:18
Alignment explanation
Indices: 678200--678259 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 18
678190 TCGAAGTTGT
678200 TTTATTTATTTATTTATTA
1 TTTATTTATTTA-TTATTA
678219 TTTATTTA-TTATTATTTA
1 TTTATTTATTTATTA-TTA
678237 TTTATTTAGTATTATTATTA
1 TTTATTTA-T-TTATTATTA
678257 TTT
1 TTT
678260 TACATATTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.08
18 14 0.38
19 8 0.22
20 6 0.16
21 6 0.16
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTATTTATTTATTATTA
Found at i:678267 original size:29 final size:33
Alignment explanation
Indices: 678202--678267 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
678192 GAAGTTGTTT
* **
678202 TATTTATTTATTTATTATTTATTTATTATTATT
1 TATTTATTTATGTATTATTTATTTATTATTACA
678235 TATTTATTTA-GTATTA-TTA-TTATT-TTACA
1 TATTTATTTATGTATTATTTATTTATTATTACA
678264 TATT
1 TATT
678268 ACATGGCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 7 0.23
30 5 0.17
31 3 0.10
32 5 0.17
33 10 0.33
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (33 bp):
TATTTATTTATGTATTATTTATTTATTATTACA
Found at i:678967 original size:24 final size:25
Alignment explanation
Indices: 678939--678993 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
678929 ATCCTCTCTT
678939 GAGTGAGAG-GAGTTGAAAGAGAAA-
1 GAGTGAGAGAGAGTT-AAAGAGAAAC
*
678963 GAGTG-GAGAGAGTTATAGAGAAAC
1 GAGTGAGAGAGAGTTAAAGAGAAAC
678987 G-GTGAGA
1 GAGTGAGA
678994 ATGAAGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.42, C:0.02, G:0.42, T:0.15
Consensus pattern (25 bp):
GAGTGAGAGAGAGTTAAAGAGAAAC
Found at i:683688 original size:13 final size:13
Alignment explanation
Indices: 683664--683702 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
683654 TATCATTGCA
683664 TCTATG-ATCAAT
1 TCTATGAATCAAT
683676 TCTATGAATCAAT
1 TCTATGAATCAAT
*
683689 TCTCTGAATCAAT
1 TCTATGAATCAAT
683702 T
1 T
683703 ATGAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 6 0.24
13 19 0.76
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (13 bp):
TCTATGAATCAAT
Found at i:683988 original size:21 final size:21
Alignment explanation
Indices: 683963--684020 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
683953 TACCGGGGAG
683963 AATAAAAATAAAATAAGAG-AA
1 AATAAAAATAAAATAAG-GTAA
*
683984 AATAAAAATAAAACAAGGTAA
1 AATAAAAATAAAATAAGGTAA
684005 AA-AAATAATAAAATAA
1 AATAAA-AATAAAATAA
684021 AAAATTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (21 bp):
AATAAAAATAAAATAAGGTAA
Found at i:684877 original size:34 final size:33
Alignment explanation
Indices: 684740--684912 Score: 145
Period size: 34 Copynumber: 4.9 Consensus size: 33
684730 TTAGTTTGTG
*
684740 CAATAAAATAAAATGTTAGTAA-GTTAGTAAGAA
1 CAATAAAATAAAAAGTTAG-AATGTTAGTAAGAA
** * *
684773 CAATAAAAATAAAAAAGTCGGTATGTTAGTATGAA
1 CAAT-AAAAT-AAAAAGTTAGAATGTTAGTAAGAA
*
684808 CAATAAAAT-AAAAGTTACAATAATAGTAAGTTAGTAAGAA
1 CAATAAAATAAAAAGTT---A-GA-A-T--GTTAGTAAGAA
*
684848 CAATAAAAATAAAAAGTTAGAATGTTAGTATGAA
1 CAAT-AAAATAAAAAGTTAGAATGTTAGTAAGAA
684882 CAATTAAAAT-AAAAGTTAGAATGTTAGTAAG
1 CAA-TAAAATAAAAAGTTAGAATGTTAGTAAG
684913 TTAGAAAAGT
Statistics
Matches: 113, Mismatches: 13, Indels: 28
0.73 0.08 0.18
Matches are distributed among these distances:
32 6 0.05
33 24 0.21
34 29 0.26
35 22 0.19
36 1 0.01
37 2 0.02
38 2 0.02
39 1 0.01
40 14 0.12
41 5 0.04
42 7 0.06
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.27
Consensus pattern (33 bp):
CAATAAAATAAAAAGTTAGAATGTTAGTAAGAA
Found at i:684890 original size:75 final size:75
Alignment explanation
Indices: 684756--684916 Score: 252
Period size: 75 Copynumber: 2.1 Consensus size: 75
684746 AATAAAATGT
* *
684756 TAGTAAGTTAGTAAGAACAATAAAAATAAAAAAGTCGGTATGTTAGTATGAACAATAAAATAAAA
1 TAGTAAGTTAGTAAGAACAATAAAAATAAAAAAGTCAGAATGTTAGTATGAACAATAAAATAAAA
684821 GTTACAATAA
66 GTTACAATAA
*
684831 TAGTAAGTTAGTAAGAACAATAAAAAT-AAAAAGTTAGAATGTTAGTATGAACAATTAAAATAAA
1 TAGTAAGTTAGTAAGAACAATAAAAATAAAAAAGTCAGAATGTTAGTATGAACAA-TAAAATAAA
* **
684895 AGTTAGAATGT
65 AGTTACAATAA
684906 TAGTAAGTTAG
1 TAGTAAGTTAG
684917 AAAAGTTAGC
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 24 0.30
75 55 0.70
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.27
Consensus pattern (75 bp):
TAGTAAGTTAGTAAGAACAATAAAAATAAAAAAGTCAGAATGTTAGTATGAACAATAAAATAAAA
GTTACAATAA
Found at i:685037 original size:19 final size:18
Alignment explanation
Indices: 685005--685053 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 18
684995 CGAATCAAAT
685005 AATACAAATAAAT-ATATAA
1 AATA-AAATAAATAATAT-A
685024 AATAAAATAGAATAATATA
1 AATAAAATA-AATAATATA
685043 AATAAAATAAA
1 AATAAAATAAA
685054 AAAGTTAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.25
19 17 0.61
20 4 0.14
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAAATAAATAATATA
Found at i:685844 original size:50 final size:50
Alignment explanation
Indices: 685767--685867 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 50
685757 AAATATATCA
* *
685767 AGACTTCCCCCAAGGCTAACCCAAGAAAGAAAGAAAATAAAGAATAAAAG
1 AGACTTCCCCCAAGGCAAACCCAAGAAAGAAAGAAAATAAAGAAGAAAAG
* **
685817 AGACTTCCCCTAAGGCAAACCTGAGAAAGAAAGAAAATAAAGAAGAAAAG
1 AGACTTCCCCCAAGGCAAACCCAAGAAAGAAAGAAAATAAAGAAGAAAAG
685867 A
1 A
685868 TCATGTTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.54, C:0.18, G:0.18, T:0.10
Consensus pattern (50 bp):
AGACTTCCCCCAAGGCAAACCCAAGAAAGAAAGAAAATAAAGAAGAAAAG
Found at i:686331 original size:61 final size:59
Alignment explanation
Indices: 686266--686460 Score: 164
Period size: 61 Copynumber: 3.2 Consensus size: 59
686256 TAAATTGTTT
686266 GTTGAAGATGACGTTATTTCTTCTTGTTGAGGAAATCGGGTTAATCAGGAAATAATTTGGG
1 GTTGAAGATGACGTT-TTTCTTCTTGTTGAGGAAATCGGGTTAATCAGGAAATAATTT-GG
* * * * * * *
686327 GTTGAAGATGACATTGTTCATCCATGTTGAGGAGATCTGGCAGCTT--TCAGATAAATTATTT--
1 GTTGAAGATGACGTTTTTC-TTCTTGTTGAGGAAATC-GG--G-TTAATCAG-GAAATAATTTGG
* * * * *
686388 GTTGAAGATGATGTTGTTCCTTCTCGTTGAGGAAATCGAGTTAATCTGGAAATAATTTGG
1 GTTGAAGATGACGTT-TTTCTTCTTGTTGAGGAAATCGGGTTAATCAGGAAATAATTTGG
686448 TGTTGAAGATGAC
1 -GTTGAAGATGAC
686461 ACTGCTTATC
Statistics
Matches: 102, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
57 2 0.02
58 9 0.09
59 3 0.03
60 4 0.04
61 65 0.64
62 4 0.04
63 4 0.04
64 9 0.09
65 2 0.02
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (59 bp):
GTTGAAGATGACGTTTTTCTTCTTGTTGAGGAAATCGGGTTAATCAGGAAATAATTTGG
Found at i:686373 original size:122 final size:123
Alignment explanation
Indices: 686195--686610 Score: 516
Period size: 122 Copynumber: 3.4 Consensus size: 123
686185 CAATTTGGAT
* * * * *
686195 ATAATCTGGTGTTGAAGACGACACTGCTCATCCATGTTGAAGATATATGGTC-GCTTTCATATAA
1 ATAATTTGGTGTTGAAGACGACACTGCTTATCCATGTTGAAGAGATATGGCCAGCTTTCAGATAA
* * *
686259 ATTGTTTGTTGAAGATGACGTTATTTCTTCTTGTTGAGGAAATCGGGTTAATCAGGAA
66 ATTGTTTGTTGAAGATGACGTTGTTCCTTCTCGTTGAGGAAATCGGGTTAATCAGGAA
* * * * *
686317 ATAATTTGGGGTTGAAGATGACATTG-TTCATCCATGTTGAGGAGATCTGG-CAGCTTTCAGATA
1 ATAATTTGGTGTTGAAGACGACACTGCTT-ATCCATGTTGAAGAGATATGGCCAGCTTTCAGATA
* * * *
686380 AATTATTTGTTGAAGATGATGTTGTTCCTTCTCGTTGAGGAAATCGAGTTAATCTGGAA
65 AATTGTTTGTTGAAGATGACGTTGTTCCTTCTCGTTGAGGAAATCGGGTTAATCAGGAA
* * *
686439 ATAATTTGGTGTTGAAGATGACACTGCTTATCCATGTTGAAGAGATCTGGCCA-CTTTTAGATAA
1 ATAATTTGGTGTTGAAGACGACACTGCTTATCCATGTTGAAGAGATATGGCCAGCTTTCAGATAA
* * * ** * * *
686503 ATTGTTTATTGAAGATGACATTGTTCCTTCTCGTTGAGAAAATTAGGTCAATCAAGAG
66 ATTGTTTGTTGAAGATGACGTTGTTCCTTCTCGTTGAGGAAATCGGGTTAATCAGGAA
* * *
686561 ATAATTTGGTGTTAAAGACGACACTGCTTATCTATGTTGAAGAGTTATGG
1 ATAATTTGGTGTTGAAGACGACACTGCTTATCCATGTTGAAGAGATATGG
686611 ATGCTTTCAT
Statistics
Matches: 253, Mismatches: 37, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
121 2 0.01
122 247 0.98
123 4 0.02
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (123 bp):
ATAATTTGGTGTTGAAGACGACACTGCTTATCCATGTTGAAGAGATATGGCCAGCTTTCAGATAA
ATTGTTTGTTGAAGATGACGTTGTTCCTTCTCGTTGAGGAAATCGGGTTAATCAGGAA
Found at i:686619 original size:244 final size:244
Alignment explanation
Indices: 686179--686619 Score: 571
Period size: 244 Copynumber: 1.8 Consensus size: 244
686169 GTTGACGACT
* * *
686179 TCGAGTCAATTTGGATATAATCTGGTGTTGAAGACGACACTGCTCATCCATGTTGAAGATATATG
1 TCGAGTCAATCTGGAAATAATCTGGTGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATATG
* * * * * * * * * *
686244 GTCGCTTTCATATAAATTGTTTGTTGAAGATGACGTTATTTCTTCTTGTTGAGGAAATCGGGTTA
66 GCCACTTTCAGATAAATTGTTTATTGAAGATGACATTATTCCTTCTCGTTGAGAAAATCAGGTCA
* * * * * *
686309 ATCAGGAAATAATTTGGGGTTGAAGATGACATTGTTCATCCATGTTGAGGAGATCTGGCAGCTTT
131 ATCAAGAAATAATTTGGGGTTAAAGACGACACTGTTCATCCATGTTGAAGAGATATGGCAGCTTT
686374 CAGATAAATTATTTGTTGAAGATGATGTTGTTCCTTCTCGTTGAGGAAA
196 CAGATAAATTATTTGTTGAAGATGATGTTGTTCCTTCTCGTTGAGGAAA
* * * * *
686423 TCGAGTTAATCTGGAAATAATTTGGTGTTGAAGATGACACTGCTTATCCATGTTGAAGAGATCTG
1 TCGAGTCAATCTGGAAATAATCTGGTGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATATG
* * *
686488 GCCACTTTTAGATAAATTGTTTATTGAAGATGACATTGTTCCTTCTCGTTGAGAAAATTAGGTCA
66 GCCACTTTCAGATAAATTGTTTATTGAAGATGACATTATTCCTTCTCGTTGAGAAAATCAGGTCA
* * * *
686553 ATCAAGAGATAATTTGGTGTTAAAGACGACACTGCTT-ATCTATGTTGAAGAGTTATGG-ATGCT
131 ATCAAGAAATAATTTGGGGTTAAAGACGACACTG-TTCATCCATGTTGAAGAGATATGGCA-GCT
686616 TTCA
194 TTCA
686620 TATGACGTTG
Statistics
Matches: 164, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
243 1 0.01
244 161 0.98
245 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (244 bp):
TCGAGTCAATCTGGAAATAATCTGGTGTTGAAGACGACACTGCTCATCCATGTTGAAGAGATATG
GCCACTTTCAGATAAATTGTTTATTGAAGATGACATTATTCCTTCTCGTTGAGAAAATCAGGTCA
ATCAAGAAATAATTTGGGGTTAAAGACGACACTGTTCATCCATGTTGAAGAGATATGGCAGCTTT
CAGATAAATTATTTGTTGAAGATGATGTTGTTCCTTCTCGTTGAGGAAA
Found at i:686944 original size:139 final size:138
Alignment explanation
Indices: 686661--687599 Score: 838
Period size: 139 Copynumber: 6.8 Consensus size: 138
686651 TAGTCATTTT
* * * * *
686661 GGATAATTTGGAGACAATACGATTCCTTCGCGT-TGAGGAAGTCTGATTGTCTGAGGATGACACT
1 GGATAATTTGGAGACAACACGGTTCC-T-ACGTATGAGGAAGTCTGATTGCCTGAGGATGACATT
* * * ** * ** * *
686725 GCTCCTTCACTTTGAGGAGATCTGGTTAGTGGATGACATTGTTCCTTTGTGTTGAGGA-AGTTTA
64 ACTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACA-TCTA
**
686789 GCCAT-TTTAG
128 GCTGTCTTTAG
* * * * ** *
686799 AAGATAATTTGGAGAAAAAATGGTTCCTTCACGT-TGAGGAAGTCTGATTTTCTGAGGATGATAT
1 -GGATAATTTGGAGACAACACGGTTCC-T-ACGTATGAGGAAGTCTGATTGCCTGAGGATGACAT
** * * * *
686863 TGTTCCTTCGCGTTGAGGAAATCTGGTCGGTGGACGACATTATTCCTACATGATAAGGACATCTA
63 TACTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACATCTA
686928 GCTGTCTTTAG
128 GCTGTCTTTAG
* * *
686939 GGATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTGCCTTAGGATAACGTTA
1 GGATAATTTGGAGACAACACGGTTCCTACGT-ATGAGGAAGTCTGATTGCCTGAGGATGACATTA
* * * * *
687004 CTCCTACGCGTTAAGGAGATATGG-CTGGTGGAC-A-ATATGTTCCTACGTGACGAGGACGTCTA
65 CTCCTTCGCGTTGAGGAGATCTGGTC-GGTGGACGACAT-TGTTCCTACGTGATGAGGACATCTA
*
687066 GCCT-TCTTTAA
128 G-CTGTCTTTAG
* * * *
687077 GGATAATTTGGAGACAACACGATTCCTACGTGATAAGGAAGTCTGATTGCCTGAGAATGGCATTA
1 GGATAATTTGGAGACAACACGGTTCCTACGT-ATGAGGAAGTCTGATTGCCTGAGGATGACATTA
* * * *
687142 CTCCTACACGTTGAGGAGATCTGGTCGGTTGACGACATTGTTCCTACGTGATGAGGACGTCTAGC
65 CTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACATCTAGC
687207 TGTCTTTAG
130 TGTCTTTAG
* * ** * * ** * ** *
687216 GGATAATTTGGAAATAACACAATTCCTACGTGATGAGGAACTCTGGTTATCTAAGGATGACGCTG
1 GGATAATTTGGAGACAACACGGTTCCTACGT-ATGAGGAAGTCTGATTGCCTGAGGATGACATTA
* ** **
687281 CTCCTTCGCGTTGAGGAGATCTGGTCGATGGAAAACATTGTTCCTACGTGATGAGGATGTCTAGC
65 CTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACATCTAGC
*
687346 GGTCTTTAG
130 TGTCTTTAG
* * * * * * *
687355 GGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGGTTGACTAAGGATGGCGTTT
1 GGATAATTTGGAGACAACACGGTTCCTACGT-ATGAGGAAGTCTGATTGCCTGAGGATGACATTA
* * * * **
687420 CTCCTTCGCATTGAGGAAATCTGGTCGGTGGACGACATTGTTCCTTCATTTTGAGGA-ATTCTAG
65 CTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACA-TCTAG
*
687484 CCGT-TTTAAG
129 CTGTCTTT-AG
** * ** * * * * *
687494 AAATAAATTGGAGACAACATAGTTCCTACATGATAAGGAAATCTGATT-CCTTAGGATGACAATA
1 GGATAATTTGGAGACAACACGGTTCCTACGT-ATGAGGAAGTCTGATTGCCTGAGGATGACATTA
* *
687558 CTCCTTCGCGTTGAGAAGATCTGGTCGGTGGACAACATTGTT
65 CTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTT
687600 TCTTCATGTT
Statistics
Matches: 667, Mismatches: 120, Indels: 27
0.82 0.15 0.03
Matches are distributed among these distances:
137 6 0.01
138 168 0.25
139 485 0.73
140 8 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (138 bp):
GGATAATTTGGAGACAACACGGTTCCTACGTATGAGGAAGTCTGATTGCCTGAGGATGACATTAC
TCCTTCGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACATCTAGCT
GTCTTTAG
Found at i:687166 original size:277 final size:277
Alignment explanation
Indices: 686661--687599 Score: 899
Period size: 277 Copynumber: 3.4 Consensus size: 277
686651 TAGTCATTTT
* * * * * * *
686661 GGATAATTTGGAGACAATAC-GATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGAC-AC
1 GGATAATTTGGAGACAACACAG-TTCCTACGTGATGAGGAAATCTGATT-CCTTAGGATGACGA-
* * * ** ** ** ** * *
686724 TGCTCCTTCACTTTGAGGAGATCTGGTTAGTGGATGACATTGTTCCTTTGTGTTGAGGAAGTTTA
63 TACTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGACGAGGACGTCTA
* * * * ** * **
686789 GCCAT-TTTAGAAGATAATTTGGAGAAAAAATGGTTCCTTCACGT--TGAGGAAGTCTGATTTTC
128 GCCGTCTTTA-AGGATAATTTGGAGACAACACAGTTCC-T-ACGTGATAAGGAAGTCTGATTGAC
* * ** ** * * *
686851 TGAGGATGATATTGTTCCTTCGCGTTGAGGAAATCTGGTCGGTGGACGACATTATTCCTACATGA
190 TAAGAATGGCATTACTCCTACACGTTGAGGAAATCTGGTCGGTGGACGACATTGTTCCTACATGA
*
686916 TAAGGACATCTAGCTGTCTTTAG
255 TGAGGACATCTAGCTGTCTTTAG
* * * *
686939 GGATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTGCCTTAGGATAACGTTA
1 GGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAATCTGATT-CCTTAGGATGACGATA
* * * *
687004 CTCCTACGCGTTAAGGAGATATGG-CTGGTGGACAATA-TGTTCCTACGTGACGAGGACGTCTAG
65 CTCCTTCGCGTTGAGGAGATCTGGTC-GGTGGACAACATTGTTCCTACGTGACGAGGACGTCTAG
* * *
687067 CCTTCTTTAAGGATAATTTGGAGACAACAC-GATTCCTACGTGATAAGGAAGTCTGATTGCCTGA
129 CCGTCTTTAAGGATAATTTGGAGACAACACAG-TTCCTACGTGATAAGGAAGTCTGATTGACTAA
* * *
687131 GAATGGCATTACTCCTACACGTTGAGGAGATCTGGTCGGTTGACGACATTGTTCCTACGTGATGA
193 GAATGGCATTACTCCTACACGTTGAGGAAATCTGGTCGGTGGACGACATTGTTCCTACATGATGA
*
687196 GGACGTCTAGCTGTCTTTAG
258 GGACATCTAGCTGTCTTTAG
* * * * * * * * *
687216 GGATAATTTGGAAATAACACAATTCCTACGTGATGAGGAACTCTGGTTATCTAAGGATGACGCTG
1 GGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAATCTGATT-CCTTAGGATGACGATA
* * * *
687281 CTCCTTCGCGTTGAGGAGATCTGGTCGATGGAAAACATTGTTCCTACGTGATGAGGATGTCTAGC
65 CTCCTTCGCGTTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGACGAGGACGTCTAGC
* * * * *
687346 GGTCTTTAGGGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGGTTGACTAAGG
130 CGTCTTTAAGGATAATTTGGAGACAACACAGTTCCTACGTGATAAGGAAGTCTGATTGACTAAGA
* * * * * * **
687411 ATGGCGTTTCTCCTTCGCATTGAGGAAATCTGGTCGGTGGACGACATTGTTCCTTCATTTTGAGG
195 ATGGCATTACTCCTACACGTTGAGGAAATCTGGTCGGTGGACGACATTGTTCCTACATGATGAGG
*
687476 A-ATTCTAGCCGT-TTTAAG
260 ACA-TCTAGCTGTCTTT-AG
** * * * * *
687494 AAATAAATTGGAGACAACATAGTTCCTACATGATAAGGAAATCTGATTCCTTAGGATGACAATAC
1 GGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAATCTGATTCCTTAGGATGACGATAC
*
687559 TCCTTCGCGTTGAGAAGATCTGGTCGGTGGACAACATTGTT
66 TCCTTCGCGTTGAGGAGATCTGGTCGGTGGACAACATTGTT
687600 TCTTCATGTT
Statistics
Matches: 543, Mismatches: 106, Indels: 25
0.81 0.16 0.04
Matches are distributed among these distances:
275 4 0.01
276 2 0.00
277 269 0.50
278 266 0.49
279 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (277 bp):
GGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAATCTGATTCCTTAGGATGACGATAC
TCCTTCGCGTTGAGGAGATCTGGTCGGTGGACAACATTGTTCCTACGTGACGAGGACGTCTAGCC
GTCTTTAAGGATAATTTGGAGACAACACAGTTCCTACGTGATAAGGAAGTCTGATTGACTAAGAA
TGGCATTACTCCTACACGTTGAGGAAATCTGGTCGGTGGACGACATTGTTCCTACATGATGAGGA
CATCTAGCTGTCTTTAG
Found at i:687452 original size:416 final size:416
Alignment explanation
Indices: 686661--687630 Score: 1058
Period size: 416 Copynumber: 2.3 Consensus size: 416
686651 TAGTCATTTT
* * * * * * * *
686661 GGATAATTTGGAGACAATACGATTCCTTCGCGTTGAGGAAGTCTGATTGTCTGAGGATGACACTG
1 GGATAATTTGGAGACAACACGATTCCTACGTGATAAGGAAGTCTGATTGCCTGAGGATGACAATA
* ** * ** * *
686726 CTCCTTCACTTTGAGGAGATCTGGTTAGTGGATGACATTGTTCCTTTGTGTTGAGGAAGTTTAGC
66 CTCCTTCACGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGAAGTCTAGC
*** * * *
686791 CATTTTAGAAGATAATTTGGAGAAAAAATGGTTCCTTCACGTTGAGGAAGTCTGATTTTCTGAGG
131 CATTTTAGAAGATAATTTGGAGAAAAAACAATTCCTTCACGTTGAGGAACTCTGATTATCTAAGG
* * * * **
686856 ATGATATTGTTCCTTCGCGTTGAGGAAATCTGGTCGGTGGACGACATTATTCCTACATGATAAGG
196 ATGACACTGCTCCTTCGCGTTGAGGAAATCTGGTCGATGGAAAACATTATTCCTACATGATAAGG
* *
686921 ACATCTAGCTGTCTTTAGGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGAT
261 ACATCTAGCGGTCTTTAGGGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGAT
* * * *
686986 TGCCTTAGGATAACGTTACTCCTACGCGTTAAGGAGATATGGCTGGTGGAC-A-ATATGTTCCTA
326 TGACTAAGGATAACGTTACTCCTACGCATTAAGGAAATATGGCTGGTGGACGACAT-TGTTCCTA
* * *
687049 CGTGACGAGGACGTCTAGCCTTCTTTAA
390 CATGACGAGGAAGTCTAGCCGT-TTTAA
* * *
687077 GGATAATTTGGAGACAACACGATTCCTACGTGATAAGGAAGTCTGATTGCCTGAGAATGGCATTA
1 GGATAATTTGGAGACAACACGATTCCTACGTGATAAGGAAGTCTGATTGCCTGAGGATGACAATA
* * *
687142 CTCCTACACGTTGAGGAGATCTGGTCGGTTGACGACATTGTTCCTACGTGATGAGGACGTCTAGC
66 CTCCTTCACGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGAAGTCTAGC
** * * *
687207 TGTCTTTAG-GGATAATTTGGA-AATAACACAATTCC-T-ACGTGATGAGGAACTCTGGTTATCT
131 CAT-TTTAGAAGATAATTTGGAGAA-AAAACAATTCCTTCACGT--TGAGGAACTCTGATTATCT
* * * *
687268 AAGGATGACGCTGCTCCTTCGCGTTGAGGAGATCTGGTCGATGGAAAACATTGTTCCTACGTGAT
192 AAGGATGACACTGCTCCTTCGCGTTGAGGAAATCTGGTCGATGGAAAACATTATTCCTACATGAT
* **
687333 GAGGATGTCTAGCGGTCTTTAGGGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTC
257 AAGGACATCTAGCGGTCTTTAGGGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTC
* ** * * * *
687398 TGGTTGACTAAGGATGGCGTTTCTCCTTCGCATTGAGGAAATCTGG-TCGGTGGACGACATTGTT
322 TGATTGACTAAGGATAACGTTACTCCTACGCATTAAGGAAATATGGCT-GGTGGACGACATTGTT
* *** *
687462 CCTTCATTTTGAGGAATTCTAGCCGTTTTAA
386 CCTACATGACGAGGAAGTCTAGCCGTTTTAA
* * * * * *
687493 GAAATAAATTGGAGACAACA-TAGTTCCTACATGATAAGGAAATCTGATT-CCTTAGGATGACAA
1 G-GATAATTTGGAGACAACACGA-TTCCTACGTGATAAGGAAGTCTGATTGCCTGAGGATGACAA
* * * * * * *
687556 TACTCCTTCGCGTTGAGAAGATCTGGTCGGTGGACAACATTGTTTCTTCATGTTGAGGAAGTCTA
64 TACTCCTTCACGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGAAGTCTA
* *
687621 GTCGTTTTAG
129 GCCATTTTAG
687631 GAGACAAATT
Statistics
Matches: 458, Mismatches: 87, Indels: 19
0.81 0.15 0.03
Matches are distributed among these distances:
414 4 0.01
415 9 0.02
416 375 0.82
417 68 0.15
418 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (416 bp):
GGATAATTTGGAGACAACACGATTCCTACGTGATAAGGAAGTCTGATTGCCTGAGGATGACAATA
CTCCTTCACGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGAAGTCTAGC
CATTTTAGAAGATAATTTGGAGAAAAAACAATTCCTTCACGTTGAGGAACTCTGATTATCTAAGG
ATGACACTGCTCCTTCGCGTTGAGGAAATCTGGTCGATGGAAAACATTATTCCTACATGATAAGG
ACATCTAGCGGTCTTTAGGGATAATTTGGAGACAACACAGTTCCTACGTGATGAGGAAGTCTGAT
TGACTAAGGATAACGTTACTCCTACGCATTAAGGAAATATGGCTGGTGGACGACATTGTTCCTAC
ATGACGAGGAAGTCTAGCCGTTTTAA
Found at i:687822 original size:15 final size:15
Alignment explanation
Indices: 687802--687832 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
687792 GAGGGAAAGG
687802 AAATATTTGAGTGAA
1 AAATATTTGAGTGAA
687817 AAATATTTGAGTGAA
1 AAATATTTGAGTGAA
687832 A
1 A
687833 CATTTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (15 bp):
AAATATTTGAGTGAA
Found at i:688040 original size:95 final size:96
Alignment explanation
Indices: 687855--688040 Score: 207
Period size: 95 Copynumber: 1.9 Consensus size: 96
687845 TGCATTTCAA
* * * * * **
687855 GGGAAATCTATCTCAAGCGATATGAAATTTGTTTTTTAAGAAAAACAATCTCAAATGTTATCAAT
1 GGGAAAACTATCTCAAGCGAGACGAAATTTGATTTTCAAGAAAAACAATCTCAAATGAGATCAAT
*** *
687920 TTTGTTTCAAGTGCAACAATTTCAAAATTTG
66 TTTGTTTCAAGAAAAACAATGTCAAAATTTG
* * *
687951 GGGAAAACTTTCTCAAGCGAGACGAAATTT-ATTTTC-AGAGAAAACAATCTCAAGTGAGATCAT
1 GGGAAAACTATCTCAAGCGAGACGAAATTTGATTTTCAAGA-AAAACAATCTCAAATGAGATCAA
688014 TTTTGTTTCAAGAAAAATC-ATGTCAAA
65 TTTTGTTTCAAGAAAAA-CAATGTCAAA
688041 CGAAGCTTTG
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
94 3 0.04
95 44 0.59
96 27 0.36
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (96 bp):
GGGAAAACTATCTCAAGCGAGACGAAATTTGATTTTCAAGAAAAACAATCTCAAATGAGATCAAT
TTTGTTTCAAGAAAAACAATGTCAAAATTTG
Found at i:691077 original size:20 final size:18
Alignment explanation
Indices: 691025--691086 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 18
691015 TCTCTCTTTC
*
691025 TTCTTTTTTTTTCTTTATT
1 TTCTTTTTTTTGCTTT-TT
691044 TTCTTTTCTCTTTGCTTTTT
1 TTCTTTT-T-TTTGCTTTTT
691064 TTCTTTGTTGTTTGCTATTTT
1 TTCTTT-TT-TTTGCT-TTTT
691085 TT
1 TT
691087 TCATTTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 7 0.19
20 16 0.43
21 14 0.38
ACGTcount: A:0.03, C:0.13, G:0.06, T:0.77
Consensus pattern (18 bp):
TTCTTTTTTTTGCTTTTT
Found at i:692019 original size:19 final size:21
Alignment explanation
Indices: 691974--692019 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 21
691964 AGATTTAAAA
691974 ATATTAAAGACAAAAAAAATG
1 ATATTAAAGACAAAAAAAATG
* *
691995 A-GTTAAA-AC-AAAACAATG
1 ATATTAAAGACAAAAAAAATG
692013 ATATTAA
1 ATATTAA
692020 TGCAACTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 5 0.24
21 1 0.05
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.22
Consensus pattern (21 bp):
ATATTAAAGACAAAAAAAATG
Found at i:696042 original size:2 final size:2
Alignment explanation
Indices: 696035--696073 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
696025 ATAAATGATT
696035 TA TA 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 TA TA T
696074 CGCACTTGCA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:698621 original size:130 final size:130
Alignment explanation
Indices: 698479--698724 Score: 343
Period size: 130 Copynumber: 1.9 Consensus size: 130
698469 AAGCATATTC
* * *
698479 CTTTTTTCAGATTTGATCTTCTC-TGAGGACCAGTGAAGCAAATCAACCAT-GATTCAATTTTCC
1 CTTTTTTCAGATTTGATCTTC-CATAAAGACCAGTGAAGCAAATCAACC-TCGATTCAATCTTCC
* * * *
698542 CTGAAGAGAAATGAAGTGAATCAAAGTTTCTAGATATGATCTACCTTGGAACGCAGCAAAGTAGA
64 CTGAAGAGAAATGAAGTAAATCAAAGTTTCCAGATATAATCTACCCTGGAACGCAGCAAAGTAGA
698607 TT
129 TT
* * *
698609 CTTTTTTCAGATTTGATCTTCCATAAAGAGCAGTGAAGTAAATCAACCTCGATTCAATCTTCTCT
1 CTTTTTTCAGATTTGATCTTCCATAAAGACCAGTGAAGCAAATCAACCTCGATTCAATCTTCCCT
* * *
698674 GAAGAGCAGTGAAGTAAATCAAAGTTTCCAGATCTAATCTACCCTGGAACG
66 GAAGAGAAATGAAGTAAATCAAAGTTTCCAGATATAATCTACCCTGGAACG
698725 TAATGGAGCA
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
129 2 0.02
130 99 0.98
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (130 bp):
CTTTTTTCAGATTTGATCTTCCATAAAGACCAGTGAAGCAAATCAACCTCGATTCAATCTTCCCT
GAAGAGAAATGAAGTAAATCAAAGTTTCCAGATATAATCTACCCTGGAACGCAGCAAAGTAGATT
Found at i:698980 original size:131 final size:131
Alignment explanation
Indices: 698529--699240 Score: 505
Period size: 131 Copynumber: 5.5 Consensus size: 131
698519 AATCAACCAT
* * * * * * *
698529 GATTCAATTTTCCCTGAAGAGAAATGAAGTGAATCAAAG-TTTCTAGATATGATCTACCTTGGAA
1 GATTCAATCTTCTCTGAAGAGCAGTGAAGTGAATCAAAGTTTTC-AGATCTAATCTACCCT-GAA
* * *** * * * * * *
698593 -CGCAGCAAAGTAGATTCTTTTT-TCAGATTTGATCTTCCAT-AAAGAGCAGT-GAAGTAAATCA
64 GAGTAGTGGAGCAGATTCTTTTTATCATATTTGATCTTCCCTGAAA-AGCAATAGAA-CAAATCT
698654 ACCTC
127 ACCTC
* *
698659 GATTCAATCTTCTCTGAAGAGCAGTGAAGTAAATCAAAGTTTCCAGATCTAATCTACCCTGGAA-
1 GATTCAATCTTCTCTGAAGAGCAGTGAAGTGAATCAAAGTTTTCAGATCTAATCTACCCT-GAAG
* * * * * * * *
698723 CGTAATGGAGCAAATCCTCCTTTTTAT-ATATTTGATCTTCCTTGAAGAGTAGTGGAACAAATCT
65 AGTAGTGGAGCAGAT--T-CTTTTTATCATATTTGATCTTCCCTGAAAAGCAATAGAACAAATCT
*
698787 ACCTG
127 ACCTC
* * * * * * *
698792 GATTCAATC-TCTCAGAAGAGAAGTGAAGTGGATCAAAATTTTCAGATCTAATATACCCTAAAGT
1 GATTCAATCTTCTCTGAAGAGCAGTGAAGTGAATCAAAGTTTTCAGATCTAATCTACCCTGAAGA
* * * * * * * *
698856 GTAGTAGAGTAGATTATTTTTTTCATATTTGATCATCCCTGAATAGCAATAGAACAAATCCACAT
66 GTAGTGGAGCAGATTCTTTTTATCATATTTGATCTTCCCTGAAAAGCAATAGAACAAATCTACCT
698921 C
131 C
* * *
698922 GATTCAATCTTCTCTGAAGAGCTGTGAAGTGAATCAAAGTTTTCAAATCTGATCTACCCTGAAGA
1 GATTCAATCTTCTCTGAAGAGCAGTGAAGTGAATCAAAGTTTTCAGATCTAATCTACCCTGAAGA
* * * * * * *
698987 GCAGCGGAGCAGATCCCTTTTAGCATATTTGATCTTCCCTGAAAAGCAACAGAACAAATATACCT
66 GTAGTGGAGCAGATTCTTTTTATCATATTTGATCTTCCCTGAAAAGCAATAGAACAAATCTACCT
699052 C
131 C
* * * * * * * *
699053 AATTAAATCTTCTCTGAAGAGTATTGAAGTGAATCAAAGTTTGCATATATGATCTACCCTGAAGA
1 GATTCAATCTTCTCTGAAGAGCAGTGAAGTGAATCAAAGTTTTCAGATCTAATCTACCCTGAAGA
* * * * *
699118 --A---AAGCGGA-GC-----A-CATATTTGATCTTCCCTGAAGAGC-ATTGAAGCAAATCTACC
66 GTAGTGGAGCAGATTCTTTTTATCATATTTGATCTTCCCTGAAAAGCAATAGAA-CAAATCTACC
699170 TC
130 TC
* * * * * * * * *
699172 GATTCAATCTTCCCTGAAGGGCAGTAAAGTGAATCAATGTTTCCATATCCAATCCA-CCTTAAGA
1 GATTCAATCTTCTCTGAAGAGCAGTGAAGTGAATCAAAGTTTTCAGATCTAATCTACCCTGAAGA
699236 GTAGT
66 GTAGT
699241 AGAACATATC
Statistics
Matches: 466, Mismatches: 101, Indels: 38
0.77 0.17 0.06
Matches are distributed among these distances:
118 11 0.02
119 77 0.17
120 2 0.00
125 1 0.00
126 5 0.01
129 7 0.02
130 102 0.22
131 158 0.34
132 54 0.12
133 43 0.09
134 6 0.01
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (131 bp):
GATTCAATCTTCTCTGAAGAGCAGTGAAGTGAATCAAAGTTTTCAGATCTAATCTACCCTGAAGA
GTAGTGGAGCAGATTCTTTTTATCATATTTGATCTTCCCTGAAAAGCAATAGAACAAATCTACCT
C
Found at i:699448 original size:3 final size:3
Alignment explanation
Indices: 699440--699492 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
699430 ATTTATTTAT
699440 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
699488 TTA TT
1 TTA TT
699493 TTACAGATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:700598 original size:2 final size:2
Alignment explanation
Indices: 700593--700632 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
700583 ACTATGAATT
700593 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
700633 GTAAGTATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:706384 original size:29 final size:28
Alignment explanation
Indices: 706351--706436 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 28
706341 TTAAAAGTAT
706351 GCCCTAATAACATATATTGAAAAAATTG-
1 GCCCTAATAACA-ATATTGAAAAAATTGA
* *
706379 GACCCTTGATAATAAGTATTGAAAAAATTGA
1 G-CCC-TAATAACAA-TATTGAAAAAATTGA
*
706410 GCCTTTAATAACAAATATTAGAAAAAA
1 GCC-CTAATAAC-AATATT-GAAAAAA
706437 AATATTGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
28 1 0.02
29 4 0.09
30 31 0.67
31 10 0.22
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.28
Consensus pattern (28 bp):
GCCCTAATAACAATATTGAAAAAATTGA
Found at i:706506 original size:28 final size:29
Alignment explanation
Indices: 706466--706530 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
706456 ACATTTATAC
* *
706466 AAATATTAGAAAAATAGGCTTC-TAATAAT
1 AAATATTAGAAAAATAAGC-CCATAATAAT
706495 AAATATTA-AAAAATAAGCCCATAATAAT
1 AAATATTAGAAAAATAAGCCCATAATAAT
706523 AAATATTA
1 AAATATTA
706531 TGGAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.73
29 8 0.24
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (29 bp):
AAATATTAGAAAAATAAGCCCATAATAAT
Found at i:707069 original size:2 final size:2
Alignment explanation
Indices: 707062--707098 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
707052 CAAATCCAAC
707062 TA 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 TA T
707099 TTGGAAGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:707264 original size:2 final size:2
Alignment explanation
Indices: 707257--707307 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
707247 ACTCCATCTA
707257 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
707299 AT AT AT AT A
1 AT AT AT AT A
707308 ATCTTATCAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:712261 original size:2 final size:2
Alignment explanation
Indices: 712256--712282 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
712246 GGCCAAAAAA
712256 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
712283 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:712287 original size:2 final size:2
Alignment explanation
Indices: 712282--712310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
712272 ACACACACAC
712282 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 A
712311 GCATTTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:714595 original size:3 final size:3
Alignment explanation
Indices: 714587--714651 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
714577 ATGTTATTTA
* * * * *
714587 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT AAT AAT AAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
714635 TAT TAT TAT ATAT TAT T
1 TAT TAT TAT -TAT TAT T
714652 TAATATTACA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:715154 original size:15 final size:15
Alignment explanation
Indices: 715117--715165 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
715107 ACAACGCAGC
*
715117 AAAGAAACAGAAA-A
1 AAAGAAAAAGAAAGA
*
715131 GAA-AAAAAGAAAGA
1 AAAGAAAAAGAAAGA
715145 AAAGAAAAAGAAAGA
1 AAAGAAAAAGAAAGA
*
715160 AGAGAA
1 AAAGAA
715166 GCTTACCGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 8 0.28
14 5 0.17
15 16 0.55
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAAGA
Found at i:717311 original size:9 final size:9
Alignment explanation
Indices: 717297--717321 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
717287 TTACATGTAA
717297 ATTTAAATT
1 ATTTAAATT
717306 ATTTAAATT
1 ATTTAAATT
717315 ATTTAAA
1 ATTTAAA
717322 AGCATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTTAAATT
Found at i:727458 original size:13 final size:12
Alignment explanation
Indices: 727440--727481 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
727430 AATAATAATA
727440 AAAAAAGAGAAAG
1 AAAAAA-AGAAAG
727453 AAAAAAAGAAAAG
1 AAAAAAAG-AAAG
*
727466 AAAGAAA-AAAG
1 AAAAAAAGAAAG
727477 AAAAA
1 AAAAA
727482 GAGGGGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 8 0.31
12 2 0.08
13 16 0.62
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Done.