Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 173 of 198
Found at i:54175935 original size:101 final size:101
Alignment explanation
Indices: 54175748--54175936 Score: 224
Period size: 101 Copynumber: 1.9 Consensus size: 101
54175738 TTAAACTGTT
* * *
54175748 TTGTATATTATTTATTTGAAATTTCTTTTTACATATTATTTATTTTAAACTTTTTATATATTATT
1 TTGTATATTATTTATTTGAAATTTCGTTTTACATATTATTTACTTTAAACTTTTTATATATTACT
* * *
54175813 TTAAATTGTCTTCTATGTTATTTATTTTAAATTGCA
66 TCAAATTGTCTTATATATTATTTATTTTAAATTGCA
* * * *
54175849 TTGTATATTATTTATTT-TAATTT-GTTTTGCATATTA-TTACTTTGAATTGTTTTATACTATTT
1 TTGTATATTATTTATTTGAAATTTCGTTTTACATATTATTTACTTTAAACT-TTTTATA-TA-TT
54175911 ACTTCAAATTGT-TCTATATATTATTT
63 ACTTCAAATTGTCT-TATATATTATTT
54175937 TGTTTTGTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
98 9 0.12
99 18 0.24
100 8 0.11
101 39 0.53
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (101 bp):
TTGTATATTATTTATTTGAAATTTCGTTTTACATATTATTTACTTTAAACTTTTTATATATTACT
TCAAATTGTCTTATATATTATTTATTTTAAATTGCA
Found at i:54177544 original size:14 final size:14
Alignment explanation
Indices: 54177525--54177555 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54177515 ATGATTGTTT
*
54177525 TAATCTAAATTTAC
1 TAATCTAAATTAAC
54177539 TAATCTAAATTAAC
1 TAATCTAAATTAAC
54177553 TAA
1 TAA
54177556 GAATGCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:54179504 original size:11 final size:13
Alignment explanation
Indices: 54179484--54179515 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
54179474 AATAAATTAA
54179484 TAAAATATCAT-T
1 TAAAATATCATAT
54179496 TAAAA-ATCATAT
1 TAAAATATCATAT
54179508 TAAAATAT
1 TAAAATAT
54179516 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:54189064 original size:43 final size:43
Alignment explanation
Indices: 54189007--54189092 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
54188997 ATACAAGTGG
54189007 GCGAGTTGTATGCCTCAGCATGTTGGTACATCTATTTCAAAGT
1 GCGAGTTGTATGCCTCAGCATGTTGGTACATCTATTTCAAAGT
54189050 GCGAGTTGTATGCCTCAGCATGTTGGTACATCTATTTCAAAGT
1 GCGAGTTGTATGCCTCAGCATGTTGGTACATCTATTTCAAAGT
54189093 AGTGATGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (43 bp):
GCGAGTTGTATGCCTCAGCATGTTGGTACATCTATTTCAAAGT
Found at i:54202257 original size:16 final size:16
Alignment explanation
Indices: 54202215--54202258 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
54202205 GAAATTTATG
54202215 TATTAAAATAATAATTT
1 TATTAAAA-AATAATTT
54202232 TA-TAATAAAATAATTT
1 TATTAA-AAAATAATTT
54202248 TATTAAAAAAT
1 TATTAAAAAAT
54202259 CTACAACCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAAAAAATAATTT
Found at i:54205134 original size:17 final size:17
Alignment explanation
Indices: 54205112--54205146 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54205102 GGAGTACTAC
54205112 AATAATAAT-ATAATCAT
1 AATAATAATCAT-ATCAT
54205129 AATAATAATCATATCAT
1 AATAATAATCATATCAT
54205146 A
1 A
54205147 GGAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAATAATCATATCAT
Found at i:54205304 original size:15 final size:14
Alignment explanation
Indices: 54205280--54205313 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
54205270 AAATGTGTCA
54205280 ATAAAAGTATGTGT
1 ATAAAAGTATGTGT
54205294 ATAATAAGTATGTGT
1 ATAA-AAGTATGTGT
54205309 A-AAAA
1 ATAAAA
54205314 AATTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 6 0.32
15 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (14 bp):
ATAAAAGTATGTGT
Found at i:54207035 original size:44 final size:44
Alignment explanation
Indices: 54206987--54207387 Score: 335
Period size: 44 Copynumber: 8.9 Consensus size: 44
54206977 GAATTGTTGC
*
54206987 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTAGTAGT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAGT
* * *
54207031 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAAATTTATAACTCGTAGCT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGA--T-T---T-GTAG-T
* * * *
54207083 TT-AATCTGTTCCCCTGCAAC-TCTAG-GAAAATAAGATTCGCTA-T
1 TTCAATCTGCTCCACTGCAACTTC-AGAG-AGATAAGATTTG-TAGT
* * * * * * *
54207126 CTTCCATCTACTCCACTGCAACTTTAGGGATATAAGATTTGTGGC
1 -TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAGT
* ** * *
54207171 TTCAATCTGTTTTACTGTAACTTCAGAGAGATAAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAGT
* *
54207215 TTCAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTAGC
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAGT
* * * *
54207259 TTCAATATGCTCTACTGCAACTTTAGAGAGATAAGATTTGCTATT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTG-TAGT
* * * * *
54207304 TTCAATCTGCTCCACTGCAACTTTAGGGAAATAAGAGTTGTGGCT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAG-T
* * *
54207349 TT-AATCTACTCCTCTGCAACTTCAGGGAGATAAGATTTG
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTG
54207388 CCACGATAAC
Statistics
Matches: 291, Mismatches: 48, Indels: 36
0.78 0.13 0.10
Matches are distributed among these distances:
43 1 0.00
44 183 0.63
45 68 0.23
46 3 0.01
47 1 0.00
48 1 0.00
49 1 0.00
50 2 0.01
51 28 0.10
52 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTTGTAGT
Found at i:54207308 original size:133 final size:132
Alignment explanation
Indices: 54206980--54207387 Score: 338
Period size: 133 Copynumber: 3.0 Consensus size: 132
54206970 GATATAGGAA
* * * * * *
54206980 TTGTTGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTAGTAGTTTCAATCTGCTCCA
1 TTGTAGCTTCAATATGCTCTACTGCAACTTTAGAGAGATAAGATTTGTAGCTTCAATCTGCTCCA
* * * * ** *
54207045 CTGCAACTTTAGGGAGATAAAATTTATA-ACTCGTAGCTTTAATCTGTTCCCCTGCAAC-TCTAG
66 CTGCAACTTCA--GAG---AAA--TA-AGAGTTGTAGCTTCAATCTACTCCTCTGCAACTTC-AG
*
54207108 -GAAAATAAGAT
122 AG-AGATAAGAT
* * * * * * * * * * **
54207119 TCGCTATCTTCCATCTACTCCACTGCAACTTTAGGGATATAAGATTTGTGGCTTCAATCTGTTTT
1 TTG-TAGCTTCAATATGCTCTACTGCAACTTTAGAGAGATAAGATTTGTAGCTTCAATCTGCTCC
* * * *
54207184 ACTGTAACTTCAGAGAGATAAGATTTGTAGCTTCAATCTGCT-CTACTGCAACTTCAGAGAGATA
65 ACTGCAACTTCAGAGAAATAAGAGTTGTAGCTTCAATCTACTCCT-CTGCAACTTCAGAGAGATA
54207248 AGAT
129 AGAT
**
54207252 TTGTAGCTTCAATATGCTCTACTGCAACTTTAGAGAGATAAGATTTGCTATTTTCAATCTGCTCC
1 TTGTAGCTTCAATATGCTCTACTGCAACTTTAGAGAGATAAGATTTG-TAGCTTCAATCTGCTCC
* * * * *
54207317 ACTGCAACTTTAGGGAAATAAGAGTTGTGGCTTTAATCTACTCCTCTGCAACTTCAGGGAGATAA
65 ACTGCAACTTCAGAGAAATAAGAGTTGTAGCTTCAATCTACTCCTCTGCAACTTCAGAGAGATAA
54207382 GAT
130 GAT
54207385 TTG
1 TTG
54207388 CCACGATAAC
Statistics
Matches: 216, Mismatches: 46, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
132 39 0.18
133 107 0.50
134 5 0.02
135 2 0.01
138 3 0.01
139 2 0.01
140 58 0.27
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (132 bp):
TTGTAGCTTCAATATGCTCTACTGCAACTTTAGAGAGATAAGATTTGTAGCTTCAATCTGCTCCA
CTGCAACTTCAGAGAAATAAGAGTTGTAGCTTCAATCTACTCCTCTGCAACTTCAGAGAGATAAG
AT
Found at i:54207372 original size:177 final size:180
Alignment explanation
Indices: 54206954--54207387 Score: 491
Period size: 177 Copynumber: 2.4 Consensus size: 180
54206944 TCGTTCTAAC
* * * * *
54206954 CCACTGCGACTTTATGGATATAGGAATTGTTGCTTCAATCTGCTCCACTGCAACTTCAGAGAGAT
1 CCACTGCAACTTTAGGGATATAAGAATTGTGGCTTCAATCT-CTCCTCTGCAACTTCAGAGAGAT
* * * *
54207019 AAGATTAGTAGTTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAAATTTATAACTCGTAGCTT
65 AAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAAA-TTAT-A-TCGTAGCTT
* * * * *
54207084 TAATCTGTTCCCCTGCAACTCTAGGAAAATAAGATTCGCTATCTTCCATCTACT
127 CAATATGCTCCACTGCAACTCTAGGAAAATAAGATTCGCTATCTTCAATCTACT
* * ** *
54207138 CCACTGCAACTTTAGGGATATAAGATTTGTGGCTTCAATCTGTTTTACTGTAACTTCAGAGAGAT
1 CCACTGCAACTTTAGGGATATAAGAATTGTGGCTTCAATCTCTCCT-CTGCAACTTCAGAGAGAT
* *
54207203 AAGATTTGTAGCTTCAATCTGCTCTACTGCAACTTCAGAGAGATAAGA-T-T-T-GTAGCTTCAA
65 AAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAAATTATATCGTAGCTTCAA
* * * * * *
54207264 TATGCTCTACTGCAACTTTA-GAGAGATAAGATTTGCTATTTTCAATCTGCT
130 TATGCTCCACTGCAACTCTAGGA-AAATAAGATTCGCTATCTTCAATCTACT
* * * *
54207315 CCACTGCAACTTTAGGGAAATAAGAGTTGTGGCTTTAATCTACTCCTCTGCAACTTCAGGGAGAT
1 CCACTGCAACTTTAGGGATATAAGAATTGTGGCTTCAATCT-CTCCTCTGCAACTTCAGAGAGAT
54207380 AAGATTTG
65 AAGATTTG
54207388 CCACGATAAC
Statistics
Matches: 212, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
176 2 0.01
177 109 0.51
178 3 0.01
181 1 0.00
182 1 0.00
183 1 0.00
184 95 0.45
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (180 bp):
CCACTGCAACTTTAGGGATATAAGAATTGTGGCTTCAATCTCTCCTCTGCAACTTCAGAGAGATA
AGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAAATTATATCGTAGCTTCAAT
ATGCTCCACTGCAACTCTAGGAAAATAAGATTCGCTATCTTCAATCTACT
Found at i:54207578 original size:51 final size:51
Alignment explanation
Indices: 54207341--54207669 Score: 293
Period size: 51 Copynumber: 6.6 Consensus size: 51
54207331 GAAATAAGAG
* ** * *
54207341 TTGTGGCTTTAATCTACTCCTCTGCAACTTCAGGGAGATAAGATTTGCCAC
1 TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTCAC
* * * * * * **
54207392 --GATAACTTCAATCCGTCCCACTGTAACTTCAGGG-GTATAGGATTTGTCGT
1 TTG-TAGCTTTAATCTGTTCCACTGCAACTTCAGGGAG-ATAAGATTTGTCAC
* * * *
54207442 TTGTAGCTTTAATCTATTCCATTGCAACTTC-GAGGAAATAAGA--T-TCGC
1 TTGTAGCTTTAATCTGTTCCACTGCAACTTCAG-GGAGATAAGATTTGTCAC
* * * * *
54207490 ---TATCTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGTAAC
1 TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTCAC
54207538 TTGTAGCTTTAATCTGTTCCACTGCAACTTCA-GGAGGATAAGATTTGTCAC
1 TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGA-GATAAGATTTGTCAC
* * * *
54207589 TTGTAACTTTAATATGTTCCAGTGCAACTTCAGGGAGATAAGATTTGTAAC
1 TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTCAC
* *
54207640 TTGTAGCTTTAATTTGTTCCACTGTAACTT
1 TTGTAGCTTTAATCTGTTCCACTGCAACTT
54207670 TAATCTGTTC
Statistics
Matches: 218, Mismatches: 45, Indels: 30
0.74 0.15 0.10
Matches are distributed among these distances:
45 31 0.14
46 1 0.00
47 1 0.00
48 5 0.02
49 3 0.01
50 37 0.17
51 136 0.62
52 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (51 bp):
TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGTCAC
Found at i:54207599 original size:147 final size:146
Alignment explanation
Indices: 54207314--54207633 Score: 355
Period size: 147 Copynumber: 2.2 Consensus size: 146
54207304 TTCAATCTGC
* * ** * *
54207314 TCCACTGCAACTTTAGGGAAATAAGAGTT-G-TGGCTTTAATCTACTCCT-CTGCAACTTCAGGG
1 TCCAGTGCAACTTCAGGGAAATAAGA-TTCGCTATCTTCAATCTGCT-CTACTGCAACTTCAGGG
* * * *
54207376 AGATAAGATTTGCCACGATAACTTCAATCCGTCCCACTGTAACTTCAGGGGTATAGGATTTGTCG
64 AGATAAGATTTGCAACGATAACTTCAATCCGTCCCACTGCAACTTCAGGGGTATAAGATTTGTCA
* * *
54207441 TTTGTAGCTTTAATCTAT
129 CTTGTAACTTTAATATAT
*
54207459 TCCATTGCAACTTC-GAGGAAATAAGATTCGCTATCTTCAATCTGCTCTACTGCAACTTCAGGGA
1 TCCAGTGCAACTTCAG-GGAAATAAGATTCGCTATCTTCAATCTGCTCTACTGCAACTTCAGGGA
* * * * *
54207523 GATAAGATTTGTAACTTG-TAGCTTTAATCTGTTCCACTGCAACTTCAGGAGG-ATAAGATTTGT
65 GATAAGATTTGCAAC--GATAACTTCAATCCGTCCCACTGCAACTTCAGG-GGTATAAGATTTGT
*
54207586 CACTTGTAACTTTAATATGT
127 CACTTGTAACTTTAATATAT
*
54207606 TCCAGTGCAACTTCAGGGAGATAAGATT
1 TCCAGTGCAACTTCAGGGAAATAAGATT
54207634 TGTAACTTGT
Statistics
Matches: 146, Mismatches: 21, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
144 3 0.02
145 25 0.17
146 39 0.27
147 75 0.51
148 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (146 bp):
TCCAGTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAATCTGCTCTACTGCAACTTCAGGGAG
ATAAGATTTGCAACGATAACTTCAATCCGTCCCACTGCAACTTCAGGGGTATAAGATTTGTCACT
TGTAACTTTAATATAT
Found at i:54207670 original size:21 final size:21
Alignment explanation
Indices: 54207641--54207690 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
54207631 ATTTGTAACT
* *
54207641 TGTAGCTTTAATTTGTTCCAC
1 TGTAACTTTAATCTGTTCCAC
54207662 TGTAACTTTAATCTGTTCCAC
1 TGTAACTTTAATCTGTTCCAC
*
54207683 TGCAACTT
1 TGTAACTT
54207691 CAAGGAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (21 bp):
TGTAACTTTAATCTGTTCCAC
Found at i:54207846 original size:102 final size:102
Alignment explanation
Indices: 54207662--54207853 Score: 296
Period size: 102 Copynumber: 1.9 Consensus size: 102
54207652 TTTGTTCCAC
* * *
54207662 TGTAACTTTAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTTGCATCTTCAATTTGCTCCAC
1 TGTAACTTTAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTCGCATATTCAATCTGCTCCAC
*
54207727 TACAACTTCAGGAAGATAAGATTTGAGATTTACATAT
66 TACAACTTAAGGAAGATAAGATTTGAGATTTACATAT
* * *
54207764 TGTAGCTTTAATCTGTTCCATTGCAACTTCAGGGAAATAAGATTCGCATATTCAATCTGCTCCAC
1 TGTAACTTTAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTCGCATATTCAATCTGCTCCAC
*
54207829 TGCAACTCTAAGG-AGATAAGATTTG
66 TACAACT-TAAGGAAGATAAGATTTG
54207854 TGGCTTTAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 77 0.95
103 4 0.05
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (102 bp):
TGTAACTTTAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTCGCATATTCAATCTGCTCCAC
TACAACTTAAGGAAGATAAGATTTGAGATTTACATAT
Found at i:54207896 original size:44 final size:43
Alignment explanation
Indices: 54207763--54207897 Score: 137
Period size: 44 Copynumber: 3.1 Consensus size: 43
54207753 GATTTACATA
* *
54207763 TTGTAGCTTTAATCTGTTCCAT-TGCAACTTCAGGGAAATAAGAT
1 TTGTAGCTTTAATCTGCTCC-TCTGCAACTTCA-GGAGATAAGAT
* * ** * * *
54207807 TCGCATATTCAATCTGCTCCACTGCAACTCTAAGGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCTCTGCAACT-TCAGGAGATAAGAT
*
54207851 TTGTGGCTTTAATCTGCTCCTCTGCAACTTCAGTGAGATAAGAT
1 TTGTAGCTTTAATCTGCTCCTCTGCAACTTCAG-GAGATAAGAT
54207895 TTG
1 TTG
54207898 CCATGATAAC
Statistics
Matches: 71, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
43 3 0.04
44 66 0.93
45 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (43 bp):
TTGTAGCTTTAATCTGCTCCTCTGCAACTTCAGGAGATAAGAT
Found at i:54214258 original size:28 final size:28
Alignment explanation
Indices: 54214227--54214280 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
54214217 CCCGAAGGTA
*
54214227 CATTTTACTAAATTGAGCTTTAGTTGTT
1 CATTTTACTAAATTGAACTTTAGTTGTT
* **
54214255 CATTTTGCTGGATTGAACTTTAGTTG
1 CATTTTACTAAATTGAACTTTAGTTG
54214281 AAAATTTCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.48
Consensus pattern (28 bp):
CATTTTACTAAATTGAACTTTAGTTGTT
Found at i:54219627 original size:17 final size:17
Alignment explanation
Indices: 54219605--54219639 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54219595 GGAGTGCTAC
54219605 AATAATAAT-ATAATCAT
1 AATAATAATCAT-ATCAT
54219622 AATAATAATCATATCAT
1 AATAATAATCATATCAT
54219639 A
1 A
54219640 GGAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAATAATCATATCAT
Found at i:54219826 original size:3 final size:3
Alignment explanation
Indices: 54219820--54219864 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
54219810 TATATTGATG
*
54219820 ATA ATA A-A ATA ATA ATAA ATA A-A ATA ATA CTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
54219864 A
1 A
54219865 AGGCAAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:54225030 original size:18 final size:18
Alignment explanation
Indices: 54225009--54225044 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54224999 GGCCCTCAAC
*
54225009 TTGATAATTATTCTCACA
1 TTGACAATTATTCTCACA
54225027 TTGACAATTATTCTCACA
1 TTGACAATTATTCTCACA
54225045 CTAGGGCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (18 bp):
TTGACAATTATTCTCACA
Found at i:54227098 original size:3 final size:3
Alignment explanation
Indices: 54227092--54227116 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54227082 AGAATCTAAA
54227092 CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT C
54227117 ATTATTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:54230204 original size:27 final size:24
Alignment explanation
Indices: 54230124--54230202 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 24
54230114 TTTTTTTTAA
54230124 AAAATTTATAATA-ATTATATTATT
1 AAAATTTATAATATA-TATATTATT
*
54230148 -TAATTTATAATATATA-ATT-TT
1 AAAATTTATAATATATATATTATT
54230169 AAAATTTATAGTAATATATAATATTATT
1 AAAA-TT-TA-TAATATAT-ATATTATT
54230197 AAAATT
1 AAAATT
54230203 ATTAAATTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
21 2 0.04
22 5 0.11
23 15 0.33
24 3 0.07
25 8 0.18
26 1 0.02
27 5 0.11
28 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
AAAATTTATAATATATATATTATT
Found at i:54230277 original size:18 final size:17
Alignment explanation
Indices: 54230239--54230282 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
54230229 AATAAATTAA
*
54230239 AAATATATAAATATATT
1 AAATATATAAAAATATT
*
54230256 AAATATATACAAAATTTT
1 AAATATATA-AAAATATT
*
54230274 AAATTTATA
1 AAATATATA
54230283 TATCAAATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATATAAAAATATT
Found at i:54230939 original size:12 final size:12
Alignment explanation
Indices: 54230922--54230955 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54230912 TTTAATAATT
54230922 AAAATAAATAAA
1 AAAATAAATAAA
*
54230934 AAAATAAATTAA
1 AAAATAAATAAA
*
54230946 AAACTAAATA
1 AAAATAAATA
54230956 TGAGTAAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:54235199 original size:19 final size:20
Alignment explanation
Indices: 54235167--54235207 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
54235157 AATGCCTCTA
54235167 AAATAATAACAAAATTA-AC
1 AAATAATAACAAAATTATAC
54235186 AAATAA-AACAAAAATTATAC
1 AAATAATAAC-AAAATTATAC
54235206 AA
1 AA
54235208 TATCTAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 13 0.65
20 4 0.20
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATAATAACAAAATTATAC
Found at i:54235239 original size:31 final size:29
Alignment explanation
Indices: 54235166--54235241 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 29
54235156 AAATGCCTCT
*
54235166 AAAATAATAACAAAATTAACAAATAAAAC
1 AAAATAATAACAATATTAACAAATAAAAC
*
54235195 AAAA-ATTATACAATATCTAAGC-AATAACAAC
1 AAAATAATA-ACAATAT-TAA-CAAATAA-AAC
*
54235226 AAAATAGTAACAATAT
1 AAAATAATAACAATAT
54235242 AATAGTGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 3 0.08
29 10 0.26
30 8 0.21
31 15 0.38
32 3 0.08
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.21
Consensus pattern (29 bp):
AAAATAATAACAATATTAACAAATAAAAC
Found at i:54237436 original size:71 final size:71
Alignment explanation
Indices: 54237304--54237448 Score: 173
Period size: 71 Copynumber: 2.0 Consensus size: 71
54237294 TATTCTTCTA
* * * * * * *
54237304 ATTTTGGTCACCTGCTAGTAATTTATTATTATTGCATACCCATTTCAGTCACTCAATTTTAATTA
1 ATTTTAGTCAACTGCTAGTAATTTAGTATTATTGCATACCCATTTCAATCACACAACTTTAATAA
54237369 ATTTTT
66 ATTTTT
* * * * * *
54237375 ATTTTAGTCAACTGCTAGTAATTTAGTGTTATTGTATGCTCATTTTAATCAGACAACTTTAATAA
1 ATTTTAGTCAACTGCTAGTAATTTAGTATTATTGCATACCCATTTCAATCACACAACTTTAATAA
54237440 ATTTTT
66 ATTTTT
54237446 ATT
1 ATT
54237449 CTGGTAATTT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (71 bp):
ATTTTAGTCAACTGCTAGTAATTTAGTATTATTGCATACCCATTTCAATCACACAACTTTAATAA
ATTTTT
Found at i:54247136 original size:3 final size:3
Alignment explanation
Indices: 54247123--54247179 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
54247113 ACTATCGGTT
* **
54247123 TTA TT- TTA TTA TTA CTA TTA TTA TTA TTA TTTA ACA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
54247168 -TA TT- TT- TTA TTA
1 TTA TTA TTA TTA TTA
54247180 ATCCATGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 8 0.18
3 33 0.75
4 3 0.07
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:54248317 original size:51 final size:50
Alignment explanation
Indices: 54248203--54248367 Score: 267
Period size: 51 Copynumber: 3.3 Consensus size: 50
54248193 CTTACGTATG
*
54248203 ATCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCTAAGCTACCACTT
1 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTT
** *
54248253 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTT
*
54248304 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTT
54248355 ATCACTTATCACT
1 ATCACTTATCACT
54248368 GATCAGAAGT
Statistics
Matches: 106, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 35 0.33
51 71 0.67
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (50 bp):
ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTT
Found at i:54252030 original size:24 final size:24
Alignment explanation
Indices: 54251998--54252044 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
54251988 TTCCATTACT
54251998 ATTATTATTA-CATTATTTACTATC
1 ATTATTATTATCA-TATTTACTATC
*
54252022 ATTATTATTATCATATTTTCTAT
1 ATTATTATTATCATATTTACTAT
54252045 ACATATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTATTATCATATTTACTATC
Found at i:54252035 original size:12 final size:12
Alignment explanation
Indices: 54251998--54252035 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54251988 TTCCATTACT
54251998 ATTATTATTA-C
1 ATTATTATTATC
*
54252009 ATTATTTACTATC
1 ATTA-TTATTATC
54252022 ATTATTATTATC
1 ATTATTATTATC
54252034 AT
1 AT
54252036 ATTTTCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.17
12 14 0.61
13 5 0.22
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:54256768 original size:21 final size:22
Alignment explanation
Indices: 54256738--54256787 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
54256728 TTTATATTTT
*
54256738 AATTTAA-TTTTAAAATTTTAA
1 AATTTAATTTTTAAAATTTCAA
* *
54256759 AATTTTATTTTTTAAATTTCAA
1 AATTTAATTTTTAAAATTTCAA
54256781 AATTTAA
1 AATTTAA
54256788 GTCATAACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTAATTTTTAAAATTTCAA
Found at i:54265183 original size:19 final size:19
Alignment explanation
Indices: 54265159--54265196 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54265149 ATAGATAATC
*
54265159 AAATAATTAAATAATTACA
1 AAATAATCAAATAATTACA
54265178 AAATAATCAAATAATTACA
1 AAATAATCAAATAATTACA
54265197 CAAGGCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATAATCAAATAATTACA
Found at i:54272906 original size:25 final size:25
Alignment explanation
Indices: 54272878--54272927 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
54272868 TTGTAGATGA
* *
54272878 TAGTTTGTTTTTTCTTCGGAACAAG
1 TAGTTTGCTTTTTCTTCAGAACAAG
54272903 TAGTTTGCTTTTTCTTCAGAACAAG
1 TAGTTTGCTTTTTCTTCAGAACAAG
54272928 GAAAAGAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (25 bp):
TAGTTTGCTTTTTCTTCAGAACAAG
Found at i:54276967 original size:4 final size:4
Alignment explanation
Indices: 54276958--54277147 Score: 380
Period size: 4 Copynumber: 47.5 Consensus size: 4
54276948 CCTTAAAGAT
54276958 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
54277006 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
54277054 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
54277102 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
54277148 GTAAGACTTG
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 186 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:54277750 original size:30 final size:29
Alignment explanation
Indices: 54277686--54277860 Score: 140
Period size: 30 Copynumber: 5.9 Consensus size: 29
54277676 GCAAAAAATA
* ** *
54277686 AAAATTACATTTTAACCCCTGTACTTTTT
1 AAAATTACATTTTGACCCCTAAACTTTCT
*
54277715 GAAATTTACATTTTGA-CCCTAAACTTTTCT
1 -AAAATTACATTTTGACCCCTAAAC-TTTCT
** *
54277745 AAAATTACATTTCAACCCTTAAACTTTCT
1 AAAATTACATTTTGACCCCTAAACTTTCT
* *
54277774 CAAAATTGCACTTTGACCCCTAAACTTTCT
1 -AAAATTACATTTTGACCCCTAAACTTTCT
* *
54277804 AAAAATTACATTTTGGCCCCT-TA-TTTCCT
1 -AAAATTACATTTTGACCCCTAAACTTT-CT
* * *
54277833 AAAATTTCATTTTTACCCCAAAAACTTT
1 AAAATTACATTTTGACCCC-TAAACTTT
54277861 ACACCCGTTA
Statistics
Matches: 114, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
28 19 0.17
29 26 0.23
30 66 0.58
31 3 0.03
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCTAAACTTTCT
Found at i:54277751 original size:59 final size:60
Alignment explanation
Indices: 54277684--54277817 Score: 164
Period size: 59 Copynumber: 2.2 Consensus size: 60
54277674 ATGCAAAAAA
** * * * *
54277684 TAAAAATTACATTTTAACCCCTGTACTTTTTGAAATTTACATTTTGA-CCCTAAACTTTTC
1 TAAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACACTTTGACCCCTAAAC-TTTC
* * *
54277744 T-AAAATTACATTTCAACCCTTAAACTTTCTCAAAATTGCACTTTGACCCCTAAACTTTC
1 TAAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACACTTTGACCCCTAAACTTTC
54277803 TAAAAATTACATTTT
1 TAAAAATTACATTTT
54277818 GGCCCCTTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 41 0.66
60 21 0.34
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (60 bp):
TAAAAATTACATTTTAACCCCTAAACTTTCTCAAAATTACACTTTGACCCCTAAACTTTC
Found at i:54278424 original size:14 final size:15
Alignment explanation
Indices: 54278400--54278429 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54278390 AGAGAAAGCG
54278400 AAAGGGAGAAGAGAA
1 AAAGGGAGAAGAGAA
54278415 AAAGGG-GAAGAGAA
1 AAAGGGAGAAGAGAA
54278429 A
1 A
54278430 TGAGGAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (15 bp):
AAAGGGAGAAGAGAA
Found at i:54279986 original size:43 final size:42
Alignment explanation
Indices: 54279815--54280057 Score: 332
Period size: 42 Copynumber: 5.8 Consensus size: 42
54279805 ACTGACACTT
* * *
54279815 AGCCTGCTAGACTTAAAGCCTGAT-TCTG-TACACCGGCACTT-
1 AGCCTGCTAGACGTAAAGTCTGATAT-TGTTTCACCGGCA-TTA
* * *
54279856 AGCCTGCTAGACATATAGTCTGACA-TGTTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
* *
54279897 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
54279939 AGCCTGCTAGACGTAAAGTCTGATATTGTTTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTG-TTTCACCGGCATTA
* * *
54279982 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCCGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
54280024 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCAC
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCAC
54280058 TGGGCAACAA
Statistics
Matches: 181, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
40 4 0.02
41 51 0.28
42 86 0.48
43 40 0.22
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (42 bp):
AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
Found at i:54279994 original size:85 final size:85
Alignment explanation
Indices: 54279815--54280054 Score: 355
Period size: 85 Copynumber: 2.9 Consensus size: 85
54279805 ACTGACACTT
* * * * * *
54279815 AGCCTGCTAGACTTAAAGCCTG--ATTCTGTACACCGGCACTT-AGCCTGCTAGACATATAGTCT
1 AGCCTGCTAGACGTAAAGTCTGAAATTAT-TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCT
*
54279877 GACA-TG-TTTCACCGGCATTA
64 GATATTGTTTTCACCGGCATTA
54279897 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGA
1 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGA
54279962 TATTGTTTTCACCGGCATTA
66 TATTGTTTTCACCGGCATTA
*
54279982 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCCGCATTAAGCCTGCTAGACGTAAAGTCTGA
1 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGA
54280047 TATTGTTT
66 TATTGTTT
54280055 CACTGGGCAA
Statistics
Matches: 145, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
82 22 0.15
83 31 0.21
84 6 0.04
85 86 0.59
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (85 bp):
AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGA
TATTGTTTTCACCGGCATTA
Found at i:54282160 original size:17 final size:17
Alignment explanation
Indices: 54282105--54282167 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
54282095 ATAATAATCG
54282105 TGTTTCAAAAATTTTCA
1 TGTTTCAAAAATTTTCA
*
54282122 TGTTCTC-AAAATTTCTCG
1 TGTT-TCAAAAATTT-TCA
54282140 TGTTTCAAAAAATTTTC-
1 TGTTTC-AAAAATTTTCA
*
54282157 TGTTTTAAAAA
1 TGTTTCAAAAA
54282168 AAAATTCATA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 5 0.12
17 18 0.45
18 10 0.25
19 7 0.17
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (17 bp):
TGTTTCAAAAATTTTCA
Found at i:54282168 original size:17 final size:18
Alignment explanation
Indices: 54282111--54282204 Score: 59
Period size: 18 Copynumber: 5.3 Consensus size: 18
54282101 ATCGTGTTTC
*
54282111 AAAAATTTTCATGTTCT-
1 AAAAATTTTCATGTTTTA
* * *
54282128 CAAAATTTCTCGTGTTTCA
1 AAAAATTT-TCATGTTTTA
54282147 AAAAATTTTC-TGTTTTAA
1 AAAAATTTTCATGTTTT-A
** * *
54282165 AAAAAAATTCAT-ATTTC
1 AAAAATTTTCATGTTTTA
* *
54282182 AAAAATATTCGTGTTTTA
1 AAAAATTTTCATGTTTTA
54282200 AAAAA
1 AAAAA
54282205 ATAAAAATAA
Statistics
Matches: 58, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
17 22 0.38
18 28 0.48
19 8 0.14
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (18 bp):
AAAAATTTTCATGTTTTA
Found at i:54282256 original size:18 final size:18
Alignment explanation
Indices: 54282230--54282522 Score: 261
Period size: 18 Copynumber: 16.6 Consensus size: 18
54282220 AAGAATCCAT
54282230 TTTTC-AAAATTCTCGTG
1 TTTTCAAAAATTCTCGTG
54282247 TTTTCAAAAATT-TCAGTG
1 TTTTCAAAAATTCTC-GTG
* *
54282265 TTTT-AAAAATTTTCATG
1 TTTTCAAAAATTCTCGTG
* *
54282282 TTTTCAAAATTTCTCATG
1 TTTTCAAAAATTCTCGTG
*
54282300 TTTT-AAAAATT-TCCGTA
1 TTTTCAAAAATTCT-CGTG
54282317 TTTTCAAAAATT-TCCGTG
1 TTTTCAAAAATTCT-CGTG
*
54282335 TTTT-AAAAAATCTTCGTG
1 TTTTCAAAAATTC-TCGTG
*
54282353 TTTTCAAAAATCCTCGTG
1 TTTTCAAAAATTCTCGTG
54282371 TTTTCAAAAATTC-CG-G
1 TTTTCAAAAATTCTCGTG
* *
54282387 TGTTTCACAAAATTTTCATG
1 T-TTTCA-AAAATTCTCGTG
*
54282407 TTTTCAAAAATTCCCGTG
1 TTTTCAAAAATTCTCGTG
54282425 TTTT-AAAAATT-TCCGTG
1 TTTTCAAAAATTCT-CGTG
*
54282442 TTTTCAAAAATTTTCGTG
1 TTTTCAAAAATTCTCGTG
* * * *
54282460 TTTTTAAGAATTTTCATG
1 TTTTCAAAAATTCTCGTG
* *
54282478 -TCTCTAAAATTCTCGTG
1 TTTTCAAAAATTCTCGTG
*
54282495 TTTT-AAAAATTTTTCGTG
1 TTTTCAAAAA-TTCTCGTG
54282513 TTTTCAAAAA
1 TTTTCAAAAA
54282523 AAATAATTGT
Statistics
Matches: 228, Mismatches: 29, Indels: 36
0.78 0.10 0.12
Matches are distributed among these distances:
16 3 0.01
17 75 0.33
18 129 0.57
19 19 0.08
20 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (18 bp):
TTTTCAAAAATTCTCGTG
Found at i:54282303 original size:53 final size:53
Alignment explanation
Indices: 54282230--54282522 Score: 273
Period size: 53 Copynumber: 5.5 Consensus size: 53
54282220 AAGAATCCAT
* *
54282230 TTTTCAAAA-TTCTCGTGTTTTCAAAAATTTCAGTGTTTTAAAAATTTTCATG
1 TTTTCAAAATTTCTCGTGTTTTCAAAAATTTCAGTGTTTTAAAAATTTCCGTG
* * *
54282282 TTTTCAAAATTTCTCATGTTTT-AAAAATTTCCGTATTTTCAAAAATTTCCGTG
1 TTTTCAAAATTTCTCGTGTTTTCAAAAATTTCAGTGTTTT-AAAAATTTCCGTG
** *
54282335 TTTT-AAAAAATCTTCGTGTTTTCAAAAATCCTC-GTGTTTTCAAAAA-TTCCGGTG
1 TTTTCAAAATTTC-TCGTGTTTTCAAAAAT-TTCAGTGTTTT-AAAAATTTCC-GTG
* * * *
54282389 TTTCACAAAATTT-TCATGTTTTCAAAAATTCCCGTGTTTTAAAAATTTCCGTG
1 TTT-TCAAAATTTCTCGTGTTTTCAAAAATTTCAGTGTTTTAAAAATTTCCGTG
* * *
54282442 TTTTCAAAAATTT-TCGTGTTTTTAAGAATTTTCA-TGTCTCT-AAAA-TTCTCGTG
1 TTTTC-AAAATTTCTCGTGTTTTCAA-AAATTTCAGTGT-TTTAAAAATTTC-CGTG
* *
54282495 TTTTAAAAATTTTTCGTGTTTTCAAAAA
1 TTTTCAAAATTTCTCGTGTTTTCAAAAA
54282523 AAATAATTGT
Statistics
Matches: 200, Mismatches: 26, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
52 43 0.22
53 93 0.47
54 57 0.28
55 2 0.01
56 5 0.03
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (53 bp):
TTTTCAAAATTTCTCGTGTTTTCAAAAATTTCAGTGTTTTAAAAATTTCCGTG
Found at i:54282344 original size:36 final size:36
Alignment explanation
Indices: 54282230--54282522 Score: 261
Period size: 35 Copynumber: 8.3 Consensus size: 36
54282220 AAGAATCCAT
*
54282230 TTTTC-AAAA-TTCTCGTGTTTTCAAAAATTTCAGTG
1 TTTTCAAAAATTTC-CGTGTTTTCAAAAATTTCCGTG
* * *
54282265 TTTT-AAAAATTTTCATGTTTTC-AAAATTTCTCATG
1 TTTTCAAAAATTTCCGTGTTTTCAAAAATTTC-CGTG
*
54282300 TTTT-AAAAATTTCCGTATTTTCAAAAATTTCCGTG
1 TTTTCAAAAATTTCCGTGTTTTCAAAAATTTCCGTG
* *
54282335 TTTTAAAAAATCTT-CGTGTTTTCAAAAA-TCCTCGTG
1 TTTTCAAAAAT-TTCCGTGTTTTCAAAAATTTC-CGTG
* *
54282371 TTTTCAAAAA-TTCCG-GTGTTTCACAAAATTTTCATG
1 TTTTCAAAAATTTCCGTGT-TTTCA-AAAATTTCCGTG
*
54282407 TTTTCAAAAATTCCCGTGTTTT-AAAAATTTCCGTG
1 TTTTCAAAAATTTCCGTGTTTTCAAAAATTTCCGTG
* * * * *
54282442 TTTTCAAAAATTTTCGTGTTTTTAAGAATTTTCATG
1 TTTTCAAAAATTTCCGTGTTTTCAAAAATTTCCGTG
* * *
54282478 -TCTCTAAAA-TTCTCGTGTTTT-AAAAATTTTTCGTG
1 TTTTCAAAAATTTC-CGTGTTTTCAAAAA-TTTCCGTG
54282513 TTTTCAAAAA
1 TTTTCAAAAA
54282523 AAATAATTGT
Statistics
Matches: 212, Mismatches: 29, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
34 18 0.08
35 105 0.50
36 77 0.36
37 10 0.05
38 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (36 bp):
TTTTCAAAAATTTCCGTGTTTTCAAAAATTTCCGTG
Found at i:54284963 original size:3 final size:3
Alignment explanation
Indices: 54284955--54284991 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
54284945 GTTTTAAATG
54284955 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54284992 TGTTGAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54290940 original size:9 final size:9
Alignment explanation
Indices: 54290926--54291112 Score: 109
Period size: 9 Copynumber: 20.9 Consensus size: 9
54290916 TAAGTATAAT
54290926 TAAGTTATG
1 TAAGTTATG
54290935 TAAGTTATG
1 TAAGTTATG
* *
54290944 ATATGATATATA
1 -TAAG-T-TATG
54290956 TAAGTTAT-
1 TAAGTTATG
54290964 TAAGTTATG
1 TAAGTTATG
*
54290973 TATG-TATG
1 TAAGTTATG
*
54290981 TGAGTTATG
1 TAAGTTATG
*
54290990 TAAGTTATCA
1 TAAGTTAT-G
* * **
54291000 TATGATAAA
1 TAAGTTATG
*
54291009 T-ATTTATG
1 TAAGTTATG
54291017 T-A-TTATG
1 TAAGTTATG
54291024 TAAGTTATG
1 TAAGTTATG
54291033 TAAGTTATG
1 TAAGTTATG
*
54291042 TGAGTTATG
1 TAAGTTATG
54291051 TGAA-TTATG
1 T-AAGTTATG
*
54291060 TAAGTTAGG
1 TAAGTTATG
*
54291069 TAAGTTTTG
1 TAAGTTATG
* * *
54291078 ATATGATATA
1 -TAAGTTATG
*
54291088 T-ATTTATG
1 TAAGTTATG
54291096 TAAGTTATG
1 TAAGTTATG
*
54291105 TAAATTAT
1 TAAGTTAT
54291113 ATATTAATTT
Statistics
Matches: 135, Mismatches: 31, Indels: 24
0.71 0.16 0.13
Matches are distributed among these distances:
7 6 0.04
8 25 0.19
9 82 0.61
10 15 0.11
11 4 0.03
12 3 0.02
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:54290988 original size:55 final size:59
Alignment explanation
Indices: 54290928--54291059 Score: 166
Period size: 55 Copynumber: 2.3 Consensus size: 59
54290918 AGTATAATTA
*
54290928 AGTTATGTAAGTTATGATATGAT-ATATATAAG-TTAT-TAAGTTATGTATG-TATGTG
1 AGTTATGTAAGTTATGATATGATAATATATAAGATTATGTAAGTTATGTAAGTTATGTG
* * *
54290983 AGTTATGTAAGTTATCATATGATAAATATTTATGTATTATGTAAGTTATGTAAGTTATGTG
1 AGTTATGTAAGTTATGATATGAT-AATATATAAG-ATTATGTAAGTTATGTAAGTTATGTG
54291044 AGTTATGTGAA-TTATG
1 AGTTATGT-AAGTTATG
54291060 TAAGTTAGGT
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
55 22 0.34
57 7 0.11
59 4 0.06
60 12 0.18
61 18 0.28
62 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.45
Consensus pattern (59 bp):
AGTTATGTAAGTTATGATATGATAATATATAAGATTATGTAAGTTATGTAAGTTATGTG
Found at i:54291065 original size:36 final size:34
Alignment explanation
Indices: 54290926--54291118 Score: 125
Period size: 36 Copynumber: 5.7 Consensus size: 34
54290916 TAAGTATAAT
*
54290926 TAAGTTATGTAAGTTATG-A-TA--TG-ATATATA
1 TAAGTTATGTAAGTTATGTATTATGTGAAT-TATG
*
54290956 TAAGTTAT-TAAGTTATGTATGTATGTGAGTTATG
1 TAAGTTATGTAAGTTATGTAT-TATGTGAATTATG
* * * **
54290990 TAAGTTATCATATGATAAATATTTATGT--ATTATG
1 TAAGTTAT-GTAAGTTATGTA-TTATGTGAATTATG
54291024 TAAGTTATGTAAGTTATGTGAGTTATGTGAATTATG
1 TAAGTTATGTAAGTTATGT-A-TTATGTGAATTATG
* * * *
54291060 TAAGTTAGGTAAGTTTTGATATGATATAT-ATTTATG
1 TAAGTTATGTAAGTTATG-TAT--TATGTGAATTATG
* *
54291096 TAAGTTATGTAAATTATATATTA
1 TAAGTTATGTAAGTTATGTATTA
54291119 ATTTAAAATA
Statistics
Matches: 127, Mismatches: 21, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
29 9 0.07
30 9 0.07
32 2 0.02
33 8 0.06
34 33 0.26
35 5 0.04
36 55 0.43
37 6 0.05
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (34 bp):
TAAGTTATGTAAGTTATGTATTATGTGAATTATG
Found at i:54291492 original size:28 final size:29
Alignment explanation
Indices: 54291461--54291658 Score: 80
Period size: 28 Copynumber: 6.3 Consensus size: 29
54291451 AATCAATTAA
*
54291461 TCAAATT-AATATAAAATCGACAATTTAT
1 TCAAATTAAATAAAAAATCGACAATTTAT
* *
54291489 TC-AATTAAATAAAAAATTGATAATTTAT
1 TCAAATTAAATAAAAAATCGACAATTTAT
* * *
54291517 TCACATAAAATCAAATAAACTAATCAAACATAATTTAT
1 T--C---AAATTAAATAAA-AAATC-GAC--AATTTAT
** *
54291555 TC-AATTAAATCGAAAATCGATAATTTAT
1 TCAAATTAAATAAAAAATCGACAATTTAT
* *
54291583 TCACATTAAATCAAATAAACTAATCAAACATAATTTAT
1 TCAAATTAAAT---A-AAA--AATC-GAC--AATTTAT
**
54291621 TC-AATTAAATCGAAAATCGACAATTTAT
1 TCAAATTAAATAAAAAATCGACAATTTAT
*
54291649 TCACATTAAA
1 TCAAATTAAA
54291659 CCGAATAAAC
Statistics
Matches: 124, Mismatches: 24, Indels: 43
0.65 0.13 0.23
Matches are distributed among these distances:
27 4 0.03
28 39 0.31
29 13 0.10
30 4 0.03
31 8 0.06
32 8 0.06
33 4 0.03
34 10 0.08
35 7 0.06
36 3 0.02
37 7 0.06
38 17 0.14
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (29 bp):
TCAAATTAAATAAAAAATCGACAATTTAT
Found at i:54291552 original size:38 final size:37
Alignment explanation
Indices: 54291508--54291701 Score: 165
Period size: 38 Copynumber: 5.7 Consensus size: 37
54291498 TAAAAAATTG
*
54291508 ATAATTTATTCACATAAAATCAAATAAACTAATCAAAC
1 ATAATTTATTCA-ATTAAATCAAATAAACTAATCAAAC
* *
54291546 ATAATTTATTCAATTAAATC----GAA--AATC---G
1 ATAATTTATTCAATTAAATCAAATAAACTAATCAAAC
54291574 ATAATTTATTCACATTAAATCAAATAAACTAATCAAAC
1 ATAATTTATTCA-ATTAAATCAAATAAACTAATCAAAC
* *
54291612 ATAATTTATTCAATTAAATC----GAA--AATC-GAC
1 ATAATTTATTCAATTAAATCAAATAAACTAATCAAAC
* *
54291642 --AATTTATTCACATTAAACCGAATAAACTAATCAAAC
1 ATAATTTATTCA-ATTAAATCAAATAAACTAATCAAAC
54291678 ATAATTTATTCAATT-AATCAAATA
1 ATAATTTATTCAATTAAATCAAATA
54291702 TATAAAGTAA
Statistics
Matches: 124, Mismatches: 12, Indels: 42
0.70 0.07 0.24
Matches are distributed among these distances:
28 22 0.18
29 15 0.12
30 2 0.02
31 8 0.06
33 8 0.06
35 8 0.06
36 9 0.07
37 18 0.15
38 34 0.27
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (37 bp):
ATAATTTATTCAATTAAATCAAATAAACTAATCAAAC
Found at i:54291556 original size:66 final size:66
Alignment explanation
Indices: 54291482--54291694 Score: 363
Period size: 66 Copynumber: 3.2 Consensus size: 66
54291472 TAAAATCGAC
** * *
54291482 AATTTATTCAATTAAATAAAAAATTGATAATTTATTCACATAAAATCAAATAAACTAATCAAACA
1 AATTTATTCAATTAAATCGAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAACA
54291547 T
66 T
54291548 AATTTATTCAATTAAATCGAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAACA
1 AATTTATTCAATTAAATCGAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAACA
54291613 T
66 T
* * *
54291614 AATTTATTCAATTAAATCGAAAATCGACAATTTATTCACATTAAACCGAATAAACTAATCAAACA
1 AATTTATTCAATTAAATCGAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAACA
54291679 T
66 T
54291680 AATTTATTCAATTAA
1 AATTTATTCAATTAA
54291695 TCAAATATAT
Statistics
Matches: 140, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 140 1.00
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (66 bp):
AATTTATTCAATTAAATCGAAAATCGATAATTTATTCACATTAAATCAAATAAACTAATCAAACA
T
Found at i:54294535 original size:126 final size:124
Alignment explanation
Indices: 54294249--54294558 Score: 433
Period size: 124 Copynumber: 2.5 Consensus size: 124
54294239 TTAGAAAGTA
* * *
54294249 AATACATAGTTGCAGCGTTTTTGGTCTAAATGCCGCTATTGCTTACCTTTTGCAGCGTTTCAACC
1 AATACATAGTTGCGGCGTTTTTGGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTTCAACC
* *** ***
54294314 AAAAACGCCACTAAAAATTTAAATTTCTATATTGAAACGGTGCCGTTTTGAAAATTTTT
66 AAAAACGCCACTAAAAAATTAAATTTCTATAAAAAAACGGTGAAATTTTGAAAATTTTT
* * * *
54294373 AATACATATTTGCGGCGTTTTTGGTCCAAACGCCGCTATTGCTTACCTTTTGCGGCGTTTCCAGC
1 AATACATAGTTGCGGCGTTTTTGGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTTCAACC
* *
54294438 AAAAACGCCACTAAAAAATTAAATTTTTGTACCAAAAAACGGTGAAATTTTGAAAATTTTT
66 AAAAACGCCACTAAAAAATTAAATTTCTATA--AAAAAACGGTGAAATTTTGAAAATTTTT
*
54294499 AATACATAGTTGCGGCGTTTTCT-GTCCAAATGCCGCTATTGCTTACCTTTTGTGGCGTTT
1 AATACATAGTTGCGGCGTTTT-TGGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTT
54294559 TTCTCATAAA
Statistics
Matches: 164, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
124 86 0.52
126 77 0.47
127 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (124 bp):
AATACATAGTTGCGGCGTTTTTGGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTTCAACC
AAAAACGCCACTAAAAAATTAAATTTCTATAAAAAAACGGTGAAATTTTGAAAATTTTT
Found at i:54294570 original size:126 final size:123
Alignment explanation
Indices: 54294249--54294577 Score: 408
Period size: 126 Copynumber: 2.6 Consensus size: 123
54294239 TTAGAAAGTA
* * * *
54294249 AATACATAGTTGCAGCGTTTTTGGTCTAAATGCCGCTATTGCTTACCTTTTGCAGCGTTTCAACC
1 AATACATAGTTGCGGCGTTTTTGGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTT-TACC
* *** ***
54294314 AAAAACGCCACTAAAAATTTAAATTTCTATATTGAAACGGTGCCGTTTTGAAAATTTTT
65 AAAAACGCCACTAAAAAATTAAATTTCTATAAAAAAACGGTGAAATTTTGAAAATTTTT
* * * *
54294373 AATACATATTTGCGGCGTTTTTGGTCCAAACGCCGCTATTGCTTACCTTTTGCGGCGTTTCCAGC
1 AATACATAGTTGCGGCGTTTTTGGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTT-TACC
* *
54294438 AAAAACGCCACTAAAAAATTAAATTTTTGTACCAAAAAACGGTGAAATTTTGAAAATTTTT
65 AAAAACGCCACTAAAAAATTAAATTTCTATA--AAAAAACGGTGAAATTTTGAAAATTTTT
* *
54294499 AATACATAGTTGCGGCGTTTTCT-GTCCAAATGCCGCTATTGCTTACCTTTTGTGGCGTTTTTCT
1 AATACATAGTTGCGGCGTTTT-TGGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTTTAC-
* *
54294563 CATAAACGCCGCTAA
64 CAAAAACGCCACTAA
54294578 TGATTGACTT
Statistics
Matches: 177, Mismatches: 24, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
124 86 0.49
126 90 0.51
127 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (123 bp):
AATACATAGTTGCGGCGTTTTTGGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTTTACCA
AAAACGCCACTAAAAAATTAAATTTCTATAAAAAAACGGTGAAATTTTGAAAATTTTT
Found at i:54294712 original size:21 final size:22
Alignment explanation
Indices: 54294677--54294722 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
54294667 TGATTGGAAA
*
54294677 TTAAGATTTTAAAATTTAA-AT
1 TTAAGATTTTAAAATATAATAT
54294698 TTAA-ATTTTAGAAATATAATAT
1 TTAAGATTTTA-AAATATAATAT
54294720 TTA
1 TTA
54294723 TGATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
TTAAGATTTTAAAATATAATAT
Found at i:54294963 original size:21 final size:22
Alignment explanation
Indices: 54294928--54294973 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
54294918 TGATTGGAAA
*
54294928 TTAAGATTTTAAAATTTAA-AT
1 TTAAGATTTTAAAATATAATAT
54294949 TTAA-ATTTTAGAAATATAATAT
1 TTAAGATTTTA-AAATATAATAT
54294971 TTA
1 TTA
54294974 TGATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
TTAAGATTTTAAAATATAATAT
Found at i:54294964 original size:251 final size:251
Alignment explanation
Indices: 54294521--54295022 Score: 952
Period size: 251 Copynumber: 2.0 Consensus size: 251
54294511 CGGCGTTTTC
*
54294521 TGTCCAAATGCCGCTATTGCTTACCTTTTGTGGCGTTTTTCTCATAAACGCCGCTAATGATTGAC
1 TGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTTTTCTCATAAACGCCGCTAATGATTGAC
54294586 TTTTACTATAAACTATTAATATATGATATGATATAAGAATATCGTATTGAATAAATCAAAGAAGA
66 TTTTACTATAAACTATTAATATATGATATGATATAAGAATATCGTATTGAATAAATCAAAGAAGA
54294651 GATTTCCATTAAGTAGTGATTGGAAATTAAGATTTTAAAATTTAAATTTAAATTTTAGAAATATA
131 GATTTCCATTAAGTAGTGATTGGAAATTAAGATTTTAAAATTTAAATTTAAATTTTAGAAATATA
*
54294716 ATATTTATGATAATTTTTTGATTCCATAGATTTACTGGAGACCTGTTTAATAATGA
196 ATATTTATGATAATTTTTTGATTCCATAGATTTACTGGAGACCGGTTTAATAATGA
*
54294772 TGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTTTTCTCATAAACGCTGCTAAT-ATTTGA
1 TGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTTTTCTCATAAACGCCGCTAATGA-TTGA
*
54294836 CTTTTACTATAAACTATTAATATATGATATGATATAAGAATATGGTATTGAATAAATCAAAGAAG
65 CTTTTACTATAAACTATTAATATATGATATGATATAAGAATATCGTATTGAATAAATCAAAGAAG
54294901 AGATTTCCATTAAGTAGTGATTGGAAATTAAGATTTTAAAATTTAAATTTAAATTTTAGAAATAT
130 AGATTTCCATTAAGTAGTGATTGGAAATTAAGATTTTAAAATTTAAATTTAAATTTTAGAAATAT
54294966 AATATTTATGATAATTTTTTGATTCCATAGATTTACTGGAGACCGGTTTAATAATGA
195 AATATTTATGATAATTTTTTGATTCCATAGATTTACTGGAGACCGGTTTAATAATGA
54295023 ATTTGAAATC
Statistics
Matches: 246, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
250 1 0.00
251 245 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (251 bp):
TGTCCAAATGCCGCTATTGCTTACCTTTTGCGGCGTTTTTCTCATAAACGCCGCTAATGATTGAC
TTTTACTATAAACTATTAATATATGATATGATATAAGAATATCGTATTGAATAAATCAAAGAAGA
GATTTCCATTAAGTAGTGATTGGAAATTAAGATTTTAAAATTTAAATTTAAATTTTAGAAATATA
ATATTTATGATAATTTTTTGATTCCATAGATTTACTGGAGACCGGTTTAATAATGA
Found at i:54295573 original size:21 final size:21
Alignment explanation
Indices: 54295544--54295591 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
54295534 TAAACATGTA
54295544 AACCCTAAACCTTAAGCCCCT
1 AACCCTAAACCTTAAGCCCCT
*
54295565 AACCTTAAACCTTAAG-CCCT
1 AACCCTAAACCTTAAGCCCCT
*
54295585 AAACCTA
1 AACCCTA
54295592 TACCCTAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.38, C:0.38, G:0.04, T:0.21
Consensus pattern (21 bp):
AACCCTAAACCTTAAGCCCCT
Found at i:54295780 original size:21 final size:21
Alignment explanation
Indices: 54295731--54295780 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
54295721 ATCTTAAATA
***
54295731 CTAAACTCTAAACTTTAAACC
1 CTAAACTCTAAACCAAAAACC
* *
54295752 CCACACTCTAAACCAAAAACC
1 CTAAACTCTAAACCAAAAACC
54295773 CTAAACTC
1 CTAAACTC
54295781 CAAGCTATAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.20
Consensus pattern (21 bp):
CTAAACTCTAAACCAAAAACC
Found at i:54295898 original size:14 final size:14
Alignment explanation
Indices: 54295858--54295898 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
54295848 ACCTTCAATA
54295858 ATAAACCCTAAAACC
1 ATAAACCCT-AAACC
**
54295873 ATAAACATTAAACC
1 ATAAACCCTAAACC
54295887 ATAAACCCTAAA
1 ATAAACCCTAAA
54295899 AAACTCAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.56, C:0.27, G:0.00, T:0.17
Consensus pattern (14 bp):
ATAAACCCTAAACC
Found at i:54297345 original size:43 final size:41
Alignment explanation
Indices: 54297298--54297525 Score: 206
Period size: 43 Copynumber: 5.3 Consensus size: 41
54297288 AAACGCCGCT
* * *
54297298 AAACGCCGCTAAAGCCTTGGACATTTAGCGGCGCTTTTCGCAG
1 AAACGCCGCTAAAGCCAT-GACCTTTAGCGGCGCTTTTC-CAA
*
54297341 AAACGCCGCTAAAGAGCAAT-ACCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCT-AA-AGCCATGACCTTTAGCGGCGCTTTT-CCAA
* ** * *
54297384 AAACGCCGCTAAAGAACAAAACCTTTAGCGACGCTTTTCCTAC
1 AAACGCCGCTAAAG-CCATGACCTTTAGCGGCGCTTTTCC-AA
* *
54297427 AAACGCCGCTAAAGCTCATGACCTTTAGCGGCGCTTCTACTAA
1 AAACGCCGCTAAAGC-CATGACCTTTAGCGGCGCTT-TTCCAA
* * * *
54297470 AAACGCCGCTAAAGAACAAGACCTTTAGCGACGCTTTTCCTAC
1 AAACGCCGCTAAAG-CCATGACCTTTAGCGGCGCTTTTCC-AA
*
54297513 AAACGCCACTAAA
1 AAACGCCGCTAAA
54297526 AGCATAACTT
Statistics
Matches: 152, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.01
42 7 0.05
43 134 0.88
44 5 0.03
45 4 0.03
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (41 bp):
AAACGCCGCTAAAGCCATGACCTTTAGCGGCGCTTTTCCAA
Found at i:54297419 original size:86 final size:87
Alignment explanation
Indices: 54297321--54297529 Score: 300
Period size: 86 Copynumber: 2.4 Consensus size: 87
54297311 GCCTTGGACA
* * * *
54297321 TTTAGCGGCGCTTTTCGC-AGAAACGCCGCTAAAGAGCAAT-ACCTTTAGCGGCGCTTTTCCCAA
1 TTTAGCGACGCTTTTC-CTACAAACGCCGCTAAAGAGCAATGACCTTTAGCGGCGCTTCTACCAA
54297384 AAACGCCGCTAAAGAACAAAACC
65 AAACGCCGCTAAAGAACAAAACC
** *
54297407 TTTAGCGACGCTTTTCCTACAAACGCCGCTAAAGCTC-ATGACCTTTAGCGGCGCTTCTACTAAA
1 TTTAGCGACGCTTTTCCTACAAACGCCGCTAAAGAGCAATGACCTTTAGCGGCGCTTCTACCAAA
*
54297471 AACGCCGCTAAAGAACAAGACC
66 AACGCCGCTAAAGAACAAAACC
*
54297493 TTTAGCGACGCTTTTCCTACAAACGCCACTAAA-AGCA
1 TTTAGCGACGCTTTTCCTACAAACGCCGCTAAAGAGCA
54297530 TAACTTTTAA
Statistics
Matches: 109, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
85 4 0.04
86 105 0.96
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (87 bp):
TTTAGCGACGCTTTTCCTACAAACGCCGCTAAAGAGCAATGACCTTTAGCGGCGCTTCTACCAAA
AACGCCGCTAAAGAACAAAACC
Found at i:54300472 original size:2 final size:2
Alignment explanation
Indices: 54300465--54300502 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
54300455 TCCGGCATCC
54300465 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54300503 GTTTCGGACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54302563 original size:13 final size:14
Alignment explanation
Indices: 54302535--54302567 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
54302525 AGTAAAATGA
54302535 TTTTTGCGGCGTTT
1 TTTTTGCGGCGTTT
*
54302549 TTTTTGTGGCGTTT
1 TTTTTGCGGCGTTT
54302563 TTTTT
1 TTTTT
54302568 TAAAAACGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.24, T:0.67
Consensus pattern (14 bp):
TTTTTGCGGCGTTT
Found at i:54302655 original size:23 final size:23
Alignment explanation
Indices: 54302611--54302683 Score: 119
Period size: 23 Copynumber: 3.1 Consensus size: 23
54302601 CAAAACGACG
**
54302611 TTATTTTGTTCTACTAAAAATTTT
1 TTATTTTG-TCTGTTAAAAATTTT
54302635 TTATTTTGTCTGTTAAAAATTTT
1 TTATTTTGTCTGTTAAAAATTTT
54302658 TTATTTTGTCTGTTAAAAATTTT
1 TTATTTTGTCTGTTAAAAATTTT
54302681 TTA
1 TTA
54302684 GTCAACTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
23 39 0.83
24 8 0.17
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.60
Consensus pattern (23 bp):
TTATTTTGTCTGTTAAAAATTTT
Found at i:54303553 original size:61 final size:63
Alignment explanation
Indices: 54303439--54303559 Score: 174
Period size: 61 Copynumber: 2.0 Consensus size: 63
54303429 TACTAACCCC
* * *
54303439 TAAACCTTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCCTAAACCCTAACACA
1 TAAACCTTATTTAATATATAAAGTAAAAAACACTAATTAATCTAAACCATAAACCCTAACACA
* * *
54303502 TAAACCTTATTT-A-ATATAAAGTAAAATACACTAATTAATCTAAATCATAAACCTTAAC
1 TAAACCTTATTTAATATATAAAGTAAAAAACACTAATTAATCTAAACCATAAACCCTAAC
54303560 CTAACACCGA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 39 0.75
62 1 0.02
63 12 0.23
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.31
Consensus pattern (63 bp):
TAAACCTTATTTAATATATAAAGTAAAAAACACTAATTAATCTAAACCATAAACCCTAACACA
Found at i:54304120 original size:41 final size:41
Alignment explanation
Indices: 54304075--54304309 Score: 355
Period size: 41 Copynumber: 5.7 Consensus size: 41
54304065 ATGTTTTTGT
**
54304075 GGCGCTTTTTTAAAAACGCCGCTAAAGCCCTGAGCATTAGC
1 GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGC
* *
54304116 GGCGC-TTCCCTAAAAACGCCGCTAAAGCCTTGAGCATTAGC
1 GGCGCTTTTCC-AAAAACGCCGCTAAAGCCCTGAGCATTAGC
*
54304157 GGCGCTTTTCCAAAAACGCCGCTAAAGACCTGAGCATTAGC
1 GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGC
*
54304198 GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTAAGCATTAGC
1 GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGC
**
54304239 GGCGCTTCCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGC
1 GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGC
** *
54304280 GGCGCTTTTTTAAAAACGCCACTAAAGCCC
1 GGCGCTTTTCCAAAAACGCCGCTAAAGCCC
54304310 CGAAAGGTCC
Statistics
Matches: 175, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 2 0.01
41 169 0.97
42 4 0.02
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (41 bp):
GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTAGC
Found at i:54304295 original size:123 final size:123
Alignment explanation
Indices: 54304075--54304306 Score: 392
Period size: 123 Copynumber: 1.9 Consensus size: 123
54304065 ATGTTTTTGT
** * *
54304075 GGCGCTTTTTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCCTAAAAACGCCGCTA
1 GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCCCCAAAAACGCCGCTA
* *
54304140 AAGCCTTGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTGAGCATTAGC
66 AAGCCCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCACTAAAGACCTGAGCATTAGC
54304198 GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCCCCAAAAACGCCGCTA
1 GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCCCCAAAAACGCCGCTA
**
54304263 AAGCCCTGAGCATTAGCGGCGCTTTTTTAAAAACGCCACTAAAG
66 AAGCCCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCACTAAAG
54304307 CCCCGAAAGG
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 101 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (123 bp):
GGCGCTTTTCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCCCCAAAAACGCCGCTA
AAGCCCTGAGCATTAGCGGCGCTTTTCCAAAAACGCCACTAAAGACCTGAGCATTAGC
Found at i:54312831 original size:18 final size:19
Alignment explanation
Indices: 54312791--54312832 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
54312781 TTTGTTGGAG
54312791 AAAATATAAAAATTAAACT
1 AAAATATAAAAATTAAACT
54312810 AAAA-ATAATAAATTAAAC-
1 AAAATATAA-AAATTAAACT
54312828 AAAAT
1 AAAAT
54312833 TTTGGATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATATAAAAATTAAACT
Found at i:54319086 original size:26 final size:25
Alignment explanation
Indices: 54319057--54319105 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
54319047 GACGGGAAGA
54319057 GAATAA-AAGTTTTGAGAGGAAAGTGG
1 GAATAACAA-TTTTGAGA-GAAAGTGG
*
54319083 GAATAACAATTTTGGGAGAAAGT
1 GAATAACAATTTTGAGAGAAAGT
54319106 AAATAGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 13 0.62
27 2 0.10
ACGTcount: A:0.43, C:0.02, G:0.31, T:0.24
Consensus pattern (25 bp):
GAATAACAATTTTGAGAGAAAGTGG
Found at i:54320643 original size:26 final size:26
Alignment explanation
Indices: 54320596--54320645 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
54320586 TATAATGAAT
* **
54320596 TGTTTTATATTATTTTAGATATTAAG
1 TGTTTTAAATTATTCCAGATATTAAG
*
54320622 TGTTTTAAATTATTCCATATATTA
1 TGTTTTAAATTATTCCAGATATTA
54320646 TTTATGTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (26 bp):
TGTTTTAAATTATTCCAGATATTAAG
Found at i:54326749 original size:19 final size:22
Alignment explanation
Indices: 54326711--54326753 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
54326701 ATATCAATTT
54326711 TAAATATATTATTATTAAATAA
1 TAAATATATTATTATTAAATAA
54326733 TAAATATA-TA-T-TTAAATAA
1 TAAATATATTATTATTAAATAA
54326752 TA
1 TA
54326754 TTTAAATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 2 0.10
22 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATATATTATTATTAAATAA
Found at i:54326920 original size:33 final size:35
Alignment explanation
Indices: 54326825--54326921 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
54326815 TTAATATTTT
*
54326825 AATATATGAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
54326860 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
54326893 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
54326922 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:54327426 original size:24 final size:24
Alignment explanation
Indices: 54327394--54327453 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
54327384 ATATAATTTT
*
54327394 TTAAAAATATAATATATATAA-ATA
1 TTAAAAATA-AATATATATAACAAA
* *
54327418 TTAAAAATAAATATTTTTAACAAA
1 TTAAAAATAAATATATATAACAAA
54327442 TTAAAAATAAAT
1 TTAAAAATAAAT
54327454 TAAAAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TTAAAAATAAATATATATAACAAA
Found at i:54329063 original size:19 final size:21
Alignment explanation
Indices: 54329039--54329086 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
54329029 TTGTTTCACA
54329039 GAAAATAG-CTT-GGTCAACG
1 GAAAATAGACTTAGGTCAACG
54329058 GAAAAT-GACTTACAGGTCAACG
1 GAAAATAGACTT--AGGTCAACG
54329080 GAAAATA
1 GAAAATA
54329087 ATCCTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 1 0.04
19 9 0.38
22 14 0.58
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.19
Consensus pattern (21 bp):
GAAAATAGACTTAGGTCAACG
Found at i:54329378 original size:31 final size:30
Alignment explanation
Indices: 54329316--54329381 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
54329306 TTTAGTCATA
54329316 TAATAAATAATTAATATAAATTATTATTTT
1 TAATAAATAATTAATATAAATTATTATTTT
*
54329346 TAATAAATTATTTAATATTTAAATT-TTA-TTT
1 TAATAAA-TAATTAATA--TAAATTATTATTTT
54329377 TAATA
1 TAATA
54329382 GTAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.22
31 16 0.50
32 3 0.09
33 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TAATAAATAATTAATATAAATTATTATTTT
Found at i:54329453 original size:15 final size:15
Alignment explanation
Indices: 54329435--54329491 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
54329425 TATCAATATT
54329435 AATATTTTAATAATA
1 AATATTTTAATAATA
*
54329450 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
54329469 AATATATTAATAATA
1 AATATTTTAATAATA
*
54329484 AATGTTTT
1 AATATTTT
54329492 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:54342405 original size:22 final size:23
Alignment explanation
Indices: 54342353--54342406 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
54342343 CGTTTTTAAT
*
54342353 TAAAATTAAAATTATATTTGTAA
1 TAAAATTAAAACTATATTTGTAA
*
54342376 TAAAATTAAAACTA-A-TTGTTA
1 TAAAATTAAAACTATATTTGTAA
54342397 TCAAAATTAA
1 T-AAAATTAA
54342407 TTGTTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 9 0.32
23 13 0.46
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
TAAAATTAAAACTATATTTGTAA
Found at i:54342407 original size:16 final size:16
Alignment explanation
Indices: 54342383--54342420 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
54342373 TAATAAAATT
*
54342383 AAAACTAATTGTTATC
1 AAAATTAATTGTTATC
*
54342399 AAAATTAATTGTTATT
1 AAAATTAATTGTTATC
54342415 AAAATT
1 AAAATT
54342421 GTATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
AAAATTAATTGTTATC
Found at i:54345318 original size:45 final size:45
Alignment explanation
Indices: 54345254--54345349 Score: 158
Period size: 45 Copynumber: 2.1 Consensus size: 45
54345244 AGCAAGGCAA
54345254 TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATAGGC
1 TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATAGGC
* *
54345299 TAATGTGAAATTT-TGAGCTAATTTTCCATTATATAAACAATCGGC
1 TAATGTGAAATTTCT-AGCTAATGTTCCATTATATAAACAATAGGC
54345344 TAATGT
1 TAATGT
54345350 TCCATTTATA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 1 0.02
45 47 0.98
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (45 bp):
TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATAGGC
Found at i:54346801 original size:10 final size:10
Alignment explanation
Indices: 54346786--54346817 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
54346776 GCCTAAAATT
54346786 ATATATAATG
1 ATATATAATG
*
54346796 ATATATAATA
1 ATATATAATG
54346806 ATATATAATG
1 ATATATAATG
54346816 AT
1 AT
54346818 GGGGATGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (10 bp):
ATATATAATG
Found at i:54347553 original size:7 final size:7
Alignment explanation
Indices: 54347541--54347578 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
54347531 GTTGAAAAAT
54347541 AAAACTA
1 AAAACTA
54347548 AAAACTA
1 AAAACTA
*
54347555 AAAACTT
1 AAAACTA
*
54347562 AAAACTT
1 AAAACTA
54347569 AAAACTA
1 AAAACTA
54347576 AAA
1 AAA
54347579 TTAACTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAACTA
Found at i:54348484 original size:43 final size:43
Alignment explanation
Indices: 54348380--54348496 Score: 112
Period size: 42 Copynumber: 2.7 Consensus size: 43
54348370 CATAGGATTC
* * * * *
54348380 CGATATGTGATTATGTGTAAAACCATGTCTGGGACATCGGCGT
1 CGATATATGATTACGTGTAAGACCATGTCTGGCACATCGGCAT
* *
54348423 C-ATATATGATTTCGTGTAAGACCATGTTTGGCACAGT-GGCAT
1 CGATATATGATTACGTGTAAGACCATGTCTGGCACA-TCGGCAT
* * * *
54348465 CGATATTTGATTACATGTAAGACTACGTCTGG
1 CGATATATGATTACGTGTAAGACCATGTCTGG
54348497 AACGTTGGCA
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 33 0.56
43 26 0.44
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
CGATATATGATTACGTGTAAGACCATGTCTGGCACATCGGCAT
Found at i:54350387 original size:28 final size:28
Alignment explanation
Indices: 54350355--54350411 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
54350345 CATATCAGCC
54350355 CATAC-ATTTT-ACAATTTCACACATTTAA
1 CATACAATTTTCAC-ATTTCACA-ATTTAA
*
54350383 CATACAATTTTCACATTTCTCAATTTAA
1 CATACAATTTTCACATTTCACAATTTAA
54350411 C
1 C
54350412 CTCTATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 12 0.46
29 12 0.46
30 2 0.08
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (28 bp):
CATACAATTTTCACATTTCACAATTTAA
Found at i:54353627 original size:21 final size:20
Alignment explanation
Indices: 54353603--54353650 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
54353593 CGGCTAATAA
*
54353603 TTAACTATTAACTAACTATGT
1 TTAACTACTAACTAACTAT-T
* *
54353624 TTAACTACTAGCTAACTCTT
1 TTAACTACTAACTAACTATT
54353644 TTAACTA
1 TTAACTA
54353651 ACCCTACTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (20 bp):
TTAACTACTAACTAACTATT
Found at i:54354426 original size:19 final size:19
Alignment explanation
Indices: 54354402--54354438 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54354392 TAATTAGGTA
* *
54354402 TTAATTAGGAGAATTTAGT
1 TTAATTAAGAGAAATTAGT
54354421 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
54354439 GAAAAAGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGT
Found at i:54354613 original size:5 final size:5
Alignment explanation
Indices: 54354574--54354638 Score: 64
Period size: 5 Copynumber: 13.2 Consensus size: 5
54354564 TTTTTATGTT
* *
54354574 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATA TTGTA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
*
54354623 TTGTA TTATA TTATA T
1 TTATA TTATA TTATA T
54354639 GTAATACCCA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
3 1 0.02
4 8 0.16
5 36 0.73
7 4 0.08
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:54358076 original size:21 final size:21
Alignment explanation
Indices: 54358050--54358114 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
54358040 GGTTTTGCCG
54358050 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
* **
54358071 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
*
54358092 TTCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
54358113 AT
1 AT
54358115 ACTGATCAGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:54365720 original size:21 final size:20
Alignment explanation
Indices: 54365694--54365740 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
54365684 ATATAAGAAC
* *
54365694 TAACTATTAACTAACTGTGTT
1 TAACTACTAACTAACTCT-TT
54365715 TAACTACTAACTAACTCTTT
1 TAACTACTAACTAACTCTTT
54365735 TAACTA
1 TAACTA
54365741 ACTTTATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (20 bp):
TAACTACTAACTAACTCTTT
Found at i:54369045 original size:12 final size:12
Alignment explanation
Indices: 54369028--54369071 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
54369018 AAAGATATAT
54369028 AATATATTCCTA
1 AATATATTCCTA
**
54369040 AATATATTTTTA
1 AATATATTCCTA
*
54369052 AATATATGCCTAA
1 AATATATTCCT-A
54369065 AATATAT
1 AATATAT
54369072 ACAATATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (12 bp):
AATATATTCCTA
Found at i:54369336 original size:20 final size:19
Alignment explanation
Indices: 54369289--54369339 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
54369279 TAAAATTGGG
*
54369289 TGCAATTTTATTTTTTTTA
1 TGCAATTTTATTTTGTTTA
*
54369308 TGTAA-TTTATATTTGTTTA
1 TGCAATTTTAT-TTTGTTTA
54369327 TGCAATTTTATTT
1 TGCAATTTTATTT
54369340 CTCTGTCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.19
19 17 0.63
20 5 0.19
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.65
Consensus pattern (19 bp):
TGCAATTTTATTTTGTTTA
Found at i:54377457 original size:60 final size:60
Alignment explanation
Indices: 54377367--54377479 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
54377357 ATTTTTAAAA
* * * * **
54377367 TTTTAGAGTTAGGACTAAATTGACAGATTTTATAAATGTTGAGGGCCAAATTTAATGAAT
1 TTTTAGAATTAGAACTAAATTGAAAAATTTTATAAACATTGAGGGCCAAATTTAATGAAT
* *
54377427 TTTTAGAATTAGAACTAAAATT-AAAAATTTTGTAAACATTGAGGGCTAAATTT
1 TTTTAGAATTAGAACT-AAATTGAAAAATTTTATAAACATTGAGGGCCAAATTT
54377480 GTTAAATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 39 0.89
61 5 0.11
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (60 bp):
TTTTAGAATTAGAACTAAATTGAAAAATTTTATAAACATTGAGGGCCAAATTTAATGAAT
Found at i:54377488 original size:60 final size:59
Alignment explanation
Indices: 54377357--54377490 Score: 135
Period size: 60 Copynumber: 2.2 Consensus size: 59
54377347 TTTTAAAAAT
* * * * * **
54377357 ATTTTTAAAATTTTAGAGTTAGGACTAAATTGACAGATTTTATAAATGTTGAGGGCCAA
1 ATTTTTAAATTTTTAGAATTAGAACTAAATTGAAAAATTTTATAAACATTGAGGGCCAA
* * * *
54377416 ATTTAATGAATTTTTAGAATTAGAACTAAAATT-AAAAATTTTGTAAACATTGAGGGCTAA
1 ATTT-TTAAATTTTTAGAATTAGAACT-AAATTGAAAAATTTTATAAACATTGAGGGCCAA
54377476 ATTTGTTAAATTTTT
1 ATTT-TTAAATTTTT
54377491 TATATTTAAG
Statistics
Matches: 59, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
59 4 0.07
60 50 0.85
61 5 0.08
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (59 bp):
ATTTTTAAATTTTTAGAATTAGAACTAAATTGAAAAATTTTATAAACATTGAGGGCCAA
Found at i:54378196 original size:22 final size:21
Alignment explanation
Indices: 54378166--54378206 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
54378156 ACTCATCATG
54378166 AAAAATAAATATAAATATTTT
1 AAAAATAAATATAAATATTTT
*
54378187 AAAAATTAAATATAAGTATT
1 AAAAA-TAAATATAAATATT
54378207 GAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAAATAAATATAAATATTTT
Found at i:54385425 original size:21 final size:21
Alignment explanation
Indices: 54385384--54385425 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
54385374 ATATCAGAAT
*
54385384 ATTATTAATGATATATTTAAA
1 ATTATTAATGATATATATAAA
*
54385405 ATTATTTAATTATATA-ATAAA
1 ATTA-TTAATGATATATATAAA
54385426 CATCAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTATTAATGATATATATAAA
Found at i:54387664 original size:18 final size:18
Alignment explanation
Indices: 54387651--54387715 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
54387641 AGCTCAGTTG
*
54387651 AAGCTGGGAGCTCATCTA
1 AAGCTGCGAGCTCATCTA
* *
54387669 AAGCTGCGAGCTCACCCA
1 AAGCTGCGAGCTCATCTA
* *
54387687 AAGAC-GCGAGCTCAACTC
1 AAG-CTGCGAGCTCATCTA
*
54387705 AAGTTGCGAGC
1 AAGCTGCGAGC
54387716 ACGTTAAAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 37 0.97
19 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.15
Consensus pattern (18 bp):
AAGCTGCGAGCTCATCTA
Found at i:54391166 original size:19 final size:19
Alignment explanation
Indices: 54391138--54391175 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
54391128 TTTTAAGAGA
54391138 ATATTGTAATTATA-ATTT
1 ATATTGTAATTATATATTT
54391156 ATATATGTAATTATATATTT
1 ATAT-TGTAATTATATATTT
54391176 TAGTGAAGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
ATATTGTAATTATATATTT
Found at i:54401140 original size:82 final size:82
Alignment explanation
Indices: 54401041--54401205 Score: 303
Period size: 82 Copynumber: 2.0 Consensus size: 82
54401031 GAAGAGAAGA
* *
54401041 AAGAAAGCGTATTATTATTTTTATTGTTATTTTCAAATAGAATAGATTATAATAAGAAAAAATTA
1 AAGAAAACATATTATTATTTTTATTGTTATTTTCAAATAGAATAGATTATAATAAGAAAAAATTA
54401106 TTTTGTTAGTATTATAT
66 TTTTGTTAGTATTATAT
*
54401123 AAGAAAACATATTATTATTTTTATTGTTATTTTCAAATAGAATAGATTATGATAAGAAAAAATTA
1 AAGAAAACATATTATTATTTTTATTGTTATTTTCAAATAGAATAGATTATAATAAGAAAAAATTA
54401188 TTTTGTTAGTATTATAT
66 TTTTGTTAGTATTATAT
54401205 A
1 A
54401206 GTTTTTTAGT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.45
Consensus pattern (82 bp):
AAGAAAACATATTATTATTTTTATTGTTATTTTCAAATAGAATAGATTATAATAAGAAAAAATTA
TTTTGTTAGTATTATAT
Found at i:54404363 original size:48 final size:48
Alignment explanation
Indices: 54404296--54404387 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
54404286 TATATAACAA
54404296 AATTTATATTACAAAGTTTGTTCAAAGTTTTAATATTGTAATGTATTT
1 AATTTATATTACAAAGTTTGTTCAAAGTTTTAATATTGTAATGTATTT
* *
54404344 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT
1 AATTTATATTACAAAGTTTGTTCAAAGTTTTAATATTGTAATGT
54404388 TGTAATGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (48 bp):
AATTTATATTACAAAGTTTGTTCAAAGTTTTAATATTGTAATGTATTT
Found at i:54405025 original size:14 final size:14
Alignment explanation
Indices: 54405006--54405040 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
54404996 CAATTTACAT
54405006 GTTAGAATAGTATC
1 GTTAGAATAGTATC
54405020 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
54405034 ATTAGAA
1 GTTAGAA
54405041 AAAAAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:54406364 original size:2 final size:2
Alignment explanation
Indices: 54406352--54406397 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
54406342 TTGGTTTAAA
54406352 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54406393 AT AT A
1 AT AT A
54406398 ATAACATGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54406956 original size:31 final size:31
Alignment explanation
Indices: 54406921--54406988 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
54406911 AATTAAATCT
54406921 AAATTAAATCAACAATAA-TAACAACAAAAA
1 AAATTAAATCAACAATAATTAACAACAAAAA
* * * *
54406951 CAAATTAAATTAACATTAATTTATAACAAAAA
1 -AAATTAAATCAACAATAATTAACAACAAAAA
54406983 AAATTA
1 AAATTA
54406989 CTTTTCTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 22 0.69
32 10 0.31
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (31 bp):
AAATTAAATCAACAATAATTAACAACAAAAA
Found at i:54407144 original size:6 final size:6
Alignment explanation
Indices: 54407133--54407171 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
54407123 GCCACTGCCC
54407133 TCTCCT TCTCCT TCTCCT TCTCCT TCTTCTCT TCTCCT T
1 TCTCCT TCTCCT TCTCCT TCTCCT TC-TC-CT TCTCCT T
54407172 ATAATGGTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 23 0.74
7 4 0.13
8 4 0.13
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (6 bp):
TCTCCT
Found at i:54420810 original size:32 final size:31
Alignment explanation
Indices: 54420750--54420812 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
54420740 TTTATTAGAA
*
54420750 AATGAGTAAATTAGTTCATTTATATTAAATT
1 AATGAGTAAATTAATTCATTTATATTAAATT
** *
54420781 AATGAGTAAATTAAATTTTTTTATTTTAAATT
1 AATGAGTAAATT-AATTCATTTATATTAAATT
54420813 TTATCTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (31 bp):
AATGAGTAAATTAATTCATTTATATTAAATT
Found at i:54428575 original size:20 final size:20
Alignment explanation
Indices: 54428530--54428577 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
54428520 CACTCGAAGC
*
54428530 AAAAGATTAAGCAAAGGGAT
1 AAAAGATTAAGCAAAGAGAT
* *
54428550 ACAAGATTAATCAAA-AGATT
1 AAAAGATTAAGCAAAGAGA-T
54428570 AAAAGATT
1 AAAAGATT
54428578 CCACAAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAAGATTAAGCAAAGAGAT
Found at i:54435594 original size:16 final size:16
Alignment explanation
Indices: 54435573--54435604 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
54435563 CCACCTTCAA
*
54435573 ACCAAAAGCTTAGTGG
1 ACCAAAAGCTCAGTGG
54435589 ACCAAAAGCTCAGTGG
1 ACCAAAAGCTCAGTGG
54435605 GGAAACAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.16
Consensus pattern (16 bp):
ACCAAAAGCTCAGTGG
Found at i:54447237 original size:16 final size:16
Alignment explanation
Indices: 54447216--54447252 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
54447206 GAACTCTTTA
*
54447216 ATTAACTTGCTGTTAT
1 ATTAACTTACTGTTAT
54447232 ATTAACTTACTGTTAT
1 ATTAACTTACTGTTAT
54447248 ATTAA
1 ATTAA
54447253 TTTGTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (16 bp):
ATTAACTTACTGTTAT
Found at i:54447260 original size:13 final size:15
Alignment explanation
Indices: 54447216--54447261 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
54447206 GAACTCTTTA
*
54447216 ATTAACTTGCTGTTAT
1 ATTAACTT-ATGTTAT
54447232 ATTAACTTACTGTTAT
1 ATTAACTTA-TGTTAT
54447248 ATTAA-TT-TGTTAT
1 ATTAACTTATGTTAT
54447261 A
1 A
54447262 AATATATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 7 0.25
15 2 0.07
16 19 0.68
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (15 bp):
ATTAACTTATGTTAT
Found at i:54450257 original size:21 final size:21
Alignment explanation
Indices: 54450233--54450284 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
54450223 ATCGGATTGA
*
54450233 TTGAATCGGTGATTGAATTAG
1 TTGAATCGGTGATTGAACTAG
54450254 TTGAATCGGTGATTGAACTAG
1 TTGAATCGGTGATTGAACTAG
54450275 TTGAATCGGT
1 TTGAATCGGT
54450285 TTTTTTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.37
Consensus pattern (21 bp):
TTGAATCGGTGATTGAACTAG
Found at i:54454322 original size:1 final size:1
Alignment explanation
Indices: 54454316--54454340 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
54454306 GGCTCGAAGG
54454316 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
54454341 CCCATCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:54455608 original size:18 final size:18
Alignment explanation
Indices: 54455546--54455609 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
54455536 TATAAAAAAT
* **
54455546 AAAAATAAATAAAAGTTA
1 AAAAATAATTAAATTTTA
*
54455564 TAAAAATTATTAAATTTTA
1 -AAAAATAATTAAATTTTA
*
54455583 ATAAAATAATTATATTTTA
1 A-AAAATAATTAAATTTTA
54455602 AAAAATAA
1 AAAAATAA
54455610 AAAAATGGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 8 0.21
19 30 0.79
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAAATAATTAAATTTTA
Found at i:54455858 original size:19 final size:18
Alignment explanation
Indices: 54455834--54455890 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
54455824 TTTTGATACG
54455834 ATAATTTTTATATTTTTTT
1 ATAATTTTT-TATTTTTTT
* **
54455853 ATAATTTTCTTACTACTTT
1 ATAATTTT-TTATTTTTTT
54455872 ATAATTTTTTTATTTTTTT
1 ATAA-TTTTTTATTTTTTT
54455891 TCTATATTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 25 0.83
20 5 0.17
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
ATAATTTTTTATTTTTTT
Found at i:54455918 original size:30 final size:29
Alignment explanation
Indices: 54455875--54455952 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 29
54455865 CTACTTTATA
*
54455875 ATTTTTTTATTTTTTTTCT-ATATTTCAAT
1 ATTTTTATATTTTTTTTCTAAT-TTTCAAT
*
54455904 ATCTTTTATATTTTTTTTCTAATTTTTAAT
1 AT-TTTTATATTTTTTTTCTAATTTTCAAT
54455934 ATTTTTAATATATTTTTTT
1 ATTTTT-ATAT-TTTTTTT
54455953 AAGTTGTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 6 0.14
30 28 0.65
31 9 0.21
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (29 bp):
ATTTTTATATTTTTTTTCTAATTTTCAAT
Found at i:54466693 original size:13 final size:13
Alignment explanation
Indices: 54466654--54466704 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
54466644 ACACTCAAAA
54466654 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* * *
54466667 TTTTCCACACCAC
1 TTTTCAAAAGCAC
54466680 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
54466693 TTTTCAAAAGCA
1 TTTTCAAAAGCA
54466705 TTGCCAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:54469080 original size:43 final size:44
Alignment explanation
Indices: 54469018--54469103 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 44
54469008 TCCTACAAGG
* *
54469018 AGTAAGAAAAAATATTGAGTTAACATACTAGTGGGAATAATATA
1 AGTAAGAAAAAATATTGAGTTAACAAACTAGAGGGAATAATATA
54469062 AGTAAGAAAAAA-ATTGAGTTAACAAACTAGAGGGAATAATAT
1 AGTAAGAAAAAATATTGAGTTAACAAACTAGAGGGAATAATAT
54469104 GTTTCCGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 28 0.70
44 12 0.30
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (44 bp):
AGTAAGAAAAAATATTGAGTTAACAAACTAGAGGGAATAATATA
Found at i:54476269 original size:2 final size:2
Alignment explanation
Indices: 54476262--54476306 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
54476252 ATGAATGATT
54476262 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54476304 TA T
1 TA T
54476307 TTCTAATGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54484459 original size:19 final size:20
Alignment explanation
Indices: 54484421--54484459 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54484411 TTTTTTTGTC
* *
54484421 AATTTAATTTGTATTTTTAA
1 AATTAAATTTGTATTATTAA
54484441 AATTAAATTTG-ATTATTAA
1 AATTAAATTTGTATTATTAA
54484460 CTTTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
AATTAAATTTGTATTATTAA
Found at i:54484959 original size:24 final size:21
Alignment explanation
Indices: 54484932--54484974 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 21
54484922 GAATATAGAC
54484932 TTCTCAAAAAGAATTATCTTAATT
1 TTCT-AAAAA-AATTA-CTTAATT
54484956 TTCTAAAAAAATTACTTAA
1 TTCTAAAAAAATTACTTAA
54484975 GAAAAGGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 5 0.26
24 4 0.21
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.40
Consensus pattern (21 bp):
TTCTAAAAAAATTACTTAATT
Found at i:54486599 original size:2 final size:2
Alignment explanation
Indices: 54486592--54486628 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54486582 TTTTGATAAT
54486592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54486629 GATGACTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54489415 original size:25 final size:25
Alignment explanation
Indices: 54489382--54489432 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
54489372 TAAAATTTTA
54489382 ATAAATTTATAACTTATATTATTTG
1 ATAAATTTATAACTTATATTATTTG
*
54489407 ATAAATTTATAATTTATATTATTTG
1 ATAAATTTATAACTTATATTATTTG
54489432 A
1 A
54489433 ACTTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (25 bp):
ATAAATTTATAACTTATATTATTTG
Found at i:54498815 original size:21 final size:21
Alignment explanation
Indices: 54498789--54498828 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54498779 TATATATATA
54498789 TAAATTTTCAAGTGATGACAT
1 TAAATTTTCAAGTGATGACAT
*
54498810 TAAATTTTTAAGTGATGAC
1 TAAATTTTCAAGTGATGAC
54498829 GTCGCACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (21 bp):
TAAATTTTCAAGTGATGACAT
Done.