Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008803.1 Hibiscus syriacus cultivar Beakdansim tig00111954_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: 1826237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1530516 original size:14 final size:14
Alignment explanation
Indices: 1530488--1530530 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
1530478 AATAAATATC
1530488 ATAAAATAAATTTTAA
1 ATAAAA-AAA-TTTAA
1530504 ATAAAAAAATTTAA
1 ATAAAAAAATTTAA
1530518 A-AAATAAAATTTA
1 ATAAA-AAAATTTA
1530531 TTTAGGTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.12
14 14 0.54
15 3 0.12
16 6 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAAAAATTTAA
Found at i:1533950 original size:138 final size:138
Alignment explanation
Indices: 1533737--1534779 Score: 1239
Period size: 138 Copynumber: 7.7 Consensus size: 138
1533727 TGTTAGTACC
* * *
1533737 CAAAGTGGTGAAAGCACGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAAAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * * *
1533802 TTGCCCTATTATGTCACTCATGTCCCCCAGGGAACTATTCATGTCAATAACTATTATTTCTGAGG
66 TTACCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGG
1533867 GGACTTGG
131 GGACTTGG
* *
1533875 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCACCTTCCATTATTTAGTTAGAGAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * * *
1533940 TTACCCTATTATATCACTCATGTCCCCCGAGGAACTATTCATGACAATACCTATTATTTCTGAGG
66 TTACCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGG
1534005 GGA-----
131 GGACTTGG
* * * * *
1534008 C----T--TGAAAGCGCGATCCCAGGGG-GCACCTTCCATTATTTTATCAGAGAATATATTATTA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * *
1534066 TTACCCTATTATGTTACTCATGTCCCCCAGGGAACTATTCATGTTAGTACCTATTATTTCTGAGG
66 TTACCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGG
1534131 GGACTTGG
131 GGACTTGG
* * * *
1534139 AAAAGTGGTGAAAGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCAGAGAATCTGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * * *
1534204 TTACCCTATTATGTCACTTATGTCCCCCAGGGAACTATTCATGGCAGCACCTATTATTTCTGAGG
66 TTACCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGG
1534269 GGACTTGG
131 GGACTTGG
* *** * *
1534277 CAAAGTGGTGAAAGCGTGTTATGGGGGGGCGCA--TTCCATTATTTTGTCAGAGAAGATATTATC
1 CAAAGTGGTGAAAGCGCGTT-CCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATC
* * * * *
1534340 ATTGCCCTATTATGTCACTCATGTCCCCTGGGGAACTATTCATGTCAGTGCCTATTATTTTTTTT
65 ATTACCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTA--TTTCTG
* *
1534405 AAGGAACTTGG
128 AGGGGACTTGG
*
1534416 CAAAGTGGTGAAAGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCA
** *
1534480 TTGTCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGGCAGTACCTATTATTTCTGAGG
66 TTACCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGG
1534545 GGACTT-G
131 GGACTTGG
** ** * * *
1534552 -AAAGT-GTG--TTC-C--T-AGGGGGGCCCTCCTTCCATTATTTTGTTAGAGAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * * * *
1534609 TTGA-CCTATTATGTCACTTATATCCCCTGGGGAACTATTCATG---G-A-ATATTATTTCTTAG
66 TT-ACCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAG
1534668 GGGACTTGG
130 GGGACTTGG
* * * * *
1534677 CAAAGTTGTTAAAGCGCGTTCCCGGGGGTGCGA-CATCCATTATTTTTTCAGAGAATATGTTATC
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGC-ACCTTCCATTATTTTGTCAGAGAATATGTTATC
* *
1534741 ATTGCCCTATTATGTCACACATGTCCCCCGGGGAACTAT
65 ATTACCCTATTATGTCACTCATGTCCCCCGGGGAACTAT
1534780 AGATGGATGG
Statistics
Matches: 771, Mismatches: 104, Indels: 65
0.82 0.11 0.07
Matches are distributed among these distances:
124 19 0.02
125 2 0.00
126 98 0.13
127 20 0.03
128 5 0.01
129 74 0.10
130 1 0.00
131 1 0.00
132 2 0.00
133 68 0.09
134 3 0.00
135 6 0.01
136 1 0.00
137 107 0.14
138 244 0.32
139 120 0.16
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (138 bp):
CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCA
TTACCCTATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGG
GGACTTGG
Found at i:1534122 original size:264 final size:265
Alignment explanation
Indices: 1533643--1534779 Score: 1276
Period size: 264 Copynumber: 4.3 Consensus size: 265
1533633 GCACGTTTCT
* * * * *
1533643 GGGGGCGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCTCTATTATATCACTCATGT
1 GGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTCATGT
* ** * * * *
1533708 CCCTCG-GGAGCACTATTCATGTTAGTACCCA--A------AGTGG---TGAAAGCACGTTCCC-
66 CCCCCGAGGA--ACTATTCATGGCAGTACCTATTATTTCTGAGGGGACTTGAAAGCGCGATCCCA
* * *
1533760 GGGGGCGCGCCTTCCATTATTTTGTCAGAAAATATGTTATCATTGCCCTATTATGTCACTCATGT
129 GGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTACCCTATTATGTCACTCATGT
* *
1533825 CCCCCAGGGAACTATTCATGTCAATAACTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGC
193 CCCCCAGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGC
1533890 GCGTTCCC
258 GCGTTCCC
* * *
1533898 GGGGGCGCACCTTCCATTATTTAGTTAGAGAATATGTTATCATTACCCTATTATATCACTCATGT
1 GGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTCATGT
* *
1533963 CCCCCGAGGAACTATTCATGACAATACCTATTATTTCTGAGGGGACTTGAAAGCGCGATCCCA-G
66 CCCCCGAGGAACTATTCATGGCAGTACCTATTATTTCTGAGGGGACTTGAAAGCGCGATCCCAGG
* * * *
1534027 GGGGCACCTTCCATTATTTTATCAGAGAATATATTATTATTACCCTATTATGTTACTCATGTCCC
131 GGGGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTACCCTATTATGTCACTCATGTCCC
* *
1534092 CCAGGGAACTATTCATGTTAGTACCTATTATTTCTGAGGGGACTTGGAAAAGTGGTGAAAGCGCG
196 CCAGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGCG
1534157 TTCCC
261 TTCCC
* * * *
1534162 GAGGGCGCGCCTTCCATTATTTTGTCAGAGAATCTGTTATCATTACCCTATTATGTCACTTATGT
1 GGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTCATGT
* * *
1534227 CCCCC-AGGGAACTATTCATGGCAGCACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAG
66 CCCCCGA-GGAACTATTCATGGCAGTACCTATTATTTCTGAGGGGACTT-G-AAAG-CGCG--A-
*** * * *
1534291 CGTGTTATGGGGGGGCGCATTCCATTATTTTGTCAGAGAAGATATTATCATTGCCCTATTATGTC
124 --TCCCA--GGGGGGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTACCCTATTATGTC
** * * * * *
1534356 ACTCATGTCCCCTGGGGAACTATTCATGTCAGTGCCTATTATTTTTTTTAAGGAACTTGGCAAAG
185 ACTCATGTCCCCCAGGGAACTATTCATGTCAGTACCTATTA--TTTCTGAGGGGACTTGGCAAAG
1534421 TGGTGAAAGCGCGTTCCC
248 TGGTGAAAGCGCGTTCCC
* **
1534439 GGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTATTATGTCACTCATGT
1 GGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTCATGT
* * * * *
1534503 CCCCCGGGGAACTATTCATGGCAGTACCTATTATTTCTGAGGGGACTTGAAAGTGTGTTCCTAGG
66 CCCCCGAGGAACTATTCATGGCAGTACCTATTATTTCTGAGGGGACTTGAAAGCGCGATCCCAGG
* * * * *
1534568 GGGGCCCTCCTTCCATTATTTTGTTAGAGAATATGTTATCATTGA-CCTATTATGTCACTTATAT
131 GGGG--CGCCTTCCATTATTTTGTCAGAGAATATATTATCATT-ACCCTATTATGTCACTCATGT
** * * * *
1534632 CCCCTGGGGAACTATTCATG---G-A-ATATTATTTCTTAGGGGACTTGGCAAAGTTGTTAAAGC
193 CCCCCAGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGC
1534692 GCGTTCCC
258 GCGTTCCC
* * * * *
1534700 GGGGGTGCGA-CATCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATTATGTCACACATG
1 GGGGGCGC-ACCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTCATG
*
1534764 TCCCCCGGGGAACTAT
65 TCCCCCGAGGAACTAT
1534780 AGATGGATGG
Statistics
Matches: 762, Mismatches: 87, Indels: 59
0.84 0.10 0.06
Matches are distributed among these distances:
254 16 0.02
255 64 0.08
256 4 0.01
261 40 0.05
262 72 0.09
263 6 0.01
264 222 0.29
265 19 0.02
266 10 0.01
267 2 0.00
268 72 0.09
269 1 0.00
272 2 0.00
273 3 0.00
274 4 0.01
275 86 0.11
276 100 0.13
277 39 0.05
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (265 bp):
GGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGTCACTCATGT
CCCCCGAGGAACTATTCATGGCAGTACCTATTATTTCTGAGGGGACTTGAAAGCGCGATCCCAGG
GGGGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTACCCTATTATGTCACTCATGTCCC
CCAGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAGCGCG
TTCCC
Found at i:1534478 original size:139 final size:137
Alignment explanation
Indices: 1534010--1534779 Score: 933
Period size: 139 Copynumber: 5.7 Consensus size: 137
1534000 TGAGGGGACT
* * * * * * *
1534010 TGAAAGCGCGATCCCAGGGGGCACCTTCCATTATTTTATCAGAGAATATATTATTATTACCCTAT
1 TGAAAGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
* * * *
1534075 TATGTTACTCATGTCCCCCAGGGAACTATTCATGTTAGTACCTATTATTTCTGAGGGGACTTGGA
66 TATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGC
1534140 AAAGTGG
131 AAAGTGG
* * *
1534147 TGAAAGCGCGTTCCCGAGGGCGCGCCTTCCATTATTTTGTCAGAGAATCTGTTATCATTACCCTA
1 TGAAAGCGCGTTCCCG-GGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * *
1534212 TTATGTCACTTATGTCCCCCAGGGAACTATTCATGGCAGCACCTATTATTTCTGAGGGGACTTGG
65 TTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGG
1534277 CAAAGTGG
130 CAAAGTGG
* *** * * *
1534285 TGAAAGCGTGTTATGGGGGGGCGCATTCCATTATTTTGTCAGAGAAGATATTATCATTGCCCTAT
1 TGAAAGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
* * * * * *
1534350 TATGTCACTCATGTCCCCTGGGGAACTATTCATGTCAGTGCCTATTATTTTTTTTAAGGAACTTG
66 TATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTA--TTTCTGAGGGGACTTG
1534415 GCAAAGTGG
129 GCAAAGTGG
*
1534424 TGAAAGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTAT
1 TGAAAGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
*
1534489 TATGTCACTCATGTCCCCCGGGGAACTATTCATGGCAGTACCTATTATTTCTGAGGGGACTT-G-
66 TATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGC
1534552 AAAGT-G
131 AAAGTGG
* * * *
1534558 T--------GTTCCTAGGGGGGCCCTCCTTCCATTATTTTGTTAGAGAATATGTTATCATTGACC
1 TGAAAGCGCGTTCC-CGGGGGG--CGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* * * * *
1534615 TATTATGTCACTTATATCCCCTGGGGAACTATTCATG---G-A-ATATTATTTCTTAGGGGACTT
63 TATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTT
*
1534675 GGCAAAGTTG
128 GGCAAAGTGG
* * * *
1534685 TTAAAGCGCGTTCCCGGGGGTGCGACATCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTCCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
1534750 TTATGTCACACATGTCCCCCGGGGAACTAT
65 TTATGTCACTCATGTCCCCCGGGGAACTAT
1534780 AGATGGATGG
Statistics
Matches: 546, Mismatches: 69, Indels: 40
0.83 0.11 0.06
Matches are distributed among these distances:
124 19 0.03
125 2 0.00
126 11 0.02
127 8 0.01
129 72 0.13
133 63 0.12
134 7 0.01
135 11 0.02
136 1 0.00
137 109 0.20
138 121 0.22
139 122 0.22
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (137 bp):
TGAAAGCGCGTTCCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGC
AAAGTGG
Found at i:1534963 original size:23 final size:23
Alignment explanation
Indices: 1534915--1534964 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1534905 TGAATTTTGA
* * *
1534915 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGAATAAAATGTGAAGG
1534938 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGAATAAAATGTGAAG-G
1534961 ATAA
1 ATAA
1534965 GTTGGTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (23 bp):
ATAAATTGAATAAAATGTGAAGG
Found at i:1535058 original size:14 final size:14
Alignment explanation
Indices: 1535039--1535069 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1535029 TGATAAGTTG
1535039 GTTTTAATGTATAT
1 GTTTTAATGTATAT
1535053 GTTTTAATGTATAT
1 GTTTTAATGTATAT
1535067 GTT
1 GTT
1535070 AAGGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:1535216 original size:34 final size:34
Alignment explanation
Indices: 1535177--1535249 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
1535167 TTAAGTTGAA
*
1535177 TTTAATGTTAAATTTCGAATACTTTAATTTGTAT
1 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
*
1535211 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACTATAATTTGTAT
1535245 TTTAA
1 TTTAA
1535250 AAACATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.53
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACTATAATTTGTAT
Found at i:1535821 original size:21 final size:21
Alignment explanation
Indices: 1535775--1535836 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1535765 AAAACCATGC
* *
1535775 AGGCTAGGCATATAA-CCTGGT
1 AGGCTAGGAATATAACCCT-GA
*
1535796 GGGCTAGGAATATAACCCTGA
1 AGGCTAGGAATATAACCCTGA
*
1535817 AGGCTAGGAATGTAACCCTG
1 AGGCTAGGAATATAACCCTG
1535837 CGGAGATGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 32 0.91
22 3 0.09
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (21 bp):
AGGCTAGGAATATAACCCTGA
Found at i:1535911 original size:42 final size:42
Alignment explanation
Indices: 1535832--1535911 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
1535822 AGGAATGTAA
* * * *
1535832 CCCTGCGGAGATGGTATATAAACTGGTGGGCTTGGCATATAC
1 CCCTGCGGAGATGGCATATAAACTGGAGAGCTAGGCATATAC
* * *
1535874 CCCTGTGGAGATGGCATCTGAACTGGAGAGCTAGGCAT
1 CCCTGCGGAGATGGCATATAAACTGGAGAGCTAGGCAT
1535912 CATCATCGGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.24
Consensus pattern (42 bp):
CCCTGCGGAGATGGCATATAAACTGGAGAGCTAGGCATATAC
Found at i:1537487 original size:24 final size:24
Alignment explanation
Indices: 1537454--1537510 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1537444 TAAATTCATG
1537454 ATAAAT-TTAA-ATTAAAAATAATA
1 ATAAATATTAACATTAAAAATAA-A
**
1537477 ATAAATATTAACATTAATTATAAA
1 ATAAATATTAACATTAAAAATAAA
*
1537501 AAAAATATTA
1 ATAAATATTA
1537511 TCATATCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.21
24 14 0.48
25 9 0.31
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAATATTAACATTAAAAATAAA
Found at i:1537625 original size:20 final size:22
Alignment explanation
Indices: 1537586--1537625 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1537576 ATAACTGTAG
*
1537586 ACAAAAGATAGATATAATTAGC
1 ACAAAAAATAGATATAATTAGC
1537608 ACAAAAAATA-AT-TAATTA
1 ACAAAAAATAGATATAATTA
1537626 CTAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (22 bp):
ACAAAAAATAGATATAATTAGC
Found at i:1537666 original size:16 final size:16
Alignment explanation
Indices: 1537638--1537705 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 16
1537628 AAATTTAAAT
*
1537638 AAATAATAATTATAT-
1 AAATAATATTTATATA
*
1537653 AAATATTATTTTATATTA
1 AAATAATA-TTTATA-TA
1537671 AAATAATATTTATAT-
1 AAATAATATTTATATA
* *
1537686 -AATTATATTAATATA
1 AAATAATATTTATATA
1537701 AAATA
1 AAATA
1537706 TAACAACTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
14 12 0.29
15 7 0.17
16 9 0.21
17 7 0.17
18 7 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATAATATTTATATA
Found at i:1537691 original size:30 final size:33
Alignment explanation
Indices: 1537638--1537705 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 33
1537628 AAATTTAAAT
*
1537638 AAATAATAATTATATAAATATTAT-TTTATATTA
1 AAATAATAATTATATAAATATTATATTAATA-TA
*
1537671 AAATAAT-ATT-TATATA-ATTATATTAATATA
1 AAATAATAATTATATAAATATTATATTAATATA
1537701 AAATA
1 AAATA
1537706 TAACAACTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 12 0.38
31 10 0.31
32 3 0.09
33 7 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
AAATAATAATTATATAAATATTATATTAATATA
Found at i:1538896 original size:12 final size:12
Alignment explanation
Indices: 1538879--1538932 Score: 81
Period size: 12 Copynumber: 4.5 Consensus size: 12
1538869 ATAAAAATAA
*
1538879 CTAACTCTTAAC
1 CTAACTCTTCAC
1538891 CTAACTCTTCAC
1 CTAACTCTTCAC
*
1538903 CTAATTCTTCAC
1 CTAACTCTTCAC
*
1538915 CTAACTCTTCAG
1 CTAACTCTTCAC
1538927 CTAACT
1 CTAACT
1538933 AAATTGATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.28, C:0.35, G:0.02, T:0.35
Consensus pattern (12 bp):
CTAACTCTTCAC
Found at i:1543514 original size:12 final size:12
Alignment explanation
Indices: 1543486--1543540 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
1543476 ATATACAAAT
1543486 ACCTAACTC-TC
1 ACCTAACTCTTC
*
1543497 ACCTAACTCTTT
1 ACCTAACTCTTC
*
1543509 ACCTAATTCTTC
1 ACCTAACTCTTC
1543521 ACCTAACTCTTC
1 ACCTAACTCTTC
*
1543533 AACTAACT
1 ACCTAACT
1543541 AAATTGCTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.35
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:1545512 original size:28 final size:27
Alignment explanation
Indices: 1545474--1545534 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
1545464 ATTTATAAAT
* *
1545474 ATTATTTTTTATTAAAATAATTTATGTA
1 ATTATTATTTATTAAAATAATTAAT-TA
*
1545502 ATTATTATTTATTAAATTAATTAATTA
1 ATTATTATTTATTAAAATAATTAATTA
1545529 ATTATT
1 ATTATT
1545535 TTTGTACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
ATTATTATTTATTAAAATAATTAATTA
Found at i:1547279 original size:42 final size:42
Alignment explanation
Indices: 1547220--1547299 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
1547210 ACCGATGATG
* * *
1547220 ATGCCCAGCCCTCCAGTTCAGATGCCATCTCCTCAGGGGTAT
1 ATGCCAAGCCCACCAGTTCAGATGCCATCTCCACAGGGGTAT
* *
1547262 ATGCCAAGCCCACCAGTTTATATGCCATCTCCACAGGG
1 ATGCCAAGCCCACCAGTTCAGATGCCATCTCCACAGGG
1547300 TTACATTCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.23
Consensus pattern (42 bp):
ATGCCAAGCCCACCAGTTCAGATGCCATCTCCACAGGGGTAT
Found at i:1547314 original size:42 final size:42
Alignment explanation
Indices: 1547220--1547329 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
1547210 ACCGATGATG
* * * * * *
1547220 ATGCCCAGCCCTCCAGTTCAGATGCCATCTCCTCAGGGGTAT
1 ATGCCAAGCCCACCAGTTTACATGCCATCTCCACAGGGGTAC
* *
1547262 ATGCCAAGCCCACCAGTTTATATGCCATCTCCACAGGGTTAC
1 ATGCCAAGCCCACCAGTTTACATGCCATCTCCACAGGGGTAC
* * * *
1547304 ATTCCTAGCCCGCCAGGTTACATGCC
1 ATGCCAAGCCCACCAGTTTACATGCC
1547330 TAGCCCGCAG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAAGCCCACCAGTTTACATGCCATCTCCACAGGGGTAC
Found at i:1547343 original size:21 final size:22
Alignment explanation
Indices: 1547295--1547343 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
1547285 GCCATCTCCA
*
1547295 CAGGGTTACATTCCTAGCCCGC
1 CAGGGTTACATGCCTAGCCCGC
1547317 CA-GGTTACATGCCTAGCCCG-
1 CAGGGTTACATGCCTAGCCCGC
1547337 CAGGGTT
1 CAGGGTT
1547344 TTATGACACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (22 bp):
CAGGGTTACATGCCTAGCCCGC
Found at i:1548184 original size:63 final size:64
Alignment explanation
Indices: 1548082--1548211 Score: 217
Period size: 63 Copynumber: 2.0 Consensus size: 64
1548072 TTTCATGCTC
* * *
1548082 ACAACCAACTTATCACTTCACATTTATTCAATTTGTCCATAATATTTTATCCAATATATTCA-A
1 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCATA
*
1548145 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCATA
1 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCATA
1548209 ACA
1 ACA
1548212 TTTTATCCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 58 0.94
64 4 0.06
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (64 bp):
ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCATA
Found at i:1548199 original size:23 final size:23
Alignment explanation
Indices: 1548167--1548252 Score: 154
Period size: 23 Copynumber: 3.7 Consensus size: 23
1548157 TCACTTCACA
* *
1548167 TTTATTCAATTTATCCATAACAT
1 TTTATCCAATTTATTCATAACAT
1548190 TTTATCCAATTTATTCATAACAT
1 TTTATCCAATTTATTCATAACAT
1548213 TTTATCCAATTTATTCATAACAT
1 TTTATCCAATTTATTCATAACAT
1548236 TTTATCCAATTTATTCA
1 TTTATCCAATTTATTCA
1548253 AACTTCACAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATCCAATTTATTCATAACAT
Found at i:1548547 original size:116 final size:116
Alignment explanation
Indices: 1548297--1548677 Score: 617
Period size: 116 Copynumber: 3.3 Consensus size: 116
1548287 ATTCAATTCC
*
1548297 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAA-GCCCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCCCCCCG
* * *
1548361 GGAACGCGCTTTCACCACTTAGGGTACTGACATGAATAGTGCCCCCGAGAG
66 GGAACGCGCTTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
* *
1548412 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGTGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCCCCCCG
* * * * *
1548477 GTAACGTGCCTTCACCACTTTGGGTACTGATATAAATAGTTCCCCCGAGGG
66 GGAACGCGCTTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
* *
1548528 ATATGGGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCCCCCCG
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCCCCCCG
1548593 GGAACGCGCTTTCACCACTTTGGGTACTGATATGAATAGTGCCCCC--GGG
66 GGAACGCGCTTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
1548642 ACATGAGTGACATAATAGGGC-ATGATAACATATTCT
1 ACATGAGTGACATAATAGGGCAATGATAACATATTCT
1548678 ATGGTACTGA
Statistics
Matches: 243, Mismatches: 22, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
113 15 0.06
114 22 0.09
115 53 0.22
116 153 0.63
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (116 bp):
ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCCCCCCG
GGAACGCGCTTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGG
Found at i:1548802 original size:180 final size:180
Alignment explanation
Indices: 1548499--1549041 Score: 781
Period size: 180 Copynumber: 3.0 Consensus size: 180
1548489 CACCACTTTG
1548499 GGTACTGATATAAATAGTTCCCCCGAGGGATATGGGTGACATAATAGGGCAATGATAACATATTC
1 GGTACTGATATAAATAGTT-CCCCGAGGGATATGGGTGACATAATA-GGCAATGATAACATATTC
1548564 TCTGACAAAATAATAGAAGGCGCCCCCCGGGAACGCGCTTTCACCACTTTGGGTACTGATATGAA
64 TCTGACAAAATAATAGAAGGCGCCCCCCGGGAACGCGCTTTCACCACTTTGGGTACTGATATGAA
1548629 TAGTGCCCCCGGGACATGAGTGACATAATAGGGC-ATGATAACATATTCTAT
129 TAGTGCCCCCGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTAT
1548680 GGTACTGATATAAATAGTTCCCCGAGGGATATGGGTGACATAATAGGTCAATGATAACATATTCT
1 GGTACTGATATAAATAGTTCCCCGAGGGATATGGGTGACATAATAGG-CAATGATAACATATTCT
* *
1548745 CTGACAAAATAATAGAAGGCGCCTCCCGGGAACACGCTTTCACCACTTTGGGTACTGATATGAAT
65 CTGACAAAATAATAGAAGGCGCCCCCCGGGAACGCGCTTTCACCACTTTGGGTACTGATATGAAT
*
1548810 AGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
130 AGTGCCCCC--GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTAT
* ** ** * * * *
1548863 GATA-AAATAATGGA-AG-GCGCCC-AAGGACATGAGTGACATAATAGGCAATGATAACATATTC
1 GGTACTGAT-ATAAATAGTTC-CCCGAGGGATATGGGTGACATAATAGGCAATGATAACATATTC
* * * *
1548924 TCTGAAAAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCACCACTTTGGGTACTGACATGA
64 TCTGACAAAATAATAGAAGGCG-CCCCCCGGGAACGCGCTTTCACCACTTTGGGTACTGATATGA
** * *
1548989 ATAGTGTCTCCGAGGGACATAAGTAACATAATAGGGCAATGATAACATATTCT
128 ATAGTG-C-CCCCGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1549042 CTGACAAAAT
Statistics
Matches: 331, Mismatches: 22, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
179 2 0.01
180 151 0.46
181 122 0.37
182 32 0.10
183 24 0.07
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (180 bp):
GGTACTGATATAAATAGTTCCCCGAGGGATATGGGTGACATAATAGGCAATGATAACATATTCTC
TGACAAAATAATAGAAGGCGCCCCCCGGGAACGCGCTTTCACCACTTTGGGTACTGATATGAATA
GTGCCCCCGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTAT
Found at i:1548926 original size:64 final size:65
Alignment explanation
Indices: 1548822--1548948 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 65
1548812 TGCCCCCGAG
*
1548822 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATAAAATAATGGAAGGCGCCCAA
1 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATGGAAGGCGCCCAA
1548887 GGACATGAGTGACATAATA-GGCAATGATAACATATTCTCTGAAAAAATAATGGAAGGCGCCC
1 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATGGAAGGCGCCC
1548949 CCCCGGGAAC
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 42 0.69
65 19 0.31
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (65 bp):
GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATGGAAGGCGCCCAA
Found at i:1548982 original size:296 final size:293
Alignment explanation
Indices: 1548297--1549179 Score: 973
Period size: 296 Copynumber: 3.0 Consensus size: 293
1548287 ATTCAATTCC
1548297 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAA-GCCCCCCCCG
1 ACATGAGTGACATAATA-GGCAATGATAACATATTCTCTGA-AAAATAAT-GAAGGCCCCCCCCG
* * * *
1548361 GGAACGCGCTTTCACCACTTAGGGTACTGACATGAATAGTGCCCCCGAGAGACATGAGTGACATA
63 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGTCCCCGAGGGACATGAGTGACATA
* * * *
1548426 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGTGCCCCCCGGTAACGTGCCTTCA
128 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCG-CCCCCGGGAACGCGCTTTCA
* * *
1548491 CCACTTTGGGTACTGATATAAATAGTTCCCCCGAGGGATATGGGTGACATAATAGGGCAATGATA
192 CCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGGATATGAGTGACATAATAGGGCAATGATA
**
1548556 ACATATTCTCTGACAAAATAATAGAAGGCGCCCCCCGGG
257 ACATATTCTCTGACAAAATAATAGAAGGCG--CCCAAGG
* * * * * * * * * * ** * *
1548595 A-ACGCGCTTTCACCACT-TTGGGTACTGATATGA-ATAGTGCCCCCG--GGA-CATG-AGTGAC
1 ACATGAG---TGA-CA-TAATAGGCAATGATA--ACATA-T-TCTCTGAAAAATAATGAAG-GCC
****** * * *** * ** * * * * *
1548653 ATAATAGGGCATGATAACAT-A-TTCTAT-GGTACTGATATAAATAGT-TCCCCGAGGGATATGG
56 CCCCCCGGGAACG-CGCCTTCACCACTTTGGGTACTGACATGAATAGTGTCCCCGAGGGACATGA
* * *
1548714 GTGACATAATAGGTCAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCCTCCCGGGAACA
120 GTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCC-CCCGGGAACG
*
1548779 CGCTTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGG
184 CGCTTTCACCACTTTGGGTACTGATATGAATAGTGCCCCCGAGGGATATGAGTGACATAATAGGG
* *
1548844 CAATGATAACATATTCTCTGATAAAATAATGGAAGGCGCCCAAGG
249 CAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCCCAAGG
1548889 ACATGAGTGACATAATAGGCAATGATAACATATTCTCTGAAAAAATAATGGAAGGCGCCCCCCCG
1 ACATGAGTGACATAATAGGCAATGATAACATATTCTCTG-AAAAATAAT-GAAGGC-CCCCCCCG
* * *
1548954 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGTCTCCGAGGGACATAAGTAACATA
63 GGAACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGTCCCCGAGGGACATGAGTGACATA
1549019 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA-GCGCCCCCGGGAACGCGCTTTCAC
128 ATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCGGGAACGCGCTTTCAC
* *
1549083 CACTTTGGGTACTGACATGAATAGTGCCCCTGAGGGATATGAGTGACATAATAGGGCAATGATAA
193 CACTTTGGGTACTGATATGAATAGTGCCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAA
1549148 CATATTCTCTGACAAAATAATAGAAGGCGCCC
258 CATATTCTCTGACAAAATAATAGAAGGCGCCC
1549180 CCCGGGAACG
Statistics
Matches: 462, Mismatches: 96, Indels: 57
0.75 0.16 0.09
Matches are distributed among these distances:
288 3 0.01
289 2 0.00
290 4 0.01
291 12 0.03
292 4 0.01
293 4 0.01
294 15 0.03
295 118 0.26
296 185 0.40
297 77 0.17
298 4 0.01
299 10 0.02
300 12 0.03
301 6 0.01
302 3 0.01
303 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (293 bp):
ACATGAGTGACATAATAGGCAATGATAACATATTCTCTGAAAAATAATGAAGGCCCCCCCCGGGA
ACGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGTCCCCGAGGGACATGAGTGACATAATA
GGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCGGGAACGCGCTTTCACCAC
TTTGGGTACTGATATGAATAGTGCCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACAT
ATTCTCTGACAAAATAATAGAAGGCGCCCAAGG
Found at i:1549234 original size:116 final size:116
Alignment explanation
Indices: 1548887--1549663 Score: 1258
Period size: 116 Copynumber: 6.7 Consensus size: 116
1548877 AGGCGCCCAA
*
1548887 GGACATGAGTGACATAATA-GGCAATGATAACATATTCTCTGAAAAAATAATGGAAGGCGCCCCC
1 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCG-CCCC
* *
1548951 CCGGGAACGCGCCTTCACCACTTTGGG-TACTGACATGAATAGTGTCTCCGAG
65 CCGGGAACGCGCCTTCACCACTTTGGGTTA-TGACATGAATAGTGCCCCCGAG
* *
1549003 GGACATAAGTAACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAA-GCG-CCCC
1 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
* *
1549066 CGGGAACGCGCTTTCACCACTTTGGG-TACTGACATGAATAGTGCCCCTGAG
66 CGGGAACGCGCCTTCACCACTTTGGGTTA-TGACATGAATAGTGCCCCCGAG
* *
1549117 GGATATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCCCCC
1 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
* * *
1549182 CGGGAACGCACCTTCACCACTTTGAGTTATGATATGAATAGTGCCCCCGAG
66 CGGGAACGCGCCTTCACCACTTTGGGTTATGACATGAATAGTGCCCCCGAG
1549233 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
1 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
* *
1549298 CGGGAACGCGCCTTCACTACTTTGGGTTATGATATGAATAGTGCCCCCGAG
66 CGGGAACGCGCCTTCACCACTTTGGGTTATGACATGAATAGTGCCCCCGAG
*
1549349 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGTGCCCCC
1 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
* *
1549414 CGGGAACGCGCCTTCACCACTTTGGGTTATGACATTAATAGTACCCCCGAG
66 CGGGAACGCGCCTTCACCACTTTGGGTTATGACATGAATAGTGCCCCCGAG
* *
1549465 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACCCCCCC
1 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
* *
1549530 CGGGAACGCGCCTTCACCACTTTGGGTTCTGACATGAATAGTTGCCCCCGAA
66 CGGGAACGCGCCTTCACCACTTTGGGTTATGACATGAATAG-TGCCCCCGAG
* * * *
1549582 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCAGACAAAATAATAGAAGGCACCCTC
1 GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
1549647 CGGGAACGCGCCTTCAC
66 CGGGAACGCGCCTTCAC
1549664 GTGAATAGTA
Statistics
Matches: 618, Mismatches: 38, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
114 103 0.17
115 3 0.00
116 390 0.63
117 122 0.20
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (116 bp):
GGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCC
CGGGAACGCGCCTTCACCACTTTGGGTTATGACATGAATAGTGCCCCCGAG
Found at i:1552872 original size:16 final size:18
Alignment explanation
Indices: 1552853--1552892 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1552843 TATAAATGAT
1552853 TAATTATATTATTTAATAA
1 TAATTATATTATTT-ATAA
*
1552872 TAATTATATTATTTATTA
1 TAATTATATTATTTATAA
1552890 TAA
1 TAA
1552893 AAATATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATTATATTATTTATAA
Found at i:1552897 original size:24 final size:23
Alignment explanation
Indices: 1552841--1552897 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
1552831 ATATTGTAAT
* *
1552841 TTTATAAATGATTAATTATATTA
1 TTTAAAAATAATTAATTATATTA
*
1552864 TTTAATAATAATTATATTAT-TTA
1 TTTAAAAATAATTA-ATTATATTA
1552887 TTATAAAAATA
1 TT-TAAAAATA
1552898 TTTGATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTAAAAATAATTAATTATATTA
Found at i:1552898 original size:18 final size:19
Alignment explanation
Indices: 1552858--1552899 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1552848 ATGATTAATT
**
1552858 ATATTATTTAATAATAATT
1 ATATTATTTAATAATAAAA
*
1552877 ATATTATTT-ATTATAAAA
1 ATATTATTTAATAATAAAA
1552895 ATATT
1 ATATT
1552900 TGATTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATTATTTAATAATAAAA
Found at i:1565671 original size:20 final size:20
Alignment explanation
Indices: 1565646--1565690 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1565636 ATTCGGTAAG
1565646 TACATGACTTTAATTGAAAA
1 TACATGACTTTAATTGAAAA
1565666 TACATGACTTTAATTGAAAA
1 TACATGACTTTAATTGAAAA
1565686 TACAT
1 TACAT
1565691 AATGCTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (20 bp):
TACATGACTTTAATTGAAAA
Found at i:1565705 original size:22 final size:20
Alignment explanation
Indices: 1565646--1565706 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
1565636 ATTCGGTAAG
*
1565646 TACATGACTTTAATTGAAAA
1 TACATAACTTTAATTGAAAA
*
1565666 TACATGACTTTAATTGAAAA
1 TACATAACTTTAATTGAAAA
*
1565686 TACATAATGCTTTAAATGAAA
1 TACATAA--CTTTAATTGAAA
1565707 GGAGAAGTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 26 0.70
22 11 0.30
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (20 bp):
TACATAACTTTAATTGAAAA
Found at i:1568089 original size:21 final size:20
Alignment explanation
Indices: 1568064--1568102 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1568054 CCATCTTGTT
*
1568064 TTTTTTGGATTTTTTTTTTGG
1 TTTTTTGG-TTTTCTTTTTGG
1568085 TTTTTTGGTTTTCTTTTT
1 TTTTTTGGTTTTCTTTTT
1568103 CTTTATCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.03, C:0.03, G:0.15, T:0.79
Consensus pattern (20 bp):
TTTTTTGGTTTTCTTTTTGG
Found at i:1568526 original size:66 final size:66
Alignment explanation
Indices: 1568413--1568552 Score: 262
Period size: 66 Copynumber: 2.1 Consensus size: 66
1568403 AATCTAGGGT
*
1568413 ATTTAATGGGAAATAAAGTTATTAGGAAATTAAGATAAGAATAAAAGATTAATCTTAAGATAATG
1 ATTTAA-GGGAAATAAAGTTATTAGGAAATTAAGATAAGAATAAAAGATTAATCTGAAGATAATG
1568478 AC
65 AC
1568480 ATTTAAGGGAAATAAAGTTATTAGGAAATTAAGATAAGAATAAAAGATTAATCTGAAGATAATGA
1 ATTTAAGGGAAATAAAGTTATTAGGAAATTAAGATAAGAATAAAAGATTAATCTGAAGATAATGA
1568545 C
66 C
1568546 ATTTAAG
1 ATTTAAG
1568553 ATAATAAGAT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
66 66 0.92
67 6 0.08
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (66 bp):
ATTTAAGGGAAATAAAGTTATTAGGAAATTAAGATAAGAATAAAAGATTAATCTGAAGATAATGA
C
Found at i:1571486 original size:16 final size:17
Alignment explanation
Indices: 1571465--1571497 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1571455 AGGTGTCACA
1571465 TTGACT-TTTCAAAACT
1 TTGACTCTTTCAAAACT
*
1571481 TTGACTCTTTTAAAACT
1 TTGACTCTTTCAAAACT
1571498 CATTGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (17 bp):
TTGACTCTTTCAAAACT
Found at i:1572124 original size:25 final size:25
Alignment explanation
Indices: 1572092--1572165 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
1572082 TACCACATAG
*
1572092 ATTTGTCCTGAAGGACTGCGTAGAA
1 ATTTGTCCTGAAGGACCGCGTAGAA
*
1572117 ATTTGTCCTGAAGGACCACGTAG-A
1 ATTTGTCCTGAAGGACCGCGTAGAA
*
1572141 ATTTGT-CTCGAAGGACCGCATAGAA
1 ATTTGTCCT-GAAGGACCGCGTAGAA
1572166 CCCTCGACTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.05
24 19 0.44
25 22 0.51
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (25 bp):
ATTTGTCCTGAAGGACCGCGTAGAA
Found at i:1572153 original size:24 final size:24
Alignment explanation
Indices: 1572060--1572157 Score: 94
Period size: 24 Copynumber: 4.1 Consensus size: 24
1572050 CACCTAAGTG
* * *
1572060 CCACGTAGAATATGAACC-GAAGTA
1 CCACGTAGAATTTG-TCCTGAAGGA
*
1572084 CCACATAG-ATTTGTCCTGAAGGA
1 CCACGTAGAATTTGTCCTGAAGGA
**
1572107 CTGCGTAGAAATTTGTCCTGAAGGA
1 CCACGTAG-AATTTGTCCTGAAGGA
1572132 CCACGTAGAATTTGT-CTCGAAGGA
1 CCACGTAGAATTTGTCCT-GAAGGA
1572156 CC
1 CC
1572158 GCATAGAACC
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
22 2 0.03
23 16 0.26
24 22 0.36
25 21 0.34
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCTGAAGGA
Found at i:1572314 original size:15 final size:15
Alignment explanation
Indices: 1572296--1572366 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
1572286 CACATAGGGT
*
1572296 ATTTTCACGTAGAAC
1 ATTTTCACATAGAAC
* *
1572311 ATTTTCACTTAGCAC
1 ATTTTCACATAGAAC
* *
1572326 ATCTTCACATAGAAG
1 ATTTTCACATAGAAC
* *
1572341 ATTTCCATATA-AAGC
1 ATTTTCACATAGAA-C
*
1572356 ATATTCACATA
1 ATTTTCACATA
1572367 CAATAAAAAT
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
14 2 0.05
15 40 0.95
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (15 bp):
ATTTTCACATAGAAC
Found at i:1578602 original size:38 final size:38
Alignment explanation
Indices: 1578560--1578638 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
1578550 ATTGACTTTG
1578560 TAAGGCATATAAAACATATAATGAAAACTTTAACTACT
1 TAAGGCATATAAAACATATAATGAAAACTTTAACTACT
*
1578598 TAAGGCATATAAAACGTATAATGAAAACTTTAACTACT
1 TAAGGCATATAAAACATATAATGAAAACTTTAACTACT
1578636 TAA
1 TAA
1578639 CAATGCATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (38 bp):
TAAGGCATATAAAACATATAATGAAAACTTTAACTACT
Found at i:1586212 original size:51 final size:50
Alignment explanation
Indices: 1586113--1586268 Score: 213
Period size: 51 Copynumber: 3.0 Consensus size: 50
1586103 GTAACTATTG
* *
1586113 AATAAAATAAAGATAATATTTTTTAATTTATCCTAATTCCTAATAAAATAAT
1 AATAAACTAAAGATAATA--TTTTAATTTATCCTAATTCTTAATAAAATAAT
* *
1586165 AATAAACTAAAGATAGTATTTTGATTCTATCCTAATTCTTAATAAAATAAT
1 AATAAACTAAAGATAATATTTTAATT-TATCCTAATTCTTAATAAAATAAT
* * *
1586216 AATAAACTAAAGATAATATTTTAACTTTATCTTAATTGTTGATAAAATAAT
1 AATAAACTAAAGATAATATTTTAA-TTTATCCTAATTCTTAATAAAATAAT
1586267 AA
1 AA
1586269 ATCTAATCCT
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
50 7 0.08
51 68 0.73
52 18 0.19
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (50 bp):
AATAAACTAAAGATAATATTTTAATTTATCCTAATTCTTAATAAAATAAT
Found at i:1587034 original size:18 final size:17
Alignment explanation
Indices: 1586992--1587034 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1586982 CTTTAGATTA
*
1586992 TTTATTTAATTATTTTC
1 TTTATTTAATTATTATC
*
1587009 TTTAATTTAATTCTTATC
1 TTT-ATTTAATTATTATC
1587027 TTATATTT
1 TT-TATTT
1587035 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 18 0.82
19 1 0.05
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATTTAATTATTATC
Found at i:1587231 original size:16 final size:15
Alignment explanation
Indices: 1587212--1587269 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
1587202 CTTTTCTAAA
1587212 ATTTAATATTTTCTTC
1 ATTTAATATTTT-TTC
*
1587228 ATTTATTTATTTTTTC
1 ATTTA-ATATTTTTTC
* *
1587244 TTTTAACATTTTTT-
1 ATTTAATATTTTTTC
1587258 ATTTTAATATTT
1 A-TTTAATATTT
1587270 CCCTCTTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 16 0.47
16 12 0.35
17 6 0.18
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTAATATTTTTTC
Found at i:1590068 original size:19 final size:20
Alignment explanation
Indices: 1590026--1590067 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1590016 AACCAGATTG
*
1590026 CCCAGATGGTACCGGTACCC
1 CCCAGATGGTACCGATACCC
1590046 CCCAGATGGTACCGATACCC
1 CCCAGATGGTACCGATACCC
1590066 CC
1 CC
1590068 ATGCCAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.14
Consensus pattern (20 bp):
CCCAGATGGTACCGATACCC
Found at i:1591653 original size:120 final size:120
Alignment explanation
Indices: 1591459--1591710 Score: 438
Period size: 120 Copynumber: 2.1 Consensus size: 120
1591449 AAGTCTTTAA
*
1591459 CTCTCGAAGAGTTATTTGGTTCACTCCTCACTCATGAAATGATGCTTCAAGATGAGGTAGACCTC
1 CTCTCGAAGATTTATTTGGTTCACTCCTCACTCATGAAATGATGCTTCAAGATGAGGTAGACCTC
*
1591524 GAGAAGATTAACGAGCCAAAGAAGGAGACT-GAGAAAAAGAAGAACATGGGAGTTG
66 GAGAAGATTAACGAGCCAAAGAAGGAGA-TGGAGAAAAACAAGAACATGGGAGTTG
*
1591579 CTCTCGAAGATTTATTTGGTTCACTCCTCACTCATGAAATGATGCTTCAAGATGAGGTATACCTC
1 CTCTCGAAGATTTATTTGGTTCACTCCTCACTCATGAAATGATGCTTCAAGATGAGGTAGACCTC
*
1591644 GAGAAGATTAACGAGCCAAAGAAGGAGATGGAGAAAAACAAGAACGTGGGAGTTG
66 GAGAAGATTAACGAGCCAAAGAAGGAGATGGAGAAAAACAAGAACATGGGAGTTG
1591699 CTCTC-AA-ATTTA
1 CTCTCGAAGATTTA
1591711 CAAGAGATGA
Statistics
Matches: 127, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
118 5 0.04
119 3 0.02
120 119 0.94
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (120 bp):
CTCTCGAAGATTTATTTGGTTCACTCCTCACTCATGAAATGATGCTTCAAGATGAGGTAGACCTC
GAGAAGATTAACGAGCCAAAGAAGGAGATGGAGAAAAACAAGAACATGGGAGTTG
Found at i:1594634 original size:23 final size:22
Alignment explanation
Indices: 1594603--1594663 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
1594593 CTGTGTGCTA
*
1594603 GGTATCGATACCCCCTTTGAATG
1 GGTACCGATACCCCC-TTGAATG
**
1594626 GGTACCGATATCATCCTTGAATG
1 GGTACCGATA-CCCCCTTGAATG
*
1594649 GGTACCAATACCCCC
1 GGTACCGATACCCCC
1594664 CGTGAGGGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 3 0.10
23 25 0.81
24 3 0.10
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.26
Consensus pattern (22 bp):
GGTACCGATACCCCCTTGAATG
Found at i:1596573 original size:16 final size:16
Alignment explanation
Indices: 1596544--1596581 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1596534 AAACACTTTG
* *
1596544 ATGTTGTTGGATTGTT
1 ATGTTTTTGAATTGTT
1596560 ATGTTTTTGAATTGTT
1 ATGTTTTTGAATTGTT
1596576 ATGTTT
1 ATGTTT
1596582 AAATTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.61
Consensus pattern (16 bp):
ATGTTTTTGAATTGTT
Found at i:1597325 original size:20 final size:20
Alignment explanation
Indices: 1597300--1597346 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1597290 GATTTCCCAA
* *
1597300 ATGGTATCGGTACCCCCTAG
1 ATGGTACCGATACCCCCTAG
1597320 ATGGTACCGATACCCCCTAG
1 ATGGTACCGATACCCCCTAG
1597340 ATGGTAC
1 ATGGTAC
1597347 ATATACCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (20 bp):
ATGGTACCGATACCCCCTAG
Found at i:1597352 original size:20 final size:20
Alignment explanation
Indices: 1597310--1597355 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1597300 ATGGTATCGG
*
1597310 TACCCCCTAGATGGTACCGA
1 TACCCCCTAGATGGTACAGA
*
1597330 TACCCCCTAGATGGTACATA
1 TACCCCCTAGATGGTACAGA
1597350 TACCCC
1 TACCCC
1597356 ATGCTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.37, G:0.15, T:0.22
Consensus pattern (20 bp):
TACCCCCTAGATGGTACAGA
Found at i:1603013 original size:123 final size:123
Alignment explanation
Indices: 1602741--1603013 Score: 336
Period size: 123 Copynumber: 2.2 Consensus size: 123
1602731 TTGTTAGAGT
* * * *
1602741 CAATGTCAACTTCACAGCGAAGGATATTAAACTCGAGCCAATGCAATTTTCAAGAATGGATTTCA
1 CAATTTCAACTTCACAACGAAGGATATTAAACTCAAGCCAATGCAATTTACAAGAATGGATTTCA
* *
1602806 ACTTCACTACGAAGGACATCCAATTAAAAGCTCAACTTCACAACGAATTAGCCATCCA
66 ACTTCACTACAAAGGACATCCAATTAAAAGCTCAACTTCACAACGAATGAGCCATCCA
* * * * * * *
1602864 CAATTTCAACTTCACACCAAAAGATATTAATCTCAAAG-CGATTCAATTTACAAGATTGGATTTC
1 CAATTTCAACTTCACAACGAAGGATATTAAACTC-AAGCCAATGCAATTTACAAGAATGGATTTC
* *
1602928 AACTTCA-TAACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCA-CCTA
65 AACTTCACT-ACAAAGGACATCCAATTAAAAGCTCAACTTCACAACGAATGAGCCATCC-A
** *
1602987 TGATTTCGACTTCACAACGAAGGATAT
1 CAATTTCAACTTCACAACGAAGGATAT
1603014 CGTACCTAAA
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
122 3 0.02
123 122 0.96
124 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.25
Consensus pattern (123 bp):
CAATTTCAACTTCACAACGAAGGATATTAAACTCAAGCCAATGCAATTTACAAGAATGGATTTCA
ACTTCACTACAAAGGACATCCAATTAAAAGCTCAACTTCACAACGAATGAGCCATCCA
Found at i:1603461 original size:270 final size:269
Alignment explanation
Indices: 1602952--1603553 Score: 931
Period size: 270 Copynumber: 2.2 Consensus size: 269
1602942 GGATATCCAA
* *
1602952 TTCAAAGCTCAACTTCACAACGAATGAGCCACCTATGATTTCGACTTCACAACGAAGGATATCGT
1 TTCAAAGCTCAACTTCACAACGAATGAGCCACCTATGATTTTGACTTCACAACGAAGGATATCGC
* *
1603017 ACCTAAAAGATTGACCCAACTTCACGAAGAATGAGTCAATTGTAACACAATAATGAAAACCAGTT
66 ACCCAAAAGATTGACCCAACTTCACGAAGAATGAGTCAATTGTAACACAACAATGAAAACCAGTT
* *
1603082 TTATACCAAAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAGAAGATGATC
131 TCATACCAAAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAAAAGATGATC
** *
1603147 CAAGAGCGACTTTCCAATACTTTAAGCCCGGTTTCAACTTCACGATGAAGGATATCGGGCTTAGG
196 CAAGAGCGACTTTCCAATACTTTAAGCCCAATTTCAACTTCACGATGAAGGATATCGGGCTCAGG
1603212 ATTTTTCAG
261 ATTTTTCAG
* * *
1603221 TTCAAAGCTCAACTTCACAATGAAGGAGCCACCTGTGATTTTGACTTCACAACGAAGGATATCGC
1 TTCAAAGCTCAACTTCACAACGAATGAGCCACCTATGATTTTGACTTCACAACGAAGGATATCGC
* *
1603286 ACCCAAAAGATTGACCCAACTTCATGATGAATGAGTC-ATCTGTAACACAACAATGAAAAACCAG
66 ACCCAAAAGATTGACCCAACTTCACGAAGAATGAGTCAAT-TGTAACACAACAATG-AAAACCAG
*
1603350 TTTCATACCAAAGTCTTTAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAAAAGATGA
129 TTTCATACCAAAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAAAAGATGA
* * * * * *
1603415 TCCAGGAGTGACTTTCCAATGCTTTGAGCCCAATTTCAACTTCACGATGAATGATATCGTGCTCA
194 TCCAAGAGCGACTTTCCAATACTTTAAGCCCAATTTCAACTTCACGATGAAGGATATCGGGCTCA
*
1603480 TGATTTTTCAG
259 GGATTTTTCAG
* *
1603491 TTCAAAGCTCAACTTCACAACGAATGAGCCA-CTCACGATTTTAACTTCACGAA-GAAGGATATC
1 TTCAAAGCTCAACTTCACAACGAATGAGCCACCT-ATGATTTTGACTTCAC-AACGAAGGATATC
1603554 ATGCCCAATG
Statistics
Matches: 302, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
268 2 0.01
269 110 0.36
270 188 0.62
271 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (269 bp):
TTCAAAGCTCAACTTCACAACGAATGAGCCACCTATGATTTTGACTTCACAACGAAGGATATCGC
ACCCAAAAGATTGACCCAACTTCACGAAGAATGAGTCAATTGTAACACAACAATGAAAACCAGTT
TCATACCAAAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTGGGCTAAAAGATGATC
CAAGAGCGACTTTCCAATACTTTAAGCCCAATTTCAACTTCACGATGAAGGATATCGGGCTCAGG
ATTTTTCAG
Found at i:1604694 original size:22 final size:22
Alignment explanation
Indices: 1604668--1604723 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
1604658 TCTCAATCTC
1604668 TTTAGATTATTTATTTAATTAT
1 TTTAGATTATTTATTTAATTAT
1604690 TTTAGATTATTTATTTAATTAT
1 TTTAGATTATTTATTTAATTAT
1604712 TTTA-ATGTATTT
1 TTTAGAT-TATTT
1604724 TATTCTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 2 0.06
22 31 0.94
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTAGATTATTTATTTAATTAT
Found at i:1604828 original size:16 final size:16
Alignment explanation
Indices: 1604810--1604839 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1604800 TATTTCCCTT
1604810 TTTTATC-TTATTTTG
1 TTTTATCTTTATTTTG
1604825 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
1604840 CCCACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:1604951 original size:18 final size:18
Alignment explanation
Indices: 1604928--1604969 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1604918 TGAAATTTAA
1604928 TATTTTCTT-CATTTATTT
1 TATTTTCTTACATTT-TTT
*
1604946 TATTTTTTTACATTTTTT
1 TATTTTCTTACATTTTTT
1604964 TATTTT
1 TATTTT
1604970 ATTATTTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTTCTTACATTTTTT
Found at i:1605110 original size:6 final size:6
Alignment explanation
Indices: 1605099--1605140 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
1605089 TGAATCGAGT
* *
1605099 ATTTGA ATTTGA ATTTTA ATTTTAA ATTTTA ATTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTT-A ATTTTA ATTTTA ATTTT
1605141 CGTAATTAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
6 28 0.82
7 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (6 bp):
ATTTTA
Found at i:1605126 original size:19 final size:19
Alignment explanation
Indices: 1605104--1605140 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1605094 CGAGTATTTG
1605104 AATTTGAATTTTAATTTTA
1 AATTTGAATTTTAATTTTA
*
1605123 AATTTTAATTTTAATTTT
1 AATTTGAATTTTAATTTT
1605141 CGTAATTAAG
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:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
AATTTGAATTTTAATTTTA
Found at i:1607193 original size:12 final size:12
Alignment explanation
Indices: 1607173--1607205 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
1607163 AAATAAAAAT
1607173 AAAAGAAAAAGCC
1 AAAA-AAAAAGCC
1607186 AAAAAAAAAGCC
1 AAAAAAAAAGCC
1607198 AAAAAAAA
1 AAAAAAAA
1607206 TCTAGAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGCC
Found at i:1614286 original size:30 final size:31
Alignment explanation
Indices: 1614252--1614328 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
1614242 ATTCAATGTT
* *
1614252 TAAGTGATCAAAACTTAATAAAACGATAA-G
1 TAAGTGACCAAAACTTAATAAAACAATAATG
* *
1614282 TAAGTAACCAAAACTTAATAAAATAATAATG
1 TAAGTGACCAAAACTTAATAAAACAATAATG
*
1614313 TAGGTGACCAAAACTT
1 TAAGTGACCAAAACTT
1614329 TTTTTTTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 25 0.62
31 15 0.38
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.25
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAAACAATAATG
Found at i:1615989 original size:23 final size:23
Alignment explanation
Indices: 1615963--1616011 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1615953 TAAATATCAC
*
1615963 TTAAAGA-AATATATAAAAATATT
1 TTAAAGATAACAT-TAAAAATATT
*
1615986 TT-AAGATAACATTAATAATATT
1 TTAAAGATAACATTAAAAATATT
1616008 TTAA
1 TTAA
1616012 TAAATAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (23 bp):
TTAAAGATAACATTAAAAATATT
Found at i:1621640 original size:27 final size:27
Alignment explanation
Indices: 1621610--1621670 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
1621600 TTATTTGATG
1621610 TTTTATCTATGAGTGTATTCA-ATTA-TT
1 TTTTATCT-TGAGTG-ATTCACATTACTT
* *
1621637 TTTTGTCTTTAGTGATTCACATTACTT
1 TTTTATCTTGAGTGATTCACATTACTT
*
1621664 TATTATC
1 TTTTATC
1621671 ATTTCTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 5 0.18
26 9 0.32
27 14 0.50
ACGTcount: A:0.23, C:0.11, G:0.10, T:0.56
Consensus pattern (27 bp):
TTTTATCTTGAGTGATTCACATTACTT
Found at i:1625803 original size:2 final size:2
Alignment explanation
Indices: 1625796--1625827 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1625786 TGTCAGAAAG
1625796 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
1625828 CTTTTATAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1627950 original size:18 final size:19
Alignment explanation
Indices: 1627923--1627965 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1627913 GGATAACAGA
*
1627923 ATACCAAAAATGA-TATCG
1 ATACCAAAAAGGAGTATCG
*
1627941 ATACCGAAAAGGAGTATCG
1 ATACCAAAAAGGAGTATCG
*
1627960 GTACCA
1 ATACCA
1627966 TAGTGTAGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (19 bp):
ATACCAAAAAGGAGTATCG
Found at i:1628021 original size:22 final size:20
Alignment explanation
Indices: 1628003--1628047 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
1627993 AAGGTATCAG
1628003 TACCATAGTATAGAAGTATCGA
1 TACCATAGTA-AG-AGTATCGA
*
1628025 TACCATGGTAAGAGTATCGA
1 TACCATAGTAAGAGTATCGA
1628045 TAC
1 TAC
1628048 TATTGAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 2 0.09
22 9 0.41
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (20 bp):
TACCATAGTAAGAGTATCGA
Found at i:1628042 original size:20 final size:22
Alignment explanation
Indices: 1627953--1628047 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 22
1627943 ACCGAAAAGG
* * *
1627953 AGTATCGGTACCATAGTGTAGT
1 AGTATCGATACCATAGTATAGA
*
1627975 AGTATCGATA-C-T-G-AAAGAA
1 AGTATCGATACCATAGTATAG-A
1627994 AGGTATC-AGTACCATAGTATAGA
1 A-GTATCGA-TACCATAGTATAGA
*
1628017 AGTATCGATACCATGGTA-AG-
1 AGTATCGATACCATAGTATAGA
1628037 AGTATCGATAC
1 AGTATCGATAC
1628048 TATTGAGCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 19 0.32
21 4 0.07
22 24 0.41
23 4 0.07
24 3 0.05
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGA
Found at i:1628042 original size:42 final size:43
Alignment explanation
Indices: 1627936--1628027 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 43
1627926 CCAAAAATGA
* * * * *
1627936 TATCGATAC-CGAA-AAGGAGTATCGGTACCATAGTGTAGTAG
1 TATCGATACTCAAAGAAAGAGTATCAGTACCATAGTATAGAAG
*
1627977 TATCGATACTGAAAGAAAG-GTATCAGTACCATAGTATAGAAG
1 TATCGATACTCAAAGAAAGAGTATCAGTACCATAGTATAGAAG
1628019 TATCGATAC
1 TATCGATAC
1628028 CATGGTAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
41 9 0.21
42 31 0.72
43 3 0.07
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (43 bp):
TATCGATACTCAAAGAAAGAGTATCAGTACCATAGTATAGAAG
Found at i:1628487 original size:54 final size:54
Alignment explanation
Indices: 1628367--1628490 Score: 135
Period size: 54 Copynumber: 2.3 Consensus size: 54
1628357 TTACCGAAAG
1628367 GGCACTGTGTGTGCAACCTCACGAAATTATAATAAGTTTATAAATTTACGTATT
1 GGCACTGTGTGTGCAACCTCACGAAATTATAATAAGTTTATAAATTTACGTATT
* * * * * * * *
1628421 GGTAGTGGGTGTGCAACC-CACATAAATTATAATAGGTTTGTGAA-TTATTGTATT
1 GGCACTGTGTGTGCAACCTCAC-GAAATTATAATAAGTTTATAAATTTA-CGTATT
*
1628475 GGCACTATGTGTGCAA
1 GGCACTGTGTGTGCAA
1628491 ACTATAGAGT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
53 6 0.11
54 50 0.89
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.35
Consensus pattern (54 bp):
GGCACTGTGTGTGCAACCTCACGAAATTATAATAAGTTTATAAATTTACGTATT
Found at i:1629312 original size:81 final size:81
Alignment explanation
Indices: 1628563--1629300 Score: 1100
Period size: 81 Copynumber: 9.1 Consensus size: 81
1628553 ACTATTCTAA
*
1628563 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCATAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
1628628 AGATTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * *
1628644 AGTAAAAGATTAATGGCCTAGCTGCGTATTTGGGAGAAAGGTGTCAATTATGTCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
1628709 AGGTTAATTACCTTTG
66 AGGTTAAATACCTTTG
* * *
1628725 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1628790 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * *
1628806 AGTAAAAAATTAATGACCTAGCTGTGCATTTGGCAG-AAGTGTGTCAATTATGCCAGCTAGATGA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAG-GTGTCAATTATGCCAGTTAGATGA
1628870 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* * *
1628887 AGTAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATACCAGTTAGATTAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
1628952 ATGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
** * * *
1628968 AGTAAAAGATTAATGGTATAACTGTGTATTTGGCAGAAAGGTGTCAATTATGCCAGTTAAATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1629033 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* ** * * *
1629049 AGTAAATGATTAATGGCCTAGCTGTATATTTTGCATAAAGGTGTCAATTATGTCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
1629114 ATGTTAAATACCTTTA
66 AGGTTAAATACCTTTG
1629130 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* *
1629195 AGATTAAATATCTTTG
66 AGGTTAAATACCTTTG
* * * * * *
1629211 AGTAAAAGAGTAATGGCTTAACTGTGTATTTGGCAGAAAGGTGTCAATTATGTCATTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
1629276 AGGTTAAATACTTTTG
66 AGGTTAAATACCTTTG
*
1629292 GGTAAAAGA
1 AGTAAAAGA
1629301 CTAAATGCTT
Statistics
Matches: 587, Mismatches: 68, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
80 2 0.00
81 582 0.99
82 3 0.01
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:1630055 original size:2 final size:2
Alignment explanation
Indices: 1630045--1630074 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1630035 CTCTCTAATC
1630045 AT AT A- 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
1630075 CTTATTCATA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1630586 original size:12 final size:12
Alignment explanation
Indices: 1630569--1630593 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1630559 TTTTTTAAAA
1630569 AAAGTCAATTTT
1 AAAGTCAATTTT
1630581 AAAGTCAATTTT
1 AAAGTCAATTTT
1630593 A
1 A
1630594 GATTTGCTTA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
AAAGTCAATTTT
Found at i:1631830 original size:18 final size:17
Alignment explanation
Indices: 1631779--1631836 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 17
1631769 AAAAAAGATA
*
1631779 ATATATATATATATAA-T
1 ATATTTATATATA-AACT
1631796 ATAAGTTTATATATAAACT
1 AT-A-TTTATATATAAACT
1631815 ATATTTATATTATAAACT
1 ATATTTATA-TATAAACT
1631833 ATAT
1 ATAT
1631837 AATTACTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
17 8 0.22
18 16 0.44
19 12 0.33
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (17 bp):
ATATTTATATATAAACT
Found at i:1631846 original size:18 final size:18
Alignment explanation
Indices: 1631803--1631859 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
1631793 AATATAAGTT
*
1631803 TATA-TATAAACTATATT
1 TATACTATAAACTATATA
*
1631820 TATATTATAAACTATATA
1 TATACTATAAACTATATA
**
1631838 -ATTACTATAAGTTATATA
1 TA-TACTATAAACTATATA
1631856 TATA
1 TATA
1631860 AATTATGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 5 0.15
18 27 0.82
19 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (18 bp):
TATACTATAAACTATATA
Found at i:1631885 original size:19 final size:20
Alignment explanation
Indices: 1631870--1631908 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1631860 AATTATGTTT
1631870 ATATG-AACTATATATGTAA
1 ATATGAAACTATATATGTAA
1631889 ATATGTAAACTATATATGTA
1 ATATG-AAACTATATATGTA
1631909 TAAACTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (20 bp):
ATATGAAACTATATATGTAA
Found at i:1631965 original size:2 final size:2
Alignment explanation
Indices: 1631952--1631984 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1631942 ATTTATATTA
1631952 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
1631985 TATTCAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1632106 original size:17 final size:18
Alignment explanation
Indices: 1632084--1632125 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
1632074 ATAGGAAATT
1632084 TTGAGAATTT-AGAGAAA
1 TTGAGAATTTAAGAGAAA
1632101 TTGAGAATTTAGAGAGAAA
1 TTGAGAATTTA-AGAGAAA
1632120 TTGAGA
1 TTGAGA
1632126 TCATTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.43
19 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (18 bp):
TTGAGAATTTAAGAGAAA
Found at i:1635150 original size:16 final size:16
Alignment explanation
Indices: 1635131--1635166 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1635121 TGAAAGACGT
*
1635131 ATTGAAAAGAAGATGG
1 ATTGAAAAGAAAATGG
1635147 ATTGAAAAGAAAATGG
1 ATTGAAAAGAAAATGG
1635163 ATTG
1 ATTG
1635167 TGACCCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.22
Consensus pattern (16 bp):
ATTGAAAAGAAAATGG
Found at i:1636152 original size:17 final size:17
Alignment explanation
Indices: 1636116--1636165 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1636106 TTGAGAGTAA
* * *
1636116 TTTAATAAAAGAAATAG
1 TTTAATGAATGAACTAG
*
1636133 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
1636150 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
1636166 TTTCCCTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:1647461 original size:18 final size:18
Alignment explanation
Indices: 1647438--1647475 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1647428 AGTTTAGGTA
*
1647438 CTAAATGTGTACTTTACC
1 CTAAATGTATACTTTACC
*
1647456 CTAAATGTATAGTTTACC
1 CTAAATGTATACTTTACC
1647474 CT
1 CT
1647476 TTAAACTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (18 bp):
CTAAATGTATACTTTACC
Found at i:1647802 original size:364 final size:363
Alignment explanation
Indices: 1647109--1647823 Score: 1014
Period size: 364 Copynumber: 2.0 Consensus size: 363
1647099 AATCGTGTAT
* * *
1647109 CCTTTAAATCTAAGGGTAAATTACATGTTTAGTACCTAAACTATAAGTTCTGGTCTATTTTAATA
1 CCTTTAAATCTAAGGGTAAATTACACGTTTAGTACCTAAACTATAACTTCTGGTCAATTTTAATA
** * *
1647174 CATAAACTTTCATTTTTTTAAACCATATCTAAAGTTTAGATTTTTTTTATTTTAGTATCATTGTT
66 CATAAACTTTCATTTTTCAAAACCATACCTAAAGTTTAGATTTTTTTTATTTTAGTATCACTGTT
* *
1647239 CAAAATTTAACGTTAAGTTTTTTTAAAAAAAAATTAAAAGTTTATATACTAAATCGGACCAAAAT
131 CAAAATTTAACGTTAAGTTTTTTTAAAAAAAAATTAAAAGTTTAGATACTAAAACGGACCAAAAT
*
1647304 TGGTAGTTTAGTAACTAAACATGTTAAGTTTTTAACAGTGTATACTAAAATGAAATAAAAACTAA
196 TGGTAGTTTAGTAACTAAACATGTTAAGTTTTTAACAGTGTATACTAAAATGAAACAAAAACTAA
* * * * * *
1647369 ATGTATGTATAGTTTTGAAAAAGTTAAAAGTTTAGGTACTAAAACGGATAAAAATTGATAGTTTA
261 ATGTAAGTATAGTTTTGAAAAAGTTAAAAGTTTAGATACTAAAACAGATAAAAACTAATAGTGTA
1647434 GGTACTAAATGTGTACTTTACCCTAAATGTATAGTTTAC
326 GGTACTAAATGTGTACTTTA-CCTAAATGTATAGTTTAC
* * *
1647473 CCTTTAAA-CTTAAGGGTAAATTACACGTTTAGTACCTAAACTATCACTTTTGGTCAATTTTAGT
1 CCTTTAAATC-TAAGGGTAAATTACACGTTTAGTACCTAAACTATAACTTCTGGTCAATTTTAAT
* *
1647537 ACCTAAACTTTCAGCTTTTTCAAAACCATGCCTAAAGTTTAGATTTTTTTTATTTTAGTA-CAAC
65 ACATAAACTTTCA--TTTTTCAAAACCATACCTAAAGTTTAGATTTTTTTTATTTTAGTATC-AC
* *
1647601 TGTTCAAAATTTAACGTTAAG-TTTTTT-AAAAAAAATT-AAAGTTTAGGTACTAAAACGGATCA
127 TGTTCAAAATTTAACGTTAAGTTTTTTTAAAAAAAAATTAAAAGTTTAGATACTAAAACGGACCA
* * *
1647663 AATTTTGTAGTTTATGT-ACTACACATGTTAAGTTTTTAACAGTG-AGTACTAAAATGAAACAAA
192 AAATTGGTAGTTTA-GTAACTAAACATGTTAAGTTTTTAACAGTGTA-TACTAAAATGAAACAAA
* * * *
1647726 AATTAAATATTAAGTAT-GTTTTTGAAAAAGTTAAAAGTTTAGATACTAAAATAGATCAAAACTA
255 AACTAAAT-GTAAGTATAG-TTTTGAAAAAGTTAAAAGTTTAGATACTAAAACAGATAAAAACTA
*
1647790 ATAGTGTAGGTACTAAATGTGTAGTTTACCTAAA
318 ATAGTGTAGGTACTAAATGTGTACTTTACCTAAA
1647824 ATTTTATAAA
Statistics
Matches: 312, Mismatches: 31, Indels: 17
0.87 0.09 0.05
Matches are distributed among these distances:
362 1 0.00
363 90 0.29
364 151 0.48
365 7 0.02
366 63 0.20
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (363 bp):
CCTTTAAATCTAAGGGTAAATTACACGTTTAGTACCTAAACTATAACTTCTGGTCAATTTTAATA
CATAAACTTTCATTTTTCAAAACCATACCTAAAGTTTAGATTTTTTTTATTTTAGTATCACTGTT
CAAAATTTAACGTTAAGTTTTTTTAAAAAAAAATTAAAAGTTTAGATACTAAAACGGACCAAAAT
TGGTAGTTTAGTAACTAAACATGTTAAGTTTTTAACAGTGTATACTAAAATGAAACAAAAACTAA
ATGTAAGTATAGTTTTGAAAAAGTTAAAAGTTTAGATACTAAAACAGATAAAAACTAATAGTGTA
GGTACTAAATGTGTACTTTACCTAAATGTATAGTTTAC
Found at i:1648006 original size:17 final size:19
Alignment explanation
Indices: 1647968--1648006 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1647958 AATTATCATT
1647968 AAAAATATAAAAATATTAA
1 AAAAATATAAAAATATTAA
*
1647987 AAAAATATAATAAT-TTAA
1 AAAAATATAAAAATATTAA
1648005 AA
1 AA
1648007 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATATAAAAATATTAA
Found at i:1648655 original size:31 final size:33
Alignment explanation
Indices: 1648617--1648713 Score: 97
Period size: 36 Copynumber: 2.8 Consensus size: 33
1648607 TTTTTATTTT
1648617 AATATAAA-TATATATTTCATAAATTAAAACAAA
1 AATA-AAAGTATATATTTCATAAATTAAAACAAA
* * *
1648650 AATAAAAGTATATATTTTATAAGTTAAGACAAAGAA
1 AATAAAAGTATATATTTCATAAATTAA-A-ACA-AA
* * *
1648686 AATAAAAATATATATTTAATAAGTTAAA
1 AATAAAAGTATATATTTCATAAATTAAA
1648714 GACAGAGATA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
32 3 0.05
33 21 0.38
34 1 0.02
35 3 0.05
36 27 0.49
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (33 bp):
AATAAAAGTATATATTTCATAAATTAAAACAAA
Found at i:1648738 original size:39 final size:37
Alignment explanation
Indices: 1648617--1648753 Score: 167
Period size: 39 Copynumber: 3.8 Consensus size: 37
1648607 TTTTTATTTT
* * *
1648617 AATATAAATATATATTTCATAAATTAAA-AC--A-AA
1 AATAAAAATATATATTTAATAAGTTAAAGACAAAGAA
* *
1648650 AATAAAAGTATATATTTTATAAGTT-AAGACAAAGAA
1 AATAAAAATATATATTTAATAAGTTAAAGACAAAGAA
*
1648686 AATAAAAATATATATTTAATAAGTTAAAGACAGAGATAA
1 AATAAAAATATATATTTAATAAGTTAAAGACA-A-AGAA
1648725 AATAAAAATATATATTTAATAAGTTAAAG
1 AATAAAAATATATATTTAATAAGTTAAAG
1648754 TAAATAATAA
Statistics
Matches: 90, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
32 2 0.02
33 23 0.26
35 1 0.01
36 25 0.28
37 6 0.07
38 1 0.01
39 32 0.36
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.31
Consensus pattern (37 bp):
AATAAAAATATATATTTAATAAGTTAAAGACAAAGAA
Found at i:1648752 original size:22 final size:22
Alignment explanation
Indices: 1648688--1648752 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
1648678 ACAAAGAAAA
1648688 TAAAAATATATATTTAATAAGT
1 TAAAAATATATATTTAATAAGT
* * * *
1648710 TAAAGACAGAGA--TAA-AA--
1 TAAAAATATATATTTAATAAGT
1648727 TAAAAATATATATTTAATAAGT
1 TAAAAATATATATTTAATAAGT
1648749 TAAA
1 TAAA
1648753 GTAAATAATA
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 8 0.27
19 5 0.17
20 5 0.17
22 12 0.40
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (22 bp):
TAAAAATATATATTTAATAAGT
Found at i:1649408 original size:15 final size:15
Alignment explanation
Indices: 1649388--1649418 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1649378 ATATGTTGAG
*
1649388 TATTTTATAATTTAA
1 TATTTTATAAATTAA
1649403 TATTTTATAAATTAA
1 TATTTTATAAATTAA
1649418 T
1 T
1649419 TTATTGATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTTATAAATTAA
Found at i:1651584 original size:15 final size:15
Alignment explanation
Indices: 1651556--1651592 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1651546 GGTAGTTAAT
* *
1651556 GGGCGAGCGGATGTG
1 GGGCGGGCGAATGTG
1651571 GGGCGGGCGAATGTG
1 GGGCGGGCGAATGTG
1651586 GGGCGGG
1 GGGCGGG
1651593 TAAGGTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.14, G:0.65, T:0.11
Consensus pattern (15 bp):
GGGCGGGCGAATGTG
Found at i:1653673 original size:28 final size:29
Alignment explanation
Indices: 1653612--1653675 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1653602 TTTGAGTCAT
1653612 TCGACTATTAAAAAATACAAAATGATCAC
1 TCGACTATTAAAAAATACAAAATGATCAC
** *
1653641 TCGACTATTAAAAGTTATAAAATGATCA-
1 TCGACTATTAAAAAATACAAAATGATCAC
1653669 TCGACTA
1 TCGACTA
1653676 GGATATGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (29 bp):
TCGACTATTAAAAAATACAAAATGATCAC
Found at i:1659031 original size:65 final size:64
Alignment explanation
Indices: 1658920--1659075 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 64
1658910 TACACTTGGG
* * * *
1658920 GTGCATC-GATACACTAATTACATTCGATGTTTCAAAAGAGCAAGGAGTGTATCGATGCATGGTC
1 GTGCATCAG-TACACAAAATACATTCGATGTTTCAAAAAAGCAAGGAGTGCATCGATGCATGG-C
1658984 T
64 T
* *
1658985 GTGCATCAGTACATAAAATACATTCGATGTTTCAATAAAATC-AGGAGTGCATCGATGCATGGCT
1 GTGCATCAGTACACAAAATACATTCGATGTTTCAA-AAAAGCAAGGAGTGCATCGATGCATGGCT
*
1659049 GTGCATCAGTACACAAAATGCATTCGA
1 GTGCATCAGTACACAAAATACATTCGA
1659076 ATTAGGGTGT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 27 0.33
65 49 0.60
66 5 0.06
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (64 bp):
GTGCATCAGTACACAAAATACATTCGATGTTTCAAAAAAGCAAGGAGTGCATCGATGCATGGCT
Found at i:1663321 original size:21 final size:21
Alignment explanation
Indices: 1663297--1663340 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1663287 TTCGGATTCG
*
1663297 GATCCAGATATTT-GGATATCC
1 GATCC-GAAATTTAGGATATCC
1663318 GATCCGAAATTTAGGATATCC
1 GATCCGAAATTTAGGATATCC
1663339 GA
1 GA
1663341 ATTCGGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (21 bp):
GATCCGAAATTTAGGATATCC
Found at i:1663365 original size:17 final size:14
Alignment explanation
Indices: 1663331--1663357 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1663321 CCGAAATTTA
1663331 GGATATCCGAATTC
1 GGATATCCGAATTC
1663345 GGATATCCGAATT
1 GGATATCCGAATT
1663358 TTTCGGATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (14 bp):
GGATATCCGAATTC
Found at i:1663420 original size:16 final size:17
Alignment explanation
Indices: 1663389--1663422 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1663379 TTACTTTAAG
1663389 TATCCGAAATTTTCGGA
1 TATCCGAAATTTTCGGA
1663406 TATCCGAAA-TTTCGGA
1 TATCCGAAATTTTCGGA
1663422 T
1 T
1663423 CGGATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (17 bp):
TATCCGAAATTTTCGGA
Found at i:1664092 original size:2 final size:2
Alignment explanation
Indices: 1664085--1664119 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1664075 CAAACCAAAG
1664085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1664120 AGCATTTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1665164 original size:2 final size:2
Alignment explanation
Indices: 1665157--1665247 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
1665147 TCAGGCCAGG
* * * *
1665157 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
* * * * *
1665197 TA TA TT TA AA T- TA AA T- TA AA TT TA T- TA -A TA T- 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
1665234 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1665248 AAATAATTAT
Statistics
Matches: 64, Mismatches: 18, Indels: 14
0.67 0.19 0.15
Matches are distributed among these distances:
1 7 0.11
2 57 0.89
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1665182 original size:17 final size:17
Alignment explanation
Indices: 1665160--1665212 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
1665150 GGCCAGGTAT
1665160 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
1665177 ATATATA---AATATTATA
1 ATATATATTTAA-ATTA-A
1665193 TATATATATTTAAATTAA
1 -ATATATATTTAAATTAA
1665211 AT
1 AT
1665213 TAAATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
14 2 0.07
15 4 0.13
16 1 0.03
17 16 0.53
18 1 0.03
19 4 0.13
20 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:1665264 original size:39 final size:38
Alignment explanation
Indices: 1665157--1665267 Score: 118
Period size: 39 Copynumber: 2.9 Consensus size: 38
1665147 TCAGGCCAGG
* * *
1665157 TATATATATATTTAAATTAA-ATATATAAATATTATATA
1 TATATATATATATAAATTAATAT-TTTTAATATTATATA
* *
1665195 TATATATTTAAATTAAATTAA-ATTTATTAATATTATATA
1 TATATATATATA-TAAATTAATATTT-TTAATATTATATA
*
1665234 TATATATATATATAAAATAATTATTTTTAATATT
1 TATATATATATATAAATTAA-TATTTTTAATATT
1665268 TATCAAGGCG
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 17 0.28
39 40 0.66
40 4 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
TATATATATATATAAATTAATATTTTTAATATTATATA
Found at i:1665330 original size:29 final size:29
Alignment explanation
Indices: 1665297--1665352 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1665287 AAACCCGTCC
1665297 CCGTCCCCATTTAGCATAAACAATTTTCG
1 CCGTCCCCATTTAGCATAAACAATTTTCG
* *
1665326 CCGTCCCCGTTTAGCATAAACAGTTTT
1 CCGTCCCCATTTAGCATAAACAATTTT
1665353 TCCCATCCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.32
Consensus pattern (29 bp):
CCGTCCCCATTTAGCATAAACAATTTTCG
Found at i:1665365 original size:29 final size:29
Alignment explanation
Indices: 1665300--1665367 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1665290 CCCGTCCCCG
* *
1665300 TCCCCATTTAGCATAAACAATTTTCGCCG
1 TCCCCGTTTAGCATAAACAATTTTCGCCA
*
1665329 TCCCCGTTTAGCATAAACAGTTTTTC-CCA
1 TCCCCGTTTAGCATAAACA-ATTTTCGCCA
*
1665358 TCCTCGTTTA
1 TCCCCGTTTA
1665368 ATTCGGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 29 0.85
30 5 0.15
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.35
Consensus pattern (29 bp):
TCCCCGTTTAGCATAAACAATTTTCGCCA
Found at i:1666079 original size:13 final size:13
Alignment explanation
Indices: 1666042--1666079 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1666032 TCCTAATGAG
1666042 CAATGTTTGAAAA
1 CAATGTTTGAAAA
*
1666055 TAAT-TTTGAAAA
1 CAATGTTTGAAAA
*
1666067 CAATGTATGAAAA
1 CAATGTTTGAAAA
1666080 ATTATGATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:1666136 original size:17 final size:18
Alignment explanation
Indices: 1666104--1666146 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
1666094 AGTTTTCATG
1666104 AAAACAACATAATTAAATC
1 AAAACAACA-AATTAAATC
1666123 AAAACAAC-AATTAAATC
1 AAAACAACAAATTAAATC
1666140 AAAACAA
1 AAAACAA
1666147 AAAAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.67
19 8 0.33
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAACAACAAATTAAATC
Found at i:1666562 original size:23 final size:23
Alignment explanation
Indices: 1666532--1666602 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
1666522 TGCATAGTGT
1666532 ATCGATGCACATTCATGGAATGC
1 ATCGATGCACATTCATGGAATGC
* *
1666555 ATCGATGCATC-TTCAT--AGTGT
1 ATCGATGCA-CATTCATGGAATGC
*
1666576 ATCGATGCATATTCA-GGTAATGC
1 ATCGATGCACATTCATGG-AATGC
1666599 ATCG
1 ATCG
1666603 GTACACTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
21 16 0.42
23 21 0.55
24 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (23 bp):
ATCGATGCACATTCATGGAATGC
Found at i:1666574 original size:44 final size:44
Alignment explanation
Indices: 1666509--1666629 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
1666499 CCCAAACGGG
* *
1666509 TGCATCGGTACAC-TGCATAGTGTATCGATGCACATTCATGG-AA
1 TGCATCGATACACTTTCATAGTGTATCGATGCACATTCA-GGTAA
* *
1666552 TGCATCGATGCA-TCTTCATAGTGTATCGATGCATATTCAGGTAA
1 TGCATCGATACACT-TTCATAGTGTATCGATGCACATTCAGGTAA
* * *
1666596 TGCATCGGTACACTTTCATAGTGGATCCATGCAC
1 TGCATCGATACACTTTCATAGTGTATCGATGCAC
1666630 TTAGCACAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
43 12 0.18
44 52 0.80
45 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
TGCATCGATACACTTTCATAGTGTATCGATGCACATTCAGGTAA
Found at i:1666581 original size:21 final size:21
Alignment explanation
Indices: 1666524--1666590 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
1666514 CGGTACACTG
1666524 CATAGTGTATCGATGCA-CATT
1 CATAGTGTATCGATGCATC-TT
* *
1666545 CATGGAATGCATCGATGCATCTT
1 CAT--AGTGTATCGATGCATCTT
*
1666568 CATAGTGTATCGATGCATATT
1 CATAGTGTATCGATGCATCTT
1666589 CA
1 CA
1666591 GGTAATGCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 20 0.53
23 17 0.45
24 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (21 bp):
CATAGTGTATCGATGCATCTT
Found at i:1672406 original size:65 final size:64
Alignment explanation
Indices: 1672311--1672448 Score: 188
Period size: 65 Copynumber: 2.1 Consensus size: 64
1672301 GTAAACTAAT
* * *
1672311 TACATTCGATGTTTCAAAAGAGCCAGGAGTGTATCGATGCATGGTCTATGCATCGATACATAAAA
1 TACATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGGT-TATGCATCGATACACAAAA
* * *
1672376 TACATTCGATGTTTCAATAA-AATCATGAGTGCATCGATGCATGGTTGTGCATCGATACACAAAA
1 TACATTCGATGTTTCAA-AAGAACCAGGAGTGCATCGATGCATGGTTATGCATCGATACACAAAA
*
1672440 TGCATTCGA
1 TACATTCGA
1672449 ATTAGGGTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 25 0.38
65 38 0.58
66 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (64 bp):
TACATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGGTTATGCATCGATACACAAAA
Found at i:1684811 original size:221 final size:219
Alignment explanation
Indices: 1684408--1684849 Score: 850
Period size: 221 Copynumber: 2.0 Consensus size: 219
1684398 CATACTACTA
1684408 AAATAACTCGAGTGTCCTTATTGTTTCTCAAGTGTCACACAAAGGCCAGTCTTATGTAATCTTAC
1 AAATAACTCGAGTGTCCTTATTGTTTCTCAAGTGTCACACAAAGGCCAGTCTTATGTAATCTTAC
1684473 CTCATAGGTTCTTATGATTATGACACAATTACCGTAAACATTACATATATCTCATATTTATTACC
66 CTCATAGGTTCTTATGATTATGACACAATTACCGTAAACATTACATATATCTCATATTTATTACC
1684538 AAGATTTTCTATAGAGCTAATGTCTTTACATGCACGCGTCAACCAATGACATGCAAGGGTAAACA
131 AAGATTTTCTATAGAGCTAATGTCTTTACATGCACGCGTCAACCAATGACATGCAAGGGTAAACA
1684603 AAGTAG-TCAATTATTCGCTATCG
196 AAGTAGTTCAATTATTCGCTATCG
1684626 AAATAACTCGAGTGTCCTTATTGTTTCTCAAGTGTCACACAAAGGCCAGTCTTATGTAATCTTAC
1 AAATAACTCGAGTGTCCTTATTGTTTCTCAAGTGTCACACAAAGGCCAGTCTTATGTAATCTTAC
1684691 CTCATAAGGTTCTTATGATTATGACACAATTACCGTAAACATTACATTATTATCTCATATTTATT
66 CTCAT-AGGTTCTTATGATTATGACACAATTACCGTAAACATTACA-TA-TATCTCATATTTATT
1684756 ACCAAGATTTTCTATAGAGCTAATGTCTTTACATGCACGCGTCAACCAATGACATGCAAGGGTAA
128 ACCAAGATTTTCTATAGAGCTAATGTCTTTACATGCACGCGTCAACCAATGACATGCAAGGGTAA
1684821 ACAAAGTAGTTCAATTATTCGCTATCG
193 ACAAAGTAGTTCAATTATTCGCTATCG
1684848 AA
1 AA
1684850 CTCATCAAAG
Statistics
Matches: 220, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
218 70 0.32
219 40 0.18
220 2 0.01
221 89 0.40
222 19 0.09
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (219 bp):
AAATAACTCGAGTGTCCTTATTGTTTCTCAAGTGTCACACAAAGGCCAGTCTTATGTAATCTTAC
CTCATAGGTTCTTATGATTATGACACAATTACCGTAAACATTACATATATCTCATATTTATTACC
AAGATTTTCTATAGAGCTAATGTCTTTACATGCACGCGTCAACCAATGACATGCAAGGGTAAACA
AAGTAGTTCAATTATTCGCTATCG
Found at i:1685561 original size:55 final size:55
Alignment explanation
Indices: 1685439--1685816 Score: 541
Period size: 55 Copynumber: 6.9 Consensus size: 55
1685429 CTATACGAGA
** * * *
1685439 ATTCATCAACTCATGATGAATT-CGTGGGT-TGTACAC-ATAGTGCATGTACT-TTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGA-AGTGCCTGTA-TGGTG
* *
1685492 ATTCATCAAATCATGATGAATTCCGTGAATATGCACACGAAGTTCCTGTATGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTATGGTG
1685547 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTATGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTATGGTG
* * *
1685602 ATTCATCAAATCATGATGAATTTCGTGAATATGCACACGAAGTGCCTGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTATGGTG
*
1685657 ATTCATCAACTCAT-ATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTATGGTG
* * *
1685711 ATTCATCAACTCATGATGAATTTCATGAATATGCACACGAAGTGCTTGTATGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTATGGTG
* * * *
1685766 ATTCATCAACTGATAATGAATTCCATGAATATGCACACAAAGTGCCTGTAT
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTAT
1685817 AACATAAATG
Statistics
Matches: 297, Mismatches: 23, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
53 21 0.07
54 59 0.20
55 216 0.73
56 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTATGGTG
Found at i:1685713 original size:164 final size:164
Alignment explanation
Indices: 1685439--1685815 Score: 553
Period size: 164 Copynumber: 2.3 Consensus size: 164
1685429 CTATACGAGA
** * * **
1685439 ATTCATCAACTCATGATGAA-TTCGTGGGT-TGTACACATAGTGCATGTACTTTGATTCATCAAA
1 ATTCATCAACTCATGATGAATTTCGTGAATATGCACACA-AGTGCCTGTACGGTGATTCATCAAA
* *
1685502 TCATGATGAATTCCGTGAATATGCACACGAAGTTCCTGTATGGTGATTCATCAACTCATGATGAA
65 TCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGGTGATTCATCAACTCATGATGAA
*
1685567 TTCCGTGAATATGCACACGAAGTGCCTGTATGGTG
130 TTCCATGAATATGCACACGAAGTGCCTGTATGGTG
* *
1685602 ATTCATCAAATCATGATGAATTTCGTGAATATGCACACGAAGTGCCTGTACGGTGATTCATCAAC
1 ATTCATCAACTCATGATGAATTTCGTGAATATGCACAC-AAGTGCCTGTACGGTGATTCATCAAA
1685667 TCAT-ATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGGTGATTCATCAACTCATGATGAA
65 TCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGGTGATTCATCAACTCATGATGAA
* *
1685731 TTTCATGAATATGCACACGAAGTGCTTGTATGGTG
130 TTCCATGAATATGCACACGAAGTGCCTGTATGGTG
* * * *
1685766 ATTCATCAACTGATAATGAATTCCATGAATATGCACACAAAGTGCCTGTA
1 ATTCATCAACTCATGATGAATTTCGTGAATATGCACAC-AAGTGCCTGTA
1685816 TAACATAAAT
Statistics
Matches: 192, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
163 19 0.10
164 141 0.73
165 31 0.16
166 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (164 bp):
ATTCATCAACTCATGATGAATTTCGTGAATATGCACACAAGTGCCTGTACGGTGATTCATCAAAT
CATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGGTGATTCATCAACTCATGATGAAT
TCCATGAATATGCACACGAAGTGCCTGTATGGTG
Found at i:1686207 original size:22 final size:20
Alignment explanation
Indices: 1686165--1686235 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 20
1686155 ATGTTGCCTA
1686165 GTATCGATACCCTTACCATG
1 GTATCGATACCCTTACCATG
*
1686185 GTATCGATACTACCTTACTATG
1 GTATCGATAC--CCTTACCATG
* * *
1686207 GTACCGACACCCCTACCA--
1 GTATCGATACCCTTACCATG
1686225 GTATCGATACC
1 GTATCGATACC
1686236 AAAATTAGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 9 0.21
20 16 0.38
22 17 0.40
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (20 bp):
GTATCGATACCCTTACCATG
Found at i:1692376 original size:55 final size:55
Alignment explanation
Indices: 1692260--1692693 Score: 548
Period size: 55 Copynumber: 7.9 Consensus size: 55
1692250 CTATACGTGA
* * ***
1692260 ATTCATCAACTCATGATGAATTTCTTG-GGCTGCACAC-ATAGTGCTTGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGA-AGTGCTTGTACGGTG
* * *
1692314 ATTCATCAACTCATGATGAATTCCGTGAATATACACATGAAGTGCCTGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCTTGTACGGTG
* * *
1692369 ATTCATCAACTCATGATGAATTCCATGAATATGCACACGAAGTGCCTGTATGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCTTGTACGGTG
* * * * *
1692424 ATTCATCAGCTCATGATGAATTCTGTGAATATGCACACGAAATGCTTATACGATG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCTTGTACGGTG
* * * * **
1692479 TTTTATTAACTCATTATGAATTCCGTGAATATGCACACGAAGTGCTTGTATAGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCTTGTACGGTG
* * ** *
1692534 ATTCATCAACTCATGATGAATTCTGTGAACATATACACGAAGTACTTGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCTTGTACGGTG
* *
1692589 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTACATGTACGGTG
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCTTGTACGGTG
** * *
1692644 ATTCATCAACTCATGATGAATTCAATGAATATGCACACAAAGTGCCTGTA
1 ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCTTGTA
1692694 GGGCACATAA
Statistics
Matches: 326, Mismatches: 52, Indels: 3
0.86 0.14 0.01
Matches are distributed among these distances:
54 25 0.08
55 300 0.92
56 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTCCGTGAATATGCACACGAAGTGCTTGTACGGTG
Found at i:1693156 original size:22 final size:23
Alignment explanation
Indices: 1693119--1693163 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1693109 CTAGTATTGA
*
1693119 TACCCTTACCATGGTATCGATAC
1 TACCCTTACCATGGTACCGATAC
*
1693142 TACCC-TACTATGGTACCGATAC
1 TACCCTTACCATGGTACCGATAC
1693164 CCCCTACCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (23 bp):
TACCCTTACCATGGTACCGATAC
Found at i:1693178 original size:95 final size:95
Alignment explanation
Indices: 1693052--1693236 Score: 273
Period size: 95 Copynumber: 1.9 Consensus size: 95
1693042 AATATTTCTA
* * * * *
1693052 TACTATGGTACCTATACCCCCCTCGGGTATCGATACCAAAAATAGGTTCGATGTTACCTAGTATT
1 TACTATGGTACCGATACCCCCCTCCGGTATCGATACCAAAAATAGATTCGATGTTACATAGTATC
1693117 GATACCCTTACCATGGTATCGATACTACCC
66 GATACCCTTACCATGGTATCGATACTACCC
* * * *
1693147 TACTATGGTACCGATA-CCCCCTACCGTTATCGATACCAAAATTAGATTCGATGTTTCATGGTAT
1 TACTATGGTACCGATACCCCCCT-CCGGTATCGATACCAAAAATAGATTCGATGTTACATAGTAT
1693211 CGATACCCTTACCATGGTATCGATAC
65 CGATACCCTTACCATGGTATCGATAC
1693237 GACCTTGTCG
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
94 6 0.08
95 74 0.93
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (95 bp):
TACTATGGTACCGATACCCCCCTCCGGTATCGATACCAAAAATAGATTCGATGTTACATAGTATC
GATACCCTTACCATGGTATCGATACTACCC
Found at i:1695501 original size:5 final size:5
Alignment explanation
Indices: 1695493--1695520 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1695483 ACAAAACAAA
1695493 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
1695521 AATTAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:1695669 original size:16 final size:16
Alignment explanation
Indices: 1695650--1695689 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1695640 AATAGGGATT
1695650 AAATTGAATAAATTCA
1 AAATTGAATAAATTCA
1695666 AAATTGAATAAATTCA
1 AAATTGAATAAATTCA
1695682 AAATTGAA
1 AAATTGAA
1695690 GGGCAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (16 bp):
AAATTGAATAAATTCA
Found at i:1696820 original size:112 final size:113
Alignment explanation
Indices: 1696671--1697210 Score: 807
Period size: 112 Copynumber: 4.8 Consensus size: 113
1696661 AGTATCAAAC
**
1696671 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
1696736 ATGAACTTTCTCTGGAAAGGCTGATCCATCAATTGATGAATTCAGGTA
66 ATGAACTTTCTCTGGAAATGCTGATCCATCAATTGACGAATTCATGTA
1696784 AAAGG-TGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1696848 ATGAACTTTCTCTGGAAATGATGATCCATCAATTGACGAATTCATGTA
66 ATGAACTTTCTCTGGAAATGCTGATCCATCAATTGACGAATTCATGTA
1696896 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1696961 ATGAACTTT-TCTGGAAAAGCTGATCCATC-ATTGACGAATTCATGT-
66 ATGAACTTTCTCTGGAAATGCTGATCCATCAATTGACGAATTCATGTA
* *
1697006 AAAGGTTAAAC-AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
1697070 ATGAA-TTTCTCTGGCAATGTTGATCCATCCAA--GATGAAATTCA--AA
66 ATGAACTTTCTCTGGAAATGCTGATCCAT-CAATTGACG-AATTCATGTA
*
1697115 CAAAGGTTGAACAAATTCTTCTCATTATGAACTTGTTCTTTCCTTCTTCAGATGAG-TCTTCTCA
1 -AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCA
* * *
1697179 TTATGAAC-TTATCTGGCAATGTTGATCCATCA
64 TTATGAACTTTCTCTGGAAATGCTGATCCATCA
1697211 GTGATGGATT
Statistics
Matches: 398, Mismatches: 19, Indels: 23
0.90 0.04 0.05
Matches are distributed among these distances:
108 3 0.01
109 76 0.19
110 29 0.07
111 76 0.19
112 141 0.35
113 73 0.18
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGCTGATCCATCAATTGACGAATTCATGTA
Found at i:1697044 original size:225 final size:221
Alignment explanation
Indices: 1696665--1697210 Score: 825
Period size: 220 Copynumber: 2.5 Consensus size: 221
1696655 TGTGATAGTA
**
1696665 TCAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
1 TCAAACAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
* * *
1696730 CTCATTATGAACTTTCTCTGGAAAGGCTGATCCATCAATTGATGAATTCAGGTAAAAGGTGAACA
66 CTCATTATGAACTTT-TCTGGAAAAGCTGATCCATC-ATTGACGAATTCAGGTAAAAGGTAAACA
1696795 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
129 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-TTTCTC
1696860 TGGAAATGATGATCCAT-CAATTGACG-AAT
193 TGGAAATGATGATCCATCCAA--GACGAAAT
*
1696889 TCATGTA-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
1 TCA--AACAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
*
1696953 TTCTCATTATGAACTTTTCTGGAAAAGCTGATCCATCATTGACGAATTCATGT-AAAGGTTAAAC
64 TTCTCATTATGAACTTTTCTGGAAAAGCTGATCCATCATTGACGAATTCAGGTAAAAGG-TAAAC
*
1697017 -AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAATTTCTC
128 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAATTTCTC
* * *
1697081 TGGCAATGTTGATCCATCCAAGATGAAAT
193 TGGAAATGATGATCCATCCAAGACGAAAT
*
1697110 TCAAACAAAGGTTGAACAAATTCTTCTCATTATGAACTTGTTCTTTCCTTCTTCAGATGAG-TCT
1 TCAAACAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTTCT
* * * *
1697174 TCTCATTATGAACTTATCTGGCAATGTTGATCCATCA
65 TCTCATTATGAACTTTTCTGGAAAAGCTGATCCATCA
1697211 GTGATGGATT
Statistics
Matches: 298, Mismatches: 17, Indels: 18
0.89 0.05 0.05
Matches are distributed among these distances:
219 1 0.00
220 75 0.25
221 44 0.15
222 65 0.22
223 18 0.06
224 22 0.07
225 72 0.24
226 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (221 bp):
TCAAACAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
CTCATTATGAACTTTTCTGGAAAAGCTGATCCATCATTGACGAATTCAGGTAAAAGGTAAACAAA
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAATTTCTCTGG
AAATGATGATCCATCCAAGACGAAAT
Found at i:1698107 original size:83 final size:84
Alignment explanation
Indices: 1697918--1698182 Score: 451
Period size: 84 Copynumber: 3.2 Consensus size: 84
1697908 TTATCTTTTG
* * ** * *
1697918 ATTCGAATGATTGTTTCTGTACTTCCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 ATTC-AATGATTGGTTCTGTCCAACCAGATCGGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1697983 TGAGCACATTCATCTTCTAA
65 TGAGCACATTCATCTTCTAA
1698003 ATTCAATGATTGGTTCTGTCCAACCAGATCGGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 ATTCAATGATTGGTTCTGTCCAACCAGATCGGATAACTCAAAGAACACTTCCAGAAGATGCTATT
*
1698068 G-GCAAATTCATCTTCTAA
66 GAGCACATTCATCTTCTAA
1698086 ATTCAATGATTGGTTCTGTCCAACCAGATCGGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 ATTCAATGATTGGTTCTGTCCAACCAGATCGGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1698151 GAGCACATTCATCTTCTAA
66 GAGCACATTCATCTTCTAA
1698170 ATTCAATGATTGG
1 ATTCAATGATTGG
1698183 ACTGGGATAT
Statistics
Matches: 171, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
83 82 0.48
84 85 0.50
85 4 0.02
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (84 bp):
ATTCAATGATTGGTTCTGTCCAACCAGATCGGATAACTCAAAGAACACTTCCAGAAGATGCTATT
GAGCACATTCATCTTCTAA
Found at i:1699291 original size:15 final size:14
Alignment explanation
Indices: 1699273--1699347 Score: 68
Period size: 15 Copynumber: 5.5 Consensus size: 14
1699263 ACCCCCTTTC
*
1699273 TTTTTCTTC-TCTT
1 TTTTTCTTCTTTTT
1699286 TTTTT-TTC-TTTT
1 TTTTTCTTCTTTTT
** *
1699298 TCATT-TTCTATTT
1 TTTTTCTTCTTTTT
1699311 TTTTTCTTCTTTTTT
1 TTTTTCTTC-TTTTT
1699326 TTTTTCTTCTTTTT
1 TTTTTCTTCTTTTT
1699340 TCTTTTCT
1 T-TTTTCT
1699348 CTTCAAGCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
12 12 0.24
13 11 0.22
14 9 0.18
15 19 0.37
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTTCTTTTT
Found at i:1699304 original size:7 final size:6
Alignment explanation
Indices: 1699269--1699350 Score: 59
Period size: 6 Copynumber: 14.0 Consensus size: 6
1699259 CTTGACCCCC
* * *
1699269 TTTCTT TTTC-T TCTC-T TTT-TT TTTCTT TTTCAT TTTCTA TTT-TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
1699313 TTTCTT CTTT-TT TTT-TT TCTTCTTT TTTCTT TTCTCTT
1 TTTCTT -TTTCTT TTTCTT T-TTC-TT TTTCTT TT-TCTT
1699351 CAAGCATAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
5 21 0.34
6 28 0.45
7 10 0.16
8 3 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:1699320 original size:26 final size:25
Alignment explanation
Indices: 1699269--1699343 Score: 78
Period size: 26 Copynumber: 2.9 Consensus size: 25
1699259 CTTGACCCCC
* *
1699269 TTTCTTTTTCTTCTCTTTTTTTTTCTT
1 TTTCATTTTCTT-T-TTTTTTCTTCTT
1699296 TTTCATTTTCTATTTTTTTTCTTCTT
1 TTTCATTTTCT-TTTTTTTTCTTCTT
** *
1699322 TTTTTTTTTCTTCTTTTTTCTT
1 TTTCATTTTCTTTTTTTTTCTT
1699344 TTCTCTTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 10 0.24
26 20 0.48
27 11 0.26
28 1 0.02
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTCATTTTCTTTTTTTTTCTTCTT
Found at i:1699347 original size:12 final size:11
Alignment explanation
Indices: 1699269--1699347 Score: 78
Period size: 10 Copynumber: 7.5 Consensus size: 11
1699259 CTTGACCCCC
1699269 TTTCTTTTTCT
1 TTTCTTTTTCT
*
1699280 TCTCTTTTT-T
1 TTTCTTTTTCT
1699290 TTTCTTTTTCAT
1 TTTCTTTTTC-T
1699302 TTTCTATTTT-T
1 TTTCT-TTTTCT
*
1699313 TTTCTTCTT-T
1 TTTCTTTTTCT
1699323 TTT-TTTTTCT
1 TTTCTTTTTCT
*
1699333 TCT-TTTTTCT
1 TTTCTTTTTCT
1699343 TTTCT
1 TTTCT
1699348 CTTCAAGCAT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
9 4 0.07
10 28 0.49
11 15 0.26
12 6 0.11
13 4 0.07
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:1710697 original size:20 final size:21
Alignment explanation
Indices: 1710674--1710714 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1710664 TATTATATGT
**
1710674 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
1710694 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
1710715 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:1712177 original size:3 final size:3
Alignment explanation
Indices: 1712169--1712266 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
1712159 AATATATATT
* *
1712169 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1712217 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1712265 TA
1 TA
1712267 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1713533 original size:16 final size:16
Alignment explanation
Indices: 1713514--1713553 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1713504 AATAGGGATT
1713514 AAATTGAATAAATTCA
1 AAATTGAATAAATTCA
1713530 AAATTGAATAAATTCA
1 AAATTGAATAAATTCA
1713546 AAATTGAA
1 AAATTGAA
1713554 GGGCAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (16 bp):
AAATTGAATAAATTCA
Found at i:1714620 original size:5 final size:5
Alignment explanation
Indices: 1714612--1714910 Score: 181
Period size: 5 Copynumber: 60.2 Consensus size: 5
1714602 TAATTTGGAC
*
1714612 ATAAA ATAAT AATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
1714663 ATAAT A-AAT A-AAT A-AAT AAATAAT ATATT ATTAT AATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT --ATAAT ATAAT ATAAT -ATAAT ATAAT
*
1714708 AATAAT A-ACAT ATAAT AT-AT AATAAT AATAAT AT-AT AATAGT A-AAT
1 -ATAAT ATA-AT ATAAT ATAAT -ATAAT -ATAAT ATAAT -ATAAT ATAAT
*
1714754 AT-AT ATACT ATAAT AT-AT A-ATAT AATAAT ATACTAT ATAAT -T-AT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT ATA--AT ATAAT ATAAT
*
1714798 ATAA- ATAAT AT-AT ACT-AT ATAAT A-ATAT ATAAT ACT-AT ATACTGT
1 ATAAT ATAAT ATAAT A-TAAT ATAAT ATA-AT ATAAT A-TAAT ATA--AT
* **
1714843 ATAA- ATACT ATAAT AT-AT ATAAT ACCAT ATAAT ATAAT AT-AT GAT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT
* *
1714890 ATAAA ATAAT ATGAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT A
1714911 AAAAAGAACC
Statistics
Matches: 238, Mismatches: 21, Indels: 70
0.72 0.06 0.21
Matches are distributed among these distances:
3 2 0.01
4 49 0.21
5 144 0.61
6 30 0.13
7 13 0.05
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:1714624 original size:3 final size:3
Alignment explanation
Indices: 1714612--1714831 Score: 119
Period size: 3 Copynumber: 73.0 Consensus size: 3
1714602 TAATTTGGAC
1714612 ATA A-A ATA ATA ATA AT- ATA AT- ATA AT- ATA AT- ATA AT- ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1714653 ATA AT- ATA AT- ATA ATAA ATAA ATAA ATAA ATA ATA TATT ATT ATA
1 ATA ATA ATA ATA ATA AT-A AT-A AT-A AT-A ATA ATA -ATA ATA ATA
*
1714698 ATA AT- ATA ATA ATA ATA ACA TATA ATA TATA ATA ATA ATA ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA ATA ATA -ATA
* * *
1714745 ATA GTA A-A TATA TATA CT- ATA ATA TATA AT- ATA ATA AT- ATA CTA
1 ATA ATA ATA -ATA -ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* *
1714789 TATA ATT AT- ATAA ATA ATA TATA CTA TATA ATA ATA TATA ATA
1 -ATA ATA ATA AT-A ATA ATA -ATA ATA -ATA ATA ATA -ATA ATA
1714832 CTATATACTG
Statistics
Matches: 177, Mismatches: 13, Indels: 54
0.73 0.05 0.22
Matches are distributed among these distances:
2 28 0.16
3 104 0.59
4 45 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Done.