Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold84
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: 4163231
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 246351 characters in sequence are not A, C, G, or T
File 6 of 11
Found at i:2303685 original size:11 final size:11
Alignment explanation
Indices: 2303664--2303700 Score: 60
Period size: 10 Copynumber: 3.5 Consensus size: 11
2303654 AATAGACATG
2303664 AAAAATG-AAT
1 AAAAATGAAAT
2303674 AAAAATGAAAT
1 AAAAATGAAAT
2303685 AAAAAT-AAAT
1 AAAAATGAAAT
2303695 AAAAAT
1 AAAAAT
2303701 TATACAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (11 bp):
AAAAATGAAAT
Found at i:2304416 original size:153 final size:154
Alignment explanation
Indices: 2304246--2304544 Score: 349
Period size: 153 Copynumber: 1.9 Consensus size: 154
2304236 AAAATCAAAG
* *
2304246 TTTTATTTAGAAAAAAAATCATTACTTTTCTTAAAAATCAAA-ATCTTATTTCGAAATAGTT-AA
1 TTTTATTTAGAAAAAAAAACACTACTTTTCTTAAAAATCAAAGATCTTATTTCGAAATAGTTGAA
*
2304309 AAAAA-TCAAAACTTTT-TAAAAAAATTTAAACTCTCCTTTAAAATGACT-TAAAAAACAAATTT
66 AAAAATTCAAAA-TTTTGTAAAAAAATTTAAA----CCTTTAAAATGACTAAAAAAAACAAATTT
*
2304371 TTATTTTTCAATATGTAAACTTTCTCCTT
126 TTATTTTTCAAAATGTAAACTTTCTCCTT
* * * * * * * *
2304400 TTTTTTTTA-AAAAAAAAACACTATTTTTCTTAAAGATTAAAGCTTTTATTTTGAAGTAGTTGAA
1 TTTTATTTAGAAAAAAAAACACTACTTTTCTTAAAAATCAAAGATCTTATTTCGAAATAGTTGAA
*** * *
2304464 AAAAATTCAAAATTTTGTTCTAAAATTTTAAGCTTTAAAATGACTAAAAAAAACAAATTTTTATT
66 AAAAATTCAAAATTTTGTAAAAAAATTTAAACCTTTAAAATGACTAAAAAAAACAAATTTTTATT
*
2304529 TTTCAAAATTTAAACT
131 TTTCAAAATGTAAACT
2304545 GTAACGTCCC
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
152 13 0.11
153 59 0.48
154 23 0.19
155 11 0.09
156 16 0.13
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (154 bp):
TTTTATTTAGAAAAAAAAACACTACTTTTCTTAAAAATCAAAGATCTTATTTCGAAATAGTTGAA
AAAAATTCAAAATTTTGTAAAAAAATTTAAACCTTTAAAATGACTAAAAAAAACAAATTTTTATT
TTTCAAAATGTAAACTTTCTCCTT
Found at i:2305568 original size:32 final size:32
Alignment explanation
Indices: 2305509--2305618 Score: 139
Period size: 32 Copynumber: 3.4 Consensus size: 32
2305499 CCATGTGCGA
*
2305509 GGCCGTGTAGGCCACATGGGCAAGGCAATTTG
1 GGCCGTGTAGGCCACATGGGCATGGCAATTTG
* * *
2305541 GGCGGTGTGGGCGACATGGGCATGGCAATTTG
1 GGCCGTGTAGGCCACATGGGCATGGCAATTTG
***
2305573 GGCCGTGTAGGCCACACAAGCATGGCAATTTG
1 GGCCGTGTAGGCCACATGGGCATGGCAATTTG
* *
2305605 GACCGTGTGGGCCA
1 GGCCGTGTAGGCCA
2305619 AAAATTTCTA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.20, C:0.22, G:0.39, T:0.19
Consensus pattern (32 bp):
GGCCGTGTAGGCCACATGGGCATGGCAATTTG
Found at i:2320545 original size:24 final size:25
Alignment explanation
Indices: 2320519--2320568 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
2320509 AAAAGAAATT
* *
2320519 AAACAAATAAATAAAAA-TATAAAT
1 AAACAAATAAACAAAAACTAAAAAT
*
2320543 AAAGAAATAAACAAAAACTAAAAAT
1 AAACAAATAAACAAAAACTAAAAAT
2320568 A
1 A
2320569 CTTAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (25 bp):
AAACAAATAAACAAAAACTAAAAAT
Found at i:2323141 original size:16 final size:16
Alignment explanation
Indices: 2323120--2323151 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2323110 ATTTTGTTGC
*
2323120 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
2323136 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
2323152 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:2323408 original size:51 final size:51
Alignment explanation
Indices: 2323350--2323537 Score: 240
Period size: 51 Copynumber: 3.7 Consensus size: 51
2323340 CGGTTCACAA
* * * *
2323350 AGTAGCCTGCACATAGTGCTACACATGTGACCATCACTATCCGATACACGT
1 AGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACGT
* * *
2323401 AGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCTGGTACGCAT
1 AGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCTGGTACACGT
* *
2323452 AGTAGCCTGCATATAGTACTACACATGTGACCTATCA-T-TCTGGTACACGT
1 AGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCTGGTACACGT
2323502 AGTAGCCTGCACATAGTACTACACACGTGACCATCA
1 AGTAGCCTGCACATAGTACTACACACGTGACCATCA
2323538 GTTTCACTTT
Statistics
Matches: 118, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
49 4 0.03
50 42 0.36
51 69 0.58
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (51 bp):
AGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACGT
Found at i:2323554 original size:101 final size:102
Alignment explanation
Indices: 2323342--2323531 Score: 267
Period size: 101 Copynumber: 1.9 Consensus size: 102
2323332 AATGATATCG
* *
2323342 GTTCACAAAGTAGCCTGCACATAGTGCTACACATGTGACCATCACTATCCGATACACGTAGTAGC
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGC
* **
2323407 CTGCACATAGTACTACACACGTGATCGAAGCTATCTG
66 CTGCACATAGTACTACACACGTGATCCAAGCTATCAC
* * * * *
2323444 GTACGCATAGTAGCCTGCATATAGTACTACACATGTGACCTATCA-T-TCTGGTACACGTAGTAG
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTATCCGATACACGTAGTAG
2323507 CCTGCACATAGTACTACACACGTGA
65 CCTGCACATAGTACTACACACGTGA
2323532 CCATCAGTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 40 0.50
102 36 0.45
103 4 0.05
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (102 bp):
GTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGC
CTGCACATAGTACTACACACGTGATCCAAGCTATCAC
Found at i:2323666 original size:11 final size:10
Alignment explanation
Indices: 2323642--2323673 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2323632 AATCGAGAAA
2323642 TTTCTCACTT
1 TTTCTCACTT
2323652 TTTCTCACTT
1 TTTCTCACTT
2323662 TTT-TC-CTT
1 TTTCTCACTT
2323670 TTTC
1 TTTC
2323674 ACTAATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.29
9 2 0.10
10 13 0.62
ACGTcount: A:0.06, C:0.28, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTCTCACTT
Found at i:2336275 original size:14 final size:15
Alignment explanation
Indices: 2336246--2336277 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2336236 AAAAACATCA
2336246 TAATTTTATCTATTT
1 TAATTTTATCTATTT
2336261 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
2336275 TAA
1 TAA
2336278 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:2340213 original size:124 final size:124
Alignment explanation
Indices: 2339993--2340243 Score: 457
Period size: 124 Copynumber: 2.0 Consensus size: 124
2339983 GAGCAAGTCA
*
2339993 TAAAATTTGTTCAAGTCACAGATTTGACTTAGGGCTTTAGACGTTCGAAAAGAAACTCGGATTTT
1 TAAAATTTGTTCAAGTCACAGATTTGACTTAGGGCTTTAGACGTTCGAAAAGAAACTCGGATTCT
* *
2340058 GACATAACCTGAAACACAATCAAATTCAAGTCAAATAAAACAAACAAATAAGAAATAAC
66 GACATAACCTGAAACACAATCAAATCCAAGTCAAATAAAAAAAACAAATAAGAAATAAC
2340117 TAAAATTTGTTCAAGTCACAGATTTGACTTAGGGCTTTAGACGTTCGAAAAGAAACTCGGATTCT
1 TAAAATTTGTTCAAGTCACAGATTTGACTTAGGGCTTTAGACGTTCGAAAAGAAACTCGGATTCT
* *
2340182 GACATAACCTGAAACACAATTAAATCCAAGTCAAATAAAAAAAACAAATAATAAATAAC
66 GACATAACCTGAAACACAATCAAATCCAAGTCAAATAAAAAAAACAAATAAGAAATAAC
2340241 TAA
1 TAA
2340244 CATAAATAAA
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 122 1.00
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (124 bp):
TAAAATTTGTTCAAGTCACAGATTTGACTTAGGGCTTTAGACGTTCGAAAAGAAACTCGGATTCT
GACATAACCTGAAACACAATCAAATCCAAGTCAAATAAAAAAAACAAATAAGAAATAAC
Found at i:2349740 original size:16 final size:16
Alignment explanation
Indices: 2349719--2349750 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2349709 TTCTTGAAAA
2349719 CAAGAAAGTGAATCTT
1 CAAGAAAGTGAATCTT
2349735 CAAGAAAGTGAATCTT
1 CAAGAAAGTGAATCTT
2349751 GATTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (16 bp):
CAAGAAAGTGAATCTT
Found at i:2350375 original size:29 final size:29
Alignment explanation
Indices: 2350333--2350389 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
2350323 ACTTCTTCAC
*
2350333 TATTTTAATGAAAAGTTAATTTTAATCCT
1 TATTTTAATGAAAACTTAATTTTAATCCT
* *
2350362 TATTTTCATTAAAACTTAATTTTAATCC
1 TATTTTAATGAAAACTTAATTTTAATCC
2350390 CTTGAAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (29 bp):
TATTTTAATGAAAACTTAATTTTAATCCT
Found at i:2350750 original size:69 final size:69
Alignment explanation
Indices: 2350563--2350808 Score: 273
Period size: 69 Copynumber: 3.5 Consensus size: 69
2350553 TGACAATTTA
* * *
2350563 TTCACTATTTTTATT-AAAATTTAATTTTAATCCCACTTTAACTAGAGAATACTCTCATAAATAA
1 TTCACTATTTTTATTAAAAAATTAATTTTAATCCCACATTAACTAGAGAATACACTC----ATAA
* *
2350627 GTGACATTTTC
62 CT--CA-CTTC
* * * * *
2350638 TTCACT-TTTTCAATAAAAAAAGTTAATTTTAATCTCACATTAACTAGAGAATACACTTATAGCT
1 TTCACTATTTT-TATTAAAAAA-TTAATTTTAATCCCACATTAACTAGAGAATACACTCATAACT
2350702 CACTTC
64 CACTTC
* *
2350708 TTCACTATTTTTATTAAAAAATTAATTTTAATCCCACTTTAACTAGAGAATACTCTCATAACTCA
1 TTCACTATTTTTATTAAAAAATTAATTTTAATCCCACATTAACTAGAGAATACACTCATAACTCA
2350773 CTTC
66 CTTC
*
2350777 TTCACTA-TTTTATTAAAAACTTAATTTTAATC
1 TTCACTATTTTTATTAAAAAATTAATTTTAATC
2350809 TCTTAAAAAA
Statistics
Matches: 149, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
68 24 0.16
69 50 0.34
70 17 0.11
71 6 0.04
73 4 0.03
74 4 0.03
75 8 0.05
76 4 0.03
77 32 0.21
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (69 bp):
TTCACTATTTTTATTAAAAAATTAATTTTAATCCCACATTAACTAGAGAATACACTCATAACTCA
CTTC
Found at i:2350814 original size:22 final size:22
Alignment explanation
Indices: 2350789--2350830 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2350779 CACTATTTTA
*
2350789 TTAAAAACTTAATTTTAATCTC
1 TTAAAAAATTAATTTTAATCTC
2350811 TTAAAAAATTAATTTTAATC
1 TTAAAAAATTAATTTTAATC
2350831 CCATATTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAAAATTAATTTTAATCTC
Found at i:2353377 original size:30 final size:30
Alignment explanation
Indices: 2353331--2353406 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
2353321 CATGTGACAT
* * *
2353331 AGCCTGTGTGTAACACACGGCCGTGCGAAC
1 AGCCCGTGTGTGACACACGGCCGTGCAAAC
*
2353361 AGCTCGTGTGTGACACACGGCCGTGCAAAC
1 AGCCCGTGTGTGACACACGGCCGTGCAAAC
*
2353391 AGCCCGAGTGTGACAC
1 AGCCCGTGTGTGACAC
2353407 GTAGTCGTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (30 bp):
AGCCCGTGTGTGACACACGGCCGTGCAAAC
Found at i:2361725 original size:73 final size:74
Alignment explanation
Indices: 2361629--2361776 Score: 289
Period size: 73 Copynumber: 2.0 Consensus size: 74
2361619 TAATATTGTG
2361629 TTTAGTTTTTAGGCTTAATTTTTATTATATATGAGCCCAATATTATATTTATTAGGTTTTATTAT
1 TTTAGTTTTTAGGCTTAATTTTTATTATATATGAGCCCAATATTATATTTATTAGGTTTTATTAT
2361694 TTTATTATC
66 TTTATTATC
2361703 TTTAGTTTTTA-GCTTAATTTTTATTATATATGAGCCCAATATTATATTTATTAGGTTTTATTAT
1 TTTAGTTTTTAGGCTTAATTTTTATTATATATGAGCCCAATATTATATTTATTAGGTTTTATTAT
2361767 TTTATTATC
66 TTTATTATC
2361776 T
1 T
2361777 ATTAATTCTG
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 63 0.85
74 11 0.15
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.57
Consensus pattern (74 bp):
TTTAGTTTTTAGGCTTAATTTTTATTATATATGAGCCCAATATTATATTTATTAGGTTTTATTAT
TTTATTATC
Found at i:2365303 original size:50 final size:52
Alignment explanation
Indices: 2365249--2365366 Score: 143
Period size: 50 Copynumber: 2.3 Consensus size: 52
2365239 TTAATAAAGT
* * * * *
2365249 CATGCATTATGTAATTCTCATGTTA-TTTAAGTTTGCATCA-TAAATT-ATGA
1 CATGCATTATGTAACTCCCATGTTAGTTAAAGGTTACATCATTAAATTAAT-A
*
2365299 CATGCATTATGTAACTCCCATGTTAGTTAAAGGTTACATCATTAAATTAATT
1 CATGCATTATGTAACTCCCATGTTAGTTAAAGGTTACATCATTAAATTAATA
*
2365351 CATGCATTAAGTAACT
1 CATGCATTATGTAACT
2365367 TATTTGTTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 23 0.40
51 12 0.21
52 21 0.36
53 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (52 bp):
CATGCATTATGTAACTCCCATGTTAGTTAAAGGTTACATCATTAAATTAATA
Found at i:2368986 original size:95 final size:95
Alignment explanation
Indices: 2368873--2369313 Score: 828
Period size: 95 Copynumber: 4.6 Consensus size: 95
2368863 ATAAAAATGG
* * * * *
2368873 GATTTTATATATTTCTTATCAGATAAAGAAATAGAATTTAATTATTATTTAAAATAGTTTTAGAT
1 GATTTTATATATTCCTTATCAGATAAGGAAATATAATTTAGTTATTATTTAAAAGAGTTTTAGAT
2368938 AAATAATAATTAAAATTCAAAATCAAAAAT
66 AAATAATAATTAAAATTCAAAATCAAAAAT
2368968 GATTTTATATATTCCTTATCAGATAAGGAAATATAATTTAGTTATTATTTAAAAGAGTTTTAGAT
1 GATTTTATATATTCCTTATCAGATAAGGAAATATAATTTAGTTATTATTTAAAAGAGTTTTAGAT
2369033 AAATAATAATTAAAATTCAAAATCAAAAAT
66 AAATAATAATTAAAATTCAAAATCAAAAAT
2369063 GATTTTATATATTCCTTATCAGATAAGGAAATATAATTTAGTTATTATTTAAAAGAGTTTTAGAT
1 GATTTTATATATTCCTTATCAGATAAGGAAATATAATTTAGTTATTATTTAAAAGAGTTTTAGAT
2369128 AAATAATAATTAAAATTCAAAATCAAAAAT
66 AAATAATAATTAAAATTCAAAATCAAAAAT
2369158 GATTTTATATATTCCTTATCAGATAAGGAAATATAATTTAGTTATTATTTAAAAGAGTTTTAGAT
1 GATTTTATATATTCCTTATCAGATAAGGAAATATAATTTAGTTATTATTTAAAAGAGTTTTAGAT
2369223 AAATAATAATTAAAATTCAAAATCAAAAAT
66 AAATAATAATTAAAATTCAAAATCAAAAAT
*
2369253 GATTTTATATATTCCTTATCAGATAAGGAAATATAATTTAGTTATTATTTAAAAGATTTTT
1 GATTTTATATATTCCTTATCAGATAAGGAAATATAATTTAGTTATTATTTAAAAGAGTTTT
2369314 TAAAATTCAA
Statistics
Matches: 340, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 340 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (95 bp):
GATTTTATATATTCCTTATCAGATAAGGAAATATAATTTAGTTATTATTTAAAAGAGTTTTAGAT
AAATAATAATTAAAATTCAAAATCAAAAAT
Found at i:2372195 original size:12 final size:12
Alignment explanation
Indices: 2372178--2372202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2372168 TAGAGACACT
2372178 ATTTTAATACTA
1 ATTTTAATACTA
2372190 ATTTTAATACTA
1 ATTTTAATACTA
2372202 A
1 A
2372203 CCTATTGGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAATACTA
Found at i:2376044 original size:22 final size:24
Alignment explanation
Indices: 2375992--2376049 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 24
2375982 TTCAAAATGT
*
2375992 TTAGAAACTAAATAATTGAAACAA
1 TTAGAAACTAAATAATTGAAAAAA
* *
2376016 -CATAAA-TAAATAATT-AAAAAA
1 TTAGAAACTAAATAATTGAAAAAA
*
2376037 TTAGAAATTAAAT
1 TTAGAAACTAAAT
2376050 TTATATTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 5 0.19
22 13 0.48
23 9 0.33
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (24 bp):
TTAGAAACTAAATAATTGAAAAAA
Found at i:2380425 original size:16 final size:16
Alignment explanation
Indices: 2380401--2380434 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2380391 ATTAAATCCT
2380401 AATTACTAAAGAAATA
1 AATTACTAAAGAAATA
* *
2380417 AATTCCTAAAGAACTA
1 AATTACTAAAGAAATA
2380433 AA
1 AA
2380435 AATAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.24
Consensus pattern (16 bp):
AATTACTAAAGAAATA
Found at i:2398376 original size:87 final size:86
Alignment explanation
Indices: 2398213--2398376 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 86
2398203 ATGAATAAGA
* * * * *
2398213 TTGAGTTCTTACTCTTAATGGATTCATAGCCCAGGATTTGGGTGGTCCTATTGAGATGGATTTGA
1 TTGAGTTATTACTCTTAATGAATTCATAGCCCAGGATTTGGGTGGTCCTATTAAGACGGACTTGA
*
2398278 TGAATTTATTGACATGTGAGG
66 TGAATTCATTGACATGTGAGG
*
2398299 TTGAGTTTATTACTCTTAATGAATTCATATCCCA-GAGTTTGGGTGGTCCTATTAAGACGGACTT
1 TTGAG-TTATTACTCTTAATGAATTCATAGCCCAGGA-TTTGGGTGGTCCTATTAAGACGGACTT
*
2398363 GATGTATTCATTGA
64 GATGAATTCATTGA
2398377 ATTTAAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
86 7 0.10
87 61 0.90
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (86 bp):
TTGAGTTATTACTCTTAATGAATTCATAGCCCAGGATTTGGGTGGTCCTATTAAGACGGACTTGA
TGAATTCATTGACATGTGAGG
Found at i:2400593 original size:8 final size:8
Alignment explanation
Indices: 2400576--2400616 Score: 52
Period size: 7 Copynumber: 5.5 Consensus size: 8
2400566 ATTTTTTTAT
2400576 AAAA-AGA
1 AAAATAGA
2400583 AAAATAG-
1 AAAATAGA
2400590 AAAATAG-
1 AAAATAGA
2400597 AAAATAGA
1 AAAATAGA
*
2400605 AAAAAAGA
1 AAAATAGA
2400613 AAAA
1 AAAA
2400617 GAGCTAGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
7 18 0.58
8 13 0.42
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (8 bp):
AAAATAGA
Found at i:2400613 original size:15 final size:14
Alignment explanation
Indices: 2400576--2400615 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
2400566 ATTTTTTTAT
2400576 AAAAAGAAAAATAGA
1 AAAAAG-AAAATAGA
*
2400591 AAATAGAAAATAGAA
1 AAAAAGAAAATAG-A
2400606 AAAAAGAAAA
1 AAAAAGAAAA
2400616 AGAGCTAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (14 bp):
AAAAAGAAAATAGA
Found at i:2402365 original size:95 final size:95
Alignment explanation
Indices: 2402202--2402395 Score: 343
Period size: 95 Copynumber: 2.0 Consensus size: 95
2402192 TGTGGAAGCA
* * *
2402202 AATTATGAGTCAATTTTAAACTTTTCTTAGGTAATTTCTCCCAAATTTTGAGCAAATTATGACCA
1 AATTATGAGCCAATTTTAAACTTTTCTTACGTAATTTCTCCCAAATTATGAGCAAATTATGACCA
2402267 CCAATTGTAAAATTAAGTGTGATTCTATCG
66 CCAATTGTAAAATTAAGTGTGATTCTATCG
*
2402297 AATTATGAGCCAATTTTAAACTTTTCTTACGTAATTTCTCCTAAATTATGAGCAAATTATGACCA
1 AATTATGAGCCAATTTTAAACTTTTCTTACGTAATTTCTCCCAAATTATGAGCAAATTATGACCA
*
2402362 CCAATTGTAAAATTAAGTGTGTTTCTATCG
66 CCAATTGTAAAATTAAGTGTGATTCTATCG
2402392 AATT
1 AATT
2402396 TTACCCATTA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (95 bp):
AATTATGAGCCAATTTTAAACTTTTCTTACGTAATTTCTCCCAAATTATGAGCAAATTATGACCA
CCAATTGTAAAATTAAGTGTGATTCTATCG
Found at i:2409766 original size:58 final size:58
Alignment explanation
Indices: 2409654--2409808 Score: 161
Period size: 58 Copynumber: 2.7 Consensus size: 58
2409644 GTCTAGTATG
* * * * * * *
2409654 TGGTACATAGTGTAAGACCACGGATGAGAGATGTCATGTAAGCATGGTATATGGTAAAA
1 TGGTA-ATAGTGTAAGACCATGGATGACAAATGCCATGGAAGCAAGGTAAATGGTAAAA
* *
2409713 TGGTAATAGTGTAAGACCATGGATGACAAATGCCATGGCAGCAAGGTAAATGGTACAA
1 TGGTAATAGTGTAAGACCATGGATGACAAATGCCATGGAAGCAAGGTAAATGGTAAAA
* * *
2409771 -GGT-ATGCAGTGTAAGACCATAGTTGACAAATGCTATGG
1 TGGTAAT--AGTGTAAGACCATGGATGACAAATGCCATGG
2409809 TAGTCAGGAA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
56 2 0.02
57 3 0.04
58 72 0.88
59 5 0.06
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.24
Consensus pattern (58 bp):
TGGTAATAGTGTAAGACCATGGATGACAAATGCCATGGAAGCAAGGTAAATGGTAAAA
Found at i:2435806 original size:16 final size:16
Alignment explanation
Indices: 2435785--2435815 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2435775 CTCCGGTATC
2435785 ATCACTAGCTGTAATA
1 ATCACTAGCTGTAATA
2435801 ATCACTAGCTGTAAT
1 ATCACTAGCTGTAAT
2435816 TTCTCAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (16 bp):
ATCACTAGCTGTAATA
Found at i:2435937 original size:184 final size:184
Alignment explanation
Indices: 2435628--2435985 Score: 671
Period size: 184 Copynumber: 1.9 Consensus size: 184
2435618 ATAACTCAGC
* * *
2435628 TAATTTCTCAATGGAGTAATCTATACATACTGGAATAAAATGTGCTGACTTTGTCAAACAATCGA
1 TAATTTCTCAAGGGAGTAATCTATACATACTGGAATAAAATGTGCTAACTTTGTCAAACAATCCA
*
2435693 CAACAACCCAAATGGCATCTTTCTTTCTCGGAGATAAGGGTAAACCCGATACAAAATCCATAGTA
66 CAACAACCCAAACGGCATCTTTCTTTCTCGGAGATAAGGGTAAACCCGATACAAAATCCATAGTA
2435758 ACCCAATCCTATTTCCACTCCGGTATCATCACTAGCTGTAATAATCACTAGCTG
131 ACCCAATCCTATTTCCACTCCGGTATCATCACTAGCTGTAATAATCACTAGCTG
2435812 TAATTTCTCAAGGGAGTAATCTATACATACTGGAATAAAATGTGCTAACTTTGTCAAACAATCCA
1 TAATTTCTCAAGGGAGTAATCTATACATACTGGAATAAAATGTGCTAACTTTGTCAAACAATCCA
*
2435877 CAACAACCCAAACGGCATCTTTCTTTCTCGGAGATAAGGGTTAACCCGATACAAAATCCATAGTA
66 CAACAACCCAAACGGCATCTTTCTTTCTCGGAGATAAGGGTAAACCCGATACAAAATCCATAGTA
2435942 ACCCAATCCTATTTCCACTCCGGTATCATCACTAGCTGTAATAA
131 ACCCAATCCTATTTCCACTCCGGTATCATCACTAGCTGTAATAA
2435986 CCCAGAAGGT
Statistics
Matches: 169, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 169 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (184 bp):
TAATTTCTCAAGGGAGTAATCTATACATACTGGAATAAAATGTGCTAACTTTGTCAAACAATCCA
CAACAACCCAAACGGCATCTTTCTTTCTCGGAGATAAGGGTAAACCCGATACAAAATCCATAGTA
ACCCAATCCTATTTCCACTCCGGTATCATCACTAGCTGTAATAATCACTAGCTG
Found at i:2444514 original size:6 final size:6
Alignment explanation
Indices: 2444503--2444545 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
2444493 AATTTATGTT
2444503 AGAATA AGAATA AGAATA AGAATA AGAATA AGAA-A AGGAATA A
1 AGAATA AGAATA AGAATA AGAATA AGAATA AGAATA A-GAATA A
2444546 AAACAATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 2 0.06
6 31 0.89
7 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (6 bp):
AGAATA
Found at i:2445930 original size:13 final size:13
Alignment explanation
Indices: 2445890--2445962 Score: 76
Period size: 13 Copynumber: 5.5 Consensus size: 13
2445880 ATGAATTATA
*
2445890 ATATGAAATGATT
1 ATATGAAATGGTT
* *
2445903 ACATAAAATGGTT
1 ATATGAAATGGTT
2445916 ATATG-AATGGATT
1 ATATGAAATGG-TT
* *
2445929 ATATAGAAATAGAT
1 ATAT-GAAATGGTT
2445943 ATATGAAATGGTT
1 ATATGAAATGGTT
2445956 ATATGAA
1 ATATGAA
2445963 GTGTCTATGC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
12 5 0.10
13 33 0.69
14 6 0.12
15 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.18, T:0.34
Consensus pattern (13 bp):
ATATGAAATGGTT
Found at i:2446794 original size:21 final size:21
Alignment explanation
Indices: 2446770--2446818 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2446760 ACTGTTTGAG
*
2446770 CACACGGGCGTATGAGGTAGC
1 CACACGGGCATATGAGGTAGC
* * *
2446791 CACATGGGCATGTGGGGTAGC
1 CACACGGGCATATGAGGTAGC
2446812 CACACGG
1 CACACGG
2446819 TCTTGGCTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.39, T:0.14
Consensus pattern (21 bp):
CACACGGGCATATGAGGTAGC
Found at i:2449034 original size:83 final size:83
Alignment explanation
Indices: 2448895--2449243 Score: 698
Period size: 83 Copynumber: 4.2 Consensus size: 83
2448885 AGGGGTGTTC
2448895 ATTCGGTTAACCGACCGGCTTCGAACCGAATTAACCATTAACCGAAAAATCATAAAAAAATTAAC
1 ATTCGGTTAACCGACCGGCTTCGAACCGAATTAACCATTAACCGAAAAATCATAAAAAAATTAAC
2448960 CGACCCCCGACCGAAAAT
66 CGACCCCCGACCGAAAAT
2448978 ATTCGGTTAACCGACCGGCTTCGAACCGAATTAACCATTAACCGAAAAATCATAAAAAAATTAAC
1 ATTCGGTTAACCGACCGGCTTCGAACCGAATTAACCATTAACCGAAAAATCATAAAAAAATTAAC
2449043 CGACCCCCGACCGAAAAT
66 CGACCCCCGACCGAAAAT
2449061 ATTCGGTTAACCGACCGGCTTCGAACCGAATTAACCATTAACCGAAAAATCATAAAAAAATTAAC
1 ATTCGGTTAACCGACCGGCTTCGAACCGAATTAACCATTAACCGAAAAATCATAAAAAAATTAAC
2449126 CGACCCCCGACCGAAAAT
66 CGACCCCCGACCGAAAAT
2449144 ATTCGGTTAACCGACCGGCTTCGAACCGAATTAACCATTAACCGAAAAATCATAAAAAAATTAAC
1 ATTCGGTTAACCGACCGGCTTCGAACCGAATTAACCATTAACCGAAAAATCATAAAAAAATTAAC
2449209 CGACCCCCGACCGAAAAT
66 CGACCCCCGACCGAAAAT
2449227 ATTCGGTTAACCGACCG
1 ATTCGGTTAACCGACCG
2449244 ATTAACCAAA
Statistics
Matches: 266, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 266 1.00
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.18
Consensus pattern (83 bp):
ATTCGGTTAACCGACCGGCTTCGAACCGAATTAACCATTAACCGAAAAATCATAAAAAAATTAAC
CGACCCCCGACCGAAAAT
Found at i:2450404 original size:29 final size:29
Alignment explanation
Indices: 2450372--2450614 Score: 163
Period size: 29 Copynumber: 8.4 Consensus size: 29
2450362 GTTGTGACCG
* * *
2450372 TCCCTTTTCATATTCCATGGTTGAAACCA
1 TCCCTTTTCATATTCGATAGTTGAAACTA
* **
2450401 TCCCTTTTCATTATT-GATAGTCGAAGTTA
1 TCCCTTTTCA-TATTCGATAGTTGAAACTA
* * * * *
2450430 T-CCTTTCTCAAATTCGAT-GGTCATCACCA
1 TCCCTTT-TCATATTCGATAGTTGA-AACTA
* * *
2450459 TCCCTTTTCATAGTT-GATGGTCGTCAAC-A
1 TCCCTTTTCATA-TTCGATAGTTG-AAACTA
* * *
2450488 TCCCTTTTCATAATCGATAGCTGAAGCTA
1 TCCCTTTTCATATTCGATAGTTGAAACTA
* * *
2450517 CCCCTTTTCATATTCAATAGTTGAAGCTA
1 TCCCTTTTCATATTCGATAGTTGAAACTA
* ** *
2450546 CCCCTTTTCATATTCGATAGCCGAAGCTA
1 TCCCTTTTCATATTCGATAGTTGAAACTA
* **
2450575 TCCCTTTTCATATTCCATAGCAGAAACTA
1 TCCCTTTTCATATTCGATAGTTGAAACTA
2450604 TCCCTTTTCAT
1 TCCCTTTTCAT
2450615 TGGTCAATGA
Statistics
Matches: 167, Mismatches: 37, Indels: 20
0.75 0.17 0.09
Matches are distributed among these distances:
28 13 0.08
29 140 0.84
30 14 0.08
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (29 bp):
TCCCTTTTCATATTCGATAGTTGAAACTA
Found at i:2450609 original size:58 final size:58
Alignment explanation
Indices: 2450487--2450614 Score: 184
Period size: 58 Copynumber: 2.2 Consensus size: 58
2450477 GGTCGTCAAC
* ** *
2450487 ATCCCTTTTCATAATCGATAGCTGAAGCTACCCCTTTTCATATTCAATAGTTGAAGCT
1 ATCCCTTTTCATAATCGATAGCCGAAGCTACCCCTTTTCATATTCAATAGCAGAAACT
* * * *
2450545 ACCCCTTTTCATATTCGATAGCCGAAGCTATCCCTTTTCATATTCCATAGCAGAAACT
1 ATCCCTTTTCATAATCGATAGCCGAAGCTACCCCTTTTCATATTCAATAGCAGAAACT
2450603 ATCCCTTTTCAT
1 ATCCCTTTTCAT
2450615 TGGTCAATGA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (58 bp):
ATCCCTTTTCATAATCGATAGCCGAAGCTACCCCTTTTCATATTCAATAGCAGAAACT
Found at i:2453920 original size:22 final size:23
Alignment explanation
Indices: 2453872--2453920 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2453862 TATTGGTATG
2453872 ATTAATGTGTCCTAATAAGTCGT
1 ATTAATGTGTCCTAATAAGTCGT
* *
2453895 -TTAATGTGTCTTAATAGGT-GT
1 ATTAATGTGTCCTAATAAGTCGT
2453916 ATTAA
1 ATTAA
2453921 AGAAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (23 bp):
ATTAATGTGTCCTAATAAGTCGT
Found at i:2463627 original size:35 final size:35
Alignment explanation
Indices: 2463573--2463695 Score: 203
Period size: 35 Copynumber: 3.5 Consensus size: 35
2463563 CCCCTTTTGA
*
2463573 GGTGTCGCCCCGAAA-GACATGTATACCATTTATAC
1 GGTGTCGCCCC-AAAGGACATGTATACCATTTACAC
2463608 GGTGTCGCCCCAAAGGACATGTATACCATTTACAC
1 GGTGTCGCCCCAAAGGACATGTATACCATTTACAC
* *
2463643 GGTGTCGCCCCGAAGGACATGTATACCATTTACAT
1 GGTGTCGCCCCAAAGGACATGTATACCATTTACAC
2463678 GGTGTCGCCCCAAAGGAC
1 GGTGTCGCCCCAAAGGAC
2463696 CAGTCCATAA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
34 3 0.04
35 80 0.96
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (35 bp):
GGTGTCGCCCCAAAGGACATGTATACCATTTACAC
Found at i:2471039 original size:18 final size:20
Alignment explanation
Indices: 2471004--2471045 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
2470994 TCTTTAGAAT
* *
2471004 TTTTTTAAAATTATTAT-AA
1 TTTTTTAAAATAAATATAAA
2471023 TTTTTTAAAA-AAATATAAA
1 TTTTTTAAAATAAATATAAA
2471042 TTTT
1 TTTT
2471046 GAAAGTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTTAAAATAAATATAAA
Found at i:2471066 original size:20 final size:21
Alignment explanation
Indices: 2471041--2471099 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
2471031 AAAAATATAA
*
2471041 ATTTTGAAAGTTTTATAAA-T
1 ATTTTGAAATTTTTATAAATT
*
2471061 ATTTTG-AATTTTTAAAAATT
1 ATTTTGAAATTTTTATAAATT
*
2471081 GTTTTGAACATTTTTATAA
1 ATTTTGAA-ATTTTTATAA
2471100 TTTGTTGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.31
20 12 0.38
21 1 0.03
22 9 0.28
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (21 bp):
ATTTTGAAATTTTTATAAATT
Found at i:2471079 original size:19 final size:20
Alignment explanation
Indices: 2471041--2471079 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2471031 AAAAATATAA
*
2471041 ATTTTGAAAGTTTTATAAAT
1 ATTTTGAAAGTTTTAAAAAT
*
2471061 ATTTTG-AATTTTTAAAAAT
1 ATTTTGAAAGTTTTAAAAAT
2471080 TGTTTTGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTTTGAAAGTTTTAAAAAT
Found at i:2476370 original size:32 final size:32
Alignment explanation
Indices: 2476334--2476397 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2476324 TAAGTGGTAG
*
2476334 GTTAAAAATATTTGAACTTGAGTTAAGCATTA
1 GTTAAAAATATTCGAACTTGAGTTAAGCATTA
*
2476366 GTTAAAAATATTCGAACTTGAGTTGAGCATTA
1 GTTAAAAATATTCGAACTTGAGTTAAGCATTA
2476398 ATGTAGAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (32 bp):
GTTAAAAATATTCGAACTTGAGTTAAGCATTA
Found at i:2477023 original size:1 final size:1
Alignment explanation
Indices: 2477019--2477044 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2477009 TTATTGATAC
2477019 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2477045 CCTGTCGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2478667 original size:30 final size:30
Alignment explanation
Indices: 2478625--2478685 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
2478615 TAACACCCCT
2478625 TTAGTCGATTCAATGACCGTCACAGATAGG
1 TTAGTCGATTCAATGACCGTCACAGATAGG
2478655 TTAGTC-AGTTCAATGACCGTCACAGATAGG
1 TTAGTCGA-TTCAATGACCGTCACAGATAGG
2478685 T
1 T
2478686 GATGTCACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (30 bp):
TTAGTCGATTCAATGACCGTCACAGATAGG
Found at i:2481745 original size:7 final size:7
Alignment explanation
Indices: 2481733--2481763 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2481723 CAAACATACA
2481733 ATTTTTC
1 ATTTTTC
2481740 ATTTTTC
1 ATTTTTC
2481747 ATTTTTC
1 ATTTTTC
2481754 ATTTTTC
1 ATTTTTC
2481761 ATT
1 ATT
2481764 CATATCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTTC
Found at i:2482675 original size:29 final size:30
Alignment explanation
Indices: 2482619--2482675 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
2482609 TAATTAAGGT
* * * *
2482619 TATATATGCTAATTTTTATTACTTTAATCA
1 TATATATACTAATTTTAATTAATCTAATCA
2482649 TATATATAC-AATTTTAATTAATCTAAT
1 TATATATACTAATTTTAATTAATCTAAT
2482676 TACAACTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.51
Consensus pattern (30 bp):
TATATATACTAATTTTAATTAATCTAATCA
Found at i:2487403 original size:96 final size:96
Alignment explanation
Indices: 2487297--2487471 Score: 269
Period size: 96 Copynumber: 1.8 Consensus size: 96
2487287 CTCTTGTTGA
* * *
2487297 ATATTTAATTGCACATTGGAAACTCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAAG
1 ATATTTAATTGCACATCGGAAACCCTCATGATCTTTTGAACTACACCAATAACATTGCACAAAAG
* *
2487362 GTGATAGCTCAATCTTATTCTCTCTATTTGG
66 GTGAGAGATCAATCTTATTCTCTCTATTTGG
* * * *
2487393 ATATTTAATTGGACATCGGAAACCCTCATGATCTTTTGAATTACACCAATAACATTTCACAATAG
1 ATATTTAATTGCACATCGGAAACCCTCATGATCTTTTGAACTACACCAATAACATTGCACAAAAG
2487458 GTGAGAGATCAATC
66 GTGAGAGATCAATC
2487472 GTACTCCTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 70 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (96 bp):
ATATTTAATTGCACATCGGAAACCCTCATGATCTTTTGAACTACACCAATAACATTGCACAAAAG
GTGAGAGATCAATCTTATTCTCTCTATTTGG
Found at i:2491932 original size:18 final size:17
Alignment explanation
Indices: 2491911--2491947 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2491901 TTTTCAATTC
2491911 TAATTTGACCCAAAATAT
1 TAATTTGACCCAAAA-AT
*
2491929 TAATTTTACCCAAAAAT
1 TAATTTGACCCAAAAAT
2491946 TA
1 TA
2491948 TTTAAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (17 bp):
TAATTTGACCCAAAAAT
Found at i:2493329 original size:31 final size:31
Alignment explanation
Indices: 2493294--2493369 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
2493284 AAATTCTGTT
* *
2493294 ATTTTAGTCACTCTGGTTTA-ATAAGTTGTCA
1 ATTTTAGTCACTCTCG-TTAGATAAGTTATCA
* *
2493325 ATTTTAGTTACTCCCGTTAGATAAGTTATCA
1 ATTTTAGTCACTCTCGTTAGATAAGTTATCA
*
2493356 ATTTTAATCACTCT
1 ATTTTAGTCACTCT
2493370 ACCGTTAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 3 0.08
31 34 0.92
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTTTAGTCACTCTCGTTAGATAAGTTATCA
Found at i:2493691 original size:13 final size:13
Alignment explanation
Indices: 2493661--2493691 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2493651 TCATATACTA
*
2493661 TTTTACTGAAAAT
1 TTTTGCTGAAAAT
2493674 TTTTGCTGAAAAT
1 TTTTGCTGAAAAT
2493687 TTTTG
1 TTTTG
2493692 GTTTAGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (13 bp):
TTTTGCTGAAAAT
Found at i:2494877 original size:100 final size:100
Alignment explanation
Indices: 2494762--2495083 Score: 439
Period size: 100 Copynumber: 3.2 Consensus size: 100
2494752 TATCCCAAAT
** * * *
2494762 ATGGTCTTACATGGGAGTTCTCATATCGAAGTCCATGTCATATCCCAGACATGGTCTTATGAGGG
1 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGAGGG
2494827 ACCTCTCATCTTGGTGCCAACGCCATGTCCCAGAC
66 ACCTCTCATCTTGGTGCCAACGCCATGTCCCAGAC
* * *
2494862 ATGGTCTTATATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGG
1 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGAGGG
* *
2494927 ACCTCTCATCTCGGTGCCAACGCCAAGTCCCAGAC
66 ACCTCTCATCTTGGTGCCAACGCCATGTCCCAGAC
* *
2494962 ATGGTCTTACATGGAAGTTCTCATAACGGTGCCCATGCCATGTCCCAGACATGGTCTTAT-ATGG
1 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGA-GG
* *
2495026 GACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCAGAC
65 GACCTCTC---ATCT---TGGTGCCAACGCCATGTCCCAGAC
*
2495068 ATGGTATTACATGGGA
1 ATGGTCTTACATGGGA
2495084 TCTCATTCCC
Statistics
Matches: 194, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
100 156 0.80
103 4 0.02
106 34 0.18
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (100 bp):
ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGAGGG
ACCTCTCATCTTGGTGCCAACGCCATGTCCCAGAC
Found at i:2495037 original size:50 final size:50
Alignment explanation
Indices: 2494744--2495083 Score: 317
Period size: 50 Copynumber: 6.7 Consensus size: 50
2494734 TCTGTACTGT
* * * * **
2494744 CAATGTCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGAAGT-C
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG--GTGC
* * * * *
2494795 C-ATGTCATATCCCAGACATGGTCTTATGA-GGGACCTCTCATCTTGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTA-CATGGGACCTCTCATATCGGTGC
* * **
2494844 CAACGCCATGTCCCAGACATGGTCTTATATGGGAGTTCTCATATCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGC
* ** *
2494894 CCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGC
* * * ** *
2494944 CAACGCCAAGTCCCAGACATGGTCTTACATGGAAGTTCTCATAACGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGC
* * *
2494994 CCATGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATAATCTCAATGATGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGC
*
2495050 CAATGCCATGTCCCAGACATGGTATTACATGGGA
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGA
2495084 TCTCATTCCC
Statistics
Matches: 234, Mismatches: 45, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
48 2 0.01
49 3 0.01
50 190 0.81
51 3 0.01
53 1 0.00
56 35 0.15
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGC
Found at i:2496666 original size:50 final size:50
Alignment explanation
Indices: 2496595--2496700 Score: 187
Period size: 50 Copynumber: 2.1 Consensus size: 50
2496585 AAACTCAAAC
2496595 AAAA-ATTTAAAAAAATCAAAAGATATATAATTGCATTATAAATTTTAAA
1 AAAACATTTAAAAAAATCAAAAGATATATAATTGCATTATAAATTTTAAA
* *
2496644 AAAACATTTAAAAAAATCAAAAGATTTATAATTGCATTGTAAATTTTAAA
1 AAAACATTTAAAAAAATCAAAAGATATATAATTGCATTATAAATTTTAAA
2496694 AAAACAT
1 AAAACAT
2496701 AAATTTATGA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
49 4 0.07
50 50 0.93
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.32
Consensus pattern (50 bp):
AAAACATTTAAAAAAATCAAAAGATATATAATTGCATTATAAATTTTAAA
Found at i:2499789 original size:20 final size:20
Alignment explanation
Indices: 2499753--2499794 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
2499743 TAACTTCTAC
2499753 TTTTTAAAATTAATTTTATAT
1 TTTTTAAAATTAATTTTA-AT
*
2499774 TTTTTAAAA-TATTTTTAAT
1 TTTTTAAAATTAATTTTAAT
2499793 TT
1 TT
2499795 ATGTATGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
21 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTAAAATTAATTTTAAT
Found at i:2500214 original size:30 final size:30
Alignment explanation
Indices: 2500180--2500247 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
2500170 TTAATTTCTA
2500180 CCAATCAGATTATGCCACGTATATAAAAGG
1 CCAATCAGATTATGCCACGTATATAAAAGG
* * * *
2500210 CCAATCATATTGTGCCACGTGTATAACAGG
1 CCAATCAGATTATGCCACGTATATAAAAGG
2500240 CCAATCAG
1 CCAATCAG
2500248 GCAACTAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (30 bp):
CCAATCAGATTATGCCACGTATATAAAAGG
Found at i:2501050 original size:22 final size:22
Alignment explanation
Indices: 2501025--2501100 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
2501015 AGAGCATTGT
2501025 AGTGCTAAACAGAGAGCACAAG
1 AGTGCTAAACAGAGAGCACAAG
** *
2501047 AGTGCTAAGTAGAGAGCAC-CG
1 AGTGCTAAACAGAGAGCACAAG
* * *
2501068 AGGTGCTGAACAGAGAGGACAAA
1 A-GTGCTAAACAGAGAGCACAAG
*
2501091 AGTACTAAAC
1 AGTGCTAAAC
2501101 CTGTACAAGT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
21 2 0.05
22 38 0.93
23 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.29, T:0.12
Consensus pattern (22 bp):
AGTGCTAAACAGAGAGCACAAG
Found at i:2504383 original size:18 final size:18
Alignment explanation
Indices: 2504347--2504382 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2504337 AATTCTAGGT
2504347 TTTTAGAAAATCTTAAAA
1 TTTTAGAAAATCTTAAAA
*
2504365 TTTTATGAAAATTTTAAA
1 TTTTA-GAAAATCTTAAA
2504383 TAATTTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTTAGAAAATCTTAAAA
Found at i:2504389 original size:21 final size:19
Alignment explanation
Indices: 2504347--2504410 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
2504337 AATTCTAGGT
*
2504347 TTTTA-GAAAATCTTAAAA
1 TTTTATGAAAATTTTAAAA
2504365 TTTTATGAAAATTTTAAATAA
1 TTTTATGAAAATTTT-AA-AA
*
2504386 TTTTATGATATATTTTTAAAA
1 TTTTATGA-A-AATTTTAAAA
2504407 TTTT
1 TTTT
2504411 CAAAGATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.13
19 8 0.21
20 2 0.05
21 16 0.41
22 3 0.08
23 5 0.13
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (19 bp):
TTTTATGAAAATTTTAAAA
Found at i:2504901 original size:20 final size:21
Alignment explanation
Indices: 2504878--2504921 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2504868 TTAAAAATTT
* *
2504878 AAAAAT-TCATAGAATTTTTA
1 AAAAATATCATAAAATTATTA
2504898 AAAAATATCATAAAATTATTA
1 AAAAATATCATAAAATTATTA
2504919 AAA
1 AAA
2504922 TTTTCATAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAAATATCATAAAATTATTA
Found at i:2506319 original size:19 final size:19
Alignment explanation
Indices: 2506282--2506325 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2506272 TAAAATTAAA
*
2506282 TAAATAATTTTTATAATTTT
1 TAAA-AATTTTAATAATTTT
2506302 TCAAAAATTTTAAT-ATTTT
1 T-AAAAATTTTAATAATTTT
2506321 TAAAA
1 TAAAA
2506326 TTTATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 9 0.41
21 3 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAAAATTTTAATAATTTT
Found at i:2508724 original size:13 final size:13
Alignment explanation
Indices: 2508698--2508736 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
2508688 AAGGCCATTG
2508698 AAGAGCAAAAAAAA
1 AAGAG-AAAAAAAA
2508712 AAGAAAGAAAAAAAA
1 AAG--AGAAAAAAAA
2508727 AAGAGAAAAA
1 AAGAGAAAAA
2508737 GGAAAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 7 0.30
14 3 0.13
15 11 0.48
16 2 0.09
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (13 bp):
AAGAGAAAAAAAA
Found at i:2515638 original size:13 final size:13
Alignment explanation
Indices: 2515620--2515653 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2515610 CAATACTTTT
* *
2515620 GAAAAGTGTTGTG
1 GAAAAGTGCTATG
2515633 GAAAAGTGCTATG
1 GAAAAGTGCTATG
2515646 GAAAAGTG
1 GAAAAGTG
2515654 ACTTTGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.24
Consensus pattern (13 bp):
GAAAAGTGCTATG
Found at i:2516078 original size:17 final size:18
Alignment explanation
Indices: 2516056--2516089 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2516046 TTCTTTATTG
2516056 CTTTTTAG-GGAAAAGCA
1 CTTTTTAGTGGAAAAGCA
2516073 CTTTTTAGTGGAAAAGC
1 CTTTTTAGTGGAAAAGC
2516090 TCATCTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (18 bp):
CTTTTTAGTGGAAAAGCA
Found at i:2519413 original size:17 final size:18
Alignment explanation
Indices: 2519391--2519428 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2519381 ATTTTAGATC
2519391 TTTTAAG-TTCAATTAGA
1 TTTTAAGTTTCAATTAGA
*
2519408 TTTTAAGTTTGAATTAGA
1 TTTTAAGTTTCAATTAGA
2519426 TTT
1 TTT
2519429 AAATCCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (18 bp):
TTTTAAGTTTCAATTAGA
Found at i:2520612 original size:39 final size:39
Alignment explanation
Indices: 2520555--2520683 Score: 159
Period size: 39 Copynumber: 3.3 Consensus size: 39
2520545 CATTTGAACA
* * *
2520555 ACTTTCAGTAGAACCAGTAGATATGGCTCGGTAGAGCAT
1 ACTTTCAGTAGAATCAGTAGGTATGGCTCGATAGAGCAT
2520594 ACTTTCAGTAGAATCAGTAGGTATGGCTCGATAGAGCAT
1 ACTTTCAGTAGAATCAGTAGGTATGGCTCGATAGAGCAT
* * * * * *
2520633 AATTTTAGTAGAATTAGTAGGTATGACACGATAGCGCAT
1 ACTTTCAGTAGAATCAGTAGGTATGGCTCGATAGAGCAT
*
2520672 ACATTTTAGTAG
1 AC-TTTCAGTAG
2520684 GTATTGCTCA
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 70 0.89
40 9 0.11
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (39 bp):
ACTTTCAGTAGAATCAGTAGGTATGGCTCGATAGAGCAT
Found at i:2528323 original size:27 final size:27
Alignment explanation
Indices: 2528282--2528636 Score: 283
Period size: 27 Copynumber: 13.1 Consensus size: 27
2528272 ATTCGTGGGC
*
2528282 AAATGATCGAAATACCCTCGAAAGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
* * * *
2528309 AAATGACCGAGATACCATTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
* *
2528336 AAATGACCAAAATACCCTC-TAAGGATA
1 AAATGACCGAAATACCCTCGAAAGG-TA
*
2528363 AAATAACCGAAATACCCTCG-AAGGATA
1 AAATGACCGAAATACCCTCGAAAGG-TA
**
2528390 ATTTGACCGAAATACCCTC-AAATGGTA
1 AAATGACCGAAATACCCTCGAAA-GGTA
** * *
2528417 AAATGACTTAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
* * * * *
2528444 AAACGATCGAAATATCTTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
*
2528471 AAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
**
2528498 AAATGAATGAAATACCCTCG-AAGGATA
1 AAATGACCGAAATACCCTCGAAAGG-TA
* ** * *
2528525 AAATTAATGAAAGACCC-CAAAAAGGTA
1 AAATGACCGAAATACCCTC-GAAAGGTA
* * * *
2528552 AAGTAACCGAAATACCTTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTA
*
2528579 AAATGACCAAAATACCCTC-AAAGGGTA
1 AAATGACCGAAATACCCTCGAAA-GGTA
** *
2528606 AAATGACTAAAATACCC-CTAAAGAGTA
1 AAATGACCGAAATACCCTCGAAAG-GTA
2528633 AAAT
1 AAAT
2528637 AATAGAAATA
Statistics
Matches: 263, Mismatches: 53, Indels: 24
0.77 0.16 0.07
Matches are distributed among these distances:
26 11 0.04
27 243 0.92
28 9 0.03
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAAGGTA
Found at i:2528349 original size:54 final size:54
Alignment explanation
Indices: 2528282--2528636 Score: 315
Period size: 54 Copynumber: 6.6 Consensus size: 54
2528272 ATTCGTGGGC
* * * *
2528282 AAATGATCGAAATACCCTCGAAAGGTAAAATGACCGAGATACCATTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTAAAATGACCGAAATACCCTCGAAGGGTA
* * * *
2528336 AAATGACCAAAATACCCTC-TAAGGATAAAATAACCGAAATACCCTCGAAGGATA
1 AAATGACCGAAATACCCTCGAAAGG-TAAAATGACCGAAATACCCTCGAAGGGTA
** ** *
2528390 ATTTGACCGAAATACCCTC-AAATGGTAAAATGACTTAAATACCCTTGAAGGGTA
1 AAATGACCGAAATACCCTCGAAA-GGTAAAATGACCGAAATACCCTCGAAGGGTA
* * * * *
2528444 AAACGATCGAAATATCTTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTAAAATGACCGAAATACCCTCGAAGGGTA
** * ** * * *
2528498 AAATGAATGAAATACCCTCG-AAGGATAAAATTAATGAAAGACCC-CAAAAAGGTA
1 AAATGACCGAAATACCCTCGAAAGG-TAAAATGACCGAAATACCCTC-GAAGGGTA
* * * * * *
2528552 AAGTAACCGAAATACCTTCGAAGGGTAAAATGACCAAAATACCCTCAAAGGGTA
1 AAATGACCGAAATACCCTCGAAAGGTAAAATGACCGAAATACCCTCGAAGGGTA
** *
2528606 AAATGACTAAAATACCC-CTAAAGAGTAAAAT
1 AAATGACCGAAATACCCTCGAAAG-GTAAAAT
2528637 AATAGAAATA
Statistics
Matches: 235, Mismatches: 58, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
53 12 0.05
54 215 0.91
55 8 0.03
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.19
Consensus pattern (54 bp):
AAATGACCGAAATACCCTCGAAAGGTAAAATGACCGAAATACCCTCGAAGGGTA
Found at i:2528430 original size:81 final size:80
Alignment explanation
Indices: 2528289--2528609 Score: 315
Period size: 81 Copynumber: 4.0 Consensus size: 80
2528279 GGCAAATGAT
* * * *
2528289 CGAAATACCCTCGAAAGGTAAAATGACCGAGATACCATTGAAGGGTAAAATGACCAAAATACCCT
1 CGAAATACCCTCG-AAGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACTAAAATACCCT
2528354 CTAAGGATAAAATAAC
65 CTAAGGATAAAATAAC
** * * *
2528370 CGAAATACCCTCGAAGGATAATTTGACCGAAATACCCTCAAATGGTAAAATGACTTAAATACCCT
1 CGAAATACCCTCGAAGG-TAAAATGACCGAAATACCCTCGAAGGGTAAAATGACTAAAATACCCT
* ** *
2528435 -TGAAGGGTAAAACGAT
65 CT-AAGGATAAAATAAC
* * * *
2528451 CGAAATATCTTCGAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGAATGAAATACCCT
1 CGAAATACCCTCGAA-GGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACTAAAATACCCT
*
2528516 CGAAGGATAAAATTAA-
65 CTAAGGATAAAA-TAAC
* * * * * * *
2528532 TGAAAGACCC-CAAAAAGGTAAAGTAACCGAAATACCTTCGAAGGGTAAAATGACCAAAATACCC
1 CGAAATACCCTC--GAAGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACTAAAATACCC
* *
2528596 TCAAAGGGTAAAAT
64 TCTAAGGATAAAAT
2528610 GACTAAAATA
Statistics
Matches: 195, Mismatches: 38, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
80 7 0.04
81 183 0.94
82 5 0.03
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.19
Consensus pattern (80 bp):
CGAAATACCCTCGAAGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACTAAAATACCCTC
TAAGGATAAAATAAC
Found at i:2528645 original size:27 final size:28
Alignment explanation
Indices: 2528576--2528650 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 28
2528566 CCTTCGAAGG
** *
2528576 GTAAAATGACCAAAATA-CCCTCAAAGG
1 GTAAAATGAATAAAATACCCCTCAAAGA
*
2528603 GTAAAATGACTAAAATACCCCT-AAAGA
1 GTAAAATGAATAAAATACCCCTCAAAGA
2528630 GTAAAAT-AATAGAAATACCCC
1 GTAAAATGAATA-AAATACCCC
2528651 CATAGGGTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
27 36 0.84
28 4 0.09
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.17
Consensus pattern (28 bp):
GTAAAATGAATAAAATACCCCTCAAAGA
Found at i:2529060 original size:34 final size:32
Alignment explanation
Indices: 2529022--2529103 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 32
2529012 TACTGCATTG
*
2529022 TACTGATACTGTATTGGGCTAAGGCTCAC--A
1 TACTGATACTGTATTGGGCTAAGGCCCACATA
2529052 T--TGATACTGTATTGGGCTAAGGCCCACACTAA
1 TACTGATACTGTATTGGGCTAAGGCCCACA-T-A
*
2529084 TACTGTTACTGTATTGGGCT
1 TACTGATACTGTATTGGGCT
2529104 TAGACCCAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 25 0.57
30 1 0.02
32 2 0.05
34 16 0.36
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (32 bp):
TACTGATACTGTATTGGGCTAAGGCCCACATA
Found at i:2529065 original size:28 final size:28
Alignment explanation
Indices: 2529023--2529089 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
2529013 ACTGCATTGT
*
2529023 ACTGATACTGTATTGGGCTAAGGCTCAC
1 ACTGATACTGTATTGGGCTAAGGCCCAC
*
2529051 ATTGATACTGTATTGGGCTAAGGCCCAC
1 ACTGATACTGTATTGGGCTAAGGCCCAC
*
2529079 ACTAATACTGT
1 ACTGATACTGT
2529090 TACTGTATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (28 bp):
ACTGATACTGTATTGGGCTAAGGCCCAC
Found at i:2529117 original size:34 final size:34
Alignment explanation
Indices: 2529056--2529122 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
2529046 CTCACATTGA
*
2529056 TACTGTATTGGGCTAAGGCCCACACTAATACTGT
1 TACTGTATTGGGCTAAGACCCACACTAATACTGT
* *
2529090 TACTGTATTGGGCTTAGACCCAGACTAATACTG
1 TACTGTATTGGGCTAAGACCCACACTAATACTG
2529123 CATGTTTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (34 bp):
TACTGTATTGGGCTAAGACCCACACTAATACTGT
Found at i:2529781 original size:26 final size:27
Alignment explanation
Indices: 2529752--2529808 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
2529742 TTATTCAGTA
*
2529752 ACAGT-CAGTGTGGGCCTTACCCCAAT
1 ACAGTACAGTGTGAGCCTTACCCCAAT
* *
2529778 ACAGTAACAGTGTGAGCCTTAGCCTAAT
1 ACAGT-ACAGTGTGAGCCTTACCCCAAT
2529806 ACA
1 ACA
2529809 TTATTAGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
28 21 0.81
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (27 bp):
ACAGTACAGTGTGAGCCTTACCCCAAT
Found at i:2535612 original size:27 final size:27
Alignment explanation
Indices: 2535574--2535950 Score: 404
Period size: 27 Copynumber: 14.0 Consensus size: 27
2535564 GATTCGTGGG
*
2535574 AAAATGACCGAAATACCCTCAAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* *
2535601 AAAATGATCGAAATACCCTTGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* **
2535628 AAAATGACCGAAATACCCTTGAAGAAT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * ** *
2535655 AAAATAACTGAAATACCCTTAAAGGAT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
2535682 AAAATGACCAAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
2535709 AAAATGACCAAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * *
2535736 AAAATGATCAAAATACCTTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
2535763 AAAATGACCGAAATACCTTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* ** *
2535790 AAAATAAATGAAATACCCTCGAAAGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* *
2535817 AAAATGACCGAAATACCCTTGAAGAG-
1 AAAATGACCGAAATACCCTCGAAGGGT
* *
2535843 AAAATGACCAAAATACCCTCTAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * * *
2535870 AAAATGATCAAAATACCC-CGAAGCGC
1 AAAATGACCGAAATACCCTCGAAGGGT
* *
2535896 AAAATAACTGAAATA-CCT-GCATAGGGT
1 AAAATGACCGAAATACCCTCG-A-AGGGT
*
2535923 AAAATGACTGAAATACCCTC-ATAGGGT
1 AAAATGACCGAAATACCCTCGA-AGGGT
2535950 A
1 A
2535951 GAATTACTAT
Statistics
Matches: 298, Mismatches: 46, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
25 3 0.01
26 39 0.13
27 253 0.85
28 3 0.01
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (27 bp):
AAAATGACCGAAATACCCTCGAAGGGT
Found at i:2536160 original size:26 final size:26
Alignment explanation
Indices: 2536131--2536211 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 26
2536121 TCTACCACAT
* *
2536131 ATACTAATACTGGTAGCTTTGCTGTG
1 ATACTATTACTGGCAGCTTTGCTGTG
* * **
2536157 ATACTGTTACTGGCAGCTTCGCTACG
1 ATACTATTACTGGCAGCTTTGCTGTG
* *
2536183 ATACTATTACTAGCAGATTTGCTGTG
1 ATACTATTACTGGCAGCTTTGCTGTG
2536209 ATA
1 ATA
2536212 TTGGTGTGTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGTG
Found at i:2536354 original size:28 final size:28
Alignment explanation
Indices: 2536314--2536368 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2536304 ACTGCATTGT
2536314 ACTGATACTGTATTGGGCTAAAGCCCAC
1 ACTGATACTGTATTGGGCTAAAGCCCAC
* *
2536342 ACTGGTACTGTATTGGGCTAAGGCCCA
1 ACTGATACTGTATTGGGCTAAAGCCCA
2536369 TATTATACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (28 bp):
ACTGATACTGTATTGGGCTAAAGCCCAC
Found at i:2537081 original size:28 final size:28
Alignment explanation
Indices: 2537040--2537110 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
2537030 GAGCCCTATT
*
2537040 CAATAACAGT-ACAGTGTGGGTCTTAACC
1 CAAT-ACAGTAACAGTGTGGGCCTTAACC
*
2537068 CAATACAGTAACAGTGTGGGCCTTAGCC
1 CAATACAGTAACAGTGTGGGCCTTAACC
* *
2537096 TAATACAGTATCAGT
1 CAATACAGTAACAGT
2537111 ACAGTGCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 5 0.13
28 33 0.87
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (28 bp):
CAATACAGTAACAGTGTGGGCCTTAACC
Found at i:2537268 original size:26 final size:26
Alignment explanation
Indices: 2537211--2537306 Score: 104
Period size: 26 Copynumber: 3.7 Consensus size: 26
2537201 CTAACACACT
* * **
2537211 AATATCGCAGCGAAGCTGCCAGTAGT
1 AATATCGCAGCAAAGCTGCGAGTAAC
* *
2537237 AGTATCGTAGCAAAGCTGCGAGTAAC
1 AATATCGCAGCAAAGCTGCGAGTAAC
*
2537263 AATATCGCAACAAAGCTGCCG-GTAAC
1 AATATCGCAGCAAAGCTG-CGAGTAAC
*
2537289 AATGTCGCAGCAAAGCTG
1 AATATCGCAGCAAAGCTG
2537307 TCAGTACAGT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 56 0.97
27 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (26 bp):
AATATCGCAGCAAAGCTGCGAGTAAC
Found at i:2545452 original size:29 final size:29
Alignment explanation
Indices: 2545419--2545475 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
2545409 CTTTGCCCCA
2545419 TTTTTAGTAATTTTTATGTTTTTGGATTC
1 TTTTTAGTAATTTTTATGTTTTTGGATTC
2545448 TTTTTAGTAATTTTTATGTTTTTGGATT
1 TTTTTAGTAATTTTTATGTTTTTGGATT
2545476 GGTATTAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.18, C:0.02, G:0.14, T:0.67
Consensus pattern (29 bp):
TTTTTAGTAATTTTTATGTTTTTGGATTC
Found at i:2545483 original size:29 final size:29
Alignment explanation
Indices: 2545422--2545483 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
2545412 TGCCCCATTT
* *
2545422 TTAGTAATTTTTATGTTTTTGGATTCTTT
1 TTAGTAATTTTTATGTTTTTGGATTCGTA
*
2545451 TTAGTAATTTTTATGTTTTTGGATTGGTA
1 TTAGTAATTTTTATGTTTTTGGATTCGTA
2545480 TTAG
1 TTAG
2545484 CTTAATCTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.19, C:0.02, G:0.18, T:0.61
Consensus pattern (29 bp):
TTAGTAATTTTTATGTTTTTGGATTCGTA
Found at i:2546289 original size:34 final size:34
Alignment explanation
Indices: 2546244--2546323 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
2546234 CTGGATACAA
* *
2546244 TGTGCTGGATGGACT-GACTTATACGGGCATATGG
1 TGTGCTGGATGGACTGGA-TCATACGAGCATATGG
* * *
2546278 TGTGCTAGATGGATTGGATCATACGAGCTTATGG
1 TGTGCTGGATGGACTGGATCATACGAGCATATGG
2546312 TGTGCTGGATGG
1 TGTGCTGGATGG
2546324 CTAATGGCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 37 0.95
35 2 0.05
ACGTcount: A:0.20, C:0.12, G:0.36, T:0.31
Consensus pattern (34 bp):
TGTGCTGGATGGACTGGATCATACGAGCATATGG
Found at i:2549913 original size:22 final size:24
Alignment explanation
Indices: 2549877--2549923 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
2549867 TATATTATTT
*
2549877 ATATAAATGATAAAAAT-AAATAG
1 ATATAAATGAAAAAAATAAAATAG
2549900 ATAT-AATGAAAAAAATAAAATAG
1 ATATAAATGAAAAAAATAAAATAG
2549923 A
1 A
2549924 AATACAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (24 bp):
ATATAAATGAAAAAAATAAAATAG
Found at i:2550766 original size:44 final size:45
Alignment explanation
Indices: 2550622--2551171 Score: 241
Period size: 44 Copynumber: 12.6 Consensus size: 45
2550612 TTTTAATCCA
* * ** ** *
2550622 CTCCACTGCAACTTCAGGAAGATAGGA-TTATCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTTAGTCTG
* * *
2550666 CTCCACTGCAACTTCAGGGAGATGAGATTTGCCATCTTTAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTTAGTCTG
*
2550711 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCCCA-C-TTAGTTTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTG-CCATCTTTAGTCTG
*
2550755 CTCCACTGCAACTTCAGGGAGATAAGA-TTAG--ATGC--GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCCAT-CTTTAGTCTG
* * * * * * *
2550796 CT-CTCTGTAACTTCAGAGAGATAAGATCTAAG--GT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCCATCTTTAGTCTG
* * * * ** *
2550839 CT-CACTACAACTTCAGCGAGATAGGA-TTACCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTTAGTCTG
* * * * *
2550882 CTCTACTGTAACTTCAGGGAGATAAAATTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTTAGTCTG
* * *
2550927 C-CTCACTGTAACTTCA-GGAGGATAAGACTAG--ATGC--GA-TCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGCCAT-CTTTAGTCTG
** * * * * *
2550968 CT-GTCTGCAACTTCAGAGAGATAAGATCTAAG--GT-TTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCCATCTTTAGTCTG
** * * ** *
2551011 CT-CACTGCAACTTCAACGAGATAGGA-TTACCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTTAGTCTG
* * * *
2551054 CTCCACTGCAATTTTAGGGAGATAAGATTTGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTTAGTCTG
2551099 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCC-TAC-TTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGCCAT-CTTTAGTCTG
* *
2551143 CTCTACTACAACTTCAGGGAGATAAGACT
1 CTCCACTGCAACTTCAGGGAGATAAGACT
2551172 CGATCTGTTA
Statistics
Matches: 387, Mismatches: 79, Indels: 80
0.71 0.14 0.15
Matches are distributed among these distances:
40 38 0.10
41 17 0.04
42 12 0.03
43 73 0.19
44 131 0.34
45 113 0.29
46 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTTAGTCTG
Found at i:2550817 original size:40 final size:40
Alignment explanation
Indices: 2550764--2550994 Score: 122
Period size: 43 Copynumber: 5.5 Consensus size: 40
2550754 GCTCCACTGC
* *
2550764 AACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTGT
1 AACTTCAGAGAGATAAGATTAGATGCAATCTGCTCTCTGT
* ** * * **
2550804 AACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCACTAC
1 AACTTCAGAGAGATAAGAT-T-A-GATGCAATCTGCTCTCTGT
* * * **
2550847 AACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCTACTGT
1 AACTTCAGAGAGATAAGATTA---GATGCAATCTGCTCT-CTGT
* * * * * *
2550891 AACTTCAGGGAGATAAAATTTGCCATCTTCAGTCTGCCTCACTGT
1 AACTTCAGAGAGATAAGATTAG--A--TGCAATCTG-CTCTCTGT
* * * *
2550936 AACTTCAG-GAGGATAAGACTAGATGCGATCTGCTGTCTGC
1 AACTTCAGAGA-GATAAGATTAGATGCAATCTGCTCTCTGT
2550976 AACTTCAGAGAGATAAGAT
1 AACTTCAGAGAGATAAGAT
2550995 CTAAGGTTTT
Statistics
Matches: 144, Mismatches: 34, Indels: 26
0.71 0.17 0.13
Matches are distributed among these distances:
40 38 0.26
41 11 0.08
42 2 0.01
43 42 0.29
44 21 0.15
45 27 0.19
46 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (40 bp):
AACTTCAGAGAGATAAGATTAGATGCAATCTGCTCTCTGT
Found at i:2550852 original size:172 final size:172
Alignment explanation
Indices: 2550627--2551127 Score: 606
Period size: 172 Copynumber: 2.9 Consensus size: 172
2550617 ATCCACTCCA
* * * * *
2550627 CTGCAACTTCAG-GAAGATAGGAT-TATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT-
1 CTGCAACTTCAGAG-AGATAAGATCTA-AGGTTTTAATCCGCT-CACTGCAACTTCAGCGAGATA
* * * *
2550689 GAGATTTGCCATCTTTAGTCTACCTC-ACTGCAACTTCA-GGAGGATAAGACTTGCCCA-CTT-A
63 G-GA-TTACCAGCTTTAATCT-CCTCTACTGCAACTTCAGGGA-GATAAAACTTG-CCATCTTCA
* *
2550750 GTTTG-CTCCACTGCAACTTCAGG-GAGATAAGATTAGATGCGATCTGCTCT
123 GTCTGCCT-CACTGCAACTTCAGGAG-GATAAGACTAGATGCGATCTGCTCT
* *
2550800 CTGTAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCACTACAACTTCAGCGAGATAGGA
1 CTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCACTGCAACTTCAGCGAGATAGGA
* * * *
2550865 TTACCGGCTTTAATCTGCTCTACTGTAACTTCAGGGAGATAAAATTTGCCATCTTCAGTCTGCCT
66 TTACCAGCTTTAATCTCCTCTACTGCAACTTCAGGGAGATAAAACTTGCCATCTTCAGTCTGCCT
* *
2550930 CACTGTAACTTCAGGAGGATAAGACTAGATGCGATCTGCTGT
131 CACTGCAACTTCAGGAGGATAAGACTAGATGCGATCTGCTCT
*
2550972 CTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCACTGCAACTTCAACGAGATAGGA
1 CTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCACTGCAACTTCAGCGAGATAGGA
* * * * * * *
2551037 TTACCGGCTTTAATCTGCTCCACTGCAATTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCT
66 TTACCAGCTTTAATCTCCTCTACTGCAACTTCAGGGAGATAAAACTTGCCATCTTCAGTCTGCCT
2551102 CACTGCAACTTCAGGAGGATAAGACT
131 CACTGCAACTTCAGGAGGATAAGACT
2551128 TGCCTACTTA
Statistics
Matches: 291, Mismatches: 28, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
170 6 0.02
171 35 0.12
172 212 0.73
173 35 0.12
174 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (172 bp):
CTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCACTGCAACTTCAGCGAGATAGGA
TTACCAGCTTTAATCTCCTCTACTGCAACTTCAGGGAGATAAAACTTGCCATCTTCAGTCTGCCT
CACTGCAACTTCAGGAGGATAAGACTAGATGCGATCTGCTCT
Found at i:2550860 original size:43 final size:43
Alignment explanation
Indices: 2550545--2551081 Score: 212
Period size: 44 Copynumber: 12.5 Consensus size: 43
2550535 CCACTCCTGG
* * * * *
2550545 TGCAACTTCAGGGAGATAAGA-CTAA--ATATGATCTGCTCTC
1 TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCTGCTCAC
* **
2550585 -GCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCACTCCAC
1 TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCTGCT-CAC
* * *
2550628 TGCAACTTCAG-GAAGATAGGAT-TATCGGCTTTAATCTGCTCCAC
1 TGCAACTTCAGAG-AGATAAGATCTA-AGGTTTTAATCTGCT-CAC
* * * **** * *
2550672 TGCAACTTCAGGGAGATGAGATTTGCCATCTTTAGTCTACCTCAC
1 TGCAACTTCAGAGAGATAAGATCTAAGGT-TTTAATCT-GCTCAC
* *** * *
2550717 TGCAACTTCAG-GAGGATAAGA-CT-TGCCCACTTAGTTTGCTCCAC
1 TGCAACTTCAGAGA-GATAAGATCTAAG--GTTTTAATCTGCT-CAC
* * *** *
2550761 TGCAACTTCAGGGAGATAAGAT-T-A-GATGCGATCTGCTCTC
1 TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCTGCTCAC
* *
2550801 TGTAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCAC
1 TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCTGCTCAC
* * * * *
2550844 TACAACTTCAGCGAGATAGGAT-TACCGGCTTTAATCTGCTCTAC
1 TGCAACTTCAGAGAGATAAGATCTA-AGGTTTTAATCTGCTC-AC
* * * * **** * *
2550888 TGTAACTTCAGGGAGATAAAATTTGCCATCTTCAGTCTGCCTCAC
1 TGCAACTTCAGAGAGATAAGATCTAAGGT-TTTAATCTG-CTCAC
* * *** **
2550933 TGTAACTTCAG-GAGGATAAGA-CT-A-GATGCGATCTGCTGTC
1 TGCAACTTCAGAGA-GATAAGATCTAAGGTTTTAATCTGCTCAC
*
2550973 TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCGCTCAC
1 TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCTGCTCAC
* * *
2551016 TGCAACTTCA-ACGAGATAGGAT-TACCGGCTTTAATCTGCTCCAC
1 TGCAACTTCAGA-GAGATAAGATCTA-AGGTTTTAATCTGCT-CAC
* * *
2551060 TGCAATTTTAGGGAGATAAGAT
1 TGCAACTTCAGAGAGATAAGAT
2551082 TTGCCATCTT
Statistics
Matches: 371, Mismatches: 92, Indels: 64
0.70 0.17 0.12
Matches are distributed among these distances:
39 19 0.05
40 45 0.12
41 17 0.05
42 14 0.04
43 87 0.23
44 126 0.34
45 58 0.16
46 5 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (43 bp):
TGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCTGCTCAC
Found at i:2550867 original size:83 final size:83
Alignment explanation
Indices: 2550758--2551039 Score: 287
Period size: 83 Copynumber: 3.3 Consensus size: 83
2550748 TAGTTTGCTC
*
2550758 CACTGCAACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGAT
1 CACTGCAACTTCAGCGAGATAAGATTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGAT
2550823 CTAAGGTTTTAATCCGCT
66 CTAAGGTTTTAATCCGCT
* * * *** *
2550841 CACTACAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCTACTGTAACTTCAGGGAGATA
1 CACTGCAACTTCAGCGAGATAAGATTA---GATGCGATCTGCTCT-CTGTAACTTCAGAGAGATA
* * **** * * *
2550906 AAATTTGCCATCTTCAGTCTGCCT
62 AGATCTAAGGT-TTTAATCCG-CT
* * * *
2550930 CACTGTAACTTCAG-GAGGATAAGACTAGATGCGATCTGCTGTCTGCAACTTCAGAGAGATAAGA
1 CACTGCAACTTCAGCGA-GATAAGATTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGA
2550994 TCTAAGGTTTTAATCCGCT
65 TCTAAGGTTTTAATCCGCT
* *
2551013 CACTGCAACTTCAACGAGATAGGATTA
1 CACTGCAACTTCAGCGAGATAAGATTA
2551040 CCGGCTTTAA
Statistics
Matches: 150, Mismatches: 41, Indels: 16
0.72 0.20 0.08
Matches are distributed among these distances:
83 46 0.31
84 8 0.05
85 22 0.15
86 21 0.14
87 23 0.15
88 8 0.05
89 22 0.15
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (83 bp):
CACTGCAACTTCAGCGAGATAAGATTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGAT
CTAAGGTTTTAATCCGCT
Found at i:2550919 original size:216 final size:216
Alignment explanation
Indices: 2550545--2550955 Score: 646
Period size: 216 Copynumber: 1.9 Consensus size: 216
2550535 CCACTCCTGG
*
2550545 TGCAACTTCAGGGAGATAAGACTAAATATGATCTGCTCTCGCAACTTCAGAGAGATAAGATCCAA
1 TGCAACTTCAGGGAGATAAGACTAAATACGATCTGCTCTCGCAACTTCAGAGAGATAAGATCCAA
* *
2550610 GGTTTTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAATCTGCTCCACTGC
66 GGTTTTAATCCACTCCACTACAACTTCAGGAAGATAGGATTACCGGCTTTAATCTGCTCCACTGC
* * *
2550675 AACTTCAGGGAGATGAGATTTGCCATCTTTAGTCTACCTCACTGCAACTTCAGGAGGATAAGACT
131 AACTTCAGGGAGATAAAATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGGATAAGACT
2550740 TGCCCACTTAGTTTGCTCCAC
196 TGCCCACTTAGTTTGCTCCAC
* * * * *
2550761 TGCAACTTCAGGGAGATAAGATTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTA
1 TGCAACTTCAGGGAGATAAGACTAAATACGATCTGCTCTC-GCAACTTCAGAGAGATAAGATCCA
* *
2550826 AGGTTTTAATCCGCT-CACTACAACTTCAGCG-AGATAGGATTACCGGCTTTAATCTGCTCTACT
65 AGGTTTTAATCCACTCCACTACAACTTCAG-GAAGATAGGATTACCGGCTTTAATCTGCTCCACT
* * *
2550889 GTAACTTCAGGGAGATAAAATTTGCCATCTTCAGTCTGCCTCACTGTAACTTCAGGAGGATAAGA
129 GCAACTTCAGGGAGATAAAATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGGATAAGA
2550954 CT
194 CT
2550956 AGATGCGATC
Statistics
Matches: 177, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
216 140 0.79
217 37 0.21
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (216 bp):
TGCAACTTCAGGGAGATAAGACTAAATACGATCTGCTCTCGCAACTTCAGAGAGATAAGATCCAA
GGTTTTAATCCACTCCACTACAACTTCAGGAAGATAGGATTACCGGCTTTAATCTGCTCCACTGC
AACTTCAGGGAGATAAAATTTGCCATCTTCAGTCTACCTCACTGCAACTTCAGGAGGATAAGACT
TGCCCACTTAGTTTGCTCCAC
Found at i:2551143 original size:89 final size:88
Alignment explanation
Indices: 2550877--2551169 Score: 276
Period size: 89 Copynumber: 3.4 Consensus size: 88
2550867 ACCGGCTTTA
* * *
2550877 ATCTGCTCTACTGTAACTTCAGGGAGATAAAATTTGCCATCTTCAGTCTGCCTCACTGTAACTTC
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* * *
2550942 AGGAGGATAAGACTAG-ATGC-G
66 AGGAGGATAAGACTTGCCTGCTT
* * * **** * * *
2550963 ATCTGCTGT-CTGCAACTTCAGAGAGATAAGATCTAAGGT-TTTAATCCG-CTCACTGCAACTTC
1 ATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* * * *
2551025 AACGA-GATAGGA-TTACCGGCTTT
66 -AGGAGGATAAGACTTGCCTGC-TT
* * *
2551048 AATCTGCTCCACTGCAATTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
1 -ATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
*
2551113 CAGGAGGATAAGACTTGCCTACTT
65 CAGGAGGATAAGACTTGCCTGCTT
*
2551137 AGTCTGCTCTACTACAACTTCAGGGAGATAAGA
1 A-TCTGCTCTACTGCAACTTCAGGGAGATAAGA
2551170 CTCGATCTGT
Statistics
Matches: 154, Mismatches: 42, Indels: 19
0.72 0.20 0.09
Matches are distributed among these distances:
82 1 0.01
83 21 0.14
84 9 0.06
85 22 0.14
86 15 0.10
87 22 0.14
88 10 0.06
89 49 0.32
90 5 0.03
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (88 bp):
ATCTGCTCTACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
AGGAGGATAAGACTTGCCTGCTT
Found at i:2563922 original size:40 final size:39
Alignment explanation
Indices: 2563850--2563936 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 39
2563840 ATAAATGCGC
* *
2563850 ATAAAAAATAAATATATATTTTCAAAAATAATT-GCAAAA
1 ATAAAAAATAAAAATACATTTTCAAAAATAATTAG-AAAA
* *
2563889 ATAAAAAATAAAAATTACATTATT-AAAATTAATTAGGAAA
1 ATAAAAAATAAAAA-TACATT-TTCAAAAATAATTAGAAAA
2563929 ATAAAAAA
1 ATAAAAAA
2563937 AACTAAATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 13 0.32
40 25 0.61
41 3 0.07
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.29
Consensus pattern (39 bp):
ATAAAAAATAAAAATACATTTTCAAAAATAATTAGAAAA
Found at i:2568119 original size:18 final size:19
Alignment explanation
Indices: 2568096--2568135 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
2568086 ATTTAATATT
2568096 AAAGTGATTAAGTTTAA-C
1 AAAGTGATTAAGTTTAATC
2568114 AAAGTGATTAAGTTTAATC
1 AAAGTGATTAAGTTTAATC
2568133 AAA
1 AAA
2568136 ATTGAACTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (19 bp):
AAAGTGATTAAGTTTAATC
Found at i:2571704 original size:71 final size:71
Alignment explanation
Indices: 2571615--2571785 Score: 202
Period size: 71 Copynumber: 2.4 Consensus size: 71
2571605 GGGAATTTTG
* * * *
2571615 TGACACCTAACTTTGAACCAAGAGGGGAAACAAAT-AACCGTTGATGTCGCAACAACCACCACTC
1 TGACATCTAACTTTGAACCAAGAGGGGAAAC-AATCAACCATCGATGTCGCAACAACAACCACTC
*
2571679 TATGTCA
65 CATGTCA
* * * *
2571686 TGACATCTAACTTCGAACCTAAAAGGGG-AACATTCAACCATCGATGTCGCGACAACAACCACTC
1 TGACATCTAACTTTGAACC-AAGAGGGGAAACAATCAACCATCGATGTCGCAACAACAACCACTC
2571750 CATGTCA
65 CATGTCA
* * *
2571757 CGATATCAAACTTTGAACCAAGAGGGGAA
1 TGACATCTAACTTTGAACCAAGAGGGGAA
2571786 GCATTCAGTG
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
70 9 0.11
71 67 0.81
72 7 0.08
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (71 bp):
TGACATCTAACTTTGAACCAAGAGGGGAAACAATCAACCATCGATGTCGCAACAACAACCACTCC
ATGTCA
Found at i:2571807 original size:71 final size:71
Alignment explanation
Indices: 2571661--2571810 Score: 158
Period size: 71 Copynumber: 2.1 Consensus size: 71
2571651 ACCGTTGATG
* * * * *
2571661 TCGCAACAACCACCACTCTATGTCATGACATCTAACTTCGAACCTAAAAGGGGAACATTCAACCA
1 TCGCGACAACAACCACTCCATGTCACGACATCAAACTTCGAACCTAAAAGGGGAACATTCAACCA
* *
2571726 TCGATG
66 TCAATA
* * * ***
2571732 TCGCGACAACAACCACTCCATGTCACGATATCAAACTTTGAACC-AAGAGGGGAAGCATTCAGTG
1 TCGCGACAACAACCACTCCATGTCACGACATCAAACTTCGAACCTAAAAGGGGAA-CATTCAACC
*
2571796 TTCAATA
65 ATCAATA
2571803 TCGCGACA
1 TCGCGACA
2571811 CCAGCTATAA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
70 9 0.14
71 55 0.86
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.21
Consensus pattern (71 bp):
TCGCGACAACAACCACTCCATGTCACGACATCAAACTTCGAACCTAAAAGGGGAACATTCAACCA
TCAATA
Found at i:2574586 original size:2 final size:2
Alignment explanation
Indices: 2574574--2574615 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
2574564 TAAAAATGAG
* * *
2574574 GA GA GA CA GA GA GA GA GA GA AA GA GA GA GA GA GA AA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2574616 TTTGTCCCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.55, C:0.02, G:0.43, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2574593 original size:14 final size:14
Alignment explanation
Indices: 2574574--2574615 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
2574564 TAAAAATGAG
*
2574574 GAGAGACAGAGAGA
1 GAGAGAAAGAGAGA
2574588 GAGAGAAAGAGAGA
1 GAGAGAAAGAGAGA
2574602 GAGAGAAAGAGAGA
1 GAGAGAAAGAGAGA
2574616 TTTGTCCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.43, T:0.00
Consensus pattern (14 bp):
GAGAGAAAGAGAGA
Found at i:2575375 original size:39 final size:39
Alignment explanation
Indices: 2575321--2575398 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
2575311 CATAGGAATT
2575321 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
*
2575360 TATTCATGAAGTCTAAAAATTAAAACTAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
2575399 AATTAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (39 bp):
TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
Found at i:2577215 original size:14 final size:13
Alignment explanation
Indices: 2577197--2577235 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2577187 ATGAAAATCC
*
2577197 CAAAAAACAAATA
1 CAAAAAAAAAATA
*
2577210 CTAAAAAAAAAAAA
1 C-AAAAAAAAAATA
2577224 CAAAAAAAAAAT
1 CAAAAAAAAAAT
2577236 TACAGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.82, C:0.10, G:0.00, T:0.08
Consensus pattern (13 bp):
CAAAAAAAAAATA
Found at i:2585580 original size:14 final size:14
Alignment explanation
Indices: 2585561--2585591 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2585551 CATGAGTTAT
*
2585561 ATAATATCAAAATA
1 ATAATAACAAAATA
2585575 ATAATAACAAAATA
1 ATAATAACAAAATA
2585589 ATA
1 ATA
2585592 TCAATATAAA
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:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAATAACAAAATA
Found at i:2594546 original size:13 final size:15
Alignment explanation
Indices: 2594523--2594554 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2594513 TTTAAATGGA
2594523 AATATGTTAATT-AT
1 AATATGTTAATTAAT
2594537 AATA-GTTAATTAAT
1 AATATGTTAATTAAT
2594551 AATA
1 AATA
2594555 AAATAGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (15 bp):
AATATGTTAATTAAT
Found at i:2617120 original size:50 final size:50
Alignment explanation
Indices: 2617039--2617215 Score: 192
Period size: 50 Copynumber: 3.4 Consensus size: 50
2617029 NNNNNNNGAT
** * * *
2617039 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTAGGTGCCAATGCCATGTCCCAGAC
** * *
2617089 ATGGTCTTACGGGGGACCTCTCATCTAGGTGCCAATGTCATGTCCCAGAT
1 ATGGTCTTACATGGGACCTCTCATCTAGGTGCCAATGCCATGTCCCAGAC
* *
2617139 ATGGTCTTACATGGGACCTCTCATAACCTCAATGATGCCAATGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCAT---CT--A-GGTGCCAATGCCATGTCCCAGAC
*
2617195 ATGGTCTTACATGGGATCTCT
1 ATGGTCTTACATGGGACCTCT
2617216 TTACCCAAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
50 63 0.60
53 2 0.02
55 1 0.01
56 39 0.37
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTAGGTGCCAATGCCATGTCCCAGAC
Found at i:2622299 original size:39 final size:40
Alignment explanation
Indices: 2622256--2622362 Score: 128
Period size: 45 Copynumber: 2.6 Consensus size: 40
2622246 TTTTCCATTA
*
2622256 TGCTATTACACCTCTATTCCATTCAACCAAACACA-AGA-T
1 TGCTATTACGCCTCTATTCCATTCAACCAAACA-ATAGATT
*
2622295 TGCTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGATT
1 TGCTATTACGCCTCTATT-C----CATTCAACCAAACAATAGATT
2622340 TGCTATTACGCCTCTATTCCATT
1 TGCTATTACGCCTCTATTCCATT
2622363 ACGCCTCTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
39 17 0.29
40 5 0.08
43 1 0.02
44 17 0.29
45 19 0.32
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.35
Consensus pattern (40 bp):
TGCTATTACGCCTCTATTCCATTCAACCAAACAATAGATT
Found at i:2622352 original size:45 final size:44
Alignment explanation
Indices: 2622275--2622364 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 44
2622265 ACCTCTATTC
2622275 CATTCAACCAAACACAAGATTGCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTGCTATTACGCCTCTATTCCATTA
*
2622319 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACA-AGA-TTGCTATTACGCCTCTATTCCATTA
2622364 C
1 C
2622365 GCCTCTAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.37
45 26 0.60
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTGCTATTACGCCTCTATTCCATTA
Found at i:2622365 original size:16 final size:16
Alignment explanation
Indices: 2622344--2622390 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
2622334 TTGATTTGCT
2622344 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
2622360 ATTACGCCTCTAATCC
1 ATTACGCCTCTATTCC
*
2622376 ATTACGCCTATATTC
1 ATTACGCCTCTATTC
2622391 TAATACAGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:2634459 original size:25 final size:26
Alignment explanation
Indices: 2634420--2634527 Score: 113
Period size: 25 Copynumber: 4.3 Consensus size: 26
2634410 TCATGTACAT
2634420 GTATGCTCA-TACGAGCTATGAG-TCG
1 GTATGCTCACT-CGAGCTATGAGATCG
2634445 GTATGCTCACTCGAG-T-TGTAGATCG
1 GTATGCTCACTCGAGCTATG-AGATCG
2634470 GTATGCTCACTCGAGCTAT-AGATCG
1 GTATGCTCACTCGAGCTATGAGATCG
* *
2634495 GTATGCTCTCAT-GAGCTAT-AAATCG
1 GTATGCTCAC-TCGAGCTATGAGATCG
*
2634520 ATATGCTC
1 GTATGCTC
2634528 TTATAAGCTA
Statistics
Matches: 74, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
23 2 0.03
24 3 0.04
25 65 0.88
26 3 0.04
27 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (26 bp):
GTATGCTCACTCGAGCTATGAGATCG
Found at i:2634560 original size:24 final size:25
Alignment explanation
Indices: 2634482--2634560 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
2634472 ATGCTCACTC
* *
2634482 GAGCTATAGATCGGTATGCTCTCAT
1 GAGCTATAAATCGATATGCTCTCAT
*
2634507 GAGCTATAAATCGATATGCTCTTAT
1 GAGCTATAAATCGATATGCTCTCAT
* * * *
2634532 AAGCTATAAATTG-TTTGCTCTCAC
1 GAGCTATAAATCGATATGCTCTCAT
2634556 GAGCT
1 GAGCT
2634561 GTGGAGTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 12 0.27
25 33 0.73
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (25 bp):
GAGCTATAAATCGATATGCTCTCAT
Found at i:2638610 original size:26 final size:26
Alignment explanation
Indices: 2638566--2638634 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
2638556 TTTACATCGT
* *
2638566 TGCTCACATGAGCTATGAAATGGGCC
1 TGCTCACACGAGCTGTGAAATGGGCC
* * *
2638592 TGCTCACACGAGTTGTGAAATTGGTC
1 TGCTCACACGAGCTGTGAAATGGGCC
*
2638618 TACTCACACGAGCTGTG
1 TGCTCACACGAGCTGTG
2638635 GGTCAGAATG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGGCC
Found at i:2639874 original size:81 final size:82
Alignment explanation
Indices: 2639767--2639931 Score: 323
Period size: 81 Copynumber: 2.0 Consensus size: 82
2639757 CTTTTTACTT
2639767 AATTAAGCATACAAACGTCAAAATTTCTTAACGAATTTTTAATATGAAAGTACTAACATCCCATA
1 AATTAAGCATACAAACGTCAAAATTTCTTAACGAATTTTTAATATGAAAGTACTAACATCCCATA
2639832 GATATTAAAATAATAAA
66 GATATTAAAATAATAAA
2639849 AATTAAGCATAC-AACGTCAAAATTTCTTAACGAATTTTTAATATGAAAGTACTAACATCCCATA
1 AATTAAGCATACAAACGTCAAAATTTCTTAACGAATTTTTAATATGAAAGTACTAACATCCCATA
2639913 GATATTAAAATAATAAA
66 GATATTAAAATAATAAA
2639930 AA
1 AA
2639932 AATAATAATT
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 71 0.86
82 12 0.14
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.30
Consensus pattern (82 bp):
AATTAAGCATACAAACGTCAAAATTTCTTAACGAATTTTTAATATGAAAGTACTAACATCCCATA
GATATTAAAATAATAAA
Found at i:2642035 original size:57 final size:55
Alignment explanation
Indices: 2641957--2642120 Score: 168
Period size: 56 Copynumber: 2.9 Consensus size: 55
2641947 AACAACTTAT
* * ** * * *
2641957 AACACCCTTTTTAAAAACTTAATTTTAGTAATAAATAACAATGGACAACAGTGATTA
1 AACACCCTTTTTGACAACTTAATTCCAATAATAAATAACAATGGACAACA--AACTA
* * * *
2642014 AACACCCTTTTTGACAGCTTAATTCCAATAATAAAGAA-AACTGGATAGCAAACTA
1 AACACCCTTTTTGACAACTTAATTCCAATAATAAATAACAA-TGGACAACAAACTA
**
2642069 AACACCCCTTTTTGACATTTTAATTCCAATAATAAATAACAATGGACAACAA
1 AACA-CCCTTTTTGACAACTTAATTCCAATAATAAATAACAATGGACAACAA
2642121 CAATTAAACC
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
55 7 0.08
56 41 0.47
57 40 0.45
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.29
Consensus pattern (55 bp):
AACACCCTTTTTGACAACTTAATTCCAATAATAAATAACAATGGACAACAAACTA
Found at i:2642288 original size:69 final size:69
Alignment explanation
Indices: 2642201--2642455 Score: 359
Period size: 69 Copynumber: 3.7 Consensus size: 69
2642191 CATTGCTACC
* * *
2642201 TCAATTGAAACATGTATTTTATACCACTAAAATGACATGGTAATGTCTTAAAATGGACAACATTA
1 TCAATTGAAACATATATTTTATACCACTAAAATGACATGATAATGTCCTAAAATGGACAACATTA
2642266 AACT
66 AACT
* * * * *
2642270 TCTATTGAAACATATATTTTATACAACTAAAATGACATGATAATATCCCAAAATGGATAACATTA
1 TCAATTGAAACATATATTTTATACCACTAAAATGACATGATAATGTCCTAAAATGGACAACATTA
2642335 AACT
66 AACT
* * *
2642339 TCAATTGAAACATATATTTTATACCACCAAAATGACATGACAATGTCCTAAAATAGACAACATTA
1 TCAATTGAAACATATATTTTATACCACTAAAATGACATGATAATGTCCTAAAATGGACAACATTA
*
2642404 AAAT
66 AACT
* * *
2642408 TCAATTGAAACATATATTTTATA-GAATCAAAATGACATTATAATGTCC
1 TCAATTGAAACATATATTTTATACCACT-AAAATGACATGATAATGTCC
2642456 AACTATGGCA
Statistics
Matches: 163, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
68 1 0.01
69 162 0.99
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (69 bp):
TCAATTGAAACATATATTTTATACCACTAAAATGACATGATAATGTCCTAAAATGGACAACATTA
AACT
Found at i:2642371 original size:138 final size:138
Alignment explanation
Indices: 2642201--2642451 Score: 396
Period size: 138 Copynumber: 1.8 Consensus size: 138
2642191 CATTGCTACC
* * ** * *
2642201 TCAATTGAAACATGTATTTTATACCACTAAAATGACATGGTAATGTCTTAAAATGGACAACATTA
1 TCAATTGAAACATATATTTTATACCACCAAAATGACATGACAATGTCCTAAAATAGACAACATTA
* *
2642266 AACTTCTATTGAAACATATATTTTATACAA-CTAAAATGACATGATAATATCCCAAAATGGATAA
66 AAATTCAATTGAAACATATATTTTATACAATC-AAAATGACATGATAATATCCCAAAATGGATAA
2642330 CATTAAACT
130 CATTAAACT
2642339 TCAATTGAAACATATATTTTATACCACCAAAATGACATGACAATGTCCTAAAATAGACAACATTA
1 TCAATTGAAACATATATTTTATACCACCAAAATGACATGACAATGTCCTAAAATAGACAACATTA
* *
2642404 AAATTCAATTGAAACATATATTTTATAGAATCAAAATGACATTATAAT
66 AAATTCAATTGAAACATATATTTTATACAATCAAAATGACATGATAAT
2642452 GTCCAACTAT
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
138 101 0.99
139 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.31
Consensus pattern (138 bp):
TCAATTGAAACATATATTTTATACCACCAAAATGACATGACAATGTCCTAAAATAGACAACATTA
AAATTCAATTGAAACATATATTTTATACAATCAAAATGACATGATAATATCCCAAAATGGATAAC
ATTAAACT
Found at i:2647206 original size:14 final size:14
Alignment explanation
Indices: 2647187--2647220 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2647177 AGAAACCCTT
2647187 AGTAAATAAGGATC
1 AGTAAATAAGGATC
2647201 AGTAAATAAGGATC
1 AGTAAATAAGGATC
*
2647215 AATAAA
1 AGTAAA
2647221 ATGCGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.21
Consensus pattern (14 bp):
AGTAAATAAGGATC
Found at i:2670474 original size:20 final size:21
Alignment explanation
Indices: 2670449--2670496 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
2670439 GATGCATAAC
2670449 AGAGGCACCAAAGTGCAGA-A
1 AGAGGCACCAAAGTGCAGACA
* *
2670469 AGAGGCACCGAAGTGTAGACA
1 AGAGGCACCAAAGTGCAGACA
2670490 A-AGGCAC
1 AGAGGCAC
2670497 TGGAGTGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.42, C:0.21, G:0.31, T:0.06
Consensus pattern (21 bp):
AGAGGCACCAAAGTGCAGACA
Found at i:2670823 original size:15 final size:17
Alignment explanation
Indices: 2670798--2670829 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2670788 AACAAATAGA
2670798 AAACAATAT-AATTTAT
1 AAACAATATAAATTTAT
2670814 AAAC-ATATAAATTTAT
1 AAACAATATAAATTTAT
2670830 TCAATAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
AAACAATATAAATTTAT
Found at i:2674748 original size:26 final size:27
Alignment explanation
Indices: 2674696--2674762 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
2674686 TGTACACCTT
*
2674696 TTACTGAAATACCCCTGATGGATAAAA
1 TTACCGAAATACCCCTGATGGATAAAA
*
2674723 TTACCGAAATACCCC-GATGGGTAAAA
1 TTACCGAAATACCCCTGATGGATAAAA
* *
2674749 TGACCAAAATACCC
1 TTACCGAAATACCC
2674763 TTTAGGGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (27 bp):
TTACCGAAATACCCCTGATGGATAAAA
Found at i:2674848 original size:54 final size:54
Alignment explanation
Indices: 2674703--2675139 Score: 538
Period size: 54 Copynumber: 8.1 Consensus size: 54
2674693 CTTTTACTGA
* * * * * **
2674703 AATACCCCTG-ATGGATAAAATTACCGAAATACCCCGAT-GGGTAAAATGACCAA
1 AATACCCCTGTA-GGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGT
* * * *
2674756 AATA-CCCTTTAGGGTAAAATGACCGTAATGTCCCTGTAGGGTAAAATGACCAT
1 AATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGT
* * * * * *
2674809 AATACCCCTATAAGGTAATATGACCGTAATGCCCATGTAGGGTAAAATAACCGT
1 AATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGT
* * *
2674863 AATACCCCTGTAGGGTAAAATGACCATAATGCCCCTATAGGGTAAAATAACTGT
1 AATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGT
* *
2674917 AATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTATAGGGTAAAATGATCGT
1 AATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGT
* ** *
2674971 AATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTGCAGGGTAAAATGACTGT
1 AATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGT
* ** * * *
2675025 AATACCCTTGTAGCATAAAATGACCATAATGCCCCTATAGGGTAAACTGATCGT
1 AATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGT
* *
2675079 AATACCCCTATAGGGTAAAATGACCGTAATGCCCTTATAGGGTAAAATGACCGT
1 AATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGT
2675133 AATACCC
1 AATACCC
2675140 TTGAGGTCAA
Statistics
Matches: 331, Mismatches: 50, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
52 23 0.07
53 23 0.07
54 285 0.86
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (54 bp):
AATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGT
Found at i:2675141 original size:27 final size:27
Alignment explanation
Indices: 2674703--2675139 Score: 466
Period size: 27 Copynumber: 16.3 Consensus size: 27
2674693 CTTTTACTGA
* * *
2674703 AATACCCCTGAT-GGATAAAATTACCGA
1 AATACCCCT-ATAGGGTAAAATGACCGT
* **
2674730 AATACCCCGAT-GGGTAAAATGACCAA
1 AATACCCCTATAGGGTAAAATGACCGT
*
2674756 AATA-CCCTTTAGGGTAAAATGACCGT
1 AATACCCCTATAGGGTAAAATGACCGT
** * *
2674782 AATGTCCCTGTAGGGTAAAATGACCAT
1 AATACCCCTATAGGGTAAAATGACCGT
* *
2674809 AATACCCCTATAAGGTAATATGACCGT
1 AATACCCCTATAGGGTAAAATGACCGT
* * * *
2674836 AATGCCCATGTAGGGTAAAATAACCGT
1 AATACCCCTATAGGGTAAAATGACCGT
* *
2674863 AATACCCCTGTAGGGTAAAATGACCAT
1 AATACCCCTATAGGGTAAAATGACCGT
* * *
2674890 AATGCCCCTATAGGGTAAAATAACTGT
1 AATACCCCTATAGGGTAAAATGACCGT
* *
2674917 AATACCCCTGTAGGGTAAAATGATCGT
1 AATACCCCTATAGGGTAAAATGACCGT
* *
2674944 AATGCCCCTATAGGGTAAAATGATCGT
1 AATACCCCTATAGGGTAAAATGACCGT
* *
2674971 AATACCCCTGTAGGGTAAAATGATCGT
1 AATACCCCTATAGGGTAAAATGACCGT
* ** *
2674998 AATGCCCCTGCAGGGTAAAATGACTGT
1 AATACCCCTATAGGGTAAAATGACCGT
* * ** *
2675025 AATACCCTTGTAGCATAAAATGACCAT
1 AATACCCCTATAGGGTAAAATGACCGT
* * *
2675052 AATGCCCCTATAGGGTAAACTGATCGT
1 AATACCCCTATAGGGTAAAATGACCGT
2675079 AATACCCCTATAGGGTAAAATGACCGT
1 AATACCCCTATAGGGTAAAATGACCGT
* *
2675106 AATGCCCTTATAGGGTAAAATGACCGT
1 AATACCCCTATAGGGTAAAATGACCGT
2675133 AATACCC
1 AATACCC
2675140 TTGAGGTCAA
Statistics
Matches: 342, Mismatches: 66, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
25 4 0.01
26 34 0.10
27 304 0.89
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (27 bp):
AATACCCCTATAGGGTAAAATGACCGT
Found at i:2675431 original size:32 final size:32
Alignment explanation
Indices: 2675375--2675616 Score: 324
Period size: 32 Copynumber: 7.6 Consensus size: 32
2675365 GCTACGATGC
* *
2675375 TACTGATGGCCTTGTGCC-AGTTATATTACCGT
1 TACTGATGGCTTTGTGCCGA-TCATATTACCGT
* * *
2675407 TATTGATGGCTTTGTACCGATTATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
2675439 TATTGATGGCTTTGTACCGGTCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
2675471 TACTGATGGCTTTGTGTCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
2675503 TACTGATGGCTTTGTGTCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
2675535 TACTGATGGCTTTGTGTCGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * *
2675567 TACTGATGGCTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
2675599 TACTGATGGCTTTGTGCC
1 TACTGATGGCTTTGTGCC
2675617 AAAAATATTA
Statistics
Matches: 192, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
32 191 0.99
33 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:2675663 original size:22 final size:21
Alignment explanation
Indices: 2675633--2675696 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
2675623 ATTACTATAC
*
2675633 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTCT
* * *
2675655 TTATAGCTTATAGCTATCCTCT
1 TTATGGCTT-TAGCCATTCTCT
2675677 TTATGGCTCTTAGCCATTCT
1 TTATGGCT-TTAGCCATTCT
2675697 AACTACTGGC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTCT
Found at i:2678801 original size:27 final size:27
Alignment explanation
Indices: 2678763--2678874 Score: 140
Period size: 27 Copynumber: 4.1 Consensus size: 27
2678753 AAAGGTTGTT
*
2678763 AAATTACCAAAATACCCCTGATGGGTA
1 AAATTATCAAAATACCCCTGATGGGTA
*
2678790 AAATTA-CTAAAATACCCCCGATGGGTA
1 AAATTATC-AAAATACCCCTGATGGGTA
*
2678817 AAATTATCGAAATA-CCCTCGATGGGTA
1 AAATTATCAAAATACCCCT-GATGGGTA
*
2678844 AAATTATCAAATTACCCCTG-TAGGGTA
1 AAATTATCAAAATACCCCTGAT-GGGTA
2678871 AAAT
1 AAAT
2678875 GAACCTAATG
Statistics
Matches: 75, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
26 5 0.07
27 65 0.87
28 5 0.07
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (27 bp):
AAATTATCAAAATACCCCTGATGGGTA
Found at i:2678894 original size:27 final size:28
Alignment explanation
Indices: 2678858--2679207 Score: 359
Period size: 27 Copynumber: 13.0 Consensus size: 28
2678848 TATCAAATTA
2678858 CCCCTGTAGGGTAAAATGAACC-TAATG
1 CCCCTGTAGGGTAAAATGAACCGTAATG
** * *
2678885 TTCCTATAGGGTAAAAT-AACCGTAATA
1 CCCCTGTAGGGTAAAATGAACCGTAATG
* *
2678912 CCCCTATAGGGTAAAATG-ACCGTGATG
1 CCCCTGTAGGGTAAAATGAACCGTAATG
* *
2678939 ACCCTGTATGGTAAAAT-AACCGTAATG
1 CCCCTGTAGGGTAAAATGAACCGTAATG
* * *
2678966 TCCTTGTAGGGTAAAAT-AATCGTAATG
1 CCCCTGTAGGGTAAAATGAACCGTAATG
* *
2678993 CCCCTGTAGGTTTAAATG-ACCGTAATG
1 CCCCTGTAGGGTAAAATGAACCGTAATG
* * *
2679020 CCCCTGTAGGGTAAAATG-ATCATAATA
1 CCCCTGTAGGGTAAAATGAACCGTAATG
*
2679047 CCCCTATAGGGTAAAATG-ACCGTAATG
1 CCCCTGTAGGGTAAAATGAACCGTAATG
* * * *
2679074 CCCTTTTAGGATAAAATG-ACCGTAATA
1 CCCCTGTAGGGTAAAATGAACCGTAATG
*
2679101 CCCCTGTAGGGTAAAAT-AACCATAATG
1 CCCCTGTAGGGTAAAATGAACCGTAATG
* *
2679128 CCCCTGTATGGTAAAATGATA--GTAATA
1 CCCCTGTAGGGTAAAATGA-ACCGTAATG
*
2679155 CCCCTGTAGGGTCAAATG-ACCGTAATG
1 CCCCTGTAGGGTAAAATGAACCGTAATG
*
2679182 CCCCTGTAGGGTAAAAT-AACTGTAAT
1 CCCCTGTAGGGTAAAATGAACCGTAAT
2679208 ACCCTCGAGG
Statistics
Matches: 266, Mismatches: 47, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.00
26 4 0.02
27 259 0.97
28 1 0.00
29 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Consensus pattern (28 bp):
CCCCTGTAGGGTAAAATGAACCGTAATG
Found at i:2678952 original size:54 final size:54
Alignment explanation
Indices: 2678858--2679211 Score: 397
Period size: 54 Copynumber: 6.6 Consensus size: 54
2678848 TATCAAATTA
*** * *
2678858 CCCCTGTAGGGTAAAATGAACC-TAATGTTCCTATAGGGTAAAATAACCGTAATA
1 CCCCTGTAGGGTAAAATG-ACCGTAATACCCCTGTAGGGTAAAATAACCGTAATG
* * *
2678912 CCCCTATAGGGTAAAATGACCGTGATGA-CCCTGTATGGTAAAATAACCGTAATG
1 CCCCTGTAGGGTAAAATGACCGTAAT-ACCCCTGTAGGGTAAAATAACCGTAATG
* * * * * * * *
2678966 TCCTTGTAGGGTAAAATAATCGTAATGCCCCTGTAGGTTTAAATGACCGTAATG
1 CCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATAACCGTAATG
* * * *
2679020 CCCCTGTAGGGTAAAATGATCATAATACCCCTATAGGGTAAAATGACCGTAATG
1 CCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATAACCGTAATG
* * * *
2679074 CCCTTTTAGGATAAAATGACCGTAATACCCCTGTAGGGTAAAATAACCATAATG
1 CCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATAACCGTAATG
* ** * *
2679128 CCCCTGTATGGTAAAATGATAGTAATACCCCTGTAGGGTCAAATGACCGTAATG
1 CCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATAACCGTAATG
* *
2679182 CCCCTGTAGGGTAAAATAACTGTAATACCC
1 CCCCTGTAGGGTAAAATGACCGTAATACCC
2679212 TCGAGGTTAA
Statistics
Matches: 250, Mismatches: 47, Indels: 6
0.83 0.16 0.02
Matches are distributed among these distances:
53 3 0.01
54 247 0.99
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (54 bp):
CCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATAACCGTAATG
Found at i:2679242 original size:23 final size:23
Alignment explanation
Indices: 2679216--2679261 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2679206 ATACCCTCGA
* *
2679216 GGTTAAATGATTGATTTTTCTGT
1 GGTTAAATGACTGATTTGTCTGT
2679239 GGTTAAATGACTGATTTGTCTGT
1 GGTTAAATGACTGATTTGTCTGT
2679262 CAGCTTTGCT
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:0.22, C:0.07, G:0.24, T:0.48
Consensus pattern (23 bp):
GGTTAAATGACTGATTTGTCTGT
Done.