Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 27 of 129
Found at i:5463135 original size:11 final size:11
Alignment explanation
Indices: 5463105--5463145 Score: 57
Period size: 10 Copynumber: 3.7 Consensus size: 11
5463095 AAAAAGTAAT
5463105 AAAATAAATAA
1 AAAATAAATAA
5463116 AAAAT-AATAA
1 AAAATAAATAA
*
5463126 AAAATAAATACC
1 AAAATAAATA-A
5463138 AAAATAAA
1 AAAATAAA
5463146 AAACTAACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.37
11 9 0.33
12 8 0.30
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:5463958 original size:6 final size:6
Alignment explanation
Indices: 5463947--5463976 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5463937 TTTTCTTTCC
5463947 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
5463977 TTATAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:5463958 original size:18 final size:18
Alignment explanation
Indices: 5463935--5463976 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5463925 TCTTTTCCTA
*
5463935 ATTTTTCTTTCCATTTTT
1 ATTTTTATTTCCATTTTT
**
5463953 ATTTTTATTTTTATTTTT
1 ATTTTTATTTCCATTTTT
5463971 ATTTTT
1 ATTTTT
5463977 TTATAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (18 bp):
ATTTTTATTTCCATTTTT
Found at i:5470142 original size:21 final size:19
Alignment explanation
Indices: 5470086--5470168 Score: 62
Period size: 21 Copynumber: 4.2 Consensus size: 19
5470076 ATTTGATCGA
*
5470086 ATAA-ATAATATTAAAAAT
1 ATAATATAATATTATAAAT
** *
5470104 ACTTTTATAATTTATATAAAT
1 A-TAATATAATAT-TATAAAT
5470125 ATAATATAAAATATTATAAAT
1 ATAATAT--AATATTATAAAT
*
5470146 AT-ATATTATATTATAATAT
1 ATAATATAATATTATAA-AT
5470165 ATAA
1 ATAA
5470169 AATTACATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
18 10 0.20
19 5 0.10
20 15 0.30
21 16 0.32
22 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAATATAATATTATAAAT
Found at i:5470173 original size:15 final size:16
Alignment explanation
Indices: 5470108--5470173 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 16
5470098 AAAAATACTT
*
5470108 TTATAATTTATATAAA
1 TTATAATATATATAAA
5470124 -TATAATATA-A-AATA
1 TTATAATATATATAA-A
*
5470138 TTATAAATATATATTATA
1 TTAT-AATATATA-TAAA
5470156 TTATAATATATA-AAA
1 TTATAATATATATAAA
5470171 TTA
1 TTA
5470174 CATAATAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
13 2 0.05
14 2 0.05
15 16 0.39
16 6 0.15
17 9 0.22
18 5 0.12
19 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATAATATATATAAA
Found at i:5470195 original size:17 final size:15
Alignment explanation
Indices: 5470169--5470211 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
5470159 TAATATATAA
*
5470169 AATTACATAATAATTT
1 AATTAAATAAT-ATTT
*
5470185 TATTAATATAATATTT
1 AATTAA-ATAATATTT
5470201 AATTAAATAAT
1 AATTAAATAAT
5470212 TAATAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 13 0.57
17 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAAATAATATTT
Found at i:5500668 original size:2 final size:2
Alignment explanation
Indices: 5500661--5500689 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5500651 TTAATAAGCT
5500661 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5500690 GGGATGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5504303 original size:10 final size:10
Alignment explanation
Indices: 5504288--5504338 Score: 57
Period size: 10 Copynumber: 4.7 Consensus size: 10
5504278 TTCGAGTGTC
5504288 TTTGTTCGTG
1 TTTGTTCGTG
5504298 TTTGTTCGTGTG
1 TTTGTTC--GTG
*
5504310 TCTTTGTTAGTG
1 --TTTGTTCGTG
5504322 TTTGTTCGTG
1 TTTGTTCGTG
5504332 TTTGTTC
1 TTTGTTC
5504339 ATCAATGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 23 0.66
12 6 0.17
14 6 0.17
ACGTcount: A:0.02, C:0.10, G:0.27, T:0.61
Consensus pattern (10 bp):
TTTGTTCGTG
Found at i:5504330 original size:24 final size:24
Alignment explanation
Indices: 5504273--5504332 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
5504263 TGGTGTTTGC
* *
5504273 GTTTGTTCGAGTGTCTTTGTTCGT
1 GTTTGTTCGTGTGTCTTTGTTAGT
5504297 GTTTGTTCGTGTGTCTTTGTTAGT
1 GTTTGTTCGTGTGTCTTTGTTAGT
5504321 GTTTGTTCGTGT
1 GTTTGTTCGTGT
5504333 TTGTTCATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.03, C:0.10, G:0.30, T:0.57
Consensus pattern (24 bp):
GTTTGTTCGTGTGTCTTTGTTAGT
Found at i:5513767 original size:52 final size:52
Alignment explanation
Indices: 5513681--5513826 Score: 188
Period size: 52 Copynumber: 2.8 Consensus size: 52
5513671 TATAACCATA
* * * *
5513681 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTTTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
5513733 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
5513785 CAAACTTACCTATTAAGGATCCTCTTT-CTCTT-GAAATTCTTC
1 CAAACTTGCCTATTAAGAATCC-CTTTCCTCTTAG-AATTCTTC
5513827 ATTTGCAAGT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
51 1 0.01
52 78 0.94
53 4 0.05
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:5514136 original size:24 final size:24
Alignment explanation
Indices: 5514099--5514180 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
5514089 GCTTTTCATA
** *
5514099 TCTCGAACTGTCAACTCTTCCATG
1 TCTCGAACCATCAACTCTTCCACG
*
5514123 TCTCGAACCATCAACTCTTCCACA
1 TCTCGAACCATCAACTCTTCCACG
* * *
5514147 TCTTGAATCTTCAACTCTTCTCACG
1 TCTCGAACCATCAACTCTTC-CACG
*
5514172 TTTCGAACC
1 TCTCGAACC
5514181 TTCAGCTTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 37 0.80
25 9 0.20
ACGTcount: A:0.23, C:0.35, G:0.09, T:0.33
Consensus pattern (24 bp):
TCTCGAACCATCAACTCTTCCACG
Found at i:5514230 original size:32 final size:31
Alignment explanation
Indices: 5514192--5514301 Score: 159
Period size: 31 Copynumber: 3.5 Consensus size: 31
5514182 TCAGCTTTTA
5514192 GATACCACTTGTTGGGGAACACCACAGCTCT
1 GATACCACTTGTTGGGGAACACCACAGCTCT
* *
5514223 GATTACCACTTATTGGGGAATACCACAGCTCT
1 GA-TACCACTTGTTGGGGAACACCACAGCTCT
*
5514255 GATACCA-TTGTTTGGGGATCACCACAGCTCT
1 GATACCACTTG-TTGGGGAACACCACAGCTCT
*
5514286 GATACCATTTGTTGGG
1 GATACCACTTGTTGGG
5514302 CTAAAAACCT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
30 2 0.03
31 37 0.52
32 32 0.45
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (31 bp):
GATACCACTTGTTGGGGAACACCACAGCTCT
Found at i:5516236 original size:20 final size:20
Alignment explanation
Indices: 5516200--5516237 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5516190 TTAAAATCAT
*
5516200 TAAATTATTTTATTTTTAAA
1 TAAATTATTTTAGTTTTAAA
5516220 TAAATT-TTTATAGTTTTA
1 TAAATTATTT-TAGTTTTA
5516238 TTATATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TAAATTATTTTAGTTTTAAA
Found at i:5516241 original size:29 final size:28
Alignment explanation
Indices: 5516205--5516264 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
5516195 ATCATTAAAT
*
5516205 TATTTTATT-T-TT-AAATAAATTTTTA
1 TATTTTATTATATTAAAATAAATTATTA
5516230 TAGTTTTATTATATTAAAATAAATTATTA
1 TA-TTTTATTATATTAAAATAAATTATTA
5516259 TATTTT
1 TATTTT
5516265 GATTTGTATC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.07
26 7 0.23
27 1 0.03
28 6 0.20
29 14 0.47
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
TATTTTATTATATTAAAATAAATTATTA
Found at i:5516282 original size:30 final size:28
Alignment explanation
Indices: 5516207--5516282 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
5516197 CATTAAATTA
*
5516207 TTTTATT-T-TTAAATAAATTTTTATAG
1 TTTTATTATATTAAATAAATTATTATAG
5516233 TTTTATTATATTAAAATAAATTATTATA-
1 TTTTATTATATT-AAATAAATTATTATAG
*
5516261 TTTTGATTTGTATCTAAATAAA
1 TTTT-A-TTATAT-TAAATAAA
5516283 CTTTCATTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 7 0.17
27 1 0.02
28 6 0.14
29 15 0.36
30 12 0.29
31 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (28 bp):
TTTTATTATATTAAATAAATTATTATAG
Found at i:5516741 original size:16 final size:17
Alignment explanation
Indices: 5516715--5516779 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 17
5516705 ATTAAAATTG
5516715 TAATAATTTTAAATTAAA
1 TAATAA-TTTAAATTAAA
*
5516733 TAA-AATTTAATTTAAA
1 TAATAATTTAAATTAAA
* *
5516749 AAATAATTTTAA-TAAA
1 TAATAATTTAAATTAAA
*
5516765 TATTAATCTTAAATT
1 TAATAAT-TTAAATT
5516780 TAATTGAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
16 21 0.57
17 12 0.32
18 4 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATAATTTAAATTAAA
Found at i:5519297 original size:12 final size:12
Alignment explanation
Indices: 5519280--5519323 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
5519270 AAAATTATAT
5519280 TTTAATTATTTA
1 TTTAATTATTTA
5519292 TTTAATTATTTA
1 TTTAATTATTTA
5519304 TTTATATATATTTA
1 TTTA-AT-TATTTA
*
5519318 TATAAT
1 TTTAAT
5519324 AGTATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 16 0.55
13 4 0.14
14 9 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTAATTATTTA
Found at i:5522446 original size:24 final size:24
Alignment explanation
Indices: 5522414--5522461 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5522404 ACACTACAAT
5522414 GAAAATTAACCAAAACAAGAAATC
1 GAAAATTAACCAAAACAAGAAATC
5522438 GAAAATTAACCAAAACAAGAAATC
1 GAAAATTAACCAAAACAAGAAATC
5522462 CATAGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.17, G:0.08, T:0.12
Consensus pattern (24 bp):
GAAAATTAACCAAAACAAGAAATC
Found at i:5530135 original size:15 final size:16
Alignment explanation
Indices: 5530099--5530135 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
5530089 ATAATCAAGG
5530099 TAATAA-TATATTTTT
1 TAATAATTATATTTTT
5530114 TAA-AATTA-ATTTTT
1 TAATAATTATATTTTT
5530128 TAATAATT
1 TAATAATT
5530136 TTGATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATAATTATATTTTT
Found at i:5531659 original size:20 final size:22
Alignment explanation
Indices: 5531626--5531669 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
5531616 AATTAAAATT
* *
5531626 TTATTTTTATTTTA-AT-TATA
1 TTATTTATAATTTATATATATA
5531646 TTATTTATAATTTATATATATA
1 TTATTTATAATTTATATATATA
5531668 TT
1 TT
5531670 TTAAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 2 0.10
22 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTTATAATTTATATATATA
Found at i:5539273 original size:12 final size:11
Alignment explanation
Indices: 5539254--5539337 Score: 70
Period size: 11 Copynumber: 7.8 Consensus size: 11
5539244 TGAAGTTTAC
5539254 CAAAATTATAT
1 CAAAATTATAT
5539265 CATAAA-T-TAT
1 CA-AAATTATAT
*
5539275 CAAAATAATAT
1 CAAAATTATAT
*
5539286 AAAAATT-TAT
1 CAAAATTATAT
*
5539296 CAAAATTGTAT
1 CAAAATTATAT
5539307 CATAAA-T-TAT
1 CA-AAATTATAT
*
5539317 CAAAATTTTAT
1 CAAAATTATAT
5539328 CAATAATTAT
1 CAA-AATTAT
5539338 CCAATTATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
9 6 0.10
10 20 0.33
11 23 0.38
12 11 0.18
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.38
Consensus pattern (11 bp):
CAAAATTATAT
Found at i:5539278 original size:21 final size:21
Alignment explanation
Indices: 5539254--5539338 Score: 102
Period size: 21 Copynumber: 4.0 Consensus size: 21
5539244 TGAAGTTTAC
5539254 CAAAATTATATCATAAATTAT
1 CAAAATTATATCATAAATTAT
* *
5539275 CAAAATAATAT-AAAAATTTAT
1 CAAAATTATATCATAAA-TTAT
*
5539296 CAAAATTGTATCATAAATTAT
1 CAAAATTATATCATAAATTAT
*
5539317 CAAAATTTTATCA-ATAATTAT
1 CAAAATTATATCATA-AATTAT
5539338 C
1 C
5539339 CAATTATTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.09
21 46 0.84
22 4 0.07
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (21 bp):
CAAAATTATATCATAAATTAT
Found at i:5539280 original size:42 final size:42
Alignment explanation
Indices: 5539215--5539327 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 42
5539205 TGCAACATTG
* * ** *
5539215 AAATTATAT-AAAAATTA-CTAAAATTTTGTTGAAGTTTACCA
1 AAATTATATCATAAATTATC-AAAATTTTATAAAAATTTACCA
** *
5539256 AAATTATATCATAAATTATCAAAATAATATAAAAATTTATCA
1 AAATTATATCATAAATTATCAAAATTTTATAAAAATTTACCA
*
5539298 AAATTGTATCATAAATTATCAAAATTTTAT
1 AAATTATATCATAAATTATCAAAATTTTAT
5539328 CAATAATTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 9 0.15
42 49 0.83
43 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (42 bp):
AAATTATATCATAAATTATCAAAATTTTATAAAAATTTACCA
Found at i:5539337 original size:10 final size:9
Alignment explanation
Indices: 5539262--5539338 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 9
5539252 ACCAAAATTA
5539262 TATCATAAAT
1 TATCA-AAAT
5539272 TATCAAAAT
1 TATCAAAAT
*
5539281 AATATAAAAATT
1 --TATCAAAA-T
5539293 TATCAAAATT
1 TATCAAAA-T
5539303 GTATCATAAAT
1 -TATCA-AAAT
5539314 TATCAAAATTT
1 TATCAAAA--T
5539325 TATCAATAAT
1 TATCAA-AAT
5539335 TATC
1 TATC
5539339 CAATTATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
9 7 0.12
10 24 0.42
11 20 0.35
12 6 0.11
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (9 bp):
TATCAAAAT
Found at i:5552769 original size:56 final size:56
Alignment explanation
Indices: 5552667--5552776 Score: 143
Period size: 56 Copynumber: 2.0 Consensus size: 56
5552657 ATAAATATCT
* * * * *
5552667 AATATCTTATAATCTTATATTTAGGTTGGATCCTTTCATTTGTAGTCAATTGATCA
1 AATATCATATAATCTTATATTTAGATTGAATCCTTTCACTTATAGTCAATTGATCA
5552723 AATATCATATAATCTTATATTTTA-ATTGAAT-CTCTTCACTTATAGTCAATTGAT
1 AATATCATATAATCTTATA-TTTAGATTGAATCCT-TTCACTTATAGTCAATTGAT
5552777 TTTAACTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 2 0.04
56 41 0.87
57 4 0.09
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (56 bp):
AATATCATATAATCTTATATTTAGATTGAATCCTTTCACTTATAGTCAATTGATCA
Found at i:5558328 original size:81 final size:81
Alignment explanation
Indices: 5558145--5558338 Score: 205
Period size: 81 Copynumber: 2.4 Consensus size: 81
5558135 TATCCAAATG
* * * * *
5558145 ATTTAGAAATA-ACGTTTGGAGGTCTTACAAATCTTAATATCCATAAATGCTCTTTTAAAAAGAA
1 ATTTA-AAATATATGTTTGGAGGACTTACAAATCTCAATATCCATAAATACTCTTCTAAAAAGAA
5558209 GCCTTGAAACTTTTAAA
65 GCCTTGAAACTTTTAAA
* *** * ** * *
5558226 ATTTAAAATATCTGCCCGGAGGGCTTACAAATCTCAATATCTGTAAGTATTCTTCTAAAAA-AAG
1 ATTTAAAATATATGTTTGGAGGACTTACAAATCTCAATATCCATAAATACTCTTCTAAAAAGAA-
*
5558290 GCTTTGAAAC-TTTAAA
65 GCCTTGAAACTTTTAAA
5558306 ATTTAAAATATTATGTTTGGAGGACTTACAAAT
1 ATTTAAAATA-TATGTTTGGAGGACTTACAAAT
5558339 TTTTTTTTAA
Statistics
Matches: 91, Mismatches: 19, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
80 23 0.25
81 68 0.75
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (81 bp):
ATTTAAAATATATGTTTGGAGGACTTACAAATCTCAATATCCATAAATACTCTTCTAAAAAGAAG
CCTTGAAACTTTTAAA
Found at i:5558676 original size:23 final size:23
Alignment explanation
Indices: 5558650--5558702 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5558640 TAAACTGAGT
* *
5558650 TTAAAGTGCCAG-TTAATCTAGGC
1 TTAAAATGCCAGCTAAAT-TAGGC
*
5558673 TTAAAATGTCAGCTAAATTAGGC
1 TTAAAATGCCAGCTAAATTAGGC
5558696 TTAAAAT
1 TTAAAAT
5558703 CTAAGTGCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (23 bp):
TTAAAATGCCAGCTAAATTAGGC
Found at i:5565340 original size:15 final size:15
Alignment explanation
Indices: 5565317--5565359 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5565307 CCCTTTTATG
*
5565317 AAATTTAAAAAAAAT
1 AAATATAAAAAAAAT
*
5565332 AAATATAAAATAACAT
1 AAATATAAAA-AAAAT
5565348 AAA-ATAAAAAAA
1 AAATATAAAAAAA
5565360 TTTCAATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 2 0.08
15 15 0.62
16 7 0.29
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATATAAAAAAAAT
Found at i:5566695 original size:14 final size:15
Alignment explanation
Indices: 5566676--5566704 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5566666 ACTATTTTTC
5566676 AAAAGG-ATTAAAAT
1 AAAAGGAATTAAAAT
5566690 AAAAGGAATTAAAAT
1 AAAAGGAATTAAAAT
5566705 TAAATATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.21
Consensus pattern (15 bp):
AAAAGGAATTAAAAT
Found at i:5567982 original size:15 final size:15
Alignment explanation
Indices: 5567940--5567997 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
5567930 TTAGGGTCCC
5567940 ATTTTAAGGTTTCAG
1 ATTTTAAGGTTTCAG
*
5567955 AGTTTTAGGGTTTCAG
1 A-TTTTAAGGTTTCAG
*
5567971 ATTTTAAAGTTTC-G
1 ATTTTAAGGTTTCAG
*
5567985 AGGTTTAAGGTTT
1 A-TTTTAAGGTTT
5567998 TTTTTTCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 2 0.06
15 20 0.56
16 14 0.39
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.47
Consensus pattern (15 bp):
ATTTTAAGGTTTCAG
Found at i:5567983 original size:31 final size:30
Alignment explanation
Indices: 5567940--5567997 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5567930 TTAGGGTCCC
* * *
5567940 ATTTTAAGGTTTCAGAGTTTTAGGGTTTCAG
1 ATTTTAAAGTTTC-GAGGTTTAAGGTTTCAG
5567971 ATTTTAAAGTTTCGAGGTTTAAGGTTT
1 ATTTTAAAGTTTCGAGGTTTAAGGTTT
5567998 TTTTTTCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.47
Consensus pattern (30 bp):
ATTTTAAAGTTTCGAGGTTTAAGGTTTCAG
Found at i:5569073 original size:15 final size:14
Alignment explanation
Indices: 5569053--5569086 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5569043 TTTGTTGATG
*
5569053 TTTTTTCTTCTTCTT
1 TTTTTTATTC-TCTT
5569068 TTTTTTATTCTCTT
1 TTTTTTATTCTCTT
5569082 TTTTT
1 TTTTT
5569087 CCCTTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTATTCTCTT
Found at i:5570484 original size:15 final size:15
Alignment explanation
Indices: 5570464--5570493 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5570454 TGTTTTTAAT
5570464 GATATGACTTTGGTG
1 GATATGACTTTGGTG
*
5570479 GATATGGCTTTGGTG
1 GATATGACTTTGGTG
5570494 TTTATAATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.37, T:0.40
Consensus pattern (15 bp):
GATATGACTTTGGTG
Found at i:5574697 original size:4 final size:4
Alignment explanation
Indices: 5574674--5574737 Score: 53
Period size: 4 Copynumber: 16.2 Consensus size: 4
5574664 TTTTATTTGG
* * *
5574674 TATT TCATT TAGT T-TT TATT TATT TGTT T-TT TATT TATGG T-TT TATT
1 TATT T-ATT TATT TATT TATT TATT TATT TATT TATT TAT-T TATT TATT
*
5574721 TGTT TATT TATT TATT T
1 TATT TATT TATT TATT T
5574738 CGAATCACAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
3 6 0.12
4 37 0.77
5 5 0.10
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:5574717 original size:27 final size:26
Alignment explanation
Indices: 5574665--5574737 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
5574655 TCGATTTCCT
* * *
5574665 TTTATTTGGTATTTCATTTAGTTTTTA
1 TTTATTT-GTTTTTTATTTAGGTTTTA
5574692 TTTATTTGTTTTTTATTTATGGTTTTA
1 TTTATTTGTTTTTTATTTA-GGTTTTA
* *
5574719 TTTGTTTATTTATTTATTT
1 TTTATTTGTTT-TTTATTT
5574738 CGAATCACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 10 0.26
27 22 0.56
28 7 0.18
ACGTcount: A:0.16, C:0.01, G:0.10, T:0.73
Consensus pattern (26 bp):
TTTATTTGTTTTTTATTTAGGTTTTA
Found at i:5574734 original size:16 final size:15
Alignment explanation
Indices: 5574674--5574737 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
5574664 TTTTATTTGG
*
5574674 TATTTCATTTAGTTTT
1 TATTT-ATTTATTTTT
*
5574690 TATTTATTTGTTTTT
1 TATTTATTTATTTTT
5574705 TATTTATGGTTTTATTTGTT
1 TATTTA----TTTATTT-TT
5574725 TATTTATTTATTT
1 TATTTATTTATTT
5574738 CGAATCACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
15 14 0.35
16 12 0.30
19 6 0.15
20 8 0.20
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.73
Consensus pattern (15 bp):
TATTTATTTATTTTT
Found at i:5580350 original size:3 final size:3
Alignment explanation
Indices: 5580344--5580371 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5580334 CTCATTTCAA
5580344 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5580372 TCTTTGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5581314 original size:9 final size:9
Alignment explanation
Indices: 5581302--5581427 Score: 83
Period size: 9 Copynumber: 14.1 Consensus size: 9
5581292 TTTGTTGTTT
*
5581302 TGATAATGA
1 TGATAATAA
* *
5581311 TGATGATGA
1 TGATAATAA
*
5581320 TGATGATAA
1 TGATAATAA
*
5581329 TAATAATAA
1 TGATAATAA
*
5581338 TAATAATAA
1 TGATAATAA
*
5581347 TAATAATAA
1 TGATAATAA
*
5581356 TAATAATAA
1 TGATAATAA
* **
5581365 TAAT-ATTT
1 TGATAATAA
*
5581373 TGATAATGA
1 TGATAATAA
* *
5581382 TGATGATGA
1 TGATAATAA
*
5581391 TGATGATAA
1 TGATAATAA
*
5581400 TAATAATAA
1 TGATAATAA
*
5581409 TAATAATAA
1 TGATAATAA
*
5581418 TAATAATAA
1 TGATAATAA
5581427 T
1 T
5581428 ATTATTATTA
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
8 5 0.05
9 98 0.95
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (9 bp):
TGATAATAA
Found at i:5581331 original size:3 final size:3
Alignment explanation
Indices: 5581325--5581428 Score: 120
Period size: 3 Copynumber: 35.0 Consensus size: 3
5581315 GATGATGATG
*
5581325 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
5581372 TTG ATA ATG ATG ATG ATG ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5581420 ATA ATA ATA
1 ATA ATA ATA
5581429 TTATTATTAT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
2 2 0.02
3 92 0.98
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:5581433 original size:3 final size:3
Alignment explanation
Indices: 5581427--5581454 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5581417 ATAATAATAA
5581427 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5581455 CATTTTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5592150 original size:21 final size:21
Alignment explanation
Indices: 5592124--5592170 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5592114 GGATAATGTA
* *
5592124 TGAAACACTTCCTTCTTTTAT
1 TGAAACACTTCATTCTTTTAC
5592145 TGAAACACTTCATTCTTTTAC
1 TGAAACACTTCATTCTTTTAC
5592166 TGAAA
1 TGAAA
5592171 TAAAATAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (21 bp):
TGAAACACTTCATTCTTTTAC
Found at i:5593025 original size:40 final size:40
Alignment explanation
Indices: 5592995--5593133 Score: 130
Period size: 41 Copynumber: 3.6 Consensus size: 40
5592985 TAATTAGATT
5592995 AGCCTTTTAAATTTAAAGTTTCATTGCCTCT-ATTCAAAAG
1 AGCCTTTTAAATTTAAAGTTTCATTGCCTCTGATT-AAAAG
* *
5593035 AGCC------ATTTAAAGTTTCATTACCTCTGATTAAAAA
1 AGCCTTTTAAATTTAAAGTTTCATTGCCTCTGATTAAAAG
* * * *
5593069 AGCCTTTTAACATTTAAAGTTTCATTGACTTTGATTAGATG
1 AGCCTTTTAA-ATTTAAAGTTTCATTGCCTCTGATTAAAAG
** *
5593110 AATCTTTTGAATTTAAAGTTTCAT
1 AGCCTTTTAAATTTAAAGTTTCAT
5593134 CACTTTTACT
Statistics
Matches: 80, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
34 28 0.35
35 3 0.04
40 18 0.22
41 31 0.39
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (40 bp):
AGCCTTTTAAATTTAAAGTTTCATTGCCTCTGATTAAAAG
Found at i:5593048 original size:34 final size:34
Alignment explanation
Indices: 5593005--5593078 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
5592995 AGCCTTTTAA
* *
5593005 ATTTAAAGTTTCATTGCCTCT-ATTCAAAAGAGCC
1 ATTTAAAGTTTCATTACCTCTGATT-AAAAAAGCC
5593039 ATTTAAAGTTTCATTACCTCTGATTAAAAAAGCC
1 ATTTAAAGTTTCATTACCTCTGATTAAAAAAGCC
*
5593073 TTTTAA
1 ATTTAA
5593079 CATTTAAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 33 0.92
35 3 0.08
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (34 bp):
ATTTAAAGTTTCATTACCTCTGATTAAAAAAGCC
Found at i:5593117 original size:41 final size:39
Alignment explanation
Indices: 5593038--5593163 Score: 119
Period size: 41 Copynumber: 3.1 Consensus size: 39
5593028 TCAAAAGAGC
* * *
5593038 CATTTAAAGTTTCATTACCTCTGATTAAAAAAGCCTTTTAA
1 CATTTAAAGTTTCATTA-CTTTGATTAGAGAA-CCTTTTAA
* *
5593079 CATTTAAAGTTTCATTGACTTTGATTAGATGAATCTTTTGA
1 CATTTAAAGTTTCATT-ACTTTGATTAGA-GAACCTTTTAA
* * *
5593120 -ATTTAAAGTTTCATCACTTTTACTTAGAGAAGCTTTTAA
1 CATTTAAAGTTTCATTACTTTGA-TTAGAGAACCTTTTAA
*
5593159 AATTT
1 CATTT
5593164 TCAGAAGTTG
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
39 15 0.21
40 23 0.32
41 31 0.43
42 3 0.04
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (39 bp):
CATTTAAAGTTTCATTACTTTGATTAGAGAACCTTTTAA
Found at i:5593227 original size:42 final size:43
Alignment explanation
Indices: 5593142--5593230 Score: 103
Period size: 42 Copynumber: 2.1 Consensus size: 43
5593132 ATCACTTTTA
* * *
5593142 CTTAGAGAAGCTTTTAAAATTTTCAGAAGTTGTCGAGCTTCTG
1 CTTAAAGAAGCTTTTAAAATTTTCAGAAGTTATCAAGCTTCTG
*
5593185 CTTAAAGAAGCTTTT-AAATTTTTA-AATGTTATCAAG-TCTCTG
1 CTTAAAGAAGCTTTTAAAATTTTCAGAA-GTTATCAAGCT-TCTG
5593227 CTTA
1 CTTA
5593231 GATGAGCCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
41 3 0.08
42 23 0.57
43 14 0.35
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (43 bp):
CTTAAAGAAGCTTTTAAAATTTTCAGAAGTTATCAAGCTTCTG
Found at i:5593376 original size:3 final size:3
Alignment explanation
Indices: 5593370--5593425 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
5593360 TTCTCATTTC
5593370 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5593418 ATT ATT AT
1 ATT ATT AT
5593426 ATTTTCATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5593456 original size:33 final size:33
Alignment explanation
Indices: 5593419--5593482 Score: 76
Period size: 32 Copynumber: 1.9 Consensus size: 33
5593409 ATTATTATTA
5593419 TTATTATATTTTCATTTCTTTGGACA-CTTTTTT
1 TTATT-TATTTTCATTTCTTTGGACATCTTTTTT
* * * *
5593452 TTATTTTTTTTCTTTTTTTTTGACATCTTTT
1 TTATTTATTTTCATTTCTTTGGACATCTTTT
5593483 CTTCATCTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (33 bp):
TTATTTATTTTCATTTCTTTGGACATCTTTTTT
Found at i:5594275 original size:7 final size:7
Alignment explanation
Indices: 5594263--5594348 Score: 61
Period size: 7 Copynumber: 11.6 Consensus size: 7
5594253 AATTGGCAGG
*
5594263 TTTTTTC
1 TTTTTTA
5594270 TTTTTT-
1 TTTTTTA
5594276 TTTCTTTA
1 TTT-TTTA
5594284 TCTTTTTA
1 T-TTTTTA
5594292 TTTTTTA
1 TTTTTTA
*
5594299 TTTTTTG
1 TTTTTTA
5594306 TTTTATT-
1 TTTT-TTA
5594313 TTTATTTA
1 TTT-TTTA
5594321 TTTTATGTTGA
1 -TTT-T-TT-A
5594332 TTTTTTA
1 TTTTTTA
5594339 -TTTTTA
1 TTTTTTA
5594345 TTTT
1 TTTT
5594349 AGTTGTTATG
Statistics
Matches: 68, Mismatches: 1, Indels: 20
0.76 0.01 0.22
Matches are distributed among these distances:
6 9 0.13
7 34 0.50
8 11 0.16
9 8 0.12
10 5 0.07
11 1 0.01
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:5594295 original size:6 final size:6
Alignment explanation
Indices: 5594286--5594348 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
5594276 TTTCTTTATC
* *
5594286 TTTTTA TTTTTTA TTTTT- TGTTTTA TTTTTA --TTTA -TTTTA TGTTGA
1 TTTTTA -TTTTTA TTTTTA T-TTTTA TTTTTA TTTTTA TTTTTA TTTTTA
5594332 TTTTTTA TTTTTA TTTT
1 -TTTTTA TTTTTA TTTT
5594349 AGTTGTTATG
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
4 4 0.09
5 5 0.11
6 27 0.57
7 11 0.23
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:5594297 original size:19 final size:19
Alignment explanation
Indices: 5594273--5594342 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
5594263 TTTTTTCTTT
*
5594273 TTTTTTCTTTATCT-TTTTA
1 TTTTTTATTT-TCTGTTTTA
*
5594292 TTTTTTATTTTTTGTTTTA
1 TTTTTTATTTTCTGTTTTA
* *
5594311 TTTTTATTTATTTTATG-TTGA
1 --TTT-TTTATTTTCTGTTTTA
5594332 TTTTTTATTTT
1 TTTTTTATTTT
5594343 TATTTTAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
18 10 0.23
19 17 0.40
21 6 0.14
22 10 0.23
ACGTcount: A:0.13, C:0.03, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTTTATTTTCTGTTTTA
Found at i:5594364 original size:3 final size:3
Alignment explanation
Indices: 5594356--5594408 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
5594346 TTTAGTTGTT
* *
5594356 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATA ATG AGG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
5594404 ATG AT
1 ATG AT
5594409 AATAATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:5594441 original size:3 final size:3
Alignment explanation
Indices: 5594435--5594475 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
5594425 ATAAAAAAAA
*
5594435 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5594476 GAAATGAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5594561 original size:3 final size:3
Alignment explanation
Indices: 5594555--5594590 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5594545 TAAAAAAATA
5594555 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5594591 TTAATGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5595078 original size:20 final size:21
Alignment explanation
Indices: 5595055--5595096 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
5595045 AATAAACAGC
5595055 AAATAAT-AGCAA-AAAAATTA
1 AAATAATCA-CAATAAAAATTA
5595075 AAATAATCACAATAAAAATTA
1 AAATAATCACAATAAAAATTA
5595096 A
1 A
5595097 TTAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.21
Consensus pattern (21 bp):
AAATAATCACAATAAAAATTA
Found at i:5595976 original size:17 final size:17
Alignment explanation
Indices: 5595957--5596017 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
5595947 AATATTTATT
*
5595957 AATTTTAAATTATTTAT
1 AATTTTAAATTATTTAA
** *
5595974 AATAAATATATT-TTTAA
1 AAT-TTTAAATTATTTAA
*
5595991 AATTATTAAATTATCTAA
1 AATT-TTAAATTATTTAA
5596009 AATTTTAAA
1 AATTTTAAA
5596018 CTTTAATAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 20 0.61
18 13 0.39
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTTAAATTATTTAA
Found at i:5596588 original size:232 final size:231
Alignment explanation
Indices: 5596068--5596723 Score: 944
Period size: 232 Copynumber: 2.8 Consensus size: 231
5596058 TGTCCTGTAT
* * *
5596068 ATCAACTCATCTTAATTTAAAACCAATTTTAAAGTAATTTATCTTTTTCAATTTATCTAGAGTTA
1 ATCAACTCATCTTAATTTAAAACCAATTTTAAAGTAATTTATCTTTTCCAATTTATCTACAATTA
*
5596133 ACATGAGTATTTAAATTTGTCACAACTTTTAAAAATATTATTTAATATTTTTAATATTTTTGATA
66 ACATGAGTATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATTTTTAATATTTTT-ATA
* *
5596198 AATAATCCTTGCATTATTTTTAGCTTTTAAATATATTTCACAAAGGAAATAT-AAAAAAAAATAT
130 AATAATCCTTGCATTATCTTTAGCTTTTAAATATATTTCACAAAGGAAATGTGAAAAAAAAATAT
**
5596262 AAATACCAAAACAACTTCAGGAAAGTTTCAACTATAC
195 AAATACCAAAACAACTTCAAAAAAGTTTCAACTATAC
* ** *
5596299 AT-ATCCTCATCTTAATTTAAAATTAATTTTAAAGTAATTTATCTTTTCTAATTTATCTACAATT
1 ATCA-ACTCATCTTAATTTAAAACCAATTTTAAAGTAATTTATCTTTTCCAATTTATCTACAATT
* *
5596363 AATATGAATATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATTTTTAATATTTTGTAT
65 AACATGAGTATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATTTTTAATATTTT-TAT
* * * * * *
5596428 AAATAATCCTTACATTATCTTCAAG-TTTTAAATATATTTCATAAAGGCAATGTGAAAAATATAT
129 AAATAATCCTTGCATTATCTT-TAGCTTTTAAATATATTTCACAAAGGAAATGTGAAAAAAAAAT
*
5596492 ATAAATACCAAAACAACTTCAAAAAAGTTTC-TCATATAC
193 ATAAATACCAAAACAACTTCAAAAAAGTTTCAAC-TATAC
* *
5596531 ATCAACTCATCTTAATTTAAAACCAAATTTAAAGTAATTTATCTTTTCCAATTTATCTGCAATTA
1 ATCAACTCATCTTAATTTAAAACCAATTTTAAAGTAATTTATCTTTTCCAATTTATCTACAATTA
* * *
5596596 ACAAGAGTATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTTAATATTTTTTTAC
66 ACATGAGTATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATTTTTAATA--TTTTTAT
* * *
5596661 AAATAATCATTGTATTATCTTTAGCTTTTAAATATATTTCACAAA-AAAATGTGAAAAACAAAA
129 AAATAATCCTTGCATTATCTTTAGCTTTTAAATATATTTCACAAAGGAAATGTGAAAAA-AAAA
5596724 ATACAAGAAC
Statistics
Matches: 374, Mismatches: 41, Indels: 18
0.86 0.09 0.04
Matches are distributed among these distances:
230 1 0.00
231 160 0.43
232 167 0.45
233 42 0.11
234 4 0.01
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (231 bp):
ATCAACTCATCTTAATTTAAAACCAATTTTAAAGTAATTTATCTTTTCCAATTTATCTACAATTA
ACATGAGTATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATTTTTAATATTTTTATAA
ATAATCCTTGCATTATCTTTAGCTTTTAAATATATTTCACAAAGGAAATGTGAAAAAAAAATATA
AATACCAAAACAACTTCAAAAAAGTTTCAACTATAC
Found at i:5610419 original size:29 final size:29
Alignment explanation
Indices: 5610387--5610445 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5610377 AATTATAGTG
* *
5610387 AAATATTTAATATGATATTTAAATTTTAA
1 AAATATTTAATATGATATATAAATTATAA
* *
5610416 AAATTTTTAATGTGATATATAAATTATAA
1 AAATATTTAATATGATATATAAATTATAA
5610445 A
1 A
5610446 TTTATTAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
AAATATTTAATATGATATATAAATTATAA
Found at i:5610446 original size:27 final size:28
Alignment explanation
Indices: 5610387--5610453 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
5610377 AATTATAGTG
* *
5610387 AAATATTTAATATGATATTTAAATTTTAA
1 AAATTTTTAATATGATATATAAA-TTTAA
* *
5610416 AAATTTTTAATGTGATATATAAA-TTAT
1 AAATTTTTAATATGATATATAAATTTAA
5610443 AAATTTATTAA
1 AAATTT-TTAA
5610454 CTAATATGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 9 0.27
28 4 0.12
29 20 0.61
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (28 bp):
AAATTTTTAATATGATATATAAATTTAA
Found at i:5610822 original size:18 final size:19
Alignment explanation
Indices: 5610801--5610839 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5610791 TATAAAATAT
* *
5610801 TTATTTTTTTCTCAC-AAA
1 TTATTCTTTTATCACTAAA
5610819 TTATTCTTTTATCACTAAA
1 TTATTCTTTTATCACTAAA
5610838 TT
1 TT
5610840 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTCTTTTATCACTAAA
Found at i:5613691 original size:21 final size:21
Alignment explanation
Indices: 5613665--5613706 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5613655 AAGATTAAAA
5613665 AGAAACCAAAATAAAGCTGAT
1 AGAAACCAAAATAAAGCTGAT
5613686 AGAAACCAAAATAAAGCTGAT
1 AGAAACCAAAATAAAGCTGAT
5613707 GGCCGAGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (21 bp):
AGAAACCAAAATAAAGCTGAT
Found at i:5622234 original size:17 final size:18
Alignment explanation
Indices: 5622212--5622246 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5622202 AATAAATATA
5622212 TAAAAA-TTAATATTTTT
1 TAAAAATTTAATATTTTT
*
5622229 TAAAAATTTATTATTTTT
1 TAAAAATTTAATATTTTT
5622247 ATTATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAAAATTTAATATTTTT
Found at i:5627232 original size:29 final size:30
Alignment explanation
Indices: 5627200--5627256 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
5627190 AAAAAAAGAT
5627200 CTTATATTTT-TATTATA-CTAAAATAAACC
1 CTTATATTTTGTATTATATCT-AAATAAACC
* *
5627229 CTTATCTTTTGTTTTATATCTAAATAAA
1 CTTATATTTTGTATTATATCTAAATAAA
5627257 TTTTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.38
30 13 0.54
31 2 0.08
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (30 bp):
CTTATATTTTGTATTATATCTAAATAAACC
Found at i:5627793 original size:6 final size:6
Alignment explanation
Indices: 5627782--5627807 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5627772 CTCACATGCC
5627782 CCGATG CCGATG CCGATG CCGATG CC
1 CCGATG CCGATG CCGATG CCGATG CC
5627808 TACCTTGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (6 bp):
CCGATG
Found at i:5629299 original size:30 final size:31
Alignment explanation
Indices: 5629259--5629320 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
5629249 AAAAAAATTA
*
5629259 TTTATCAATAAAATAGTTATT-TTAT-TTTAT
1 TTTATCAATAAAATA-ATATTATTATATTTAT
*
5629289 TTTATTAATAAAATAATATTATTATATTTAT
1 TTTATCAATAAAATAATATTATTATATTTAT
5629320 T
1 T
5629321 AATAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 4 0.14
30 18 0.64
31 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (31 bp):
TTTATCAATAAAATAATATTATTATATTTAT
Found at i:5629340 original size:26 final size:26
Alignment explanation
Indices: 5629285--5629340 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
5629275 TTATTTTATT
**
5629285 TTAT-TTTATTAATAAAATAATATTA
1 TTATATTTATTAATAAAATAATAAAA
*
5629310 TTATATTTATTAATAATAT-ATAAAA
1 TTATATTTATTAATAAAATAATAAAA
5629335 TCTATA
1 T-TATA
5629341 CACTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTATATTTATTAATAAAATAATAAAA
Found at i:5629629 original size:18 final size:18
Alignment explanation
Indices: 5629589--5629629 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5629579 TTCTTTTCTC
*
5629589 TAAAAAACTATTTTTCTA
1 TAAAAAACTATTTTTATA
* *
5629607 AAAAAAACTATTTTTATT
1 TAAAAAACTATTTTTATA
5629625 TAAAA
1 TAAAA
5629630 TCCAATGAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAAAACTATTTTTATA
Found at i:5629754 original size:13 final size:14
Alignment explanation
Indices: 5629736--5629764 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5629726 AAAGCATGTT
5629736 TTTAATT-TAATTC
1 TTTAATTGTAATTC
5629749 TTTAATTGTAATTC
1 TTTAATTGTAATTC
5629763 TT
1 TT
5629765 ACTAGATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTAATTGTAATTC
Found at i:5639416 original size:14 final size:14
Alignment explanation
Indices: 5639388--5639428 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5639378 ATACTTATAT
5639388 AATTATATATTTAAA
1 AATTATAT-TTTAAA
*
5639403 TATTATATTTTAAA
1 AATTATATTTTAAA
*
5639417 AATAATATTTTA
1 AATTATATTTTA
5639429 TTAATTTCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTATATTTTAAA
Found at i:5639999 original size:3 final size:3
Alignment explanation
Indices: 5639984--5640114 Score: 79
Period size: 3 Copynumber: 41.7 Consensus size: 3
5639974 TTTTAATTTA
* * * *
5639984 ATT ATT TTT ATT ATT ATG ATG ATT ATG ATT ATT ATT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* * *
5640030 ATCT ATT AAT ATT TTT ATTT ATTT ATCT ATT ATT ATT -TT TTT AATT
1 AT-T ATT ATT ATT ATT A-TT A-TT AT-T ATT ATT ATT ATT ATT -ATT
* *
5640076 ATCT ATT AAT A-T ATT -TT ATT ATTT ATCT ATT ATT TTT AT
1 AT-T ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT ATT AT
5640115 CTTTTTTTCT
Statistics
Matches: 103, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
2 6 0.06
3 70 0.68
4 27 0.26
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5640056 original size:24 final size:23
Alignment explanation
Indices: 5640011--5640107 Score: 133
Period size: 24 Copynumber: 4.2 Consensus size: 23
5640001 GATGATTATG
* *
5640011 ATTATTATTATTATTATTTATCT
1 ATTAATATTTTTATTATTTATCT
5640034 ATTAATATTTTTATTTATTTATCT
1 ATTAATATTTTTA-TTATTTATCT
* *
5640058 ATTATTATTTTT-TTAATTATCT
1 ATTAATATTTTTATTATTTATCT
5640080 ATTAATATATTTTATTATTTATCT
1 ATTAATAT-TTTTATTATTTATCT
5640104 ATTA
1 ATTA
5640108 TTTTTATCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
22 16 0.25
23 15 0.23
24 34 0.52
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTAATATTTTTATTATTTATCT
Found at i:5640098 original size:46 final size:47
Alignment explanation
Indices: 5640011--5640114 Score: 158
Period size: 46 Copynumber: 2.2 Consensus size: 47
5640001 GATGATTATG
*
5640011 ATTATTATTATTATTATTTATCTATTAATATTTTTATTTATTTATCT
1 ATTATTATTATTATTAATTATCTATTAATATTTTTATTTATTTATCT
*
5640058 ATTATTATT-TTTTTAATTATCTATTAATATATTTTA-TTATTTATCT
1 ATTATTATTATTATTAATTATCTATTAATAT-TTTTATTTATTTATCT
*
5640104 ATTATTTTTAT
1 ATTATTATTAT
5640115 CTTTTTTTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
46 37 0.71
47 15 0.29
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (47 bp):
ATTATTATTATTATTAATTATCTATTAATATTTTTATTTATTTATCT
Found at i:5641214 original size:48 final size:48
Alignment explanation
Indices: 5641114--5641207 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
5641104 TAAAGATAAA
** * *
5641114 AAAAATATTTTTAAAGGAAAGTTGATTGTATCAATTTCCTTTGAATAC
1 AAAAATATTTTTAAAGGAAAGTTGAAAGTATCAATTTCCTCTGAAAAC
* *
5641162 AAAAATTTTTTTAAATGAAAGTTGAAAGTATCAATTTCC-CTGAAAA
1 AAAAATATTTTTAAAGGAAAGTTGAAAGTATCAATTTCCTCTGAAAA
5641208 ATAAAAAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 5 0.12
48 35 0.88
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.37
Consensus pattern (48 bp):
AAAAATATTTTTAAAGGAAAGTTGAAAGTATCAATTTCCTCTGAAAAC
Found at i:5641225 original size:58 final size:58
Alignment explanation
Indices: 5641162--5641298 Score: 177
Period size: 58 Copynumber: 2.3 Consensus size: 58
5641152 CTTTGAATAC
*
5641162 AAAAATTTTTTTAAATGAAAGTTGAAAGTATCAATTTCCCTGAAAAATAAAA-AGTTAA
1 AAAAATTTTTTTAAA-AAAAGTTGAAAGTATCAATTTCCCTGAAAAATAAAATAGTTAA
** * * **
5641220 AAAAATAGTTTTAGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTTTAA
1 AAAAATTTTTTTA-AAAAAAGTTGAAAGTATCAATTTCCCTGAAAAATAAAATAGTTAA
5641279 ATAAAATTTTTTTAAAAAAA
1 A-AAAATTTTTTTAAAAAAA
5641299 TATTTTAGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
58 44 0.66
59 13 0.19
60 10 0.15
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (58 bp):
AAAAATTTTTTTAAAAAAAGTTGAAAGTATCAATTTCCCTGAAAAATAAAATAGTTAA
Found at i:5641282 original size:13 final size:13
Alignment explanation
Indices: 5641264--5641289 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5641254 TTTTCCTTAA
5641264 AAATAAAATTTTT
1 AAATAAAATTTTT
5641277 AAATAAAATTTTT
1 AAATAAAATTTTT
5641290 TTAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATAAAATTTTT
Found at i:5641298 original size:14 final size:16
Alignment explanation
Indices: 5641272--5641304 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5641262 AAAAATAAAA
5641272 TTTTTAAATAAAAT-T
1 TTTTTAAATAAAATAT
5641287 TTTTTAAA-AAAATAT
1 TTTTTAAATAAAATAT
5641302 TTT
1 TTT
5641305 AGAAAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTTAAATAAAATAT
Found at i:5641368 original size:72 final size:74
Alignment explanation
Indices: 5641218--5641368 Score: 191
Period size: 72 Copynumber: 2.1 Consensus size: 74
5641208 ATAAAAAGTT
* **
5641218 AAAAAAATAGTTTTAGAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTTTAAATAA
1 AAAAAAATAGTTTTAGAAAAAAGTTGAAAGTATCAATTTGCCTTAAAAATAAAATTTCCAAATAA
***
5641283 AATTTTTTT
66 AATTTTGAG
* *
5641292 AAAAAAATA-TTTTAG-AAAAAGTTGAAAGTATCAATTTGCCTTGAAAGTAAAATTTCCAAA-AA
1 AAAAAAATAGTTTTAGAAAAAAGTTGAAAGTATCAATTTGCCTTAAAAATAAAATTTCCAAATAA
*
5641354 TATCTTTGAG
66 AAT-TTTGAG
5641364 AAAAA
1 AAAAA
5641369 TTTGAAAGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 4 0.06
72 48 0.72
73 6 0.09
74 9 0.13
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (74 bp):
AAAAAAATAGTTTTAGAAAAAAGTTGAAAGTATCAATTTGCCTTAAAAATAAAATTTCCAAATAA
AATTTTGAG
Found at i:5641400 original size:57 final size:54
Alignment explanation
Indices: 5641294--5641408 Score: 149
Period size: 57 Copynumber: 2.1 Consensus size: 54
5641284 ATTTTTTTAA
**
5641294 AAAAATATTTTAGAAAAAGTTGAAAGTATCAATTTGCCTTGAAAGTAAAATTTCC
1 AAAAATATTTTAGAAAAAGTTGAAAGTATCAATTTGCCTCAAAAGTAAAATTT-C
* ** *
5641349 AAAAATATCTTTGAGAAAAATTTGAAAGTATCAATTTTTCTCAAAATTAAAATTTC
1 AAAAATAT-TTT-AGAAAAAGTTGAAAGTATCAATTTGCCTCAAAAGTAAAATTTC
5641405 AAAA
1 AAAA
5641409 TTAAAAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
55 8 0.15
56 8 0.15
57 36 0.69
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.34
Consensus pattern (54 bp):
AAAAATATTTTAGAAAAAGTTGAAAGTATCAATTTGCCTCAAAAGTAAAATTTC
Found at i:5641414 original size:130 final size:130
Alignment explanation
Indices: 5641179--5641414 Score: 309
Period size: 129 Copynumber: 1.8 Consensus size: 130
5641169 TTTTTAAATG
5641179 AAAGTTGAAAGTATCAATTTCCCTGAAAAATAAAAAGTTAAAAAAATAGTTTTAGAAAAAAGTTG
1 AAAGTTGAAAGTATCAATTTCCCTGAAAAATAAAAAGTTAAAAAAATAGTTTTAGAAAAAAGTTG
* **
5641244 AAAGTATCAATTTTCCTTAAAAATAAAATTTTTAAATAAAATTTTTTTAAAAAAATATTTTAGAA
66 AAAGTATCAATTTTCCTCAAAAATAAAATTTCAAAATAAAATTTTTTTAAAAAAATATTTTAGAA
* * * ** *
5641309 AAAGTTGAAAGTATCAATTTGCCTTG-AAAGT-AAAATTTCCAAAAATA-TCTTT-GAGAAAAAT
1 AAAGTTGAAAGTATCAATTT-CCCTGAAAAATAAAAAGTTAAAAAAATAGT-TTTAGA-AAAAAG
* *
5641370 TTGAAAGTATCAATTTTTCTCAAAATTAAAATTTCAAAATTAAAA
63 TTGAAAGTATCAATTTTCCTCAAAAATAAAATTTCAAAA-TAAAA
5641415 AAAAAATTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
128 3 0.03
129 55 0.60
130 29 0.32
131 4 0.04
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (130 bp):
AAAGTTGAAAGTATCAATTTCCCTGAAAAATAAAAAGTTAAAAAAATAGTTTTAGAAAAAAGTTG
AAAGTATCAATTTTCCTCAAAAATAAAATTTCAAAATAAAATTTTTTTAAAAAAATATTTTAGAA
Found at i:5641464 original size:64 final size:66
Alignment explanation
Indices: 5641349--5641471 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 66
5641339 TAAAATTTCC
* * * *
5641349 AAAAATATCTTTGAGAAAAATTTGAAAGTATCAATTTTTCTCAAAATTAAAATT-TCAAAATTAA
1 AAAAAAATCTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTCAAAAATAAAATTATCAAAATTAA
5641413 A
66 A
* *
5641414 AAAAAAAT-TTTGAGAAAAAGTTGGAAGTACCAA-TTTTCTTTAAAAATAAAATTATCAA
1 AAAAAAATCTTTGAGAAAAAGTTGAAAGTACCAATTTTTC-TCAAAAATAAAATTATCAA
5641472 GAAAAGCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 5 0.10
64 34 0.68
65 11 0.22
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.33
Consensus pattern (66 bp):
AAAAAAATCTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTCAAAAATAAAATTATCAAAATTAA
A
Found at i:5641646 original size:5 final size:5
Alignment explanation
Indices: 5641636--5641664 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5641626 TCATTATTCT
5641636 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5641665 TCCTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:5645156 original size:6 final size:6
Alignment explanation
Indices: 5645135--5645172 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
5645125 TTAATAAAAT
* *
5645135 AGTTCG AATCCG AGTTCG AGTTCG AGTTCG AGTTCG AG
1 AGTTCG AGTTCG AGTTCG AGTTCG AGTTCG AGTTCG AG
5645173 CATGAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (6 bp):
AGTTCG
Found at i:5649068 original size:8 final size:9
Alignment explanation
Indices: 5649042--5649079 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
5649032 CTTCTTGGTC
5649042 TTTCATTTT
1 TTTCATTTT
*
5649051 TGTCATTTT
1 TTTCATTTT
*
5649060 TTTTATTTT
1 TTTCATTTT
5649069 TTTCATTTT
1 TTTCATTTT
5649078 TT
1 TT
5649080 CCAAACACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTCATTTT
Found at i:5652111 original size:44 final size:43
Alignment explanation
Indices: 5652056--5652252 Score: 189
Period size: 44 Copynumber: 4.5 Consensus size: 43
5652046 AAGTTCTGTT
5652056 GCCTCTATTTAGAGGAGC-TATTTATTTTTTCAAAAAATCATTGA
1 GCCTCTATTTAGAGGAGCTTATTTATTTTTTC--AAAATCATTGA
* * *
5652100 GCCTCTGTTTAGAGGAACTTTATTTATTTTTTCAAAATCGTTGA
1 GCCTCTATTTAGAGGAGC-TTATTTATTTTTTCAAAATCATTGA
* * * * * *
5652144 ACCTCTGTTTAGAAGAGCTTTGTTTATTTTTTTAAAGTCATTGA
1 GCCTCTATTTAGAGGAGC-TTATTTATTTTTTCAAAATCATTGA
* * * * *
5652188 GCCTCTACTTAGAGGAGCTTTGTTTATTTTACTCAAAGTCATTAA
1 GCCTCTATTTAGAGGAGC-TTATTTATTTT-TTCAAAATCATTGA
* *
5652233 GCCTCTACTTATAGGAGCTT
1 GCCTCTATTTAGAGGAGCTT
5652253 TGATCAAAAT
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
44 91 0.69
45 28 0.21
46 13 0.10
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (43 bp):
GCCTCTATTTAGAGGAGCTTATTTATTTTTTCAAAATCATTGA
Found at i:5652468 original size:6 final size:6
Alignment explanation
Indices: 5652459--5652499 Score: 50
Period size: 7 Copynumber: 6.8 Consensus size: 6
5652449 TCATTTTTCT
5652459 TTTTAA TTTTAA -TTTAA -TTTAA TTTTTAA TTTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA -TTTTAA TTTTA
5652500 TTATTTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.30
6 11 0.33
7 12 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:5652514 original size:10 final size:9
Alignment explanation
Indices: 5652495--5652626 Score: 52
Period size: 9 Copynumber: 13.7 Consensus size: 9
5652485 TAATTTTTAA
5652495 TTTTATTAT
1 TTTTATTAT
5652504 TTTTCATTAT
1 TTTT-ATTAT
* *
5652514 TATTATGAT
1 TTTTATTAT
* *
5652523 TATTATTGT
1 TTTTATTAT
5652532 TATTTATCTAT
1 T-TTTAT-TAT
**
5652543 TAATATT-T
1 TTTTATTAT
*
5652551 ATTTATTTAT
1 TTTTA-TTAT
5652561 TTATATATTAT
1 TT-T-TATTAT
*
5652572 TATTATTA-
1 TTTTATTAT
5652580 TTTTAGTTAT
1 TTTTA-TTAT
* *
5652590 CTATTAATAT
1 -TTTTATTAT
5652600 ATTTTATTAT
1 -TTTTATTAT
*
5652610 TTATCTATTAC
1 TT-T-TATTAT
5652621 TTTTAT
1 TTTTAT
5652627 CTTTTTTTTC
Statistics
Matches: 91, Mismatches: 20, Indels: 24
0.67 0.15 0.18
Matches are distributed among these distances:
8 7 0.08
9 32 0.35
10 30 0.33
11 20 0.22
12 2 0.02
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATTAT
Found at i:5652515 original size:3 final size:3
Alignment explanation
Indices: 5652497--5652610 Score: 72
Period size: 3 Copynumber: 35.7 Consensus size: 3
5652487 ATTTTTAATT
* * *
5652497 TTA TTA TTT TTCA TTA TTA TTA TGA TTA TTA TTG TTA TTTA TCTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA
*
5652545 ATA TTTA TTTA TTTA TTTA TATA TTA TTA TTA TTA TT- TTA GTTA TCTA
1 TTA -TTA -TTA -TTA -TTA T-TA TTA TTA TTA TTA TTA TTA -TTA T-TA
*
5652593 TTA ATA -TA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
5652611 TATCTATTAC
Statistics
Matches: 92, Mismatches: 9, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
2 6 0.07
3 55 0.60
4 31 0.34
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5652575 original size:49 final size:48
Alignment explanation
Indices: 5652510--5652619 Score: 139
Period size: 51 Copynumber: 2.2 Consensus size: 48
5652500 TTATTTTTCA
* * *
5652510 TTATTATTATGATTATTATTGTTATTTATCTATTAATATTTATTTATTTAT
1 TTATTATTATTATTATTA-TGTTAGTTATCTATTAATATAT-TTTA-TTAT
*
5652561 TTATATATTATTATTATTATTTTAGTTATCTATTAATATATTTTATTAT
1 TTAT-TATTATTATTATTATGTTAGTTATCTATTAATATATTTTATTAT
5652610 TTATCTATTA
1 TTAT-TATTA
5652620 CTTTTATCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
49 13 0.25
50 4 0.08
51 23 0.43
52 13 0.25
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (48 bp):
TTATTATTATTATTATTATGTTAGTTATCTATTAATATATTTTATTAT
Found at i:5652618 original size:8 final size:7
Alignment explanation
Indices: 5652496--5652618 Score: 53
Period size: 8 Copynumber: 17.3 Consensus size: 7
5652486 AATTTTTAAT
5652496 TTTATTA
1 TTTATTA
5652503 TTT-TTCA
1 TTTATT-A
5652510 -TTATTA
1 TTTATTA
*
5652516 -TTATGA
1 TTTATTA
5652522 -TTATTA
1 TTTATTA
*
5652528 -TTGTTA
1 TTTATTA
5652534 TTTATCTA
1 TTTAT-TA
*
5652542 -TTAATA
1 TTTATTA
5652548 TTTATTTA
1 TTTA-TTA
5652556 TTTATTTA
1 TTTA-TTA
*
5652564 TATATTA
1 TTTATTA
5652571 -TTATTA
1 TTTATTA
*
5652577 TTATTTTA
1 TT-TATTA
*
5652585 GTTATCTA
1 TTTAT-TA
*
5652593 TTAATATA
1 TTTAT-TA
5652601 TTTTATTA
1 -TTTATTA
5652609 TTTATCTA
1 TTTAT-TA
5652617 TT
1 TT
5652619 ACTTTTATCT
Statistics
Matches: 90, Mismatches: 15, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
6 27 0.30
7 26 0.29
8 33 0.37
9 4 0.04
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTATTA
Found at i:5653467 original size:3 final size:3
Alignment explanation
Indices: 5653461--5653498 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
5653451 AGTTTTTTTT
5653461 TTA TTA TT- TTA TATA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
5653499 TATTGATTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5653470 original size:12 final size:12
Alignment explanation
Indices: 5653455--5653561 Score: 60
Period size: 12 Copynumber: 8.7 Consensus size: 12
5653445 TTTCAAAGTT
*
5653455 TTTTTTTTATTA
1 TTTTATTTATTA
*
5653467 TTTTATATATTA
1 TTTTATTTATTA
5653479 TTATTA-TTATTA
1 TT-TTATTTATTA
5653491 TTATTATTTATTGA
1 TT-TTATTTATT-A
** *
5653505 TTAGATTAGAATTA
1 TTTTATT--TATTA
**
5653519 TTTGGTATTCCTTA
1 TTT--TATTTATTA
5653533 TTTTATTT-TTA
1 TTTTATTTATTA
5653544 TTTTA-TT-TTA
1 TTTTATTTATTA
5653554 TTTTATTT
1 TTTTATTT
5653562 TTAATGATTT
Statistics
Matches: 76, Mismatches: 11, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
10 10 0.13
11 10 0.13
12 27 0.36
13 11 0.14
14 12 0.16
15 3 0.04
16 3 0.04
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:5653540 original size:5 final size:5
Alignment explanation
Indices: 5653530--5653562 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
5653520 TTGGTATTCC
5653530 TTATT TTATTT TTATT TTATT TTATT TTATT TT
1 TTATT TTA-TT TTATT TTATT TTATT TTATT TT
5653563 TAATGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:5656272 original size:37 final size:37
Alignment explanation
Indices: 5656222--5656297 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
5656212 ATATAATGGT
5656222 CTATCACTTGTTTCTTATGAGCCCTTCAAATTTCAAA
1 CTATCACTTGTTTCTTATGAGCCCTTCAAATTTCAAA
5656259 CTATCACTTGTTTCTTATGAGCCCTTCAAATTTCAAA
1 CTATCACTTGTTTCTTATGAGCCCTTCAAATTTCAAA
5656296 CT
1 CT
5656298 GACATTTTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.41
Consensus pattern (37 bp):
CTATCACTTGTTTCTTATGAGCCCTTCAAATTTCAAA
Found at i:5657458 original size:75 final size:75
Alignment explanation
Indices: 5657335--5657618 Score: 328
Period size: 75 Copynumber: 3.8 Consensus size: 75
5657325 CATTTACGGT
* * * * *
5657335 ATTGTTAATTCAGTGAAAGTAAAACACTAATGCTGTCTGCAATGTTCTCCATTTTGGTTTGTGTA
1 ATTGTTAACTCAGGGAATGGAAAACACTAATGCTGTCTGCAGTGTTCTCCATTTTGGTTTGTGTA
5657400 ATCTACTTGG
66 ATCTACTTGG
*
5657410 ATTGTTAACTCAGGGAATGGAAAACACTAATGCTGTTTGCAGTGTTCTCCATTTTGGTTTGTGTA
1 ATTGTTAACTCAGGGAATGGAAAACACTAATGCTGTCTGCAGTGTTCTCCATTTTGGTTTGTGTA
5657475 ATCTACTTGG
66 ATCTACTTGG
* * * * *
5657485 ATT-TGTAACTCAGGGAATGGAAAGCAC-----CTGTCTGCAGTCTTTTCCATTTTGGTTTATGG
1 ATTGT-TAACTCAGGGAATGGAAAACACTAATGCTGTCTGCAGTGTTCTCCATTTTGGTTTGTGT
5657544 AATCTACTTGG
65 AATCTACTTGG
* * * * * *
5657555 ATTGTTAATTCAGGGAATGGAAGGAAAACAGTAATGATCTCTGCAGTGTTTTCTATTTTGGTTT
1 ATTGTTAACTCAGGGAAT----GGAAAACACTAATGCTGTCTGCAGTGTTCTCCATTTTGGTTT
5657619 TGTGGATTCT
Statistics
Matches: 179, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
70 53 0.30
71 1 0.01
74 8 0.04
75 93 0.52
79 24 0.13
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (75 bp):
ATTGTTAACTCAGGGAATGGAAAACACTAATGCTGTCTGCAGTGTTCTCCATTTTGGTTTGTGTA
ATCTACTTGG
Found at i:5663985 original size:22 final size:23
Alignment explanation
Indices: 5663951--5663995 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
5663941 AAATATTTAT
*
5663951 AAATGTTAATTAAAGATA-ATAA
1 AAATATTAATTAAAGATATATAA
* *
5663973 AAATATTATTTAAATATATATAA
1 AAATATTAATTAAAGATATATAA
5663996 TGTATTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AAATATTAATTAAAGATATATAA
Found at i:5664200 original size:2 final size:2
Alignment explanation
Indices: 5664193--5664223 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5664183 AAAGAAAACA
5664193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5664224 CTTAGTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5673377 original size:4 final size:4
Alignment explanation
Indices: 5673368--5673394 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5673358 GCTTACGAGT
5673368 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
5673395 TTGATATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:5673893 original size:24 final size:24
Alignment explanation
Indices: 5673833--5673895 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
5673823 TGGTTCCAGT
* *
5673833 ACCCCTGCCTTCGGTGCCACGAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
** *
5673857 ATGCCTGCTTTTGGTGCCACAAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
*
5673881 ACCCCTCCCTTTGGT
1 ACCCCTGCCTTTGGT
5673896 TCAACTGGAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.13, C:0.40, G:0.22, T:0.25
Consensus pattern (24 bp):
ACCCCTGCCTTTGGTGCCACAAGC
Found at i:5674093 original size:24 final size:24
Alignment explanation
Indices: 5674064--5674246 Score: 201
Period size: 24 Copynumber: 7.6 Consensus size: 24
5674054 TGGTTCCAGT
*
5674064 ACCCCTGCCTTTGGTGCCACAACC
1 ACCCCTGCCTTTGGTGCCACAAGC
*
5674088 ACCCCTG-CTTTCGGTGCCACAAGT
1 ACCCCTGCCTTT-GGTGCCACAAGC
*
5674112 ACCCCTGCCTTCGGTGCCACAAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
* * * *
5674136 GCCCCTACCTTCGGTGCCACGAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
5674160 ACCCCTG-CTTTCGGTGCCACAAGC
1 ACCCCTGCCTTT-GGTGCCACAAGC
**
5674184 ATGCCTG-CTTTCGGTGCCACAAGC
1 ACCCCTGCCTTT-GGTGCCACAAGC
* * *
5674208 ACCCCTCCCTTTGGTTCCCCAAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
*
5674232 ACCCCTCCCTTTGGT
1 ACCCCTGCCTTTGGT
5674247 TTAACTGGAA
Statistics
Matches: 137, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
23 7 0.05
24 123 0.90
25 7 0.05
ACGTcount: A:0.15, C:0.43, G:0.20, T:0.22
Consensus pattern (24 bp):
ACCCCTGCCTTTGGTGCCACAAGC
Found at i:5674132 original size:48 final size:48
Alignment explanation
Indices: 5674064--5674237 Score: 222
Period size: 48 Copynumber: 3.6 Consensus size: 48
5674054 TGGTTCCAGT
* * *
5674064 ACCCCTGCCTTTGGTGCCACAACCACCCCTGCTTTCGGTGCCACAAGT
1 ACCCCTGCCTTCGGTGCCACAAGCACCCCTGCTTTCGGTGCCACAAGC
* * * *
5674112 ACCCCTGCCTTCGGTGCCACAAGCGCCCCTACCTTCGGTGCCACGAGC
1 ACCCCTGCCTTCGGTGCCACAAGCACCCCTGCTTTCGGTGCCACAAGC
* **
5674160 ACCCCTGCTTTCGGTGCCACAAGCATGCCTGCTTTCGGTGCCACAAGC
1 ACCCCTGCCTTCGGTGCCACAAGCACCCCTGCTTTCGGTGCCACAAGC
* * * *
5674208 ACCCCTCCCTTTGGTTCCCCAAGCACCCCT
1 ACCCCTGCCTTCGGTGCCACAAGCACCCCT
5674238 CCCTTTGGTT
Statistics
Matches: 105, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 105 1.00
ACGTcount: A:0.16, C:0.44, G:0.20, T:0.21
Consensus pattern (48 bp):
ACCCCTGCCTTCGGTGCCACAAGCACCCCTGCTTTCGGTGCCACAAGC
Found at i:5674164 original size:72 final size:72
Alignment explanation
Indices: 5674064--5674237 Score: 240
Period size: 72 Copynumber: 2.4 Consensus size: 72
5674054 TGGTTCCAGT
* * *
5674064 ACCCCTGCCTTTGGTGCCACAACCACCCCTGCTTTCGGTGCCACAAGTACCCCTGCCTTCGGTGC
1 ACCCCTACCTTTGGTGCCACAAGCACCCCTGCTTTCGGTGCCACAAGCACCCCTGCCTTCGGTGC
5674129 CACAAGC
66 CACAAGC
* * * ** *
5674136 GCCCCTACCTTCGGTGCCACGAGCACCCCTGCTTTCGGTGCCACAAGCATGCCTGCTTTCGGTGC
1 ACCCCTACCTTTGGTGCCACAAGCACCCCTGCTTTCGGTGCCACAAGCACCCCTGCCTTCGGTGC
5674201 CACAAGC
66 CACAAGC
* * *
5674208 ACCCCTCCCTTTGGTTCCCCAAGCACCCCT
1 ACCCCTACCTTTGGTGCCACAAGCACCCCT
5674238 CCCTTTGGTT
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
72 87 1.00
ACGTcount: A:0.16, C:0.44, G:0.20, T:0.21
Consensus pattern (72 bp):
ACCCCTACCTTTGGTGCCACAAGCACCCCTGCTTTCGGTGCCACAAGCACCCCTGCCTTCGGTGC
CACAAGC
Found at i:5674322 original size:351 final size:351
Alignment explanation
Indices: 5673836--5674848 Score: 1785
Period size: 351 Copynumber: 2.9 Consensus size: 351
5673826 TTCCAGTACC
* * ** * * * *
5673836 CCTGCCTTCGGTGCCACGAGCATGCCTGCTTTTGGTGCCACAAGCACCCCTCCCTTTGGTTCAAC
1 CCTGCTTTCGGTGCCACAAGCACCCCTCCCTTTGGTTCCACAAGCACCCCTCCCTTTGGTTTAAC
*
5673901 TGGAAGTCCAGCATTTGGGAGCACTGGAACTGCATTTAGTGTCTCTAATTCCCCAGTCTTTGGAA
66 TGGAAGTCCAGCATTTGGGAGCACTGGAACTGCATTTGGTGTCTCTAATTCCCCAGTCTTTGGAA
* *
5673966 CAGGAGGCATGATGCAGCAATCACAGCCTGCATTTGGTAGTGGTATATTTGGTTCCTCTGCTTCT
131 CAGGAGGCACGATGCAGCAATCACAGCCTGCATCTGGTAGTGGTATATTTGGTTCCTCTGCTTCT
*
5674031 TTTGGTTCAACTCAGTCTGCATTTGGTTCCAGTACCCCTGCCTTTGGTGCCACAACCACCCCTGC
196 TTTGGTTCAACTCAGTCTGCATTTGGTTCCAGTACCCCTGCCTTTGGTGCCACAAGCACCCCTGC
* *
5674096 TTTCGGTGCCACAAGTACCCCTGCCTTCGGTGCCACAAGCGCCCCTACCTTCGGTGCCACGAGCA
261 TTTCGGTGCCACAAGTACCCCTGCCTTCGGTGCCACAAGCACCCCTGCCTTCGGTGCCACGAGCA
* *
5674161 CCCCTGCTTTCGGTGCCACAAGCATG
326 CCCCTACCTTCGGTGCCACAAGCATG
*
5674187 CCTGCTTTCGGTGCCACAAGCACCCCTCCCTTTGGTTCCCCAAGCACCCCTCCCTTTGGTTTAAC
1 CCTGCTTTCGGTGCCACAAGCACCCCTCCCTTTGGTTCCACAAGCACCCCTCCCTTTGGTTTAAC
5674252 TGGAAGTCCAGCATTTGGGAGCACTGGAACTGCATTTGGTGTCTCTAATTCCCCAGTCTTTGGAA
66 TGGAAGTCCAGCATTTGGGAGCACTGGAACTGCATTTGGTGTCTCTAATTCCCCAGTCTTTGGAA
*
5674317 CAGGAGGCACGATGCAGCAATCACAGCTTGCATCTGGTAGTGGTATATTTGGTTCCTCTGCTTCT
131 CAGGAGGCACGATGCAGCAATCACAGCCTGCATCTGGTAGTGGTATATTTGGTTCCTCTGCTTCT
*
5674382 TTTGGTGCAACTCAGTCTGCATTTGGTTCCAGTACCCCTGCCTTTGGTGCCACAAGCACCCCTGC
196 TTTGGTTCAACTCAGTCTGCATTTGGTTCCAGTACCCCTGCCTTTGGTGCCACAAGCACCCCTG-
* * * *
5674447 CTTT-GGTGCCACAAGCACCCCTGCTTTCGGTGCCACAAGTACCCCTGCCTTCGGTGCCATGAGC
260 CTTTCGGTGCCACAAGTACCCCTGCCTTCGGTGCCACAAGCACCCCTGCCTTCGGTGCCACGAGC
* *
5674511 GCCCCTACCTTCGGTGCCACGAGCATG
325 ACCCCTACCTTCGGTGCCACAAGCATG
5674538 CCTGCTTTCGGTGCCACAAGCACCCCTCCCTTTGGTTCCACAAGCACCCCTCCCTTTGGTTTAAC
1 CCTGCTTTCGGTGCCACAAGCACCCCTCCCTTTGGTTCCACAAGCACCCCTCCCTTTGGTTTAAC
5674603 TGGAAGTCCAGCATTTGGGAGCACTGGAACTGCATTTGGTGTCTCTAATTCCCCAGTCTTTGGAA
66 TGGAAGTCCAGCATTTGGGAGCACTGGAACTGCATTTGGTGTCTCTAATTCCCCAGTCTTTGGAA
5674668 CAGGAGGCACGATGCAGCAATCACAGCCTGCATCTGGTAGTGGTATATTTGGTTCCTCTGCTTCT
131 CAGGAGGCACGATGCAGCAATCACAGCCTGCATCTGGTAGTGGTATATTTGGTTCCTCTGCTTCT
5674733 TTTGGTTCAACTCAGTCTGCATTTGGTTCCAGTACCCCTGCCTTTGGTGCCACAAGCACCCCTGC
196 TTTGGTTCAACTCAGTCTGCATTTGGTTCCAGTACCCCTGCCTTTGGTGCCACAAGCACCCCTGC
5674798 TTTCGGTGCCACAAGTACCCCTGCCTTCGGTGCCACAAGCACCCCTGCCTT
261 TTTCGGTGCCACAAGTACCCCTGCCTTCGGTGCCACAAGCACCCCTGCCTT
5674849 TGGTTCAACT
Statistics
Matches: 629, Mismatches: 31, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
350 4 0.01
351 621 0.99
352 4 0.01
ACGTcount: A:0.17, C:0.32, G:0.22, T:0.28
Consensus pattern (351 bp):
CCTGCTTTCGGTGCCACAAGCACCCCTCCCTTTGGTTCCACAAGCACCCCTCCCTTTGGTTTAAC
TGGAAGTCCAGCATTTGGGAGCACTGGAACTGCATTTGGTGTCTCTAATTCCCCAGTCTTTGGAA
CAGGAGGCACGATGCAGCAATCACAGCCTGCATCTGGTAGTGGTATATTTGGTTCCTCTGCTTCT
TTTGGTTCAACTCAGTCTGCATTTGGTTCCAGTACCCCTGCCTTTGGTGCCACAAGCACCCCTGC
TTTCGGTGCCACAAGTACCCCTGCCTTCGGTGCCACAAGCACCCCTGCCTTCGGTGCCACGAGCA
CCCCTACCTTCGGTGCCACAAGCATG
Found at i:5674503 original size:72 final size:72
Alignment explanation
Indices: 5674412--5674597 Score: 255
Period size: 72 Copynumber: 2.6 Consensus size: 72
5674402 ATTTGGTTCC
*
5674412 AGTACCCCTGCCTTTGGTGCCACAAGCACCCCTGCCTTTGGTGCCACAAGCACCCCTGCTTTCGG
1 AGTACCCCTGCCTTTGGTGCCACAAGCACCCCTACCTTTGGTGCCACAAGCACCCCTGCTTTCGG
5674477 TGCCACA
66 TGCCACA
* ** * * * **
5674484 AGTACCCCTGCCTTCGGTGCCATGAGCGCCCCTACCTTCGGTGCCACGAGCATGCCTGCTTTCGG
1 AGTACCCCTGCCTTTGGTGCCACAAGCACCCCTACCTTTGGTGCCACAAGCACCCCTGCTTTCGG
5674549 TGCCACA
66 TGCCACA
* * * *
5674556 AGCACCCCTCCCTTTGGTTCCACAAGCACCCCTCCCTTTGGT
1 AGTACCCCTGCCTTTGGTGCCACAAGCACCCCTACCTTTGGT
5674598 TTAACTGGAA
Statistics
Matches: 96, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 96 1.00
ACGTcount: A:0.15, C:0.41, G:0.21, T:0.23
Consensus pattern (72 bp):
AGTACCCCTGCCTTTGGTGCCACAAGCACCCCTACCTTTGGTGCCACAAGCACCCCTGCTTTCGG
TGCCACA
Found at i:5674598 original size:24 final size:24
Alignment explanation
Indices: 5674415--5674597 Score: 217
Period size: 24 Copynumber: 7.6 Consensus size: 24
5674405 TGGTTCCAGT
5674415 ACCCCTGCCTTTGGTGCCACAAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
5674439 ACCCCTGCCTTTGGTGCCACAAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
*
5674463 ACCCCTG-CTTTCGGTGCCACAAGT
1 ACCCCTGCCTTT-GGTGCCACAAGC
* **
5674487 ACCCCTGCCTTCGGTGCCATGAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
* * * *
5674511 GCCCCTACCTTCGGTGCCACGAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
**
5674535 ATGCCTG-CTTTCGGTGCCACAAGC
1 ACCCCTGCCTTT-GGTGCCACAAGC
* *
5674559 ACCCCTCCCTTTGGTTCCACAAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
*
5674583 ACCCCTCCCTTTGGT
1 ACCCCTGCCTTTGGT
5674598 TTAACTGGAA
Statistics
Matches: 137, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
23 7 0.05
24 123 0.90
25 7 0.05
ACGTcount: A:0.15, C:0.42, G:0.21, T:0.23
Consensus pattern (24 bp):
ACCCCTGCCTTTGGTGCCACAAGC
Found at i:5674795 original size:24 final size:24
Alignment explanation
Indices: 5674766--5674852 Score: 140
Period size: 24 Copynumber: 3.6 Consensus size: 24
5674756 TGGTTCCAGT
5674766 ACCCCTGCCTTTGGTGCCACAAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
*
5674790 ACCCCTG-CTTTCGGTGCCACAAGT
1 ACCCCTGCCTTT-GGTGCCACAAGC
*
5674814 ACCCCTGCCTTCGGTGCCACAAGC
1 ACCCCTGCCTTTGGTGCCACAAGC
5674838 ACCCCTGCCTTTGGT
1 ACCCCTGCCTTTGGT
5674853 TCAACTGGAT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
23 4 0.07
24 50 0.88
25 3 0.05
ACGTcount: A:0.15, C:0.41, G:0.21, T:0.23
Consensus pattern (24 bp):
ACCCCTGCCTTTGGTGCCACAAGC
Found at i:5674992 original size:24 final size:24
Alignment explanation
Indices: 5674953--5675034 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
5674943 TCGAGCATAC
5674953 CTGCTTTTGGCA-CTTCCAGCACTT
1 CTGCTTTTGG-AGCTTCCAGCACTT
*
5674977 CTGCTTTTGGAGCTT-CA--AGTT
1 CTGCTTTTGGAGCTTCCAGCACTT
* * * *
5674998 CTG-TTTATGGGGGTTCAAGCACTC
1 CTGCTTT-TGGAGCTTCCAGCACTT
5675022 CTGCTTTTGGAGC
1 CTGCTTTTGGAGC
5675035 ATCTTCTACT
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
20 3 0.07
21 12 0.27
22 1 0.02
23 3 0.07
24 22 0.50
25 3 0.07
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.38
Consensus pattern (24 bp):
CTGCTTTTGGAGCTTCCAGCACTT
Found at i:5675285 original size:2 final size:2
Alignment explanation
Indices: 5675261--5675305 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
5675251 TAGGAAGTTC
* * *
5675261 AT AT CT AT AT CT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5675303 AT A
1 AT A
5675306 ATTAAATTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5676715 original size:738 final size:738
Alignment explanation
Indices: 5675293--5677391 Score: 3568
Period size: 738 Copynumber: 2.8 Consensus size: 738
5675283 ATATATATAT
* *
5675293 ATATATATATATAATTAAATTCTTTTGAGTTCTCATGTAGGAACTCAATCTTCTGCACCGGCATT
1 ATATCTATATATAATTAAATTCTTTTGAGTTCTCATGTAGGAACTCAATCTTCTGCACCGGCATA
*
5675358 TGGAAGCACCAGCTTTGGCCAGTCACCATTTGGGGGTCAACGTGGGGGAAGTAGAGTAGCTCCTT
66 TGGAAGCACCAGCTTTGGCCAGTCACCATTTGGGTGTCAACGTGGGGGAAGTAGAGTAGCTCCTT
5675423 ACACACCTACAGCTGAAGCAGATAGTGGGAGTAGTACACAGCCAGCTGGAAAGTTGGAGTCAATA
131 ACACACCTACAGCTGAAGCAGATAGTGGGAGTAGTACACAGCCAGCTGGAAAGTTGGAGTCAATA
*
5675488 TCAGCGATGCCTGTTTGTAAAGATAAAAGTCATGAGGAGCTGAGATGGGAGGATTATCAGTTAGG
196 TCAGCGATGCCTGTTTATAAAGATAAAAGTCATGAGGAGCTGAGATGGGAGGATTATCAGTTAGG
*
5675553 AGATAAAGGTGCCTTCGTAAAATATTGCAAAACCCTGAAAGTTAATCATTCTTCTTTTCTGTGCT
261 AGATAAAGGTACCTTCGTAAAATATTGCAAAACCCTGAAAGTTAATCATTCTTCTTTTCTGTGCT
5675618 TGACTTTGACTACCTTGCTGTATTAATTTGAAATTTCAGGTGGACCACAGCCAGCTGCTCAGCCT
326 TGACTTTGACTACCTTGCTGTATTAATTTGAAATTTCAGGTGGACCACAGCCAGCTGCTCAGCCT
5675683 TCTGGAGGGATTGGCTTTGGTGTGTCAGCTGCACCCACAAGTCCTTTTGGCTCTTCTTCAACATT
391 TCTGGAGGGATTGGCTTTGGTGTGTCAGCTGCACCCACAAGTCCTTTTGGCTCTTCTTCAACATT
*
5675748 TGGTCAAACATCTGTAAATCCTTTCTCCGGCACTAGTACCAATCCATTTAGTCCAAAGCCTCCAT
456 TGGTCAAACATCTGTAAATCCTTTCTTCGGCACTAGTACCAATCCATTTAGTCCAAAGCCTCCAT
* *
5675813 CCTTTAATAGTACAGGTCTCACATCCTCGACTGTTACATCAAATCCTTTTCAATCGACATGTAGT
521 CCTTTAATAGTACAGGTCTCACATCCTCGACTGCTACATCAAATCCTTTTCAATCAACATGTAGT
5675878 CCTTTTGGAACCACTACATTTGGAGCCCAGAGTTGTCCTTTTGGTGAGTAATCAAGTCTCCACGA
586 CCTTTTGGAACCACTACATTTGGAGCCCAGAGTTGTCCTTTTGGTGAGTAATCAAGTCTCCACGA
*
5675943 TTAATTATAAACTTTGAAATTACTTAATACAGTTTGGGAGAAAATATATATTTTCATAGGCTTCC
651 TTAATAATAAACTTTGAAATTACTTAATACAGTTTGGGAGAAAATATATATTTTCATAGGCTTCC
5676008 ACCTTTTGAGTACTAGGAAGTTC
716 ACCTTTTGAGTACTAGGAAGTTC
5676031 ATATCTATATATAATTAAATTCTTTTGAGTTCTCATGTAGGAACTCAATCTTCTGCACCGGCATA
1 ATATCTATATATAATTAAATTCTTTTGAGTTCTCATGTAGGAACTCAATCTTCTGCACCGGCATA
5676096 TGGAAGCACCAGCTTTGGCCAGTCACCATTTGGGTGTCAACGTGGGGGAAGTAGAGTAGCTCCTT
66 TGGAAGCACCAGCTTTGGCCAGTCACCATTTGGGTGTCAACGTGGGGGAAGTAGAGTAGCTCCTT
*
5676161 ACACACCTACAACTGAAGCAGATAGTGGGAGTAGTACACAGCCAGCTGGAAAGTTGGAGTCAATA
131 ACACACCTACAGCTGAAGCAGATAGTGGGAGTAGTACACAGCCAGCTGGAAAGTTGGAGTCAATA
*
5676226 TCAGCGATGCCTGTTTATAAAGATAAAAGTCATGAGGAGCTGAGATGGGAGGATTATCGGTTAGG
196 TCAGCGATGCCTGTTTATAAAGATAAAAGTCATGAGGAGCTGAGATGGGAGGATTATCAGTTAGG
5676291 AGATAAAGGTACCTTCGTAAAATATTGCAAAACCCTGAAAGTTAATCATTCTTCTTTTCTGTGCT
261 AGATAAAGGTACCTTCGTAAAATATTGCAAAACCCTGAAAGTTAATCATTCTTCTTTTCTGTGCT
5676356 TGACTTTGACTACCTTGCTGTATTAATTTGAAATTTCAGGTGGACCACAGCCAGCTGCTCAGCCT
326 TGACTTTGACTACCTTGCTGTATTAATTTGAAATTTCAGGTGGACCACAGCCAGCTGCTCAGCCT
5676421 TCTGGAGGGATTGGCTTTGGTGTGTCAGCTGCACCCACAAGTCCTTTTGGCTCTTCTTCAACATT
391 TCTGGAGGGATTGGCTTTGGTGTGTCAGCTGCACCCACAAGTCCTTTTGGCTCTTCTTCAACATT
* *
5676486 TGGTCAAACATCTGTAAATCCTTTCTTCGGCACTAGTACGAGTCCATTTAGTCCAAAGCCTCCAT
456 TGGTCAAACATCTGTAAATCCTTTCTTCGGCACTAGTACCAATCCATTTAGTCCAAAGCCTCCAT
* * *
5676551 CCTTTAATAGTATAGGTCTCACATCCTTGATTGCTACATCAAATCCTTTTCAATCAACATGTAGT
521 CCTTTAATAGTACAGGTCTCACATCCTCGACTGCTACATCAAATCCTTTTCAATCAACATGTAGT
* *
5676616 CCTTTTGGAGCCACTACATTTGGAGCCCGGAGTTGTCCTTTTGGTGAGTAATCAAGTCTCCACGA
586 CCTTTTGGAACCACTACATTTGGAGCCCAGAGTTGTCCTTTTGGTGAGTAATCAAGTCTCCACGA
5676681 TTAATAATAAACTTTGAAATTACTTAATACAGTTTGGGAGAAAATATATATTTTCATAGGCTTCC
651 TTAATAATAAACTTTGAAATTACTTAATACAGTTTGGGAGAAAATATATATTTTCATAGGCTTCC
5676746 ACCTTTTGAGTACTAGGAAGTTC
716 ACCTTTTGAGTACTAGGAAGTTC
* * * * *
5676769 ATATCTACATCTATATATATATATATATGTGTGTGTGTGTGTGTTATATATATATAATTAAATTC
1 ATATCT--A--TATATA-AT-TA-A-A--T-TCT-T-T-TGAG---T-TCT-CAT--GT--A---
**
5676834 TTTTGAGTTCTCATGTAGGAACTCAATCTTCTGCACCGGCATATGGAAGCACCAGCTTTGGCCAG
40 ----G-GAACTC-------AA-----TCTTCTGCACCGGCATATGGAAGCACCAGCTTTGGCCAG
5676899 TCACCATTTGGGTGTCAACGTGGGGGAAGTAGAGTAGCTCCTTACACACCTACAGCTGAAGCAGA
88 TCACCATTTGGGTGTCAACGTGGGGGAAGTAGAGTAGCTCCTTACACACCTACAGCTGAAGCAGA
*
5676964 TAGTGGGAGTAGTACACAGCCAGCTGGAAAGTTGGAGTCAATATCAGCGATGCCTGTCTATAAAG
153 TAGTGGGAGTAGTACACAGCCAGCTGGAAAGTTGGAGTCAATATCAGCGATGCCTGTTTATAAAG
5677029 ATAAAAGTCATGAGGAGCTGAGATGGGAGGATTATCAGTTAGGAGATAAAGGTACCTTCGTAAAA
218 ATAAAAGTCATGAGGAGCTGAGATGGGAGGATTATCAGTTAGGAGATAAAGGTACCTTCGTAAAA
5677094 TATTGCAAAACCCTGAAAGTTAATCATTCTTCTTTTCTGTGCTTGACTTTGACTACCTTGCTGTA
283 TATTGCAAAACCCTGAAAGTTAATCATTCTTCTTTTCTGTGCTTGACTTTGACTACCTTGCTGTA
5677159 TTAATTTGAAATTTCAGGTGGACCACAGCCAGCTGCTCAGCCTTCTGGAGGGATTGGCTTTGGTG
348 TTAATTTGAAATTTCAGGTGGACCACAGCCAGCTGCTCAGCCTTCTGGAGGGATTGGCTTTGGTG
*
5677224 TGTCAGCTGCACCCACAAATCCTTTTGGCTCTTCTTCAACATTTGGTCAAACATCTGTAAATCCT
413 TGTCAGCTGCACCCACAAGTCCTTTTGGCTCTTCTTCAACATTTGGTCAAACATCTGTAAATCCT
5677289 TTCTTCGGCACTAGTACCAATCCATTTAGTCCAAAGCCTCCATCCTTTAATAGTACAGGTCTCAC
478 TTCTTCGGCACTAGTACCAATCCATTTAGTCCAAAGCCTCCATCCTTTAATAGTACAGGTCTCAC
5677354 ATCCTCGACTGCTACATCAAATCCTTTTCAATCAACAT
543 ATCCTCGACTGCTACATCAAATCCTTTTCAATCAACAT
5677392 CATCAAGCCT
Statistics
Matches: 1284, Mismatches: 34, Indels: 43
0.94 0.02 0.03
Matches are distributed among these distances:
738 726 0.57
740 1 0.00
742 6 0.00
743 2 0.00
744 2 0.00
745 1 0.00
746 1 0.00
748 1 0.00
749 2 0.00
750 1 0.00
751 1 0.00
752 3 0.00
755 1 0.00
756 2 0.00
757 2 0.00
759 1 0.00
761 1 0.00
768 1 0.00
769 4 0.00
776 2 0.00
781 523 0.41
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (738 bp):
ATATCTATATATAATTAAATTCTTTTGAGTTCTCATGTAGGAACTCAATCTTCTGCACCGGCATA
TGGAAGCACCAGCTTTGGCCAGTCACCATTTGGGTGTCAACGTGGGGGAAGTAGAGTAGCTCCTT
ACACACCTACAGCTGAAGCAGATAGTGGGAGTAGTACACAGCCAGCTGGAAAGTTGGAGTCAATA
TCAGCGATGCCTGTTTATAAAGATAAAAGTCATGAGGAGCTGAGATGGGAGGATTATCAGTTAGG
AGATAAAGGTACCTTCGTAAAATATTGCAAAACCCTGAAAGTTAATCATTCTTCTTTTCTGTGCT
TGACTTTGACTACCTTGCTGTATTAATTTGAAATTTCAGGTGGACCACAGCCAGCTGCTCAGCCT
TCTGGAGGGATTGGCTTTGGTGTGTCAGCTGCACCCACAAGTCCTTTTGGCTCTTCTTCAACATT
TGGTCAAACATCTGTAAATCCTTTCTTCGGCACTAGTACCAATCCATTTAGTCCAAAGCCTCCAT
CCTTTAATAGTACAGGTCTCACATCCTCGACTGCTACATCAAATCCTTTTCAATCAACATGTAGT
CCTTTTGGAACCACTACATTTGGAGCCCAGAGTTGTCCTTTTGGTGAGTAATCAAGTCTCCACGA
TTAATAATAAACTTTGAAATTACTTAATACAGTTTGGGAGAAAATATATATTTTCATAGGCTTCC
ACCTTTTGAGTACTAGGAAGTTC
Found at i:5677538 original size:84 final size:81
Alignment explanation
Indices: 5677449--5677609 Score: 234
Period size: 84 Copynumber: 2.0 Consensus size: 81
5677439 AGTTCATCTT
* * *
5677449 CAACTCCTACATTTGGAACTGGTTCATCA-TTCTTTAATTTGTCTGTCACTCTTTCTTTTTCAAC
1 CAACTCCTACATTTGGAACTGGTTCATCACTT-TTTAATTCGTCTATCACTC---CATTTTCAAC
5677513 TTCACCATCCATTTTTGGTA
62 TTCACCATCCATTTTTGGTA
* *
5677533 CAACTCCTACATTTGGAACTGGTTCATCACTTTTTAGTTCGTCTATCACTCCATTTTCATCTTCA
1 CAACTCCTACATTTGGAACTGGTTCATCACTTTTTAATTCGTCTATCACTCCATTTTCAACTTCA
5677598 CCATCCATTTTT
66 CCATCCATTTTT
5677610 TATGCTGGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
81 24 0.34
84 45 0.63
85 2 0.03
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.44
Consensus pattern (81 bp):
CAACTCCTACATTTGGAACTGGTTCATCACTTTTTAATTCGTCTATCACTCCATTTTCAACTTCA
CCATCCATTTTTGGTA
Found at i:5682715 original size:30 final size:30
Alignment explanation
Indices: 5682610--5682715 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 30
5682600 ATTAATTTAT
* *
5682610 ATTAAAAGTTTATTT-AAGTATAAATTAAAA
1 ATTAAAAATTTATTTGAA-TACAAATTAAAA
* ** *
5682640 ATTAAAAAATTATTAAAATACAAATTAAAT
1 ATTAAAAATTTATTTGAATACAAATTAAAA
* ** *
5682670 GTTAAGTACTTATTTGAATACAAATTAAAA
1 ATTAAAAATTTATTTGAATACAAATTAAAA
5682700 ATTAAAAATTTATTTG
1 ATTAAAAATTTATTTG
5682716 TGTTCAAATT
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
30 57 0.97
31 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (30 bp):
ATTAAAAATTTATTTGAATACAAATTAAAA
Found at i:5684221 original size:15 final size:16
Alignment explanation
Indices: 5684192--5684222 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5684182 TTACAAATAT
5684192 TAAATATTAAAAAAAA
1 TAAATATTAAAAAAAA
5684208 TAAATATTAAAAAAA
1 TAAATATTAAAAAAA
5684223 CAGGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAATATTAAAAAAAA
Found at i:5690760 original size:7 final size:7
Alignment explanation
Indices: 5690748--5690785 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
5690738 AGTATATATT
5690748 TAAAAAA
1 TAAAAAA
5690755 TAAAAAA
1 TAAAAAA
**
5690762 T-AAATT
1 TAAAAAA
5690768 TAAAAAA
1 TAAAAAA
5690775 TAAAAAA
1 TAAAAAA
5690782 TAAA
1 TAAA
5690786 TTATTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 4 0.15
7 22 0.85
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAAAAA
Found at i:5690770 original size:20 final size:20
Alignment explanation
Indices: 5690745--5690787 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
5690735 TTTAGTATAT
5690745 ATTTAAAAAATAAAAAATAA
1 ATTTAAAAAATAAAAAATAA
5690765 ATTTAAAAAATAAAAAATAA
1 ATTTAAAAAATAAAAAATAA
5690785 ATT
1 ATT
5690788 ATTATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
ATTTAAAAAATAAAAAATAA
Found at i:5690986 original size:15 final size:16
Alignment explanation
Indices: 5690966--5690996 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
5690956 TATATTTTGT
5690966 AAATTTTAAT-TAATA
1 AAATTTTAATATAATA
5690981 AAATTTTAATATAATA
1 AAATTTTAATATAATA
5690997 GAGATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTTTAATATAATA
Found at i:5705146 original size:2 final size:2
Alignment explanation
Indices: 5705139--5705168 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5705129 GTTTGTAGAG
5705139 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
5705169 CATCTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5706309 original size:60 final size:60
Alignment explanation
Indices: 5706236--5706356 Score: 197
Period size: 60 Copynumber: 2.0 Consensus size: 60
5706226 ACTTCTTTCA
* *
5706236 TTGTGTGCATGCAAAATGATGTATGAATATGCTTTTTTATAGTCCAATTTACTACAGGTT
1 TTGTGTGCATGCAAAATGATGTATAAATATGCTCTTTTATAGTCCAATTTACTACAGGTT
* * *
5706296 TTGTGTGCATGCAAAATGGTGTATAAATATGCTCTTTTATAGTCCAATTTAGTGCAGGTT
1 TTGTGTGCATGCAAAATGATGTATAAATATGCTCTTTTATAGTCCAATTTACTACAGGTT
5706356 T
1 T
5706357 GGAATTCACT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (60 bp):
TTGTGTGCATGCAAAATGATGTATAAATATGCTCTTTTATAGTCCAATTTACTACAGGTT
Found at i:5709939 original size:3 final size:3
Alignment explanation
Indices: 5709931--5709966 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5709921 TGATGGACTT
5709931 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
1 CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA CTA
5709967 GTATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CTA
Found at i:5711350 original size:16 final size:16
Alignment explanation
Indices: 5711329--5711362 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5711319 TCTGAATATG
*
5711329 TTTAAAAAAATATCAC
1 TTTAAAAAAAAATCAC
5711345 TTTAAAAAAAAATCAC
1 TTTAAAAAAAAATCAC
5711361 TT
1 TT
5711363 CTGAATGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (16 bp):
TTTAAAAAAAAATCAC
Found at i:5721173 original size:2 final size:2
Alignment explanation
Indices: 5721166--5721194 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5721156 GAGATTTATG
5721166 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5721195 ACTTTTGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5721787 original size:23 final size:23
Alignment explanation
Indices: 5721761--5721808 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
5721751 TTGGAAGTGA
5721761 TTGTTTTGGTGCAGATGATTTCT
1 TTGTTTTGGTGCAGATGATTTCT
*
5721784 TTGTTTTGGTGCGGATGATTTCT
1 TTGTTTTGGTGCAGATGATTTCT
5721807 TT
1 TT
5721809 CCTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.10, C:0.08, G:0.27, T:0.54
Consensus pattern (23 bp):
TTGTTTTGGTGCAGATGATTTCT
Found at i:5729815 original size:23 final size:22
Alignment explanation
Indices: 5729770--5729818 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
5729760 TAATCAAATC
*
5729770 CTTATTTAATATATGAATTGAG
1 CTTATTTAATATATGAATCGAG
* *
5729792 CTTATTTTTATATATTAATCGAG
1 CTTA-TTTAATATATGAATCGAG
5729815 CTTA
1 CTTA
5729819 ATTGAACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (22 bp):
CTTATTTAATATATGAATCGAG
Done.