Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008439.1 Hibiscus syriacus cultivar Beakdansim tig00111238_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: 2703160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:321851 original size:155 final size:156
Alignment explanation
Indices: 321550--321863 Score: 612
Period size: 155 Copynumber: 2.0 Consensus size: 156
321540 TTTTTCGATC
321550 AAAGTATTTGAGAGCAGCACAAGAGCTTCTCGATGAAGTTGTTAACGTTGGGCATGGGTCAAAAA
1 AAAGTATTTGAGAGCAG-ACAAGAGCTTCTCGATGAAGTTGTTAACGTTGGGCATGGGTCAAAAA
321615 CTGGCCCTTCTGAGGGGACCAAAGAGAAGATAAAGGTGAACAAAGAATCAAAGGATGATGTGACC
65 CTGGCCCTTCTGAGGGGACCAAAGAGAAGATAAAGGTGAACAAAGAATCAAAGGATGATGTGACC
321680 GGAGGAGAGGGGTCAAGTGCCTGTAAA
130 GGAGGAGAGGGGTCAAGTGCCTGTAAA
321707 AAAGTATTTGAGAGCAG-CAAGAGCTTCTCGATGAAGTTGTTAACGTTGGGCATGGGTCAAAAAC
1 AAAGTATTTGAGAGCAGACAAGAGCTTCTCGATGAAGTTGTTAACGTTGGGCATGGGTCAAAAAC
321771 TGGCCCTTCTGAGGGGACCAAAGAGAAGATAAAGGTGAACAAAGAATCAAAGGATGATGTGACCG
66 TGGCCCTTCTGAGGGGACCAAAGAGAAGATAAAGGTGAACAAAGAATCAAAGGATGATGTGACCG
321836 GAGGAGAGGGGTCAAGTGCCTGTAAA
131 GAGGAGAGGGGTCAAGTGCCTGTAAA
321862 AA
1 AA
321864 CGGGGATAAA
Statistics
Matches: 157, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
155 140 0.89
157 17 0.11
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.19
Consensus pattern (156 bp):
AAAGTATTTGAGAGCAGACAAGAGCTTCTCGATGAAGTTGTTAACGTTGGGCATGGGTCAAAAAC
TGGCCCTTCTGAGGGGACCAAAGAGAAGATAAAGGTGAACAAAGAATCAAAGGATGATGTGACCG
GAGGAGAGGGGTCAAGTGCCTGTAAA
Found at i:323625 original size:13 final size:13
Alignment explanation
Indices: 323607--323631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
323597 CGCGGCGCCA
323607 TTGTTGCCTGATT
1 TTGTTGCCTGATT
323620 TTGTTGCCTGAT
1 TTGTTGCCTGAT
323632 CCAAGTCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.24, T:0.52
Consensus pattern (13 bp):
TTGTTGCCTGATT
Found at i:323827 original size:21 final size:21
Alignment explanation
Indices: 323763--323828 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
323753 TTCAAGGATA
* * *
323763 TATATATTTATATAGCTGGTT
1 TATATATATATATAGGTAGTT
* *
323784 TATATATATACT-T--GCAGTA
1 TATATATATA-TATAGGTAGTT
323803 TATATATATATATAGGTAGTT
1 TATATATATATATAGGTAGTT
323824 TATAT
1 TATAT
323829 GTTCTTACAT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
18 1 0.03
19 13 0.38
21 19 0.56
22 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.48
Consensus pattern (21 bp):
TATATATATATATAGGTAGTT
Found at i:331488 original size:75 final size:75
Alignment explanation
Indices: 331365--331512 Score: 253
Period size: 75 Copynumber: 2.0 Consensus size: 75
331355 AGCTACTGTC
*
331365 TTCTATCATCCTTTGATCAACTTCTGGCACATTTAAATTATTTCTGGAAATCGTAGGATCCTTTC
1 TTCTATCATCCTTTGATCAACTTCTGGAACATTTAAATTATTTCTGGAAATCGTAGGATCCTTTC
331430 ATGCTTCATG
66 ATGCTTCATG
* *
331440 TTCTATCATCCTTTGATTAACTTTTGGAAC-TTCTAAATTATTTCTGGAAATCGTAGGATCCTTT
1 TTCTATCATCCTTTGATCAACTTCTGGAACATT-TAAATTATTTCTGGAAATCGTAGGATCCTTT
331504 CATGCTTCA
65 CATGCTTCA
331513 AGTTGAATCC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 2 0.03
75 67 0.97
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (75 bp):
TTCTATCATCCTTTGATCAACTTCTGGAACATTTAAATTATTTCTGGAAATCGTAGGATCCTTTC
ATGCTTCATG
Found at i:344179 original size:15 final size:15
Alignment explanation
Indices: 344159--344190 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
344149 TGAATCTCTA
344159 GTTGATGATTTTGTT
1 GTTGATGATTTTGTT
*
344174 GTTGATGGTTTTGTT
1 GTTGATGATTTTGTT
344189 GT
1 GT
344191 AGCGGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.00, G:0.31, T:0.59
Consensus pattern (15 bp):
GTTGATGATTTTGTT
Found at i:355087 original size:138 final size:138
Alignment explanation
Indices: 354839--355092 Score: 384
Period size: 138 Copynumber: 1.8 Consensus size: 138
354829 GTGCAGCTTA
* * * *
354839 AGCAGGATGCAAGAGAGAGTCAAAAGTTGCCGGAAGTGATTCCAAAGGTCGAAGACACACATTTA
1 AGCAGGATACAAGAGAAAGTCAAAAGTTACCGGAAGTGATTCCAAAGGTCGAAGAAACACATTTA
*
354904 GATCGTCAATCAGAAGCAGGGAATCACATAGCAATAGACCAACTAGATACCACAGCTTCCATTTG
66 GATCATCAATCAGAAGCAGGGAATCACATAGCAATAGACCAACTAGATACCACAGCTTCCATTTG
354969 TTCACATG
131 TTCACATG
* * * * *
354977 AGCAGGATACAGGAGAAAGTCTAAAGTTATCTGAAGTGATTCCAAATGTCGAAGAAACACATTCT
1 AGCAGGATACAAGAGAAAGTCAAAAGTTACCGGAAGTGATTCCAAAGGTCGAAGAAACACATT-T
* *
355042 -GATCATCAATCAGAAGCAGGGAATCACATGGCAATAGATCAACTAGATACC
65 AGATCATCAATCAGAAGCAGGGAATCACATAGCAATAGACCAACTAGATACC
355093 GCTGCTGAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
138 102 0.99
139 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (138 bp):
AGCAGGATACAAGAGAAAGTCAAAAGTTACCGGAAGTGATTCCAAAGGTCGAAGAAACACATTTA
GATCATCAATCAGAAGCAGGGAATCACATAGCAATAGACCAACTAGATACCACAGCTTCCATTTG
TTCACATG
Found at i:368955 original size:18 final size:17
Alignment explanation
Indices: 368923--368969 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
368913 TATTAATGGA
368923 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
368940 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
368958 G-AATAAAAATAA
1 GTAA-AAAAATAA
368970 TGTGTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:369079 original size:39 final size:39
Alignment explanation
Indices: 368996--369080 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
368986 AATATTTACT
* *
368996 AAAATAAATAAAATAATAAATATATAATACTAAGTAAAA
1 AAAATAAATAAAATAATAAATAAATAATACTAAGAAAAA
* * *
369035 CAAATAAA-AAAATAA-AGATATAAATGATATTAAGAAAAA
1 AAAATAAATAAAATAATA-A-ATAAATAATACTAAGAAAAA
369074 AAAATAA
1 AAAATAA
369081 TAGGAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
37 1 0.03
38 8 0.21
39 29 0.76
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (39 bp):
AAAATAAATAAAATAATAAATAAATAATACTAAGAAAAA
Found at i:369130 original size:51 final size:51
Alignment explanation
Indices: 369075--369175 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
369065 TAAGAAAAAA
* *
369075 AAATAATAGGAAAAATAAAATAAAGTAA-AAATATA-ATATATATATATAAAT
1 AAATAAAAAGAAAAATAAAAT--AGTAAGAAATATATATATATATATATAAAT
* * *
369126 AAATAAAAATAAAAATAGAATATTAAGAAATATATATATATATATATAAA
1 AAATAAAAAGAAAAATAAAATAGTAAGAAATATATATATATATATATAAA
369176 GACGTATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
49 4 0.09
50 7 0.16
51 32 0.74
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (51 bp):
AAATAAAAAGAAAAATAAAATAGTAAGAAATATATATATATATATATAAAT
Found at i:369163 original size:47 final size:45
Alignment explanation
Indices: 369109--369212 Score: 136
Period size: 47 Copynumber: 2.3 Consensus size: 45
369099 GTAAAAATAT
*
369109 AATATATATATATAAATAAATAAAAATAAAAATAGAATATTAAGAA
1 AATATATATATATAAATAAAGAAAAAT-AAAATAGAATATTAAGAA
* *** *
369155 ATATATATATATATATATAAAGACGTATAAAATATAATATTAAGAA
1 A-ATATATATATATAAATAAAGAAAAATAAAATAGAATATTAAGAA
369201 AATATATATATA
1 AATATATATATA
369213 CATAGTAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 11 0.22
46 19 0.37
47 21 0.41
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.33
Consensus pattern (45 bp):
AATATATATATATAAATAAAGAAAAATAAAATAGAATATTAAGAA
Found at i:369175 original size:43 final size:46
Alignment explanation
Indices: 369112--369221 Score: 138
Period size: 46 Copynumber: 2.5 Consensus size: 46
369102 AAAATATAAT
* *
369112 ATATATATATAAATAAATAAA-A-ATA-AAAATAGAATATTAAGAA
1 ATATATATATATATATATAAAGACATATAAAATAGAATATTAAGAA
* *
369155 ATATATATATATATATATAAAGACGTATAAAATATAATATTAAGAA
1 ATATATATATATATATATAAAGACATATAAAATAGAATATTAAGAA
*
369201 A-ATATATATATACATAGTAAA
1 ATATATATATATATATA-TAAA
369222 TGGAGAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
43 19 0.33
44 1 0.02
45 16 0.28
46 22 0.38
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (46 bp):
ATATATATATATATATATAAAGACATATAAAATAGAATATTAAGAA
Found at i:369254 original size:2 final size:2
Alignment explanation
Indices: 369242--369310 Score: 79
Period size: 2 Copynumber: 35.0 Consensus size: 2
369232 TTAATACATT
* * *
369242 TA TA CA TA TA TA TA TA TA TG TA TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
369284 TA TA TA TA -A TGA TA TA -A GA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
369311 ATAAAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
1 2 0.04
2 53 0.93
3 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:369314 original size:14 final size:14
Alignment explanation
Indices: 369247--369333 Score: 70
Period size: 14 Copynumber: 6.1 Consensus size: 14
369237 ACATTTATAC
*
369247 ATATATATATATAT
1 ATATATATATAAAT
* * *
369261 GTATATGTATATAT
1 ATATATATATAAAT
*
369275 ATATATATATATAT
1 ATATATATATAAAT
369289 ATA-ATGATATAAGAT
1 ATATAT-ATATAA-AT
*
369304 ATATATA-ATAAAA
1 ATATATATATAAAT
369317 ATAATATAATATAAAT
1 AT-ATAT-ATATAAAT
369333 A
1 A
369334 AAAAAGGAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
13 5 0.08
14 40 0.67
15 7 0.12
16 8 0.13
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (14 bp):
ATATATATATAAAT
Found at i:369323 original size:25 final size:27
Alignment explanation
Indices: 369275--369325 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
369265 ATGTATATAT
* *
369275 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
369302 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATAAAATAATATAA
369326 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:369364 original size:20 final size:20
Alignment explanation
Indices: 369328--369366 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
369318 TAATATAATA
*
369328 TAAATAAAAAAGGAATATAG
1 TAAATAAAAAAGAAATATAG
369348 TAAATAAATAAA-AAATATA
1 TAAATAAA-AAAGAAATATA
369367 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (20 bp):
TAAATAAAAAAGAAATATAG
Found at i:370891 original size:110 final size:109
Alignment explanation
Indices: 370740--370941 Score: 332
Period size: 110 Copynumber: 1.8 Consensus size: 109
370730 GAAATTGGCT
*
370740 CTGAAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAG
1 CTGAAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAG
* *
370805 TTCAATATCCTTCGCTGTGAAGTTGAAGTTTACTCTGAATGAAA
66 TCCAATATCCCTCGCTGTGAAGTTGAAGTTTACTCTGAATGAAA
* * * *
370849 CTGAAAAGTTGTTTGTTGACAATCAGTCGCCCTTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGA
1 CTGAAAA-TTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGA
370914 GTCCAATATCCCTCGCTGTGAAGTTGAA
65 GTCCAATATCCCTCGCTGTGAAGTTGAA
370942 ATTGGCTCTG
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
109 7 0.08
110 78 0.92
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (109 bp):
CTGAAAATTGTTTGTTGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAG
TCCAATATCCCTCGCTGTGAAGTTGAAGTTTACTCTGAATGAAA
Found at i:375244 original size:23 final size:23
Alignment explanation
Indices: 375225--375308 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
375215 CTCGTATAAA
*
375225 TGCACCGAAGTGCCACGTATAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
375248 TACACCGAAGTTCCACATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
375271 TGCACCGAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
375294 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
375309 TATAATAATG
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:376319 original size:21 final size:21
Alignment explanation
Indices: 376287--376329 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
376277 TGTTTGTTTA
376287 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
376308 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
376329 A
1 A
376330 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:378980 original size:21 final size:21
Alignment explanation
Indices: 378948--378990 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
378938 TGTTTGTTTA
378948 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
378969 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
378990 A
1 A
378991 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:388074 original size:15 final size:13
Alignment explanation
Indices: 388046--388070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
388036 CATGATATTA
388046 AGAAAAAAATAAT
1 AGAAAAAAATAAT
388059 AGAAAAAAATAA
1 AGAAAAAAATAA
388071 AATAAAGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AGAAAAAAATAAT
Found at i:388074 original size:18 final size:18
Alignment explanation
Indices: 388051--388107 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 18
388041 TATTAAGAAA
388051 AAAATAATAGAAAAAAAT
1 AAAATAATAGAAAAAAAT
*
388069 AAAATAA-AG-TAAAAAT
1 AAAATAATAGAAAAAAAT
* * *
388085 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAAAAAAT
388104 AAAA
1 AAAA
388108 ACAAAAATAG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 11 0.37
17 3 0.10
18 8 0.27
19 8 0.27
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAATAATAGAAAAAAAT
Found at i:388100 original size:10 final size:10
Alignment explanation
Indices: 388083--388173 Score: 62
Period size: 10 Copynumber: 9.3 Consensus size: 10
388073 TAAAGTAAAA
388083 ATAT-AATAT
1 ATATAAATAT
*
388092 ATATAAATAA
1 ATATAAATAT
* * *
388102 ATAAAAACAA
1 ATATAAATAT
*
388112 AAATAGAATAT
1 ATATA-AATAT
*
388123 -TATATATAT
1 ATATAAATAT
*
388132 ATATATATAT
1 ATATAAATAT
*
388142 ATATATATAT
1 ATATAAATAT
*
388152 ATATAAAGAT
1 ATATAAATAT
*
388162 GTATAAA-AT
1 ATATAAATAT
388171 ATA
1 ATA
388174 ATATTAAGAA
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
9 12 0.18
10 51 0.77
11 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (10 bp):
ATATAAATAT
Found at i:388130 original size:2 final size:2
Alignment explanation
Indices: 388119--388156 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
388109 CAAAAATAGA
388119 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
388157 AAGATGTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:388236 original size:2 final size:2
Alignment explanation
Indices: 388224--388270 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
388214 TTAATACATC
* *
388224 TA TA CA TA TA TA TA TA TA TA TA TA TA TA -A TGA TA TA -A GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
388265 TA TA TA
1 TA TA TA
388271 ATAAAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:388274 original size:14 final size:14
Alignment explanation
Indices: 388231--388293 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 14
388221 ATCTATACAT
*
388231 ATATATATATATAT
1 ATATATATATATAA
388245 ATATATAATGATATAA
1 ATATAT-AT-ATATAA
388261 GATATATATA-ATAA
1 -ATATATATATATAA
*
388275 AAATAATATAATATAA
1 ATAT-ATAT-ATATAA
388291 ATA
1 ATA
388294 AAAAAAGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 3 0.08
14 14 0.35
15 4 0.10
16 13 0.32
17 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:388283 original size:25 final size:27
Alignment explanation
Indices: 388235--388285 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
388225 ATACATATAT
* *
388235 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
388262 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATAAAATAATATAA
388286 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:388288 original size:23 final size:23
Alignment explanation
Indices: 388231--388329 Score: 64
Period size: 23 Copynumber: 4.3 Consensus size: 23
388221 ATCTATACAT
* *
388231 ATAT-ATATATATATATATATAATG
1 ATATAATATATATA-ATA-AAAATA
388255 ATATAAGATATATATAATAAAAATA
1 ATAT-A-ATATATATAATAAAAATA
* *
388280 ATATAATATAAATAA-AAAAAGGA
1 ATATAATATATATAATAAAAA-TA
* *
388303 ATATAGTAAATA-AAT-AAAA-A
1 ATATAATATATATAATAAAAATA
388323 ATATAAT
1 ATATAAT
388330 TAAAAGTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
20 7 0.11
22 11 0.18
23 19 0.31
24 5 0.08
25 8 0.13
26 3 0.05
27 9 0.15
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
ATATAATATATATAATAAAAATA
Found at i:388333 original size:21 final size:21
Alignment explanation
Indices: 388268--388333 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
388258 TAAGATATAT
*
388268 ATAATAAAAATAATATAATATAA
1 ATAA-AAAAAGAATATAAT-TAA
*
388291 ATAAAAAAAGGAATAT-AGTAA
1 ATAAAAAAA-GAATATAATTAA
388312 ATAAATAAAA-AATATAATTAA
1 ATAAA-AAAAGAATATAATTAA
388333 A
1 A
388334 AGTATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.14
21 13 0.35
22 10 0.27
23 9 0.24
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
ATAAAAAAAGAATATAATTAA
Found at i:388385 original size:13 final size:13
Alignment explanation
Indices: 388367--388402 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
388357 TAATATAAAA
388367 GTAAAATTAAAGG
1 GTAAAATTAAAGG
388380 GTAAAATTAAA-G
1 GTAAAATTAAAGG
388392 GT-AAATTAAAG
1 GTAAAATTAAAG
388403 ATTAAGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.36
12 3 0.14
13 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.25
Consensus pattern (13 bp):
GTAAAATTAAAGG
Found at i:400849 original size:19 final size:19
Alignment explanation
Indices: 400825--400863 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
400815 TCAGATGTTA
*
400825 TACATACAGGGAAGCACTG
1 TACATACAAGGAAGCACTG
400844 TACATACAAGGAAGCACTG
1 TACATACAAGGAAGCACTG
400863 T
1 T
400864 GTTCACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (19 bp):
TACATACAAGGAAGCACTG
Found at i:400953 original size:16 final size:16
Alignment explanation
Indices: 400906--400959 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
400896 GATTAAGATC
*
400906 GGAATACAACATTCTC
1 GGAATACAACATTCTA
400922 GGAATACAACATTCTA
1 GGAATACAACATTCTA
400938 GGAATACAACATTCTA
1 GGAATACAACATTCTA
*
400954 AGAATA
1 GGAATA
400960 TCCTCTAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (16 bp):
GGAATACAACATTCTA
Found at i:403738 original size:9 final size:9
Alignment explanation
Indices: 403724--403753 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
403714 GCAGAAGCAT
403724 TGACAACGA
1 TGACAACGA
403733 TGACAACGA
1 TGACAACGA
403742 TGACAACGA
1 TGACAACGA
403751 TGA
1 TGA
403754 GTGAGAGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (9 bp):
TGACAACGA
Found at i:415722 original size:19 final size:19
Alignment explanation
Indices: 415698--415736 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
415688 TCAGATGTTA
*
415698 TACATACAGGGAAGCACTG
1 TACATACAAGGAAGCACTG
415717 TACATACAAGGAAGCACTG
1 TACATACAAGGAAGCACTG
415736 T
1 T
415737 GTTCACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (19 bp):
TACATACAAGGAAGCACTG
Found at i:415826 original size:16 final size:16
Alignment explanation
Indices: 415779--415832 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
415769 GATTAAGATC
*
415779 GGAATACAACATTCTC
1 GGAATACAACATTCTA
415795 GGAATACAACATTCTA
1 GGAATACAACATTCTA
415811 GGAATACAACATTCTA
1 GGAATACAACATTCTA
*
415827 AGAATA
1 GGAATA
415833 TCCTCTAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (16 bp):
GGAATACAACATTCTA
Found at i:418612 original size:9 final size:9
Alignment explanation
Indices: 418598--418627 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
418588 GCAGAAGCAT
418598 TGACAACGA
1 TGACAACGA
418607 TGACAACGA
1 TGACAACGA
418616 TGACAACGA
1 TGACAACGA
418625 TGA
1 TGA
418628 GTGAGAGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (9 bp):
TGACAACGA
Found at i:434648 original size:15 final size:16
Alignment explanation
Indices: 434619--434648 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
434609 TGAAATTGAA
434619 ATTTTAAAAAGATAAT
1 ATTTTAAAAAGATAAT
434635 ATTTTAAAAA-ATAA
1 ATTTTAAAAAGATAA
434649 GGTAAACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTTTAAAAAGATAAT
Found at i:440543 original size:16 final size:16
Alignment explanation
Indices: 440522--440557 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
440512 TCAATAAAAG
440522 TTCGAGAGTTATAAAT
1 TTCGAGAGTTATAAAT
440538 TTC--GAGTTATAAAT
1 TTCGAGAGTTATAAAT
440552 TTCGAG
1 TTCGAG
440558 TGTTCATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 14 0.78
16 4 0.22
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (16 bp):
TTCGAGAGTTATAAAT
Found at i:440546 original size:14 final size:14
Alignment explanation
Indices: 440527--440558 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
440517 AAAAGTTCGA
440527 GAGTTATAAATTTC
1 GAGTTATAAATTTC
440541 GAGTTATAAATTTC
1 GAGTTATAAATTTC
440555 GAGT
1 GAGT
440559 GTTCATCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (14 bp):
GAGTTATAAATTTC
Found at i:441877 original size:820 final size:820
Alignment explanation
Indices: 440221--442219 Score: 3138
Period size: 820 Copynumber: 2.4 Consensus size: 820
440211 TCGCCAAACT
* * * *
440221 TGTTAGAAATCAAATTTAATTATGAAAAAGTCAATAAAGACGGTTATAAA-AATAAAGAAAATAT
1 TGTTAGAAATCAAACTTAATTATGAAAAAGTCAAAAAAGACGGCTATAAAGCA-AAAG-AAATAT
* * * *
440285 ATAAGTTGCATGGATACACAAATAACTACGTGGATAATAAAGTGATAGCAACTTGAATTACAAAG
64 ACAAGTTGCATGGATACACAAATAACCACGTGGATAATAAAGTGGTAGCAACTTGAATTGCAAAG
* * *
440350 AATTGCTTAATTATTAAAATAAGTGAGAGCGAAAGAAAAATAAAGAAATTTGAGAGATAGGTTGT
129 AATTGCTTAATTATTAAGATAAGTGAGAGCGAAAGAAAAATAGAGAGATTTGAGAGATAGGTTGT
* * *
440415 AAAGCTTAGCAAAACGTTAAATAGTGGGGTTGTATTTGTAAACTAGCAGTAGCTAGTATTGTAAT
194 GAAGCTTAGCAAAGCTTTAAATAGTGGGGTTGTATTTGTAAACTAGCAGTAGCTAGTATTGTAAT
*
440480 ATTGAGGTAGTGTCGTTGTAACGTATTTTGTTTCAATAAAAGTTCGAGAGTTATAAATTTCGAGT
259 ATTGAGGTAGTGTCGTTGTAACGTATTTTGTTTCAAT-AAA-----A-AG-T-TCAA----GAGT
*
440545 TATAAATTTCGAGTGT-TCATCTACGTTTCCAACAAGTGGTATCAGAGCTTGGTTCAAGTTCAAC
311 TATAAATTTCGAGTGTCT-ATCTACGCTTCCAACAAGTGGTATCAGAGCTTGGTTCAAGTTCAAC
* * * *
440609 GTGGTGGAGAATATGACCAACATGATTCAACCACAAATTCCGAGATTGACAAAGATAAATTATGG
375 GTGGTGAAGAAGATGACCAACATGATTCAACCACAAATTCCAAGATTGACAAAGACAAATTATGG
* * * *
440674 CAACTGGAGTATTTAAATGAAGGCGTTTCTAGGCTCCCAAGATTGTTGAGATATCATCGAGGATG
440 CAACTAGAGCATTCAAATGAAGGCGTTGCTAGGCTCCCAAGATTGTTGAGATATCATCGAGGATG
* * * *
440739 GTTACACCGAGCCTGAAAATATAGCAGCAGAAGCAGTCTTGACCAATGAAGGCAATAAGGTATTG
505 GTTACACCGAGCCTGAAAATACAACAGCAGAAGCAGTCATGACCAATGAAGGCAATAAGATATTG
* * * * *
440804 AATGAATCCCGAAAAAGAGATTAAAGAGCGTTGTTCTTTATTTTTCAAGGAGTATATGAATTTAC
570 AAGGAATCCCGAAAAAGAGATAAAAGAGCGTTATTCTTTATTTTTCAAGGAGTATACGAATCTAC
*
440869 CTTTGAAAAAAATTATGATGTGAAGACCGCAAAATAAGCGTGAAAGAGTTTGCAAAAATCTTAAG
635 CTTTGAAAAAAATTATGATGTGAAGACCGCAAAATAAGCGTGAAAGAGTTTGCAAAAAACTTAAG
* *
440934 GTGTCAAAAAAGCAAAGAAGAATACATAGCCGCAGCAGCGTGCACTTGTCAAGAAATGAATAATC
700 GTGTCAAAAAAGCAAAGAAGAATACATAGCCGCAGCAACGTGCACTTGTCAAAAAATGAATAATC
*
440999 GCTTGGAGATGATAAGCGGAGAAAAGCTCGGAATATAAAATCAAGTTTGAGAGAAG
765 GCTTGGAGATGATAAGCGGAGAAAAGCTCGGAATAGAAAATCAAGTTTGAGAGAAG
* * *
441055 TGTTAGAAATCAAACTTAATTATGAAAAAGTCAACAAAGACGGCAATAAAGCAAATGAAATATAC
1 TGTTAGAAATCAAACTTAATTATGAAAAAGTCAAAAAAGACGGCTATAAAGCAAAAGAAATATAC
* *
441120 AAGTTGCATGGATACACAAATAACCACGCGGATAATAAAGTGGTAGCAACTTTAATTGCAAAGAA
66 AAGTTGCATGGATACACAAATAACCACGTGGATAATAAAGTGGTAGCAACTTGAATTGCAAAGAA
* * * *
441185 TTGCTTAATTATTAAGAGAAGCGAGAGAGAAAGAAAAATAGAGAGATTTGAGATATAGGTTGTGA
131 TTGCTTAATTATTAAGATAAGTGAGAGCGAAAGAAAAATAGAGAGATTTGAGAGATAGGTTGTGA
** * * *
441250 AGCTTAATAAAGCTTTAAATAGCGGAGTTGTATTTGTAAACTAGCAGTAGCTAGTATTATAATAT
196 AGCTTAGCAAAGCTTTAAATAGTGGGGTTGTATTTGTAAACTAGCAGTAGCTAGTATTGTAATAT
*
441315 TGATGTAGTGTCGTTGTAACGTATTTTGTTTCAATAAAAAGTTCAAGAGTTATAAATTTCGAGTG
261 TGAGGTAGTGTCGTTGTAACGTATTTTGTTTCAATAAAAAGTTCAAGAGTTATAAATTTCGAGTG
*
441380 TCTATCTACGCTTCCAACAAGTGGTATCAGAGCTTGGTTCGAGTTCAACGTGGTGAAGAAGATGA
326 TCTATCTACGCTTCCAACAAGTGGTATCAGAGCTTGGTTCAAGTTCAACGTGGTGAAGAAGATGA
*
441445 CCAACATGATTCAACCATAAATTCCAAGATTGACAAAGACAAATTATGGCAACTAGAGCATTCAA
391 CCAACATGATTCAACCACAAATTCCAAGATTGACAAAGACAAATTATGGCAACTAGAGCATTCAA
*
441510 ATGAAGGTGTTGCTAGGCTCCCAAGATTGTTGAGATATCATCGAGGATGGTTACACCGAGCCTGA
456 ATGAAGGCGTTGCTAGGCTCCCAAGATTGTTGAGATATCATCGAGGATGGTTACACCGAGCCTGA
* * *
441575 AAATGCAACAGCAGAAGCAGTCATGACCAATGAAGGCAATAAGATATTGAAGGAATCCTGGAAAA
521 AAATACAACAGCAGAAGCAGTCATGACCAATGAAGGCAATAAGATATTGAAGGAATCCCGAAAAA
*
441640 GAGATAAAAGAGCGTTATTCTTTATTTTTCAAGGAGTATACGAATCTACCTTTGAAAAAATTTAT
586 GAGATAAAAGAGCGTTATTCTTTATTTTTCAAGGAGTATACGAATCTACCTTTGAAAAAAATTAT
* * *
441705 GATGTGAAGACCGCAAAATAAGTGTGGAAGAGTTTGCAAAAAACTTAAGGTGTCGAAAAAGCAAA
651 GATGTGAAGACCGCAAAATAAGCGTGAAAGAGTTTGCAAAAAACTTAAGGTGTCAAAAAAGCAAA
*
441770 GAAGAATACATAGCCGCAGCAATGTGCACTTGTCAAAAAATGAATAATCGCTTGGAGATGATAAG
716 GAAGAATACATAGCCGCAGCAACGTGCACTTGTCAAAAAATGAATAATCGCTTGGAGATGATAAG
* * *
441835 CGGAGAAAAGCTCGGAATGGAAAATCAAGTTTGGGGGAAG
781 CGGAGAAAAGCTCGGAATAGAAAATCAAGTTTGAGAGAAG
* *
441875 TGTTAGAAATCAAACTTAATTATGAAAAAGTCAAAAAAGACGACTATAAAGCAAAGGAAATATAC
1 TGTTAGAAATCAAACTTAATTATGAAAAAGTCAAAAAAGACGGCTATAAAGCAAAAGAAATATAC
* * * *
441940 AAGTTGCATGGATACGCAAATAACCACGTGGATAATAAAGTGGCAACAACTTGAATTGCAATGAA
66 AAGTTGCATGGATACACAAATAACCACGTGGATAATAAAGTGGTAGCAACTTGAATTGCAAAGAA
442005 TTGCTTAATTATTAAGATAAGTGAGAGCGAAAGAAAAATAGAGAGATTTGAGAGATAGGTTGTGA
131 TTGCTTAATTATTAAGATAAGTGAGAGCGAAAGAAAAATAGAGAGATTTGAGAGATAGGTTGTGA
* *
442070 AGCTTAGCAAAGCTTTAAATAGTGGGGTTGTATTTGTAAACTAGCAGCAGTTAGTATTGTAATAT
196 AGCTTAGCAAAGCTTTAAATAGTGGGGTTGTATTTGTAAACTAGCAGTAGCTAGTATTGTAATAT
* * *
442135 TGAGGTAGTGTCGTTGTAGCGTATTTTGTTTCAATAAAAAGTTCGAGAGTTATAAATTCCGAGTG
261 TGAGGTAGTGTCGTTGTAACGTATTTTGTTTCAATAAAAAGTTCAAGAGTTATAAATTTCGAGTG
*
442200 TCCATCTACGCTTCCAACAA
326 TCTATCTACGCTTCCAACAA
442220 ACCTTTCTTC
Statistics
Matches: 1072, Mismatches: 91, Indels: 18
0.91 0.08 0.02
Matches are distributed among these distances:
820 795 0.74
821 1 0.00
824 3 0.00
825 1 0.00
826 2 0.00
827 1 0.00
832 3 0.00
833 216 0.20
834 49 0.05
835 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (820 bp):
TGTTAGAAATCAAACTTAATTATGAAAAAGTCAAAAAAGACGGCTATAAAGCAAAAGAAATATAC
AAGTTGCATGGATACACAAATAACCACGTGGATAATAAAGTGGTAGCAACTTGAATTGCAAAGAA
TTGCTTAATTATTAAGATAAGTGAGAGCGAAAGAAAAATAGAGAGATTTGAGAGATAGGTTGTGA
AGCTTAGCAAAGCTTTAAATAGTGGGGTTGTATTTGTAAACTAGCAGTAGCTAGTATTGTAATAT
TGAGGTAGTGTCGTTGTAACGTATTTTGTTTCAATAAAAAGTTCAAGAGTTATAAATTTCGAGTG
TCTATCTACGCTTCCAACAAGTGGTATCAGAGCTTGGTTCAAGTTCAACGTGGTGAAGAAGATGA
CCAACATGATTCAACCACAAATTCCAAGATTGACAAAGACAAATTATGGCAACTAGAGCATTCAA
ATGAAGGCGTTGCTAGGCTCCCAAGATTGTTGAGATATCATCGAGGATGGTTACACCGAGCCTGA
AAATACAACAGCAGAAGCAGTCATGACCAATGAAGGCAATAAGATATTGAAGGAATCCCGAAAAA
GAGATAAAAGAGCGTTATTCTTTATTTTTCAAGGAGTATACGAATCTACCTTTGAAAAAAATTAT
GATGTGAAGACCGCAAAATAAGCGTGAAAGAGTTTGCAAAAAACTTAAGGTGTCAAAAAAGCAAA
GAAGAATACATAGCCGCAGCAACGTGCACTTGTCAAAAAATGAATAATCGCTTGGAGATGATAAG
CGGAGAAAAGCTCGGAATAGAAAATCAAGTTTGAGAGAAG
Found at i:450748 original size:21 final size:21
Alignment explanation
Indices: 450722--450768 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
450712 AATATGTAAA
450722 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
450743 TCGCATTGCTATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
450764 TCGCA
1 TCGCA
450769 ACGCGAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:450836 original size:20 final size:20
Alignment explanation
Indices: 450619--450847 Score: 159
Period size: 19 Copynumber: 11.6 Consensus size: 20
450609 AAATGACCAA
* *
450619 CAAATTCGCAATGCG-ATCT
1 CAAATTCGCAACGCGAATTT
* *
450638 CAAATTCGCAATGCG-ATCT
1 CAAATTCGCAACGCGAATTT
*
450657 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACGCGAATTT
* * *
450677 CAATTTCGCAACTC-AGTTT
1 CAAATTCGCAACGCGAATTT
* *
450696 CCAATTTCACAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
** *
450719 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
** * *
450737 CCAAATTCGCATTGCTATTTT
1 -CAAATTCGCAACGCGAATTT
**
450758 CCAAATTCGCAACGCGAAAGT
1 -CAAATTCGCAACGCGAATTT
*
450779 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
*
450798 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
450817 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
450837 -AATTTCGCAAC
1 CAAATTCGCAAC
450848 AGGTTTTAGT
Statistics
Matches: 174, Mismatches: 27, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
18 1 0.01
19 82 0.47
20 56 0.32
21 33 0.19
22 1 0.01
23 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:451175 original size:25 final size:25
Alignment explanation
Indices: 451141--451190 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
451131 ATTATTTTTC
*
451141 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
451166 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
451191 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:451309 original size:20 final size:20
Alignment explanation
Indices: 451283--451356 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
451273 TTCACTACAT
*
451283 GAAAGTCAAATTCCCAACGC
1 GAAAGTCAAATTCGCAACGC
* * *
451303 GATAGTCAAATTTGCAACGT
1 GAAAGTCAAATTCGCAACGC
*
451323 GAAAATCAAATTCGCAACGC
1 GAAAGTCAAATTCGCAACGC
451343 GAAAGTCAAATTCG
1 GAAAGTCAAATTCG
451357 GTTTGCGATT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
GAAAGTCAAATTCGCAACGC
Found at i:451326 original size:40 final size:40
Alignment explanation
Indices: 451263--451355 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
451253 TAAGCGTTGT
* *
451263 GATAGTCAAATTCACTACATGAAAGTCAAATTCCCAACGC
1 GATAGTCAAATTCACAACATGAAAATCAAATTCCCAACGC
** * *
451303 GATAGTCAAATTTGCAACGTGAAAATCAAATTCGCAACGC
1 GATAGTCAAATTCACAACATGAAAATCAAATTCCCAACGC
*
451343 GAAAGTCAAATTC
1 GATAGTCAAATTC
451356 GGTTTGCGAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.23
Consensus pattern (40 bp):
GATAGTCAAATTCACAACATGAAAATCAAATTCCCAACGC
Found at i:454065 original size:24 final size:24
Alignment explanation
Indices: 454031--454084 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
454021 CCATCACATC
454031 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
454055 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
454079 ATCAAA
1 ATCAAA
454085 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:454098 original size:24 final size:24
Alignment explanation
Indices: 454031--454098 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
454021 CCATCACATC
* * *
454031 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
454055 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
454079 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
454099 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:454231 original size:12 final size:12
Alignment explanation
Indices: 454210--454243 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
454200 GGTTGTGGGT
*
454210 TTTGAGATTGTG
1 TTTGATATTGTG
454222 TTTGATATTGTG
1 TTTGATATTGTG
*
454234 TTTGGTATTG
1 TTTGATATTG
454244 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:455037 original size:20 final size:20
Alignment explanation
Indices: 455007--455078 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
454997 TGAAATTCAG
455007 TTGCGAATTTGACTTTCGCT
1 TTGCGAATTTGACTTTCGCT
455027 TTGC-AACTTTGACTTTCG-T
1 TTGCGAA-TTTGACTTTCGCT
* *
455046 GTTGCGAATTTGACTATCGCG
1 -TTGCGAATTTGACTTTCGCT
455067 TTGCGAATTTGA
1 TTGCGAATTTGA
455079 AAAATCGCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
19 3 0.07
20 41 0.89
21 2 0.04
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCT
Found at i:455150 original size:20 final size:20
Alignment explanation
Indices: 455101--455154 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
455091 CGATTTACAT
455101 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
455121 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
455141 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
455155 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:458642 original size:2 final size:2
Alignment explanation
Indices: 458635--458679 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
458625 TAACTTAGTT
458635 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
458677 TA T
1 TA T
458680 TATTTTTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:463843 original size:17 final size:17
Alignment explanation
Indices: 463798--463834 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
463788 TAATTCAAAG
463798 GTGGGAGGTGGGTGGTT
1 GTGGGAGGTGGGTGGTT
463815 GTGGGAGGTGGGTGGTT
1 GTGGGAGGTGGGTGGTT
463832 GTG
1 GTG
463835 ATGAGTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.00, G:0.65, T:0.30
Consensus pattern (17 bp):
GTGGGAGGTGGGTGGTT
Found at i:474065 original size:20 final size:20
Alignment explanation
Indices: 473984--474074 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
473974 TTCTAGATTT
*
473984 GCAACGCGATTTTGACTATC
1 GCAACGCGATTTTGACAATC
** *
474004 GCATTGCGATTTTAGAAAATC
1 GCAACGCGATTTT-GACAATC
* * *
474025 ACAACGCGAATATGTA-AATC
1 GCAACGCGATTTTG-ACAATC
* *
474045 GCAACGCGATTCTGACTATC
1 GCAACGCGATTTTGACAATC
474065 GCAACGCGAT
1 GCAACGCGAT
474075 AATACAAAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.73
21 14 0.25
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (20 bp):
GCAACGCGATTTTGACAATC
Found at i:474418 original size:19 final size:19
Alignment explanation
Indices: 474394--474430 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
474384 TTATTTTGGA
*
474394 TTTTTCACTATCGCAACAT
1 TTTTTCAATATCGCAACAT
474413 TTTTTCAATATCGCAACA
1 TTTTTCAATATCGCAACA
474431 ACACATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTTTCAATATCGCAACAT
Found at i:475833 original size:36 final size:36
Alignment explanation
Indices: 475792--475867 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
475782 ATTTTCGGGA
*
475792 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
475828 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
475864 TTTT
1 TTTT
475868 TTTTGCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:479162 original size:21 final size:22
Alignment explanation
Indices: 479138--479179 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
479128 ATTATATTGA
479138 AAAAAAT-AAGTATTTAATTTG
1 AAAAAATAAAGTATTTAATTTG
479159 AAAAAATAAAGTATTTAATTT
1 AAAAAATAAAGTATTTAATTT
479180 TATTTCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
AAAAAATAAAGTATTTAATTTG
Found at i:479678 original size:60 final size:60
Alignment explanation
Indices: 479565--479679 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 60
479555 ACGTAGTTAA
* * **
479565 AAAGCCTAATTATCGATGTAGGTAATCGTTGTTACTTAGGGAAATTTCGGTAATCGCGTG
1 AAAGCCTAATTACCGATGTAGGTAATAGTTGTTACTTAGGGAAATTTAAGTAATCGCGTG
*
479625 AAAGCCTAATTACCGATGTAGGTAATATTTGTTACTTAGGGAAATTTAAGTAATC
1 AAAGCCTAATTACCGATGTAGGTAATAGTTGTTACTTAGGGAAATTTAAGTAATC
479680 CTTGTTCGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (60 bp):
AAAGCCTAATTACCGATGTAGGTAATAGTTGTTACTTAGGGAAATTTAAGTAATCGCGTG
Found at i:489825 original size:5 final size:5
Alignment explanation
Indices: 489815--489843 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
489805 TAATTGGTCG
489815 ATTTA ATTTA ATTTA ATTTA ATTTA ATTT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTT
489844 TGGTTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:489967 original size:7 final size:7
Alignment explanation
Indices: 489955--489980 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
489945 CATGGATTTG
489955 GTTGCCA
1 GTTGCCA
489962 GTTGCCA
1 GTTGCCA
489969 GTTGCCA
1 GTTGCCA
489976 GTTGC
1 GTTGC
489981 AAGGTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.27, G:0.31, T:0.31
Consensus pattern (7 bp):
GTTGCCA
Found at i:497196 original size:66 final size:66
Alignment explanation
Indices: 497090--497221 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
497080 AGCCGGAAAT
497090 GCAGAAGTTATTGTTCTTAGTGATTCAGATGAAGAGAACGAAATTTCGATATCTCTGTCAACTCT
1 GCAGAAGTTATTGTTCTTAGTGATTCAGATGAAGAGAACGAAATTTCGATATCTCTGTCAACTCT
497155 G
66 G
*
497156 GCAGAAGTTATTGTTCTTAGTGATTCAGATGACGAGAACGAAATTTCGATATCTCTGTCAACTCT
1 GCAGAAGTTATTGTTCTTAGTGATTCAGATGAAGAGAACGAAATTTCGATATCTCTGTCAACTCT
497221 G
66 G
497222 TTATCATTCT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (66 bp):
GCAGAAGTTATTGTTCTTAGTGATTCAGATGAAGAGAACGAAATTTCGATATCTCTGTCAACTCT
G
Found at i:500785 original size:12 final size:12
Alignment explanation
Indices: 500768--500792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
500758 AAAAGTTGTG
500768 GTTTACCATTGA
1 GTTTACCATTGA
500780 GTTTACCATTGA
1 GTTTACCATTGA
500792 G
1 G
500793 ACAAGATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTTACCATTGA
Found at i:514822 original size:16 final size:16
Alignment explanation
Indices: 514801--514831 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
514791 TCAAAAAAAT
514801 TTCATCCATCACCCGA
1 TTCATCCATCACCCGA
*
514817 TTCATCTATCACCCG
1 TTCATCCATCACCCG
514832 CCAATCATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.42, G:0.06, T:0.29
Consensus pattern (16 bp):
TTCATCCATCACCCGA
Found at i:519706 original size:4 final size:4
Alignment explanation
Indices: 519697--519722 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
519687 CAATCTTCAA
519697 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
519723 CCACAGGCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:528435 original size:30 final size:29
Alignment explanation
Indices: 528379--528436 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
528369 TGCTGATTTT
*
528379 TTTTAGTTTAGTGTCTAACGTTTATTTCA
1 TTTTAGTTTAGTGTCTAAAGTTTATTTCA
* *
528408 TTTTAGTTTGGTGTCTAATATTTTATTTC
1 TTTTAGTTTAGTGTCTAA-AGTTTATTTC
528437 GTTACTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.59
Consensus pattern (29 bp):
TTTTAGTTTAGTGTCTAAAGTTTATTTCA
Found at i:528548 original size:12 final size:12
Alignment explanation
Indices: 528531--528555 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
528521 TTTTTTTAAA
528531 AAAAATAATATT
1 AAAAATAATATT
528543 AAAAATAATATT
1 AAAAATAATATT
528555 A
1 A
528556 TATTTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAATAATATT
Found at i:536369 original size:20 final size:22
Alignment explanation
Indices: 536346--536391 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 22
536336 AGATGTTTTT
*
536346 TTTATAATTTT-TATTAAT-AA
1 TTTATAATTTTATATCAATGAA
536366 -TT-TAATTTTATATCAATGAA
1 TTTATAATTTTATATCAATGAA
536386 TTTATA
1 TTTATA
536392 TAGTTTTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 7 0.33
19 8 0.38
20 2 0.10
21 2 0.10
22 2 0.10
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTATAATTTTATATCAATGAA
Found at i:539889 original size:21 final size:20
Alignment explanation
Indices: 539803--539960 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
539793 AAATGACCAA
**
539803 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
539822 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
539842 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
539862 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
539883 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
539904 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
539924 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
539945 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
539961 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:539989 original size:20 final size:20
Alignment explanation
Indices: 539928--540156 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
539918 GATTTTCAAG
* ** *
539928 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
539948 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
539968 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
539988 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
540008 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
540028 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
540048 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
540068 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
540088 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
540108 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
540128 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
540148 AATCACAAC
1 AATCGCAAC
540157 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:540888 original size:24 final size:24
Alignment explanation
Indices: 540849--540895 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
540839 AAATTTGGTC
540849 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
540873 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
540896 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:541087 original size:12 final size:12
Alignment explanation
Indices: 541070--541094 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
541060 ATATAATCCT
541070 GAAGAAGAAAAA
1 GAAGAAGAAAAA
541082 GAAGAAGAAAAA
1 GAAGAAGAAAAA
541094 G
1 G
541095 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:543456 original size:53 final size:53
Alignment explanation
Indices: 543393--543600 Score: 321
Period size: 53 Copynumber: 3.8 Consensus size: 53
543383 GCAACGAGAG
*
543393 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAAAATCGCAATGCGGAAATGAA
543446 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGGAAATGAA
*
543503 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGGAAATGAA
*
543556 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCG
543601 ATTTTCATTT
Statistics
Matches: 147, Mismatches: 2, Indels: 12
0.91 0.01 0.07
Matches are distributed among these distances:
52 13 0.09
53 80 0.54
55 3 0.02
57 35 0.24
58 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGGAAATGAA
Found at i:543462 original size:19 final size:19
Alignment explanation
Indices: 543393--543582 Score: 274
Period size: 19 Copynumber: 10.4 Consensus size: 19
543383 GCAACGAGAG
543393 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
543412 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
543426 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
543446 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
543465 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
543484 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
543503 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
543522 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
543536 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
543556 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
543575 AATCGCAA
1 AATCGCAA
543583 CGAGAGAATC
Statistics
Matches: 155, Mismatches: 4, Indels: 24
0.85 0.02 0.13
Matches are distributed among these distances:
14 22 0.14
15 1 0.01
16 2 0.01
17 4 0.03
19 97 0.63
20 29 0.19
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:543614 original size:72 final size:70
Alignment explanation
Indices: 543379--543582 Score: 233
Period size: 72 Copynumber: 2.9 Consensus size: 70
543369 CGGAAATTAC
* *
543379 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCG
1 AATCGCAACGAGACAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-
543438 GAAATGAA
64 G-AATGAA
*
543446 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAA--CG--A-GACAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
543510 ATGCGAAATGAA
61 A-GCG-AATGAA
*
543522 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAACGAGACAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
543583 CGAGAGAATC
Statistics
Matches: 123, Mismatches: 3, Indels: 17
0.86 0.02 0.12
Matches are distributed among these distances:
67 8 0.07
69 2 0.02
71 14 0.11
72 64 0.52
74 3 0.02
76 16 0.13
77 16 0.13
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (70 bp):
AATCGCAACGAGACAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
ATGAA
Found at i:543659 original size:53 final size:52
Alignment explanation
Indices: 543591--543726 Score: 254
Period size: 53 Copynumber: 2.6 Consensus size: 52
543581 AACGAGAGAA
*
543591 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
543643 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
543696 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
543727 AGTCATTTTT
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
52 31 0.38
53 51 0.62
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:543734 original size:19 final size:19
Alignment explanation
Indices: 543591--543726 Score: 166
Period size: 19 Copynumber: 7.6 Consensus size: 19
543581 AACGAGAGAA
*
543591 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
543610 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
543626 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
543643 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
543663 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
543679 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
543696 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
543715 TCGCATTGCGAT
1 TCGCATTGCGAT
543727 AGTCATTTTT
Statistics
Matches: 101, Mismatches: 5, Indels: 22
0.79 0.04 0.17
Matches are distributed among these distances:
14 12 0.12
16 14 0.14
17 12 0.12
18 2 0.02
19 46 0.46
20 15 0.15
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:543852 original size:14 final size:14
Alignment explanation
Indices: 543833--543869 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
543823 CATCAATTAC
543833 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
543847 ACAAATCATCTTTT
1 ACAAATCAACTTTT
543861 ACAAATCAA
1 ACAAATCAA
543870 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:545269 original size:19 final size:19
Alignment explanation
Indices: 545227--545399 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
545217 TAGTTTACTT
* *
545227 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
545247 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
545266 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
545285 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
545304 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
545323 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
545337 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
545356 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
545370 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
545389 TCGCAATGCGA
1 TCGCAACGCGA
545400 TTTTGTCGTT
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 20 0.16
15 2 0.02
16 4 0.03
17 4 0.03
18 2 0.02
19 84 0.66
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:545341 original size:33 final size:33
Alignment explanation
Indices: 545299--545394 Score: 165
Period size: 33 Copynumber: 2.9 Consensus size: 33
545289 AACGCGAAAC
545299 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
*
545332 CAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
* *
545365 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 CAAAATCGCAACGCGAAATGAAAATCGCAA
545395 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.10
Consensus pattern (33 bp):
CAAAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:545389 original size:52 final size:52
Alignment explanation
Indices: 545261--545399 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
545251 AACGCGAAAT
* * * *
545261 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
545313 GA-AAT-GAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACG--AAAATCGCAATGCGAAACCAAAATCGCAACGA
*
545365 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
545400 TTTTGTCGTT
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 7 0.10
51 3 0.04
52 47 0.69
53 3 0.04
54 8 0.12
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:545414 original size:14 final size:14
Alignment explanation
Indices: 545395--545450 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
545385 AAAATCGCAA
545395 TGCGATTTTGTCGT
1 TGCGATTTTGTCGT
545409 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-G--T--CGT
*
545428 TGCGATTCTGTCGT
1 TGCGATTTTGTCGT
545442 TGCGATTTT
1 TGCGATTTT
545451 CATTTCGCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.07, C:0.16, G:0.29, T:0.48
Consensus pattern (14 bp):
TGCGATTTTGTCGT
Found at i:545430 original size:19 final size:18
Alignment explanation
Indices: 545406--545467 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
545396 GCGATTTTGT
545406 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-GTTTCG
*
545425 CGTTGCGATTCTG--T--
1 CGTTGCGATTTTGTTTCG
*
545439 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTT-GTTTCG
545458 CGTTGCGATT
1 CGTTGCGATT
545468 CTCTCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 11 0.31
16 1 0.03
17 1 0.03
18 1 0.03
19 21 0.60
ACGTcount: A:0.08, C:0.19, G:0.27, T:0.45
Consensus pattern (18 bp):
CGTTGCGATTTTGTTTCG
Found at i:545440 original size:33 final size:33
Alignment explanation
Indices: 545395--545499 Score: 149
Period size: 33 Copynumber: 3.2 Consensus size: 33
545385 AAAATCGCAA
* *
545395 TGCGATTTTGTCGTTGCGATTTTGGTTTCGCGT
1 TGCGATTCTGTCGTTGCGATTTTAGTTTCGCGT
545428 TGCGATTCTGTCGTTGCGATTTTCA-TTTCGCGT
1 TGCGATTCTGTCGTTGCGATTTT-AGTTTCGCGT
* *
545461 TGCGATTCTCTCGTTGCGATTTTAAGTTTCGTGT
1 TGCGATTCTGTCGTTGCGATTTT-AGTTTCGCGT
545495 TGCGA
1 TGCGA
545500 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
33 53 0.82
34 12 0.18
ACGTcount: A:0.10, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTCTGTCGTTGCGATTTTAGTTTCGCGT
Found at i:545477 original size:14 final size:14
Alignment explanation
Indices: 545425--545481 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
545415 TTTGGTTTCG
*
545425 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
545439 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
545458 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
545472 CGTTGCGATT
1 CGTTGCGATT
545482 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:545756 original size:93 final size:93
Alignment explanation
Indices: 545597--545912 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
545587 TCAGGGTATT
545597 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
545662 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
545690 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
545755 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
545783 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
545848 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
545876 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
545913 AAGCAATCTA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:547628 original size:20 final size:20
Alignment explanation
Indices: 547597--547693 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
547587 TTTTGGTTGA
547597 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
547617 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
547637 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
547656 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
547671 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
547691 AAT
1 AAT
547694 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:547649 original size:21 final size:21
Alignment explanation
Indices: 547595--547659 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
547585 TCTTTTGGTT
547595 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
547616 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
547636 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
547657 GAA
1 GAA
547660 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:547663 original size:14 final size:14
Alignment explanation
Indices: 547644--547700 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
547634 GAGAAATGAA
547644 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
547658 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
547677 AATCGCAACGAGAG
1 AATCGCAACGAGAG
547691 AATCGCAACG
1 AATCGCAACG
547701 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:547676 original size:33 final size:33
Alignment explanation
Indices: 547595--547717 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
547585 TCTTTTGGTT
*
547595 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
547636 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
547669 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
547702 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
547718 TTCTCGTTGC
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:547893 original size:33 final size:33
Alignment explanation
Indices: 547851--547921 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
547841 AATACTAACT
547851 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
547884 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
547917 TGAAA
1 TGAAA
547922 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:548326 original size:20 final size:20
Alignment explanation
Indices: 548301--548492 Score: 253
Period size: 20 Copynumber: 9.6 Consensus size: 20
548291 CTTTAAAAAT
*
548301 CGCGTTGCGATTTACGAATA
1 CGCGTTGCGATTTACGGATA
548321 CGCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
*
548342 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
548361 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
548381 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
548401 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
548421 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
548441 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
548461 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
548481 CGCGTTGCGATT
1 CGCGTTGCGATT
548493 CTGGAAAATC
Statistics
Matches: 153, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
19 2 0.01
20 148 0.97
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:549189 original size:16 final size:17
Alignment explanation
Indices: 549151--549196 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
549141 TGTTTATGAG
*
549151 GGAATTGAAATCTGTGAA
1 GGAATTGGAATCTGT-AA
549169 GGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
549185 GGAATTGGAATC
1 GGAATTGGAATC
549197 CAATTCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:549742 original size:5 final size:5
Alignment explanation
Indices: 549726--549776 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
549716 TTCACCCTAA
* * *
549726 ACCCG AACCCG ACCCG ACCCG ACCCT ACCTG ACCTG A-CC- ACCCG ACCCG
1 ACCCG -ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG
549775 AC
1 AC
549777 TCAACCTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
3 1 0.03
4 3 0.08
5 30 0.77
6 5 0.13
ACGTcount: A:0.24, C:0.55, G:0.16, T:0.06
Consensus pattern (5 bp):
ACCCG
Found at i:549869 original size:26 final size:26
Alignment explanation
Indices: 549840--549907 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
549830 TTCATACGAC
549840 CCGACCCGAATATATGAATTAGAAAT
1 CCGACCCGAATATATGAATTAGAAAT
*
549866 CCGACCCGCATATATGAATTAGAAAT
1 CCGACCCGAATATATGAATTAGAAAT
549892 CCGACCCGAATTATAT
1 CCGACCCGAA-TATAT
549908 ATATTTTCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 34 0.87
27 5 0.13
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24
Consensus pattern (26 bp):
CCGACCCGAATATATGAATTAGAAAT
Found at i:560800 original size:5 final size:6
Alignment explanation
Indices: 560784--560809 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
560774 AGAAAAAATT
560784 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
560810 GTAATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:561013 original size:109 final size:109
Alignment explanation
Indices: 560892--561110 Score: 411
Period size: 109 Copynumber: 2.0 Consensus size: 109
560882 TGTAAACATA
*
560892 AGTATGATTATTTTTGTTATAGTTTTAATTAGTTAGAACTTTTTAGTATAATTACCAATATTTAA
1 AGTATGACTATTTTTGTTATAGTTTTAATTAGTTAGAACTTTTTAGTATAATTACCAATATTTAA
560957 TTTATTGATCAATTTATTATGAAATAACCCTTCTAACTAAACTT
66 TTTATTGATCAATTTATTATGAAATAACCCTTCTAACTAAACTT
*
561001 AGTATGACTATTTTTGTTATAGTTTTAATTAGTTAGAACTTTTTAGTATAATTACCAATCTTTAA
1 AGTATGACTATTTTTGTTATAGTTTTAATTAGTTAGAACTTTTTAGTATAATTACCAATATTTAA
*
561066 TTTATTGATCAATTTATTATGAAATAACCCTTCTAACTCAACTT
66 TTTATTGATCAATTTATTATGAAATAACCCTTCTAACTAAACTT
561110 A
1 A
561111 TTTCGTATAT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (109 bp):
AGTATGACTATTTTTGTTATAGTTTTAATTAGTTAGAACTTTTTAGTATAATTACCAATATTTAA
TTTATTGATCAATTTATTATGAAATAACCCTTCTAACTAAACTT
Found at i:582213 original size:24 final size:25
Alignment explanation
Indices: 582167--582213 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
582157 TAATATAGAG
* * *
582167 TATTTGAAAATCAATATATATTTTT
1 TATTTGAAAATAAATACAAATTTTT
582192 TATTTG-AAATAAATACAAATTT
1 TATTTGAAAATAAATACAAATTT
582214 ATATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
TATTTGAAAATAAATACAAATTTTT
Found at i:584168 original size:21 final size:21
Alignment explanation
Indices: 584135--584174 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
584125 TCATTGAATT
*
584135 TTATTATCTTTTCTATTTCAA
1 TTATTATCTTTTCAATTTCAA
584156 TTATTATAC-TTTCAATTTC
1 TTATTAT-CTTTTCAATTTC
584175 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTATCTTTTCAATTTCAA
Found at i:585634 original size:21 final size:22
Alignment explanation
Indices: 585590--585642 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
585580 AGACCAACGG
*
585590 GCTGAAAACC--GGTAGAACCG
1 GCTGAAAACCGGGGTAGAACCA
585610 GCTGAAAACCGGGGT-GAACCA
1 GCTGAAAACCGGGGTAGAACCA
585631 GCTGAAAACCGG
1 GCTGAAAACCGG
585643 CAAAATCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 10 0.33
21 17 0.57
22 3 0.10
ACGTcount: A:0.34, C:0.25, G:0.32, T:0.09
Consensus pattern (22 bp):
GCTGAAAACCGGGGTAGAACCA
Found at i:586582 original size:18 final size:17
Alignment explanation
Indices: 586559--586605 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
586549 ATAATTAAAA
586559 ATTTTAAATTATTTATAT
1 ATTTTAAATTATTT-TAT
586577 ATTTTAAATTTATTTTAT
1 ATTTTAAA-TTATTTTAT
*
586595 ATTTTATATTA
1 ATTTTAAATTA
586606 AAAATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 3 0.11
18 18 0.67
19 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTAAATTATTTTAT
Found at i:586610 original size:25 final size:25
Alignment explanation
Indices: 586568--586618 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
586558 AATTTTAAAT
** *
586568 TATTTATATATTTTAAATTTATTTTA
1 TATTTATATATTAAAAATAT-TTTTA
586594 TATTT-TATATTAAAAATATTTTTA
1 TATTTATATATTAAAAATATTTTTA
586618 T
1 T
586619 CTCTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 11 0.50
26 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTTATATATTAAAAATATTTTTA
Found at i:591861 original size:24 final size:24
Alignment explanation
Indices: 591834--591885 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
591824 TGAAAACAGG
591834 AATAAAGAGAGGAAGAGAATATGC
1 AATAAAGAGAGGAAGAGAATATGC
591858 AATAAAGAGAGGAAGAGAATATGC
1 AATAAAGAGAGGAAGAGAATATGC
591882 AATA
1 AATA
591886 TGGTAAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.56, C:0.04, G:0.27, T:0.13
Consensus pattern (24 bp):
AATAAAGAGAGGAAGAGAATATGC
Found at i:594562 original size:27 final size:27
Alignment explanation
Indices: 594532--594598 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
594522 TCTCTCTACT
594532 AAATAACTAAATCTTCTAAAACTGAAC
1 AAATAACTAAATCTTCTAAAACTGAAC
594559 AAATAACTAAATCTTCTAAAACTGAAC
1 AAATAACTAAATCTTCTAAAACTGAAC
594586 AAATAACTAAATC
1 AAATAACTAAATC
594599 CGATCATCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.54, C:0.18, G:0.03, T:0.25
Consensus pattern (27 bp):
AAATAACTAAATCTTCTAAAACTGAAC
Found at i:601934 original size:16 final size:17
Alignment explanation
Indices: 601910--601941 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
601900 TTACTATTAA
601910 ATTTAAATTATATTTTG
1 ATTTAAATTATATTTTG
601927 ATTT-AATTATATTTT
1 ATTTAAATTATATTTT
601942 ATTATCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTAAATTATATTTTG
Found at i:602641 original size:47 final size:46
Alignment explanation
Indices: 602587--602700 Score: 158
Period size: 47 Copynumber: 2.4 Consensus size: 46
602577 TAAAAATAAA
* **
602587 TTATTTTTCTTTTTTACAATTATTTT-AATCGAGTTTAAATTATATTT
1 TTATTTTTATTTTTTACAATTATTTTAAAT-GAGTTTAAA-TATACAT
602634 TTATTTTTATTTTTTACAATTATTTTAAATGAGTTTAAATATACAT
1 TTATTTTTATTTTTTACAATTATTTTAAATGAGTTTAAATATACAT
*
602680 TAATTTTTATTGTTTTACAAT
1 TTATTTTTATT-TTTTACAAT
602701 GTTTGTTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
46 15 0.25
47 43 0.70
48 3 0.05
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (46 bp):
TTATTTTTATTTTTTACAATTATTTTAAATGAGTTTAAATATACAT
Found at i:605971 original size:36 final size:37
Alignment explanation
Indices: 605899--605972 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
605889 GTTGAAAAAT
* *
605899 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATATTCTTTAAAAAAATTAAAATCATAAA
* *
605936 ATTTATATA-ATTCTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATATATATTCTTTAAAAAAATT-AAAATCATAAA
605972 A
1 A
605973 AAGGTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 19 0.59
37 13 0.41
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (37 bp):
ATTTATATATATTCTTTAAAAAAATTAAAATCATAAA
Found at i:613230 original size:23 final size:23
Alignment explanation
Indices: 613203--613246 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
613193 TAAACAACTG
*
613203 AAAACGTACCATAAAGGTAAAGA
1 AAAACGTACCATAAAGATAAAGA
**
613226 AAAACGTGTCATAAAGATAAA
1 AAAACGTACCATAAAGATAAA
613247 ATGAGACATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.11, G:0.16, T:0.16
Consensus pattern (23 bp):
AAAACGTACCATAAAGATAAAGA
Found at i:614490 original size:60 final size:60
Alignment explanation
Indices: 614379--614525 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 60
614369 GAACATATGA
* * *
614379 ATAGTTGAGTGACCATTTTGTAACTTTTAACAATCGATGGACTAAAAAAAGCAACGCCCT
1 ATAGTTGAGGGAACATTTTGTAACTTTTAACAATCGATGGACTAAAAAAAGCAACACCCT
* * * * ** * *
614439 ATAGTTGAGGGATCATTTTGTAACTTTTAATAGTCAGA-GGATTTCATAAAGCAACACCTT
1 ATAGTTGAGGGAACATTTTGTAACTTTTAACAATC-GATGGACTAAAAAAAGCAACACCCT
*
614499 ATACTTGAGGGAACATTTT-TATACTTT
1 ATAGTTGAGGGAACATTTTGTA-ACTTT
614526 ACCCATTAAG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
59 2 0.03
60 69 0.95
61 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (60 bp):
ATAGTTGAGGGAACATTTTGTAACTTTTAACAATCGATGGACTAAAAAAAGCAACACCCT
Found at i:619502 original size:31 final size:31
Alignment explanation
Indices: 619464--619526 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
619454 GAGGTTTCTG
*
619464 CAAATAATACTAGGAGACTCATGTAAGGCAT
1 CAAATAATACAAGGAGACTCATGTAAGGCAT
* *
619495 CAAATAATACAAGGATATTCATGTAAGGCAT
1 CAAATAATACAAGGAGACTCATGTAAGGCAT
619526 C
1 C
619527 GCATCTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (31 bp):
CAAATAATACAAGGAGACTCATGTAAGGCAT
Found at i:621439 original size:7 final size:7
Alignment explanation
Indices: 621427--621452 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
621417 ACAGTGGCCG
621427 GAAGAAA
1 GAAGAAA
621434 GAAGAAA
1 GAAGAAA
621441 GAAGAAA
1 GAAGAAA
621448 GAAGA
1 GAAGA
621453 GCAACATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:630151 original size:27 final size:27
Alignment explanation
Indices: 630112--630167 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
630102 CCCGGACTCG
*
630112 AAAATATTTTATATATAATTAATATAA
1 AAAATATTATATATATAATTAATATAA
630139 AAAATATTATATATATAATTAATATAA
1 AAAATATTATATATATAATTAATATAA
630166 AA
1 AA
630168 GATAAGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAATATTATATATATAATTAATATAA
Found at i:630179 original size:27 final size:27
Alignment explanation
Indices: 630122--630179 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
630112 AAAATATTTT
** *
630122 ATATATAATTAATATAAAAAATATTAT
1 ATATATAATTAATATAAAAAATAAGAA
*
630149 ATATATAATTAATATAAAAGATAAGAA
1 ATATATAATTAATATAAAAAATAAGAA
630176 ATAT
1 ATAT
630180 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
ATATATAATTAATATAAAAAATAAGAA
Found at i:630941 original size:2 final size:2
Alignment explanation
Indices: 630934--630962 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
630924 TATTTATTTC
630934 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 T
630963 GCATTAAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:641388 original size:14 final size:14
Alignment explanation
Indices: 641369--641398 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
641359 ATATAAAATT
641369 TTAAATTTTTTAAA
1 TTAAATTTTTTAAA
641383 TTAAATTTTTTAAA
1 TTAAATTTTTTAAA
641397 TT
1 TT
641399 TTTATAAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAAATTTTTTAAA
Found at i:641808 original size:2 final size:2
Alignment explanation
Indices: 641801--641828 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
641791 TCTTGTTAAA
641801 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
641829 CACAAGAATA
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:654101 original size:2 final size:2
Alignment explanation
Indices: 654094--654124 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
654084 ACGTATCTTA
654094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
654125 GTCCTAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:655050 original size:20 final size:20
Alignment explanation
Indices: 655021--655059 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
655011 AAAGCTCATA
*
655021 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
655041 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
655060 GTGGTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:679417 original size:23 final size:24
Alignment explanation
Indices: 679372--679417 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
679362 TGTTGATGAA
*
679372 TTGAACATATAAATAAATTTGTTC
1 TTGAACATATAAATAAATATGTTC
* *
679396 TTGAACGT-TAAATGAATATGTT
1 TTGAACATATAAATAAATATGTT
679418 TATAAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (24 bp):
TTGAACATATAAATAAATATGTTC
Found at i:679530 original size:2 final size:2
Alignment explanation
Indices: 679525--679554 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
679515 ATATATTAAA
679525 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
679555 ACCTTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:680726 original size:57 final size:57
Alignment explanation
Indices: 680638--680880 Score: 362
Period size: 57 Copynumber: 4.3 Consensus size: 57
680628 CACAGTTTCC
*
680638 AAAATCGCGTTGCAATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
1 AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
* * * *
680695 AAAATCGTGTTGCGATAGTACTGTTTACCTATGTCGGTAAGTAGCGTTGTGAATTTG
1 AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
* * *
680752 TAAATCTCGTTGCGATAGTACTGTTTACCTGTATCGGTAATTAGCGTTGCGAATTT-
1 AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
* *
680808 ATAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGGGAATTTA
1 A-AAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
**
680866 AAAATATCGTTGCGA
1 AAAATCGCGTTGCGA
680881 ATTTATAAAT
Statistics
Matches: 166, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
57 165 0.99
58 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (57 bp):
AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
Found at i:680882 original size:20 final size:20
Alignment explanation
Indices: 680850--680900 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
680840 TATCGGTAAT
*
680850 TAGCGTTGGGAATTTAAAAA
1 TAGCGTTGCGAATTTAAAAA
* *
680870 TATCGTTGCGAATTTATAAA
1 TAGCGTTGCGAATTTAAAAA
*
680890 TCGCGTTGCGA
1 TAGCGTTGCGA
680901 TAGTACTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (20 bp):
TAGCGTTGCGAATTTAAAAA
Found at i:680893 original size:77 final size:77
Alignment explanation
Indices: 680796--681209 Score: 639
Period size: 77 Copynumber: 5.4 Consensus size: 77
680786 CGGTAATTAG
* *
680796 CGTTGCGAATTTATAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGGGA
1 CGTTGCGAATTTATAAATCGCGTTGCGATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGA
* *
680861 ATTTAAAAATAT
66 ATTTGAAAATCT
*
680873 CGTTGCGAATTTATAAATCGCGTTGCGATAGTACTGTTTACCTAGGTCGGTAATTAGCGTTGCGA
1 CGTTGCGAATTTATAAATCGCGTTGCGATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGA
*
680938 ATTTGAAAACCT
66 ATTTGAAAATCT
* *
680950 CGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATGTCGGTAATTAACGTTGCGA
1 CGTTGCGAATTTATAAATCGCGTTGCGATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGA
*
681015 ATTTAAAAATCT
66 ATTTGAAAATCT
* *
681027 CATTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGA
1 CGTTGCGAATTTATAAATCGCGTTGCGATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGA
681092 ATTTGAAAATCT
66 ATTTGAAAATCT
* * * * * *
681104 CGTTGCGAATTTGTAAATCGCGTTGTGATAGTATTGTTTATCTATATCGGTAATTAGCGTTACGA
1 CGTTGCGAATTTATAAATCGCGTTGCGATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGA
*
681169 ATTTGAAAATCG
66 ATTTGAAAATCT
* *
681181 CGTTGCGAATTTAGAAAATCACGTTGCGA
1 CGTTGCGAATTTA-TAAATCGCGTTGCGA
681210 ATTTGGAAAA
Statistics
Matches: 311, Mismatches: 25, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
77 299 0.96
78 12 0.04
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.36
Consensus pattern (77 bp):
CGTTGCGAATTTATAAATCGCGTTGCGATAGTACTGTTTACCTATGTCGGTAATTAGCGTTGCGA
ATTTGAAAATCT
Done.