Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 181 of 206
Found at i:55164525 original size:9 final size:10
Alignment explanation
Indices: 55164482--55164513 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
55164472 TAATAATTAT
55164482 AATAATAAAC
1 AATAATAAAC
55164492 AAT-ATAAAC
1 AATAATAAAC
55164501 AAT-ATAAAC
1 AATAATAAAC
55164510 AATA
1 AATA
55164514 TAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 18 0.86
10 3 0.14
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (10 bp):
AATAATAAAC
Found at i:55164525 original size:18 final size:18
Alignment explanation
Indices: 55164480--55164527 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
55164470 TATAATAATT
*
55164480 ATAATAATAAACAATATA
1 ATAAAAATAAACAATATA
*
55164498 A-ACAATATAAACAATATA
1 ATA-AAAATAAACAATATA
55164516 ATAAAAATAAAC
1 ATAAAAATAAAC
55164528 TAAAAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAAATAAACAATATA
Found at i:55166286 original size:45 final size:45
Alignment explanation
Indices: 55166067--55166375 Score: 181
Period size: 45 Copynumber: 7.0 Consensus size: 45
55166057 CTTCGCTGCA
* * *
55166067 AGTACAGGAAGGCAAGATCTGCCATATTCAGTCTGCTCCACTGT-
1 AGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTC
* * * * * *
55166111 A-AACCTAGGGAGGCAA-AACTGGTGTCTTC-GATCTGCTTCGCTGTC
1 AGTA-C-AGGAAGGCAAGATCTGCTATCTTCAG-TCTGCTCCGCTGTC
* * ** * * *
55166156 AGTACAGGAAGGCAAGATCTGTTATCTTTAACCTACTCCACT-AC
1 AGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTC
* * * * * *
55166200 TG-CCAAGAGAGGCAAG-GCTGGTATCTTC-GATCTGCTTCGCTGTC
1 AGTACAGGA-AGGCAAGATCTGCTATCTTCAG-TCTGCTCCGCTGTC
* *
55166244 AGTACAGAAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTG-C
1 AGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTC
* * * * * * * *
55166288 A-AACCCAGGGAGGCAAG-GCTGGTATCTTCAATCTGCTTCTCTGTT
1 AGTA--CAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTC
*
55166333 AGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTCCGCTG
1 AGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTG
55166376 CAAACTCAGG
Statistics
Matches: 189, Mismatches: 58, Indels: 35
0.67 0.21 0.12
Matches are distributed among these distances:
43 23 0.12
44 81 0.43
45 82 0.43
46 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27
Consensus pattern (45 bp):
AGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGTC
Found at i:55166353 original size:177 final size:177
Alignment explanation
Indices: 55166040--55166360 Score: 500
Period size: 177 Copynumber: 1.8 Consensus size: 177
55166030 GGCGATAAGA
* * *
55166040 CTGGTGTCTTTGATCTACTTCGCTGCAAGTACAGGAAGGCAAGATCTGCCATATTCAGTCTGCTC
1 CTGGTATCTTCGATCTACTTCGCTGCAAGTACAGAAAGGCAAGATCTGCCATATTCAGTCTGCTC
* * * *
55166105 CACTGTAAACCTAGGGAGGCAAAACTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCA
66 CACTGCAAACCCAGGGAGGCAAAACTGGTATCTTCAATCTGCTTCGCTGTCAGTACAGGAAGGCA
55166170 AGATCTGTTATCTTTAACCTACTCCACTACTGCCAAGAGAGGCAAGG
131 AGATCTGTTATCTTTAACCTACTCCACTACTGCCAAGAGAGGCAAGG
* *
55166217 CTGGTATCTTCGATCTGCTTCGCTGTC-AGTACAGAAAGGCAAGATCTGCTATATTCAGTCTGCT
1 CTGGTATCTTCGATCTACTTCGCTG-CAAGTACAGAAAGGCAAGATCTGCCATATTCAGTCTGCT
* ** * *
55166281 CCGCTGCAAACCCAGGGAGGCAAGGCTGGTATCTTCAATCTGCTTCTCTGTTAGTACAGGAAGGC
65 CCACTGCAAACCCAGGGAGGCAAAACTGGTATCTTCAATCTGCTTCGCTGTCAGTACAGGAAGGC
55166346 AAGATCTGTTATCTT
130 AAGATCTGTTATCTT
55166361 CAGTCTGCTC
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
177 128 0.99
178 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (177 bp):
CTGGTATCTTCGATCTACTTCGCTGCAAGTACAGAAAGGCAAGATCTGCCATATTCAGTCTGCTC
CACTGCAAACCCAGGGAGGCAAAACTGGTATCTTCAATCTGCTTCGCTGTCAGTACAGGAAGGCA
AGATCTGTTATCTTTAACCTACTCCACTACTGCCAAGAGAGGCAAGG
Found at i:55166386 original size:45 final size:45
Alignment explanation
Indices: 55166252--55166393 Score: 144
Period size: 45 Copynumber: 3.2 Consensus size: 45
55166242 TCAGTACAGA
* *
55166252 AAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAAACCCAGG
1 AAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAGG
* * * * * * ** *
55166297 GAGGCAAG-GCTGGTATCTTCAATCTGCTTCTCTG-TTAGTACAGG
1 AAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCAAACT-CAGG
*
55166341 AAGGCAAGATCTGTTATCTTCAGTCTGCTCCGCTGCAAACTCAGG
1 AAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAGG
*
55166386 AAAGCAAG
1 AAGGCAAG
55166394 GCTGAAGTTT
Statistics
Matches: 73, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
43 1 0.01
44 31 0.42
45 39 0.53
46 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (45 bp):
AAGGCAAGATCTGCTATCTTCAGTCTGCTCCGCTGCAAACTCAGG
Found at i:55166393 original size:89 final size:88
Alignment explanation
Indices: 55166040--55166397 Score: 396
Period size: 89 Copynumber: 4.0 Consensus size: 88
55166030 GGCGATAAGA
* * * *
55166040 CTGGTGTCTTTGATCTACTTCGCTG-CAAGTACAGGAAGGCAAGATCTGCCATATTCAGTCTGCT
1 CTGGTATCTTCGATCTGCTTCGCTGTC-AGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCT
* * **
55166104 CCACTGTAAACCTAGGGAGGCAAAA
65 CCACTGCAAACC-AGGAAGGCAAGG
* * * * ** *
55166129 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTTAACCTACTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTC
* ** *
55166194 CACTAC-TGCCAAGAGAGGCAAGG
66 CACTGCAAACCAGGA-AGGCAAGG
*
55166217 CTGGTATCTTCGATCTGCTTCGCTGTCAGTACAGAAAGGCAAGATCTGCTATATTCAGTCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTC
* *
55166282 CGCTGCAAACCCAGGGAGGCAAGG
66 CACTGCAAA-CCAGGAAGGCAAGG
* * * * *
55166306 CTGGTATCTTCAATCTGCTTCTCTGTTAGTACAGGAAGGCAAGATCTGTTATCTTCAGTCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTC
* *
55166371 CGCTGCAAACTCAGGAAAGCAAGG
66 CACTGCAAAC-CAGGAAGGCAAGG
55166395 CTG
1 CTG
55166398 AAGTTTCACC
Statistics
Matches: 225, Mismatches: 39, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
87 2 0.01
88 70 0.31
89 148 0.66
90 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27
Consensus pattern (88 bp):
CTGGTATCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTC
CACTGCAAACCAGGAAGGCAAGG
Found at i:55167672 original size:15 final size:15
Alignment explanation
Indices: 55167652--55167698 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
55167642 CCTTAGCCTC
55167652 TCCATTTTTACTTTT
1 TCCATTTTTACTTTT
55167667 TCCATTTTT-CATTTT
1 TCCATTTTTAC-TTTT
* *
55167682 TCTATTTTTATTTTT
1 TCCATTTTTACTTTT
55167697 TC
1 TC
55167699 ACATCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 27 0.96
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCCATTTTTACTTTT
Found at i:55167712 original size:30 final size:29
Alignment explanation
Indices: 55167655--55167713 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
55167645 TAGCCTCTCC
55167655 ATTTTTACTTTTTCCATTTTTCATTTTTCT
1 ATTTTTACTTTTTCCATTTTT-ATTTTTCT
* *
55167685 ATTTTTATTTTTTCACATCTTTTTTTTTT
1 ATTTTTACTTTTTC-CAT-TTTTATTTTT
55167714 GCAACTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.52
31 8 0.32
32 4 0.16
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (29 bp):
ATTTTTACTTTTTCCATTTTTATTTTTCT
Found at i:55168208 original size:18 final size:17
Alignment explanation
Indices: 55168179--55168287 Score: 62
Period size: 17 Copynumber: 6.4 Consensus size: 17
55168169 CCCAGCGGGG
55168179 TTTTTTCTTTTTCTCTT
1 TTTTTTCTTTTTCTCTT
*
55168196 TTTTTTCTGTTTTTTCTT
1 TTTTTTCT-TTTTCTCTT
* ** *
55168214 CTTTTTC-CCTCCT-TT
1 TTTTTTCTTTTTCTCTT
* * *
55168229 TTTTTTGTTTTTGTGTT
1 TTTTTTCTTTTTCTCTT
* * *
55168246 TTGTTT-TTGTTCTTTT
1 TTTTTTCTTTTTCTCTT
55168262 TTTCTTTCTTTTTTCCTCTT
1 TTT-TTTC-TTTTT-CTCTT
55168282 TTTTTT
1 TTTTTT
55168288 TTGAATTGAA
Statistics
Matches: 66, Mismatches: 19, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
15 7 0.11
16 13 0.20
17 18 0.27
18 14 0.21
19 7 0.11
20 7 0.11
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTTTTCTCTT
Found at i:55168218 original size:9 final size:8
Alignment explanation
Indices: 55168179--55168273 Score: 50
Period size: 9 Copynumber: 10.8 Consensus size: 8
55168169 CCCAGCGGGG
55168179 TTTTTTCT
1 TTTTTTCT
*
55168187 TTTTCTCTT
1 TTTTTTC-T
55168196 TTTTTTCT
1 TTTTTTCT
55168204 GTTTTTTCT
1 -TTTTTTCT
55168213 TCTTTTTCCCT
1 T-TTTTT--CT
55168224 CCTTTTTT-T
1 --TTTTTTCT
55168233 TTGTTTT-T
1 TT-TTTTCT
* *
55168241 GTGTTTTGT
1 -TTTTTTCT
55168250 TTTTGTTCT
1 TTTT-TTCT
55168259 TTTTTTCT
1 TTTTTTCT
55168267 TTCTTTT
1 TT-TTTT
55168274 TTCCTCTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 23
0.71 0.05 0.23
Matches are distributed among these distances:
7 2 0.03
8 26 0.37
9 34 0.49
11 2 0.03
12 5 0.07
13 1 0.01
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (8 bp):
TTTTTTCT
Found at i:55168239 original size:29 final size:29
Alignment explanation
Indices: 55168178--55168240 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
55168168 CCCCAGCGGG
* *
55168178 GTTTTTTCTTTTTCTCTTTTTTTTCTGTT
1 GTTTTTTCTTTTTCCCTCTTTTTTCTGTT
55168207 -TTTTCTTCTTTTTCCCTCCTTTTTT-T-TT
1 GTTTT-TTCTTTTTCCCT-CTTTTTTCTGTT
55168235 GTTTTT
1 GTTTTT
55168241 GTGTTTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
28 7 0.24
29 16 0.55
30 6 0.21
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (29 bp):
GTTTTTTCTTTTTCCCTCTTTTTTCTGTT
Found at i:55168247 original size:13 final size:13
Alignment explanation
Indices: 55168231--55168255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55168221 CCTCCTTTTT
55168231 TTTTGTTTTTGTG
1 TTTTGTTTTTGTG
55168244 TTTTGTTTTTGT
1 TTTTGTTTTTGT
55168256 TCTTTTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (13 bp):
TTTTGTTTTTGTG
Found at i:55168285 original size:12 final size:10
Alignment explanation
Indices: 55168181--55168288 Score: 56
Period size: 11 Copynumber: 9.9 Consensus size: 10
55168171 CAGCGGGGTT
55168181 TTTTCTTTTTC
1 TTTT-TTTTTC
55168192 TCTTTTTTTTC
1 T-TTTTTTTTC
55168203 TGTTTTTTCTTC
1 T-TTTTTT-TTC
** *
55168215 TTTTTCCCTCC
1 TTTTT-TTTTC
*
55168226 TTTTTTTTTG
1 TTTTTTTTTC
55168236 TTTTTGTGTTT-
1 TTTTT-T-TTTC
*
55168247 TGTTTTTGTTC
1 T-TTTTTTTTC
55168258 TTTTTTTCTTTC
1 -TTTTTT-TTTC
**
55168270 TTTTTTCCTC
1 TTTTTTTTTC
55168280 TTTTTTTTT
1 TTTTTTTTT
55168289 TGAATTGAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
10 17 0.23
11 39 0.53
12 18 0.24
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.79
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:55173282 original size:9 final size:9
Alignment explanation
Indices: 55173270--55173300 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
55173260 AATTATAATA
55173270 ATAAACAAT
1 ATAAACAAT
55173279 ATAAACAAT
1 ATAAACAAT
55173288 ATAAACAAT
1 ATAAACAAT
55173297 ATAA
1 ATAA
55173301 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (9 bp):
ATAAACAAT
Found at i:55173309 original size:9 final size:10
Alignment explanation
Indices: 55173266--55173297 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
55173256 TAATAATTAT
55173266 AATAATAAAC
1 AATAATAAAC
55173276 AAT-ATAAAC
1 AATAATAAAC
55173285 AAT-ATAAAC
1 AATAATAAAC
55173294 AATA
1 AATA
55173298 TAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 18 0.86
10 3 0.14
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (10 bp):
AATAATAAAC
Found at i:55173309 original size:18 final size:18
Alignment explanation
Indices: 55173264--55173311 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
55173254 TATAATAATT
*
55173264 ATAATAATAAACAATATA
1 ATAAAAATAAACAATATA
*
55173282 A-ACAATATAAACAATATA
1 ATA-AAAATAAACAATATA
55173300 ATAAAAATAAAC
1 ATAAAAATAAAC
55173312 TAAAAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAAATAAACAATATA
Found at i:55176425 original size:21 final size:20
Alignment explanation
Indices: 55176397--55176452 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
55176387 GATCAACACT
55176397 TTTGAGCTTCTGTTAAGCTC
1 TTTGAGCTTCTGTTAAGCTC
* *
55176417 TTATGAGCTTTTGTTCAGCTC
1 TT-TGAGCTTCTGTTAAGCTC
55176438 TTTCGAGCTTCTGTT
1 TTT-GAGCTTCTGTT
55176453 GGCGTGTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 28 0.90
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (20 bp):
TTTGAGCTTCTGTTAAGCTC
Found at i:55184929 original size:16 final size:17
Alignment explanation
Indices: 55184908--55184943 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
55184898 TCAGCTCCTA
55184908 TTTTAATTTCG-ATTAT
1 TTTTAATTTCGAATTAT
*
55184924 TTTTAATTTTGAATTAT
1 TTTTAATTTCGAATTAT
55184941 TTT
1 TTT
55184944 CAACCTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTAATTTCGAATTAT
Found at i:55186064 original size:98 final size:98
Alignment explanation
Indices: 55185895--55186091 Score: 376
Period size: 98 Copynumber: 2.0 Consensus size: 98
55185885 TCTAATTACC
55185895 TAAGTAGATTAAAAATTAGTATCTAATCACCTATCATATCAGCTTCCAGATCTGGTGGAATTTTC
1 TAAGTAGATTAAAAATTAGTATCTAATCACCTATCATATCAGCTTCCAGATCTGGTGGAATTTTC
*
55185960 TGTAATATTTAGATTTTCCCTGATTTTTTGTTT
66 TGTAATATTTAGATTTTCCCTGATTTTTGGTTT
55185993 TAAGTAGATTAAAAATTAGTATCTAATCACCTATCATATCAGCTTCCAGATCTGGTGGAATTTTC
1 TAAGTAGATTAAAAATTAGTATCTAATCACCTATCATATCAGCTTCCAGATCTGGTGGAATTTTC
*
55186058 TGTAATATTTGGATTTTCCCTGATTTTTGGTTT
66 TGTAATATTTAGATTTTCCCTGATTTTTGGTTT
55186091 T
1 T
55186092 TATAAAATAT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (98 bp):
TAAGTAGATTAAAAATTAGTATCTAATCACCTATCATATCAGCTTCCAGATCTGGTGGAATTTTC
TGTAATATTTAGATTTTCCCTGATTTTTGGTTT
Found at i:55186389 original size:54 final size:55
Alignment explanation
Indices: 55186301--55186413 Score: 203
Period size: 54 Copynumber: 2.1 Consensus size: 55
55186291 TATCATTGAC
*
55186301 CATTGGTCAACTAACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
1 CATTAGTCAACTAACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
55186356 CATTAGTCAACT-ACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
1 CATTAGTCAACTAACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
55186410 -ATTA
1 CATTA
55186414 AGGTGGCAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
53 4 0.07
54 42 0.74
55 11 0.19
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (55 bp):
CATTAGTCAACTAACTGCCACATCTAATTCTGATTTATTTGATAAAGATTAAAAG
Found at i:55195815 original size:127 final size:127
Alignment explanation
Indices: 55195589--55195850 Score: 488
Period size: 127 Copynumber: 2.1 Consensus size: 127
55195579 AGCCTGTTGT
* *
55195589 TTAATTTGCAGAGCCTACAATTCGCTGGTCAAGTGCATAAAGAAGGCAGCATCATGCAAAATGGG
1 TTAATTTTCAGAGCCTACAATTCGCTGGTCAAGTGCATAAAGAAGGCAGCATCATGCAAAATGGA
*
55195654 GATAACATGCCATGTTACCAAGTAAACGCAGATCCGAAGGTGATTATCTGAGCATCCATGCC
66 GATAACATGCCATGTTACCAAGTAAACGCAGATCCGAAGGTGATTATCTGAGCACCCATGCC
55195716 TTAATTTTCAGAGCCTACAATTCGCTGGTCAAGTGCATAAAGAAGGCAGCATCATGCAAAATGGA
1 TTAATTTTCAGAGCCTACAATTCGCTGGTCAAGTGCATAAAGAAGGCAGCATCATGCAAAATGGA
55195781 GATAACATGCCATGTTACCAAGTAAACGCAGATCCGAAGGTGATTATCTGAGCACCCATGCC
66 GATAACATGCCATGTTACCAAGTAAACGCAGATCCGAAGGTGATTATCTGAGCACCCATGCC
*
55195843 TTATTTTT
1 TTAATTTT
55195851 TCTTGCTGGT
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 131 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (127 bp):
TTAATTTTCAGAGCCTACAATTCGCTGGTCAAGTGCATAAAGAAGGCAGCATCATGCAAAATGGA
GATAACATGCCATGTTACCAAGTAAACGCAGATCCGAAGGTGATTATCTGAGCACCCATGCC
Found at i:55200189 original size:10 final size:10
Alignment explanation
Indices: 55200176--55200202 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55200166 ATTAAATTTT
55200176 AAAAATATAG
1 AAAAATATAG
55200186 AAAAATATAG
1 AAAAATATAG
55200196 AAAAATA
1 AAAAATA
55200203 AAAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (10 bp):
AAAAATATAG
Found at i:55201302 original size:24 final size:25
Alignment explanation
Indices: 55201270--55201324 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
55201260 ATAATAAAAA
*
55201270 TATAATTTTATTA-TTTTAATAGTT
1 TATAATTTTATAATTTTTAATAGTT
* *
55201294 TATATTTTTATAATTTTTAATAGAT
1 TATAATTTTATAATTTTTAATAGTT
55201319 TA-AATT
1 TATAATT
55201325 AATTTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
TATAATTTTATAATTTTTAATAGTT
Found at i:55208512 original size:20 final size:20
Alignment explanation
Indices: 55208478--55208519 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
55208468 AACCATCTAA
** *
55208478 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
55208498 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
55208518 AT
1 AT
55208520 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:55210555 original size:13 final size:14
Alignment explanation
Indices: 55210536--55210575 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
55210526 CAATGGCATA
55210536 GAAATAATATAAAC
1 GAAATAATATAAAC
55210550 -AAATAA-ATAAAC
1 GAAATAATATAAAC
55210562 GAAATTAATATAAA
1 GAAA-TAATATAAA
55210576 AAAACAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.26
13 9 0.39
14 3 0.13
15 5 0.22
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (14 bp):
GAAATAATATAAAC
Found at i:55210880 original size:9 final size:9
Alignment explanation
Indices: 55210866--55210931 Score: 98
Period size: 9 Copynumber: 7.2 Consensus size: 9
55210856 TTGGGTAATT
55210866 TTCGGGTAA
1 TTCGGGTAA
55210875 TTCGGGTAA
1 TTCGGGTAA
55210884 TTTTCGGGTAA
1 --TTCGGGTAA
*
55210895 TTCGGTTAA
1 TTCGGGTAA
55210904 -TCGGGTAA
1 TTCGGGTAA
55210912 TTCGGGTAA
1 TTCGGGTAA
55210921 TTCGGGTAA
1 TTCGGGTAA
55210930 TT
1 TT
55210932 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
8 7 0.13
9 36 0.69
11 9 0.17
ACGTcount: A:0.21, C:0.11, G:0.30, T:0.38
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:55210883 original size:20 final size:18
Alignment explanation
Indices: 55210866--55210931 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 18
55210856 TTGGGTAATT
55210866 TTCGGGTAATTCGGGTAA
1 TTCGGGTAATTCGGGTAA
*
55210884 TTTTCGGGTAATTCGGTTAA
1 --TTCGGGTAATTCGGGTAA
55210904 -TCGGGTAATTCGGGTAA
1 TTCGGGTAATTCGGGTAA
55210921 TTCGGGTAATT
1 TTCGGGTAATT
55210932 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.37
18 10 0.23
20 17 0.40
ACGTcount: A:0.21, C:0.11, G:0.30, T:0.38
Consensus pattern (18 bp):
TTCGGGTAATTCGGGTAA
Found at i:55211723 original size:23 final size:23
Alignment explanation
Indices: 55211677--55211731 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
55211667 ATGATGCCAC
**
55211677 ATAATAATATTAATAATATGAAA
1 ATAATAATATTAATAATAAAAAA
55211700 ATAATTAAT-TTAATAATAAAAAA
1 ATAA-TAATATTAATAATAAAAAA
55211723 ACTAA-AATA
1 A-TAATAATA
55211732 ACAAATAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
24 7 0.26
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
ATAATAATATTAATAATAAAAAA
Found at i:55212127 original size:22 final size:21
Alignment explanation
Indices: 55212092--55212187 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 21
55212082 AAAAGGTATC
* *
55212092 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
55212113 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* * *
55212136 TGCATATCATA--TCTAAGAC
1 TACAAATCATATCTCTAAGAT
*
55212155 TACATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
55212174 TGCATATCATATCT
1 TACAAATCATATCT
55212188 AAGATTGCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
19 34 0.54
21 4 0.06
22 15 0.24
23 10 0.16
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:55212135 original size:23 final size:22
Alignment explanation
Indices: 55212092--55212149 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
55212082 AAAAGGTATC
* *
55212092 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
55212113 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
55212136 TGCATATCATATCT
1 TACAAATCATATCT
55212150 AAGACTACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:55212152 original size:19 final size:19
Alignment explanation
Indices: 55212128--55212200 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
55212118 AATCATATCT
55212128 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
55212147 TCTAAGACTACATATCATA
1 TCTAAGATTGCATATCATA
55212166 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
55212185 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
55212201 CTTGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55216111 original size:144 final size:144
Alignment explanation
Indices: 55215886--55216169 Score: 498
Period size: 144 Copynumber: 2.0 Consensus size: 144
55215876 TAAGGTAGAT
**
55215886 TAGTAATAATGTGTAACCCTATATAGTATATACAACTATGTTACTATAATGTACATTTGTATATT
1 TAGTAATAATGTGTAACCCTATATAGTATATACAACTATGCCACTATAATGTACATTTGTATATT
* *
55215951 AATGATACGTAACCTTAAAC-CTTAAATGTGCAACTAACCTTATCGTATATTATTGTTATACTTA
66 AATGATACGCAACCTTAAACTC-TAAATGTGCAACTAACCTTATCATATATTATTGTTATACTTA
*
55216015 TATCCTTACCTTATA
130 TACCCTTACCTTATA
55216030 TAGTAATAATGTGTAACCCTATATAGTATATACAACTATGCCACTATAATGTACATTTGTATATT
1 TAGTAATAATGTGTAACCCTATATAGTATATACAACTATGCCACTATAATGTACATTTGTATATT
*
55216095 AATGATACGCAACCTTAAACTCTAAATGTGCAGCTAACCTTATCATATATTATTGTTATACTTAT
66 AATGATACGCAACCTTAAACTCTAAATGTGCAACTAACCTTATCATATATTATTGTTATACTTAT
55216160 ACCCTTACCT
131 ACCCTTACCT
55216170 CAATTTAGAC
Statistics
Matches: 133, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
144 132 0.99
145 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (144 bp):
TAGTAATAATGTGTAACCCTATATAGTATATACAACTATGCCACTATAATGTACATTTGTATATT
AATGATACGCAACCTTAAACTCTAAATGTGCAACTAACCTTATCATATATTATTGTTATACTTAT
ACCCTTACCTTATA
Found at i:55221813 original size:119 final size:119
Alignment explanation
Indices: 55221602--55221840 Score: 390
Period size: 119 Copynumber: 2.0 Consensus size: 119
55221592 TGGCTCAGCC
55221602 AGAATCTGCCGTACCATATGTTGTTTATAGTGATGCGTCTTTAAATGGTTTGGGTTGTGTACTGA
1 AGAATCTGCCGTACCATATGTTGTTTATAGTGATGCGTCTTTAAATGGTTTGGGTTGTGTACTGA
* * * *
55221667 TGTAGTCAGGAAAGATAGTAGCTTATGCTTCTTGATAATTAATGCGGCATGAGA
66 TGCAGTCAGGAAAGATAGTAGCCTATGCTTCTTGAAAATTAATACGGCATGAGA
*
55221721 AGAATCTAG-CGTACCGTATGTTGTTTATAGTGATGCGTCTTTAAATGGTTTGGGTTGTGTACTG
1 AGAATCT-GCCGTACCATATGTTGTTTATAGTGATGCGTCTTTAAATGGTTTGGGTTGTGTACTG
* * *
55221785 ATGCAGTCAGGAAAGGTAGTAGCCTATGCTTTTTGAAAATTAATACTGCATGAGA
65 ATGCAGTCAGGAAAGATAGTAGCCTATGCTTCTTGAAAATTAATACGGCATGAGA
55221840 A
1 A
55221841 AATTTATTCT
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
119 110 0.99
120 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.36
Consensus pattern (119 bp):
AGAATCTGCCGTACCATATGTTGTTTATAGTGATGCGTCTTTAAATGGTTTGGGTTGTGTACTGA
TGCAGTCAGGAAAGATAGTAGCCTATGCTTCTTGAAAATTAATACGGCATGAGA
Found at i:55222477 original size:19 final size:21
Alignment explanation
Indices: 55222443--55222483 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
55222433 ATGAAACGGG
*
55222443 AAATTTTTGAATTTG-TAGCA
1 AAATGTTTGAATTTGTTAGCA
55222463 AAATGTTTG-ATTTGTTAGCA
1 AAATGTTTGAATTTGTTAGCA
55222483 A
1 A
55222484 GTGAAAGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (21 bp):
AAATGTTTGAATTTGTTAGCA
Found at i:55224543 original size:41 final size:42
Alignment explanation
Indices: 55224467--55224560 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 42
55224457 TCAACTCTCG
*
55224467 CGAGCTTCTGTTTAACTCATATGAGTTTCCGTTCAGCTC-TA
1 CGAGCTTCTATTTAACTCATATGAGTTTCCGTTCAGCTCTTA
* *
55224508 TTGAGCTTCTATTTAAC-CTTATGAGTTTCCGTTCAGCTCTTA
1 -CGAGCTTCTATTTAACTCATATGAGTTTCCGTTCAGCTCTTA
55224550 CGAGCTTCTAT
1 CGAGCTTCTAT
55224561 GCAGCTCTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
41 31 0.66
42 16 0.34
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.41
Consensus pattern (42 bp):
CGAGCTTCTATTTAACTCATATGAGTTTCCGTTCAGCTCTTA
Found at i:55224549 original size:21 final size:21
Alignment explanation
Indices: 55224486--55224549 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
55224476 GTTTAACTCA
55224486 TATGAGTTTCCGTTCAGCTC-
1 TATGAGTTTCCGTTCAGCTCT
* ** * *
55224506 TATTGAGCTTCTATTTAAC-CT
1 TA-TGAGTTTCCGTTCAGCTCT
55224527 TATGAGTTTCCGTTCAGCTCT
1 TATGAGTTTCCGTTCAGCTCT
55224548 TA
1 TA
55224550 CGAGCTTCTA
Statistics
Matches: 31, Mismatches: 10, Indels: 5
0.67 0.22 0.11
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.44
Consensus pattern (21 bp):
TATGAGTTTCCGTTCAGCTCT
Found at i:55224565 original size:21 final size:21
Alignment explanation
Indices: 55224541--55224581 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
55224531 AGTTTCCGTT
55224541 CAGCTCTTACGAGCTTCTATG
1 CAGCTCTTACGAGCTTCTATG
55224562 CAGCTCTTACGAGCTTCTAT
1 CAGCTCTTACGAGCTTCTAT
55224582 TCAACCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (21 bp):
CAGCTCTTACGAGCTTCTATG
Found at i:55228480 original size:3 final size:3
Alignment explanation
Indices: 55228467--55228524 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
55228457 ATTACTTAAC
* * * * * * *
55228467 TAT TTT TAT TAT TAT TGT TAT TAT TAT TAA TGT TAC TAT AAT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55228515 TAT TAT TAT T
1 TAT TAT TAT T
55228525 TGTATTAGTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:55234327 original size:19 final size:17
Alignment explanation
Indices: 55234294--55234334 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
55234284 ATTATTTGAA
*
55234294 TTTTATATTTTATAATT
1 TTTTATATTTTATAACT
55234311 TTTTATGATTCTTATAACT
1 TTTTAT-ATT-TTATAACT
55234330 TTTTA
1 TTTTA
55234335 ATAATCAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 3 0.14
19 12 0.57
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (17 bp):
TTTTATATTTTATAACT
Found at i:55234433 original size:19 final size:20
Alignment explanation
Indices: 55234411--55234459 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
55234401 TTTCTTGGAA
55234411 TTTTTAATAAT-TCTATA-AT
1 TTTTTAATAATAT-TATATAT
* *
55234430 TTTTTAAAAATATTTTATAT
1 TTTTTAATAATATTATATAT
55234450 TTTTTAATAA
1 TTTTTAATAA
55234460 CAACTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTAATAATATTATATAT
Found at i:55252835 original size:20 final size:20
Alignment explanation
Indices: 55252801--55252842 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
55252791 AACTATTTAA
** *
55252801 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
55252821 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
55252841 AT
1 AT
55252843 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:55257208 original size:22 final size:22
Alignment explanation
Indices: 55257180--55257221 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
55257170 TATAAAGAAT
55257180 ATATAAAAGAAAAACT-TAAAAA
1 ATATAAAA-AAAAACTCTAAAAA
55257202 ATATAAAAAAAAACTCTAAA
1 ATATAAAAAAAAACTCTAAA
55257222 CTTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.19
Consensus pattern (22 bp):
ATATAAAAAAAAACTCTAAAAA
Found at i:55259931 original size:2 final size:2
Alignment explanation
Indices: 55259924--55259953 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
55259914 TGGCTTGTAT
55259924 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55259954 TCGCTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55267242 original size:23 final size:23
Alignment explanation
Indices: 55267197--55267242 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
55267187 AATGCAACAA
* *
55267197 GAGACCAGCAACAGTTCAGCATG
1 GAGACCAGCAACAGCTCAACATG
*
55267220 GAGACCAGCAGCAGCTCAACATG
1 GAGACCAGCAACAGCTCAACATG
55267243 AAGATCGGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.28, G:0.26, T:0.11
Consensus pattern (23 bp):
GAGACCAGCAACAGCTCAACATG
Found at i:55271713 original size:23 final size:23
Alignment explanation
Indices: 55271683--55271728 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
55271673 AATGCAACAA
* *
55271683 GAGACCAGCAGCAGTTCAGCATG
1 GAGACCAGCAGCAGCTCAACATG
55271706 GAGACCAGCAGCAGCTCAACATG
1 GAGACCAGCAGCAGCTCAACATG
55271729 AAGATTGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.11
Consensus pattern (23 bp):
GAGACCAGCAGCAGCTCAACATG
Found at i:55275050 original size:19 final size:20
Alignment explanation
Indices: 55275017--55275070 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
55275007 AAAAAATATA
55275017 AATTTTAATATTTTT-ATAAAT
1 AATTTTAA-ATTTTTGA-AAAT
55275038 -ATTTTAAATTTTTGAAAAT
1 AATTTTAAATTTTTGAAAAT
*
55275057 AATTTTGAATTTTT
1 AATTTTAAATTTTT
55275071 TTTTTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
AATTTTAAATTTTTGAAAAT
Found at i:55289822 original size:24 final size:24
Alignment explanation
Indices: 55289785--55289848 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
55289775 CCAAACACTC
* *
55289785 ACACTCAGTTCTCTGCGCAGCCAA
1 ACACTCAGTCCTCTGCCCAGCCAA
*
55289809 ACACTCAATCCTCTGCCCAGCCAA
1 ACACTCAGTCCTCTGCCCAGCCAA
55289833 ACACTCAGTCCT-TGCC
1 ACACTCAGTCCTCTGCC
55289849 TGCCAACCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 4 0.11
24 32 0.89
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.20
Consensus pattern (24 bp):
ACACTCAGTCCTCTGCCCAGCCAA
Found at i:55290872 original size:15 final size:15
Alignment explanation
Indices: 55290852--55290886 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
55290842 GGAGAATTTA
55290852 AAAGAATTTGAAGTC
1 AAAGAATTTGAAGTC
55290867 AAAGAATTTGAAGTC
1 AAAGAATTTGAAGTC
55290882 AAAGA
1 AAAGA
55290887 GCTCGGTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (15 bp):
AAAGAATTTGAAGTC
Found at i:55303462 original size:23 final size:24
Alignment explanation
Indices: 55303436--55303481 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
55303426 TTCTAACATA
*
55303436 TGAGTATTGA-AAAAACAAATGTG
1 TGAGAATTGAGAAAAACAAATGTG
*
55303459 TGAGAATTGAGAAATACAAATGT
1 TGAGAATTGAGAAAAACAAATGT
55303482 TTGTTTCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (24 bp):
TGAGAATTGAGAAAAACAAATGTG
Found at i:55303709 original size:36 final size:36
Alignment explanation
Indices: 55303658--55303777 Score: 195
Period size: 36 Copynumber: 3.3 Consensus size: 36
55303648 GTTAGCCATG
* *
55303658 TATACCAGCAGCCATGTATAACAACATAAGCAACAA
1 TATACCAGCAACCATGTATACCAACATAAGCAACAA
*
55303694 TATACCAGCAACCATGTATACCAACATAAGTAACAA
1 TATACCAGCAACCATGTATACCAACATAAGCAACAA
**
55303730 TATACCAGCAGTCATGTATACCAACATAAGCAACAA
1 TATACCAGCAACCATGTATACCAACATAAGCAACAA
55303766 TATACCAGCAAC
1 TATACCAGCAAC
55303778 AATATTACAA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 76 1.00
ACGTcount: A:0.46, C:0.26, G:0.10, T:0.18
Consensus pattern (36 bp):
TATACCAGCAACCATGTATACCAACATAAGCAACAA
Found at i:55303735 original size:20 final size:20
Alignment explanation
Indices: 55303710--55303772 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
55303700 AGCAACCATG
55303710 TATACCAACATAAGTAACAA
1 TATACCAACATAAGTAACAA
* *
55303730 TATACCAGC---AGT--CATG
1 TATACCAACATAAGTAACA-A
*
55303746 TATACCAACATAAGCAACAA
1 TATACCAACATAAGTAACAA
55303766 TATACCA
1 TATACCA
55303773 GCAACAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
15 2 0.06
16 8 0.25
17 3 0.09
19 2 0.06
20 15 0.47
21 2 0.06
ACGTcount: A:0.48, C:0.24, G:0.08, T:0.21
Consensus pattern (20 bp):
TATACCAACATAAGTAACAA
Found at i:55307083 original size:42 final size:41
Alignment explanation
Indices: 55307024--55307109 Score: 145
Period size: 42 Copynumber: 2.1 Consensus size: 41
55307014 TTTAGGCAGT
*
55307024 GTTTCTCTGTTATCAATCGCTGCTGATAAATGTCATCATGGG
1 GTTTCTCTGTTATCAATCACTGCTGAT-AATGTCATCATGGG
*
55307066 GTTTCTCTGTTATCAATCACTGCTGATAATGTCATCATGTG
1 GTTTCTCTGTTATCAATCACTGCTGATAATGTCATCATGGG
55307107 GTT
1 GTT
55307110 ACTTCTGGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
41 16 0.38
42 26 0.62
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (41 bp):
GTTTCTCTGTTATCAATCACTGCTGATAATGTCATCATGGG
Found at i:55311285 original size:9 final size:9
Alignment explanation
Indices: 55311271--55311300 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
55311261 TCGAACTAGC
55311271 ATTAATCGA
1 ATTAATCGA
55311280 ATTAATCGA
1 ATTAATCGA
*
55311289 ATTATTCGA
1 ATTAATCGA
55311298 ATT
1 ATT
55311301 GTATAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (9 bp):
ATTAATCGA
Found at i:55326939 original size:25 final size:25
Alignment explanation
Indices: 55326855--55326924 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 25
55326845 CCAATATCGA
* * * *
55326855 GAAGCTTCGAAGAGCCATTAATTAG
1 GAAGCTCCGGAGAGCCTTTAATCAG
* *
55326880 GAAGCTCATGAAAGAGCCTTTAATCAG
1 GAAGCTC-CG-GAGAGCCTTTAATCAG
55326907 GAAGCTCCGGAGAGCCTT
1 GAAGCTCCGGAGAGCCTT
55326925 ATATCGGGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
25 14 0.38
26 2 0.05
27 21 0.57
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (25 bp):
GAAGCTCCGGAGAGCCTTTAATCAG
Found at i:55326945 original size:25 final size:25
Alignment explanation
Indices: 55326855--55326946 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 25
55326845 CCAATATCGA
* * *
55326855 GAAGCTTCGAAGAGCCATTAATTAG
1 GAAGCTCCGAAGAGCCTTTAATCAG
*
55326880 GAAGCTCATGAAAGAGCCTTTAATCAG
1 GAAGCTC-CG-AAGAGCCTTTAATCAG
* *
55326907 GAAGCTCCGGAGAGCC-TTATATCGG
1 GAAGCTCCGAAGAGCCTTTA-ATCAG
* *
55326932 GATGCTCCTAAGAGC
1 GAAGCTCCGAAGAGC
55326947 TACGACGTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 3 0.06
25 28 0.52
26 2 0.04
27 21 0.39
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.22
Consensus pattern (25 bp):
GAAGCTCCGAAGAGCCTTTAATCAG
Found at i:55327019 original size:24 final size:25
Alignment explanation
Indices: 55326986--55327046 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
55326976 ACAACCAAAT
* *
55326986 CGGGATGCTCATAAGAACTAT-TAA
1 CGGGAAGCTCATAAGAACCATATAA
**
55327010 CGGGAAGCTCGCAAGAACCATATAA
1 CGGGAAGCTCATAAGAACCATATAA
55327035 CGGGAAGCTCAT
1 CGGGAAGCTCAT
55327047 GAGAGCCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (25 bp):
CGGGAAGCTCATAAGAACCATATAA
Found at i:55327041 original size:25 final size:24
Alignment explanation
Indices: 55326998--55327044 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
55326988 GGATGCTCAT
*
55326998 AAGAACTATTAACGGGAAGCTCGC
1 AAGAACCATTAACGGGAAGCTCGC
55327022 AAGAACCATATAACGGGAAGCTC
1 AAGAACCAT-TAACGGGAAGCTC
55327045 ATGAGAGCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.15
Consensus pattern (24 bp):
AAGAACCATTAACGGGAAGCTCGC
Found at i:55329222 original size:26 final size:26
Alignment explanation
Indices: 55329193--55329268 Score: 91
Period size: 26 Copynumber: 2.9 Consensus size: 26
55329183 TTTCATCCCT
* * *
55329193 ATTTTACCCCCAGCAAAATTTTGATG
1 ATTTTACCCCTAGTAAAATTTTGACG
*
55329219 ATTTTA-CCCTTGATAAAATTTTGACG
1 ATTTTACCCCTAG-TAAAATTTTGACG
*
55329245 ATTTTACCCCTGGTAAAATTTTGA
1 ATTTTACCCCTAGTAAAATTTTGA
55329269 GAAAATATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
25 4 0.09
26 34 0.79
27 5 0.12
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTGACG
Found at i:55332029 original size:18 final size:15
Alignment explanation
Indices: 55331992--55332021 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55331982 TCTAAGTTTA
55331992 AAAAAATAATTACAT
1 AAAAAATAATTACAT
55332007 AAAAAATAATTACAT
1 AAAAAATAATTACAT
55332022 CATTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAAATAATTACAT
Found at i:55333187 original size:14 final size:15
Alignment explanation
Indices: 55333168--55333201 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
55333158 CTGAATCTAT
55333168 TTTGGGCCACTGTA-
1 TTTGGGCCACTGTAG
*
55333182 TTTGGGCCTCTGTAG
1 TTTGGGCCACTGTAG
55333197 TTTGG
1 TTTGG
55333202 TTTATTTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.09, C:0.18, G:0.32, T:0.41
Consensus pattern (15 bp):
TTTGGGCCACTGTAG
Found at i:55334083 original size:267 final size:267
Alignment explanation
Indices: 55333537--55334054 Score: 743
Period size: 267 Copynumber: 1.9 Consensus size: 267
55333527 ATATTCAGTC
55333537 TTTTAAATTGCAATGTTAGGGAAACAAGATTCGCCATCGTAGCTTCAATATGTTCTACTACACCG
1 TTTTAAATTGCAATGTTAGGGAAACAAGATTCGCCATCGTAGCTTCAATATGTTCTACTACACCG
* * * *
55333602 CCAGGGGAGTAAGAGTCGCCGTTGTGGCTTTAATCTGCTCCACCGTAATGCCAAAGAGATAGAAT
66 CCAGGGAAGTAAGAGTCACCGTCGTGGCTTTAATCTGCTCCACCATAATGCCAAAGAGATAGAAT
* *
55333667 TCACTGCCCACAGCTTCAATCCGCTTCACTTCAGCTAATCCAAGCCTTAACGCTAGGGAGATAAG
131 TCACTGCCCACAGCTTCAATCCGCTTCACTTCAGCTAATCCAAGCCTTAACGCCAAGGAGATAAG
* * * * * *
55333732 ATTCACCGCCGTGGCTTCAATTTGCTCCGCTACAATGCTAGGGAAGTAAGATTCGTCGTTATGGT
196 ATTCACCGCCGTGGCTTCAATCTGCTCCACTACAACGCCAGGGAAGTAAAATTCATCGTTATGGT
55333797 TTCAATA
261 TTCAATA
* * * *
55333804 TTTTAAATTGCAATGTT-GGAGAAACGAGATTTGCCGTCGTAGCTTCAATCTGTT-TCACTACAC
1 TTTTAAATTGCAATGTTAGG-GAAACAAGATTCGCCATCGTAGCTTCAATATGTTCT-ACTACAC
* * * * *
55333867 CGCTAGGGAAGTAAGATTCACCGTCGTGGTTTTAATCTGCTCCACTATAATGCCAAAGAGATAGG
64 CGCCAGGGAAGTAAGAGTCACCGTCGTGGCTTTAATCTGCTCCACCATAATGCCAAAGAGATAGA
* *
55333932 ATTCGCTGCCCACAGCTTCAATCCGCTTCACTTCAGCTAATCCAAGCCTTAATGCCAAGGAGATA
129 ATTCACTGCCCACAGCTTCAATCCGCTTCACTTCAGCTAATCCAAGCCTTAACGCCAAGGAGATA
* * * * * *
55333997 AGATTCACTGTCGTGGTTTCAATCTGCTCTACTATAACGCCAGGGGAGTAAAATTCAT
194 AGATTCACCGCCGTGGCTTCAATCTGCTCCACTACAACGCCAGGGAAGTAAAATTCAT
55334055 TGTTGTGGCT
Statistics
Matches: 220, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
266 3 0.01
267 217 0.99
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (267 bp):
TTTTAAATTGCAATGTTAGGGAAACAAGATTCGCCATCGTAGCTTCAATATGTTCTACTACACCG
CCAGGGAAGTAAGAGTCACCGTCGTGGCTTTAATCTGCTCCACCATAATGCCAAAGAGATAGAAT
TCACTGCCCACAGCTTCAATCCGCTTCACTTCAGCTAATCCAAGCCTTAACGCCAAGGAGATAAG
ATTCACCGCCGTGGCTTCAATCTGCTCCACTACAACGCCAGGGAAGTAAAATTCATCGTTATGGT
TTCAATA
Found at i:55334198 original size:43 final size:44
Alignment explanation
Indices: 55334131--55334266 Score: 134
Period size: 44 Copynumber: 3.1 Consensus size: 44
55334121 ATTGCCAGCA
55334131 CAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCT
1 CAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCT
* * * * * **
55334175 CAGGGAGACAAG-GCTGGTATCTTCGATCTACTTGACTG-T-CAAT
1 CAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGC--T
* * *
55334218 ACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTACTGCT
1 -CAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCT
55334263 CAGG
1 CAGG
55334267 GAGATAAGTC
Statistics
Matches: 70, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 21 0.30
44 26 0.37
45 19 0.27
46 1 0.01
47 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (44 bp):
CAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCT
Found at i:55346251 original size:12 final size:13
Alignment explanation
Indices: 55346227--55346275 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
55346217 AATGGCATAT
55346227 AAATAATATAAAC
1 AAATAATATAAAC
55346240 AAATAA-ATAAAC
1 AAATAATATAAAC
*
55346252 AAAATGAATATATAAA
1 -AAAT-AATATA-AAC
55346268 AAATAATA
1 AAATAATA
55346276 ATCCATGGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.19
13 10 0.32
14 6 0.19
15 7 0.23
16 2 0.06
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (13 bp):
AAATAATATAAAC
Found at i:55346856 original size:19 final size:16
Alignment explanation
Indices: 55346816--55346848 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55346806 ATATATAAGT
55346816 TAAAAAAATAATTACA
1 TAAAAAAATAATTACA
55346832 TAAAAAAATAATTACA
1 TAAAAAAATAATTACA
55346848 T
1 T
55346849 CATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAAAATAATTACA
Found at i:55348017 original size:14 final size:15
Alignment explanation
Indices: 55347998--55348031 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
55347988 CTGAATCTTT
55347998 TTTGGGCCACTGTA-
1 TTTGGGCCACTGTAG
*
55348012 TTTGGGCCTCTGTAG
1 TTTGGGCCACTGTAG
55348027 TTTGG
1 TTTGG
55348032 TTTATTGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.09, C:0.18, G:0.32, T:0.41
Consensus pattern (15 bp):
TTTGGGCCACTGTAG
Found at i:55355523 original size:16 final size:17
Alignment explanation
Indices: 55355491--55355523 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
55355481 ATTTTATATG
*
55355491 TTAATTAATAGAAGCAT
1 TTAATTAATAAAAGCAT
55355508 TTAATT-ATAAAAGCAT
1 TTAATTAATAAAAGCAT
55355524 GAAGAAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (17 bp):
TTAATTAATAAAAGCAT
Found at i:55368683 original size:20 final size:20
Alignment explanation
Indices: 55368658--55368695 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55368648 ATGCTAACAA
55368658 AGGCACCAAAGTGCAATCAG
1 AGGCACCAAAGTGCAATCAG
*
55368678 AGGCACCGAAGTGCAATC
1 AGGCACCAAAGTGCAATC
55368696 CCGTACAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGCACCAAAGTGCAATCAG
Found at i:55369517 original size:18 final size:18
Alignment explanation
Indices: 55369474--55369536 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 18
55369464 TTTAAATGTT
55369474 AAAAATAATTAAAAT-AAG
1 AAAAA-AATTAAAATAAAG
*
55369492 TAATAAAATTAAAATAAAAG
1 -AAAAAAATTAAAAT-AAAG
55369512 AAAAAAAGGTTAAAATATAAG
1 AAAAAAA--TTAAAATA-AAG
55369533 AAAA
1 AAAA
55369537 CATAATGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 9 0.24
19 10 0.27
20 4 0.11
21 14 0.38
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (18 bp):
AAAAAAATTAAAATAAAG
Found at i:55370519 original size:39 final size:39
Alignment explanation
Indices: 55370462--55370580 Score: 139
Period size: 39 Copynumber: 3.0 Consensus size: 39
55370452 TACTTTCTAT
* *
55370462 TTGGCATGATTCGAGTGGATCAGCTCTTATGAGCTTCTG
1 TTGGCATGTTTCGGGTGGATCAGCTCTTATGAGCTTCTG
*
55370501 TTGGCATGTTTCGGGTGGACCAGCTCTTATGAGCTTCTG
1 TTGGCATGTTTCGGGTGGATCAGCTCTTATGAGCTTCTG
** * * * **
55370540 TTTGGTGTATTTCAGTTGGATCAAATCTTATGAGCTTCTG
1 -TTGGCATGTTTCGGGTGGATCAGCTCTTATGAGCTTCTG
55370580 T
1 T
55370581 CTAGTTTGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 37 0.54
40 31 0.46
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (39 bp):
TTGGCATGTTTCGGGTGGATCAGCTCTTATGAGCTTCTG
Found at i:55375533 original size:12 final size:12
Alignment explanation
Indices: 55375516--55375568 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
55375506 TCGAATAAGC
55375516 ATGTATATATAT
1 ATGTATATATAT
55375528 ATGTATATATAT
1 ATGTATATATAT
*
55375540 AATGCTAGAATATAT
1 -ATG-TA-TATATAT
**
55375555 ATACATATATAT
1 ATGTATATATAT
55375567 AT
1 AT
55375569 AAAAGTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 20 0.59
13 4 0.12
14 4 0.12
15 6 0.18
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (12 bp):
ATGTATATATAT
Found at i:55376431 original size:41 final size:41
Alignment explanation
Indices: 55376354--55376492 Score: 201
Period size: 41 Copynumber: 3.4 Consensus size: 41
55376344 GACTTTAAGT
**
55376354 CTAGCAGGCTAATTGCCGGT--TCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
55376393 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* **
55376434 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAGT
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
55376475 CTAGCGGGCTATGTGCCG
1 CTAGCAGGCTACGTGCCG
55376493 TTGAATTTGT
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 18 0.20
41 73 0.80
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:55382264 original size:11 final size:11
Alignment explanation
Indices: 55382248--55382330 Score: 96
Period size: 11 Copynumber: 7.5 Consensus size: 11
55382238 AGCATGAAGA
55382248 TGGTGTTGTTT
1 TGGTGTTGTTT
55382259 TGGTGTTGTTT
1 TGGTGTTGTTT
*
55382270 GTGATGTTGTTTT
1 -TGGTGTTG-TTT
*
55382283 TTGTGTTGTTT
1 TGGTGTTGTTT
* *
55382294 TGATGCTG-TT
1 TGGTGTTGTTT
55382304 TGGTGTTGTTT
1 TGGTGTTGTTT
*
55382315 TGATGTTGTTT
1 TGGTGTTGTTT
55382326 TGGTG
1 TGGTG
55382331 CTACTTTTGT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
10 8 0.14
11 35 0.59
12 13 0.22
13 3 0.05
ACGTcount: A:0.04, C:0.01, G:0.34, T:0.61
Consensus pattern (11 bp):
TGGTGTTGTTT
Found at i:55382304 original size:35 final size:31
Alignment explanation
Indices: 55382250--55382332 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 31
55382240 CATGAAGATG
*
55382250 GTGTTGTTTTGGTGTTGTTTGTGATGTTGTTTTTT
1 GTGTTGTTTTGGTGCTGTTTG-G-TGTTG--TTTT
*
55382285 GTGTTGTTTTGATGCTGTTTGGTGTTGTTTT
1 GTGTTGTTTTGGTGCTGTTTGGTGTTGTTTT
55382316 GATGTTGTTTTGGTGCT
1 G-TGTTGTTTTGGTGCT
55382333 ACTTTTGTGG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
31 5 0.11
32 14 0.32
33 5 0.11
34 1 0.02
35 19 0.43
ACGTcount: A:0.04, C:0.02, G:0.33, T:0.61
Consensus pattern (31 bp):
GTGTTGTTTTGGTGCTGTTTGGTGTTGTTTT
Found at i:55382309 original size:21 final size:22
Alignment explanation
Indices: 55382251--55382330 Score: 117
Period size: 21 Copynumber: 3.6 Consensus size: 22
55382241 ATGAAGATGG
55382251 TGTTGTTTTGGTGTTGTTTGTGA
1 TGTTGTTTTGGTGTTGTTT-TGA
*
55382274 TGTTGTTTTTTGTGTTGTTTTGA
1 TGTTG-TTTTGGTGTTGTTTTGA
*
55382297 TGCTG-TTTGGTGTTGTTTTGA
1 TGTTGTTTTGGTGTTGTTTTGA
55382318 TGTTGTTTTGGTG
1 TGTTGTTTTGGTG
55382331 CTACTTTTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
21 19 0.37
22 7 0.14
23 12 0.24
24 13 0.25
ACGTcount: A:0.04, C:0.01, G:0.33, T:0.62
Consensus pattern (22 bp):
TGTTGTTTTGGTGTTGTTTTGA
Found at i:55382416 original size:41 final size:42
Alignment explanation
Indices: 55382371--55382461 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 42
55382361 CAGCTCTTTA
55382371 TGTTTTTATTAT-ATTTTTAATTTGTGTATTGTTTTAAGAAT
1 TGTTTTTATTATCATTTTTAATTTGTGTATTGTTTTAAGAAT
* * * * * * *
55382412 TG-TTTTAGTGTCATTTTTTATTTGTTTCTTGTTTTAATATT
1 TGTTTTTATTATCATTTTTAATTTGTGTATTGTTTTAAGAAT
55382453 TGTTTTTAT
1 TGTTTTTAT
55382462 GTTTTTAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
40 7 0.17
41 28 0.70
42 5 0.12
ACGTcount: A:0.19, C:0.02, G:0.12, T:0.67
Consensus pattern (42 bp):
TGTTTTTATTATCATTTTTAATTTGTGTATTGTTTTAAGAAT
Found at i:55382824 original size:22 final size:22
Alignment explanation
Indices: 55382782--55382824 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
55382772 ATACTCTTCG
*
55382782 TACTTTTAAATTTTAGTATTTT
1 TACTTTTAAATTTTAGAATTTT
55382804 TACTTTT-AATTTTAAGAATTT
1 TACTTTTAAATTTT-AGAATTT
55382825 AACCCCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (22 bp):
TACTTTTAAATTTTAGAATTTT
Found at i:55386701 original size:49 final size:49
Alignment explanation
Indices: 55386634--55386732 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
55386624 CATAAAACCG
55386634 AAATAAGTAATAACAAAAAAAAATGGCATATGATTAGGTATCCAGAAAT
1 AAATAAGTAATAACAAAAAAAAATGGCATATGATTAGGTATCCAGAAAT
55386683 AAATAAGTAATAACAAAAAAAAATGGCATATGATTAGGTATCCAGAAAT
1 AAATAAGTAATAACAAAAAAAAATGGCATATGATTAGGTATCCAGAAAT
55386732 A
1 A
55386733 GTTAAGACAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (49 bp):
AAATAAGTAATAACAAAAAAAAATGGCATATGATTAGGTATCCAGAAAT
Found at i:55390804 original size:71 final size:71
Alignment explanation
Indices: 55390688--55390844 Score: 287
Period size: 71 Copynumber: 2.2 Consensus size: 71
55390678 TAACACTCAA
55390688 AATTTATCAATATCACTTTAACAGTAGGCATGATTAATATCACATGTTTACTCATAGCATCGTAA
1 AATTTATCAATATCACTTTAACAGTAGGCATGATTAATATCACATGTTTACTCATAGCATCGTAA
55390753 CAATTC
66 CAATTC
*
55390759 AATTTATCAATATCACTTTAACAGTAGGCATGATTAATATCACATGTTTACTCATAGCATTGTAA
1 AATTTATCAATATCACTTTAACAGTAGGCATGATTAATATCACATGTTTACTCATAGCATCGTAA
**
55390824 TGATTC
66 CAATTC
55390830 AATTTATCAATATCA
1 AATTTATCAATATCA
55390845 ATAAACACAT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 83 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (71 bp):
AATTTATCAATATCACTTTAACAGTAGGCATGATTAATATCACATGTTTACTCATAGCATCGTAA
CAATTC
Found at i:55404451 original size:14 final size:14
Alignment explanation
Indices: 55404432--55404458 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55404422 ATTTGCCTAC
55404432 TTATTTTTTTATTG
1 TTATTTTTTTATTG
55404446 TTATTTTTTTATT
1 TTATTTTTTTATT
55404459 TATTTTACTA
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:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (14 bp):
TTATTTTTTTATTG
Found at i:55415083 original size:2 final size:2
Alignment explanation
Indices: 55415076--55415107 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
55415066 GTGTAACTGG
*
55415076 AT AT AT AT AT AT AT AC 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
55415108 GAACTGTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55416948 original size:2 final size:2
Alignment explanation
Indices: 55416941--55416970 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55416931 GCAACAATTA
*
55416941 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55416971 GTAATGCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55419645 original size:2 final size:2
Alignment explanation
Indices: 55419638--55419671 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55419628 TTAAATAACT
55419638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55419672 CATCATCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55437668 original size:102 final size:101
Alignment explanation
Indices: 55437461--55437794 Score: 408
Period size: 100 Copynumber: 3.3 Consensus size: 101
55437451 TATCGATGAA
*
55437461 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCAC-GTGTAGTACT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACTGTGTAGTACT
* *
55437525 AAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGAT
66 AAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGAT
* * *
55437561 CACGTGTGCAGTACTGTGTGAAGGCTACCACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCAC-TGTGTAGTAC
* *
55437626 TAAGTGAAGGATACTATGTGTACCGAAAAGCTTTGGT
65 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGAT
* * * * * * * *
55437663 CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCG-TAAA-ACTTGATCACGTGTGCAGTG
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCAC-TGTGTAGTA
* * * *
55437726 CTATGTGAAGGCTACTACGTGAACCCTAAAA-C-TTGAT
64 CTAAGTGAAGGCTACTATGTGTA-CCGAAAAGCTTTGAT
*
55437763 CACGTGTGTAGTACTATGTGAAGGCTACTACG
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACG
55437795 CGTATCGAAT
Statistics
Matches: 202, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
100 84 0.42
101 37 0.18
102 81 0.40
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (101 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACTGTGTAGTACT
AAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGAT
Found at i:55437735 original size:50 final size:50
Alignment explanation
Indices: 55437461--55437794 Score: 300
Period size: 51 Copynumber: 6.6 Consensus size: 50
55437451 TATCGATGAA
* * * * *
55437461 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGAT
* * * * *
55437512 CAC--GTGTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGAT
* * * * *** *
55437561 CACGTGTGCAGTACTGTGTGAAGGCTACCACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
* * * * * *
55437612 CACATGTGTAGTACTAAGTGAAGGATACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGAT
* * *
55437663 CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
* * *
55437713 CACGTGTGCAGTGCTATGTGAAGGCTACTACGTGAACCCTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
55437763 CACGTGTGTAGTACTATGTGAAGGCTACTACG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACG
55437795 CGTATCGAAT
Statistics
Matches: 225, Mismatches: 48, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
47 1 0.00
48 2 0.01
49 38 0.17
50 78 0.35
51 99 0.44
52 6 0.03
53 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
Found at i:55437827 original size:202 final size:202
Alignment explanation
Indices: 55437461--55437828 Score: 431
Period size: 202 Copynumber: 1.8 Consensus size: 202
55437451 TATCGATGAA
* * ** * *
55437461 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACGTGTAGTACTA
1 CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCGATAAATAATGATCACGTGTAGTACTA
* * * *
55437526 AGTGAAGGCTACAATGTGTACCGAGAAGCTTTGATCACGTGTGCAGTACTGTGTGAAGGCTACCA
66 AGTGAAGGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGCAGTACTATGTGAAGGCTACCA
* * ** * *
55437591 CGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGATACTATGTGTACCGAAAAG
131 CGCGAATCGATAAATAAAAGTAACATGGGTAGTACTAAGTGAAGGATACTATGTGTACCGAAAAG
55437656 CTTTGGT
196 CTTTGGT
* *
55437663 CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCG-TAAA-ACTTGATCACGTGTGCAGTG
1 CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCGATAAATA-ATGATCACGTGT--AGTA
* * * *
55437726 CTATGTGAAGGCTACTACGTGAACCCTA-AAAC-TTGATCACGTGTGTAGTACTATGTGAAGGCT
63 CTAAGTGAAGGCTACAACGTGAA-CCGAGAAACTTTGATCACGTGTGCAGTACTATGTGAAGGCT
* * *
55437789 ACTACGCGTATCGA-ATGATAAAAGTAACATGGGTAGTACT
127 ACCACGCGAATCGATA-AATAAAAGTAACATGGGTAGTACT
55437829 GTGTGAAAAA
Statistics
Matches: 136, Mismatches: 25, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
200 1 0.01
201 15 0.11
202 92 0.68
203 25 0.18
204 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (202 bp):
CACGTGTGTAGTACTCTATGAAGGCTACTACGTAAACCGATAAATAATGATCACGTGTAGTACTA
AGTGAAGGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGCAGTACTATGTGAAGGCTACCA
CGCGAATCGATAAATAAAAGTAACATGGGTAGTACTAAGTGAAGGATACTATGTGTACCGAAAAG
CTTTGGT
Found at i:55440791 original size:56 final size:50
Alignment explanation
Indices: 55440501--55440797 Score: 240
Period size: 50 Copynumber: 5.8 Consensus size: 50
55440491 GATAATAACA
* ** ** * *
55440501 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAAATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * * ** *
55440550 TGCCAATGTCATATCCCAGATATGGTCTTACATGAGAATTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
55440600 TGCCCATGCCATGTCCCAGACATGGTCTTA-AGGGGGACCTTTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGG
* **
55440650 TGTCAACGCCATGTCTTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* **
55440700 TGCCAACGCCATGTCCCAGACATAGTCTTGTATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * * *
55440755 ATGCCAATGCCTTGTCCCAGACATGGTTTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
55440798 TTACCCAAAT
Statistics
Matches: 199, Mismatches: 39, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.20
50 116 0.58
51 1 0.01
53 5 0.03
55 2 0.01
56 35 0.18
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:55444422 original size:18 final size:18
Alignment explanation
Indices: 55444388--55444422 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55444378 ACATGCTCAC
*
55444388 ATAATCACTTATCACATA
1 ATAATCACTTATAACATA
*
55444406 ATAATCACTTTTAACAT
1 ATAATCACTTATAACAT
55444423 GTTTAACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATCACTTATAACATA
Found at i:55446672 original size:29 final size:29
Alignment explanation
Indices: 55446632--55446723 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
55446622 CTGGGCATAC
* * *
55446632 GCCCGTATGCTTCACACGGTCATGTGATA
1 GCCCGTGTGCTTCACACAGCCATGTGATA
*
55446661 GCCTGTGTGCTTCACACAGCCATGTGATA
1 GCCCGTGTGCTTCACACAGCCATGTGATA
* *
55446690 GCCCGTGT-CCTCTACAC-GACTATGTGATA
1 GCCCGTGTGCTTC-ACACAG-CCATGTGATA
55446719 GCCCG
1 GCCCG
55446724 AGTCCTAGGC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.07
29 50 0.93
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (29 bp):
GCCCGTGTGCTTCACACAGCCATGTGATA
Found at i:55447675 original size:36 final size:36
Alignment explanation
Indices: 55447608--55447676 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
55447598 AATATATCAA
* *
55447608 TGGATAACGCTCATTTGAGCTTCTTCAGTATATTGG
1 TGGATAACGCTCAGTTGAACTTCTTCAGTATATTGG
* *
55447644 TGGATATCGCTC-GTTGAACTTCATTCGGTATAT
1 TGGATAACGCTCAGTTGAACTTC-TTCAGTATAT
55447677 GTAATATAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 8 0.29
36 20 0.71
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (36 bp):
TGGATAACGCTCAGTTGAACTTCTTCAGTATATTGG
Found at i:55451378 original size:30 final size:30
Alignment explanation
Indices: 55451312--55451391 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
55451302 AAACTAAGAT
*
55451312 ATATAAAATTATTTAAATAATTATGTTGTA
1 ATATAAAATTATATAAATAATTATGTTGTA
* *
55451342 ATATAAAATTATATAATTATGTTATGATT-TA
1 ATATAAAATTATATAAATA-ATTATG-TTGTA
55451373 A-ATAAAATTACTTATAAAT
1 ATATAAAATTA--TATAAAT
55451392 CCGTGTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 26 0.62
31 8 0.19
32 8 0.19
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (30 bp):
ATATAAAATTATATAAATAATTATGTTGTA
Found at i:55474922 original size:20 final size:21
Alignment explanation
Indices: 55474884--55474922 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
55474874 CACCAAAAAG
*
55474884 AACAAGCAACAAACGGAGAAA
1 AACAAGCAACAAACCGAGAAA
*
55474905 AACAA-CAAGAAACCGAGA
1 AACAAGCAACAAACCGAGA
55474923 TCCAAAGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.62, C:0.21, G:0.18, T:0.00
Consensus pattern (21 bp):
AACAAGCAACAAACCGAGAAA
Found at i:55477310 original size:12 final size:12
Alignment explanation
Indices: 55477295--55477320 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55477285 AAAATTAATA
55477295 AAATATTAAATT
1 AAATATTAAATT
55477307 AAATATTAAATT
1 AAATATTAAATT
55477319 AA
1 AA
55477321 TATAATAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATTAAATT
Found at i:55480278 original size:15 final size:15
Alignment explanation
Indices: 55480258--55480288 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55480248 GTTCATATTG
*
55480258 TCCAACCTCTTTAGA
1 TCCAACATCTTTAGA
55480273 TCCAACATCTTTAGA
1 TCCAACATCTTTAGA
55480288 T
1 T
55480289 TTTCCAATCT
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:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (15 bp):
TCCAACATCTTTAGA
Found at i:55480982 original size:2 final size:2
Alignment explanation
Indices: 55480977--55481008 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
55480967 AAAAATAGAT
55480977 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55481009 CATCATCCCT
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):
TA
Found at i:55481056 original size:88 final size:83
Alignment explanation
Indices: 55480906--55481065 Score: 248
Period size: 88 Copynumber: 1.9 Consensus size: 83
55480896 AATCAAATTT
* *
55480906 TATATTATATATATATATACCATTCCTCCTTTTAGATTGTGTGTCTTAAAACAATTTCTGAAAAA
1 TATATTATATATATATATACCATCCCTCCGTTTAGATTGTGTGTCTTAAAACAATTTCTGAAAAA
55480971 ATAGATTATATATATATA
66 ATAGATTATATATATATA
*
55480989 TATATATATATATATATATACATCATCCCTCCGTTTAGATTGTGTTTGTCTTAAAACAATTTTTG
1 TATAT-TATATATATATATAC--CATCCCTCCGTTTAGATTGTG--TGTCTTAAAACAATTTCTG
55481054 AAAAAATAGATT
61 AAAAAATAGATT
55481066 GGTTTTTTGA
Statistics
Matches: 69, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
83 5 0.07
84 15 0.22
86 19 0.28
88 30 0.43
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (83 bp):
TATATTATATATATATATACCATCCCTCCGTTTAGATTGTGTGTCTTAAAACAATTTCTGAAAAA
ATAGATTATATATATATA
Found at i:55486028 original size:27 final size:28
Alignment explanation
Indices: 55485998--55486055 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
55485988 TTTGAAAATT
* *
55485998 AAAATATATAAACATTT-AAAATATATA
1 AAAACATAAAAACATTTAAAAATATATA
* *
55486025 AAAACATAAAAATATTTAAAAATATTTA
1 AAAACATAAAAACATTTAAAAATATATA
55486053 AAA
1 AAA
55486056 TAAAAAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAACATAAAAACATTTAAAAATATATA
Found at i:55486029 original size:19 final size:19
Alignment explanation
Indices: 55485996--55486057 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 19
55485986 TATTTGAAAA
55485996 TTAAAATATAT--AAACAT
1 TTAAAATATATAAAAACAT
55486013 TTAAAATATATAAAAACA-
1 TTAAAATATATAAAAACAT
* * *
55486031 TAAAAATATTTAAAAATAT
1 TTAAAATATATAAAAACAT
55486050 TTAAAATA
1 TTAAAATA
55486058 AAAAAACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 11 0.29
18 15 0.39
19 12 0.32
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAAATATATAAAAACAT
Found at i:55486034 original size:17 final size:17
Alignment explanation
Indices: 55485997--55486046 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
55485987 ATTTGAAAAT
* **
55485997 TAAAATATATAAACATT
1 TAAAATATATAAAAACA
55486014 TAAAATATATAAAAACA
1 TAAAATATATAAAAACA
*
55486031 TAAAAATATTTAAAAA
1 T-AAAATATATAAAAA
55486047 TATTTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATATATAAAAACA
Found at i:55486038 original size:35 final size:35
Alignment explanation
Indices: 55485998--55486071 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 35
55485988 TTTGAAAATT
*
55485998 AAAATA-TATAAACATTTAAAATATATAAAAAC-ATA
1 AAAATATTAAAAACATTTAAAATA-A-AAAAACTATA
*
55486033 AAAATATTTAAAAATATTTAAAATAAAAAAACTATA
1 AAAATA-TTAAAAACATTTAAAATAAAAAAACTATA
55486069 AAA
1 AAA
55486072 GTTTAAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 12 0.35
36 7 0.21
37 15 0.44
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (35 bp):
AAAATATTAAAAACATTTAAAATAAAAAAACTATA
Found at i:55486044 original size:10 final size:10
Alignment explanation
Indices: 55486011--55486055 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
55486001 ATATATAAAC
55486011 ATTT-AAAAT
1 ATTTAAAAAT
* *
55486020 ATATAAAAAC
1 ATTTAAAAAT
55486030 A--TAAAAAT
1 ATTTAAAAAT
55486038 ATTTAAAAAT
1 ATTTAAAAAT
55486048 ATTTAAAA
1 ATTTAAAA
55486056 TAAAAAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
8 7 0.23
9 3 0.10
10 20 0.67
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
ATTTAAAAAT
Found at i:55486062 original size:27 final size:26
Alignment explanation
Indices: 55485996--55486064 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
55485986 TATTTGAAAA
* *
55485996 TTAAAATATATAAACATTTAAAATAT
1 TTAAAATAAAAAAACATTTAAAATAT
* *
55486022 ATAAAA-ACATAAAAATATTTAAAAATAT
1 TTAAAATA-A-AAAAACATTT-AAAATAT
55486050 TTAAAATAAAAAAAC
1 TTAAAATAAAAAAAC
55486065 TATAAAAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
25 1 0.03
26 5 0.15
27 13 0.39
28 13 0.39
29 1 0.03
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (26 bp):
TTAAAATAAAAAAACATTTAAAATAT
Found at i:55486071 original size:9 final size:8
Alignment explanation
Indices: 55485992--55486071 Score: 54
Period size: 9 Copynumber: 9.4 Consensus size: 8
55485982 GCATTATTTG
55485992 AAAAT-TA
1 AAAATATA
55485999 AAATATATA
1 AAA-ATATA
* *
55486008 AACATTTA
1 AAAATATA
55486016 AAATATATA
1 AAA-ATATA
*
55486025 AAAACATA
1 AAAATATA
55486033 AAAATATTTA
1 AAAATA--TA
*
55486043 AAAATATTT
1 AAAATA-TA
*
55486052 AAAATAAA
1 AAAATATA
55486060 AAAACTATA
1 AAAA-TATA
55486069 AAA
1 AAA
55486072 GTTTAAGAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
7 3 0.05
8 21 0.37
9 25 0.44
10 8 0.14
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAATATA
Found at i:55486180 original size:11 final size:11
Alignment explanation
Indices: 55486164--55486193 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
55486154 TTAAAAAAAA
55486164 ATAGATTTTTT
1 ATAGATTTTTT
*
55486175 ATAGATTATTT
1 ATAGATTTTTT
55486186 ATAGATTT
1 ATAGATTT
55486194 AAAAAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (11 bp):
ATAGATTTTTT
Found at i:55488621 original size:22 final size:23
Alignment explanation
Indices: 55488585--55488627 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
55488575 ACTCTTTTTC
*
55488585 AAAAGGTTGATGGTCAAATTTGA
1 AAAAGATTGATGGTCAAATTTGA
55488608 AAAAGATTGA-GGTCAAATTT
1 AAAAGATTGATGGTCAAATTT
55488628 AACTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (23 bp):
AAAAGATTGATGGTCAAATTTGA
Found at i:55489045 original size:29 final size:29
Alignment explanation
Indices: 55489013--55489073 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
55489003 TAAAAAACAT
*
55489013 ATAAAATTA-TTAAATGTTAA-AATAGAATA
1 ATAAAATTATTTAAA-ATTAATAATA-AATA
55489042 ATAAAATTATTTAAAATTAATAATAAATA
1 ATAAAATTATTTAAAATTAATAATAAATA
55489071 ATA
1 ATA
55489074 TGACAGGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
ATAAAATTATTTAAAATTAATAATAAATA
Found at i:55492903 original size:9 final size:9
Alignment explanation
Indices: 55492874--55492949 Score: 89
Period size: 9 Copynumber: 8.4 Consensus size: 9
55492864 GTAGTGATTC
55492874 AATTCGGTT
1 AATTCGGTT
*
55492883 AATTCAGTT
1 AATTCGGTT
*
55492892 AATTCGGGT
1 AATTCGGTT
* *
55492901 AATCCGATT
1 AATTCGGTT
*
55492910 AACTCGGTT
1 AATTCGGTT
*
55492919 AATTCGGGT
1 AATTCGGTT
*
55492928 AATCCGGTT
1 AATTCGGTT
55492937 AATTCGGTT
1 AATTCGGTT
55492946 AATT
1 AATT
55492950 TTTAACCAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (9 bp):
AATTCGGTT
Found at i:55492919 original size:27 final size:27
Alignment explanation
Indices: 55492889--55492949 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
55492879 GGTTAATTCA
55492889 GTTAATTCGGGTAATCCGATTAACTCG
1 GTTAATTCGGGTAATCCGATTAACTCG
* *
55492916 GTTAATTCGGGTAATCCGGTTAATTCG
1 GTTAATTCGGGTAATCCGATTAACTCG
55492943 GTTAATT
1 GTTAATT
55492950 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
GTTAATTCGGGTAATCCGATTAACTCG
Found at i:55494580 original size:25 final size:27
Alignment explanation
Indices: 55494550--55494617 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
55494540 AAAATTGGTA
55494550 AGACATTTTCCATTCT-TCTCTAAGCA-
1 AGACATTTTCCATTCTCT-TCTAAGCAC
55494576 A-ACATTTTCCATTCTCTTCTAAGCAGC
1 AGACATTTTCCATTCTCTTCTAAGCA-C
55494603 AGACATTTTCCATTC
1 AGACATTTTCCATTC
55494618 CTCAAAGCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 22 0.58
26 2 0.05
27 1 0.03
28 13 0.34
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.38
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAAGCAC
Found at i:55497097 original size:15 final size:15
Alignment explanation
Indices: 55497072--55497119 Score: 87
Period size: 15 Copynumber: 3.1 Consensus size: 15
55497062 TAAGTGGTAC
55497072 TTTCAATGCTTTCATT
1 TTTC-ATGCTTTCATT
55497088 TTTCATGCTTTCATT
1 TTTCATGCTTTCATT
55497103 TTTCATGCTTTCATT
1 TTTCATGCTTTCATT
55497118 TT
1 TT
55497120 AAGTGGTACT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 28 0.88
16 4 0.12
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (15 bp):
TTTCATGCTTTCATT
Found at i:55497101 original size:8 final size:8
Alignment explanation
Indices: 55497071--55497116 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
55497061 ATAAGTGGTA
55497071 CTTTCAATG
1 CTTTC-ATG
55497080 CTTTCAT-
1 CTTTCATG
*
55497087 TTTTCATG
1 CTTTCATG
55497095 CTTTCAT-
1 CTTTCATG
*
55497102 TTTTCATG
1 CTTTCATG
55497110 CTTTCAT
1 CTTTCAT
55497117 TTTAAGTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
7 12 0.39
8 14 0.45
9 5 0.16
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (8 bp):
CTTTCATG
Found at i:55498656 original size:28 final size:27
Alignment explanation
Indices: 55498612--55498683 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
55498602 TTGAAATTTT
*
55498612 AGTTTGTTGGATTTTGATATATGTCTTGA
1 AGTTTGTTGGATATTGAT-TATGT-TTGA
*
55498641 A-TTTGTTGGATATTGATTATGTTTTA
1 AGTTTGTTGGATATTGATTATGTTTGA
*
55498667 AGCTTGTTGGATATTGA
1 AGTTTGTTGGATATTGA
55498684 ATTTATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 4 0.10
27 19 0.49
28 15 0.38
29 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.24, T:0.51
Consensus pattern (27 bp):
AGTTTGTTGGATATTGATTATGTTTGA
Found at i:55498699 original size:35 final size:36
Alignment explanation
Indices: 55498651--55498719 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
55498641 ATTTGTTGGA
55498651 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
55498687 TATT-ATTATGTTTTAAGCTTGTTGGATATTGAA
1 TATTGATTATGTTTTAAGCTTGTTGGATATTGAA
55498720 ATGGTTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (36 bp):
TATTGATTATGTTTTAAGCTTGTTGGATATTGAATT
Found at i:55499777 original size:71 final size:72
Alignment explanation
Indices: 55499658--55499800 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 72
55499648 TTGATACATT
*
55499658 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
55499723 TTGGATA
66 TTGGATA
*
55499730 TATGTGGTGTAATATTATGCAC-TAGACAATGTTGTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
55499794 TTGGATA
66 TTGGATA
55499801 ATATTATTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 47 0.68
72 22 0.32
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (72 bp):
TATGTGGTGTAATATTATGCACTTAGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
TTGGATA
Found at i:55500062 original size:32 final size:33
Alignment explanation
Indices: 55500026--55500110 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
55500016 AACTTTTCCG
* * *
55500026 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
55500058 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
55500090 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
55500111 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:55500109 original size:14 final size:15
Alignment explanation
Indices: 55500087--55500163 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
55500077 TTACCAAACA
55500087 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
55500101 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
55500116 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
55500136 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
55500150 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
55500164 ACTGCCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:55500128 original size:20 final size:20
Alignment explanation
Indices: 55500103--55500142 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55500093 AATATTTTCC
*
55500103 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55500123 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55500143 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55500148 original size:34 final size:35
Alignment explanation
Indices: 55500091--55500157 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
55500081 CAAACACCAG
*
55500091 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
55500126 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
55500158 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:55500164 original size:14 final size:14
Alignment explanation
Indices: 55500126--55500165 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
55500116 ACAGAAAAGT
*
55500126 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
55500140 AAATCATTTTACGG
1 AAAACATTTTACAG
55500154 AAAACATTTTAC
1 AAAACATTTTAC
55500166 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:55517034 original size:20 final size:21
Alignment explanation
Indices: 55516988--55517034 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
55516978 CAAGATAAAT
*
55516988 ATTAATTTAATTTAATATTAAG
1 ATTAA-TTAATTTAATAGTAAG
*
55517010 A-TAATTACTTTAATAGTAA-
1 ATTAATTAATTTAATAGTAAG
55517029 ATTAAT
1 ATTAAT
55517035 AAAATACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 3 0.14
22 1 0.05
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (21 bp):
ATTAATTAATTTAATAGTAAG
Found at i:55525340 original size:35 final size:35
Alignment explanation
Indices: 55525280--55525363 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 35
55525270 TACACGGTTA
* * *
55525280 ACCATCCAGCACACCAGATGTTCATAAGAGCTAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
* *
55525315 ACCACCCAACACACTAGATGCTCATAAGAGCCAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
*
55525350 ACCATCCAATACAC
1 ACCATCCAACACAC
55525364 AAGAAACAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (35 bp):
ACCATCCAACACACCAGATGCTCATAAGAGCCAGT
Done.