Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008739.1 Hibiscus syriacus cultivar Beakdansim tig00111817_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 827959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:413849 original size:80 final size:76
Alignment explanation
Indices: 413754--414265 Score: 579
Period size: 80 Copynumber: 6.6 Consensus size: 76
413744 GAGGAGTCGA
* * * *
413754 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAATCAATCTTTTAATGTTATTATTAACTT
1 TCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATC--TT--TGTTATTCTTGACTT
*
413819 CCTCGCGAAGAGAAG
62 CCTCGTGAAGAGAAG
*
413834 TCAATCTTT-TCTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTTCT
1 TCAATCTTTGT-TATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCT
*
413898 CGTGAAGAAAAG
65 CGTGAAGAGAAG
* * * *
413910 TTAATCTTTCAATGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGACTC
1 TCAATC-TT---TGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTT
*
413975 CCTCGTGAAGAGGAG
62 CCTCGTGAAGAGAAG
* *
413990 TTAATCTTTGTTTATTCTTGACTCCCTCGTGAAGA-AGAGTCAATCTTTCAATGTTATTCTTAAC
1 TCAATCTTTG-TTATTCTTGACTCCCTCGTGAAGAGA-AGTCAATC-TT---TGTTATTCTTGAC
* * *
414054 TTTCTCGTGAAAAGAAA
60 TTCCTCGTGAAGAGAAG
* *
414071 TCAATC-TTGTTATTCTTGACTCCCTTGTGAAGAG--GTCAATCTTTGTTATTCTTGACTCCCTC
1 TCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTC
*
414133 GTGAAGAAAAG
66 GTGAAGAGAAG
* *
414144 TCAATCTTTGTTATTCTTGACTCCCTCGTGAAAAGGAGTCAATCTTTGTTATTCTTGAC-TCCTC
1 TCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTC
414208 GTGAAGAGGAA-
66 GTGAAGA-GAAG
* *
414219 TCAATTTTTCAGTATTATTCTTGACTTCCTCGTGAAGAGAAGTCAAT
1 TCAATCTTT--G--TTATTCTTGACTCCCTCGTGAAGAGAAGTCAAT
414266 ATTTCAGTAT
Statistics
Matches: 373, Mismatches: 38, Indels: 43
0.82 0.08 0.09
Matches are distributed among these distances:
73 30 0.08
74 26 0.07
75 19 0.05
76 59 0.16
77 40 0.11
78 4 0.01
79 56 0.15
80 109 0.29
81 30 0.08
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (76 bp):
TCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTC
GTGAAGAGAAG
Found at i:413967 original size:118 final size:118
Alignment explanation
Indices: 413754--414357 Score: 683
Period size: 118 Copynumber: 5.1 Consensus size: 118
413744 GAGGAGTCGA
* * *
413754 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAA-TCAATCTTTTAATGTTATTATTAACT
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGA-AAAGTCAATCTTTCAATGTTATTCTTGACT
*
413818 TCCTCGCGAAGAGAAGTCAATCTTT-TCTATTCTTGACTCCCTCGTGAAGAGAAG
65 TCCTCGTGAAGAGAAGTCAATCTTTGT-TATTCTTGACTCCCTCGTGAAGAGAAG
* *
413872 TCAATCTTTGTTATTCTTGACTTTCTCGTGAAGAAAAGTTAATCTTTCAATGTTATTCTTGACTT
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAAAAGTCAATCTTTCAATGTTATTCTTGACTT
* *
413937 CCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAG
66 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAG
* * * *
413990 TTAATCTTTGTTTATTCTTGACTCCCTCGTGAAGAAGAGTCAATCTTTCAATGTTATTCTTAACT
1 TCAATCTTTG-TTATTCTTGACTTCCTCGTGAAGAAAAGTCAATCTTTCAATGTTATTCTTGACT
* * * *
414055 TTCTCGTGAAAAGAAATCAATC-TTGTTATTCTTGACTCCCTTGTGAAGAG--G
65 TCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAG
* *
414106 TCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAAAAGTCAATC-TT---TGTTATTCTTGACTC
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAAAAGTCAATCTTTCAATGTTATTCTTGACTT
* *
414167 CCTCGTGAAAAGGAGTCAATCTTTGTTATTCTTGACT-CCTCGTGAAGAGGAA-
66 CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGA-GAAG
* * *
414219 TCAATTTTTCAGTATTATTCTTGACTTCCTCGTGAAGAGAAGTCAATATTTCAGTAT-TTCCATT
1 TCAATCTTT--G--TTATTCTTGACTTCCTCGTGAAGAAAAGTCAATCTTTCA--ATGTT--ATT
* ** * * **
414283 CTTGACTTTCTTATGAAGAGAAATCAATCTCTCAGTATGGCCATTCTTGACTTTCTCGTGAAGAG
58 CTTGACTTCCTCGTGAAGAGAAGTCAATCT-T-TGT-T----ATTCTTGACTCCCTCGTGAAGAG
414348 AAG
116 AAG
414351 TCAATCT
1 TCAATCT
414358 CTCAGTATTT
Statistics
Matches: 417, Mismatches: 41, Indels: 42
0.83 0.08 0.08
Matches are distributed among these distances:
111 41 0.10
112 16 0.04
113 8 0.02
114 2 0.00
115 34 0.08
116 10 0.02
117 34 0.08
118 142 0.34
119 68 0.16
122 2 0.00
123 1 0.00
124 26 0.06
125 1 0.00
126 2 0.00
127 1 0.00
131 13 0.03
132 16 0.04
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (118 bp):
TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAAAAGTCAATCTTTCAATGTTATTCTTGACTT
CCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGAAG
Found at i:414300 original size:45 final size:45
Alignment explanation
Indices: 414194--414786 Score: 418
Period size: 45 Copynumber: 13.3 Consensus size: 45
414184 AATCTTTGTT
* *
414194 ATTCTTGAC-TCCTCGTGAAGAGGAA-TCAATTTTTCAGTA-TT--
1 ATTCTTGACTTTCTCGTGAAGA-GAAGTCAATCTTTCAGTATTTCC
* *
414235 ATTCTTGACTTCCTCGTGAAGAGAAGTCAATATTTCAGTATTTCC
1 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTCC
** * * **
414280 ATTCTTGACTTTCTTATGAAGAGAAATCAATCTCTCAGTATGGCC
1 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTCC
* *
414325 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTCTCAGTATTTTC
1 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTCC
* * * ***
414370 ATTCTTGACTTTCTCATGAAGAGAAGTCAACCTCTCAGTATTGGA
1 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTCC
* * *
414415 ATTCCTGACTTTCTCGTGAAAAGAAGTCAATTTTTCAGTATTGT-C
1 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATT-TCC
* * * *
414460 -TTCCTTGATTTTCTCGTGAAGA-AGAGTCAATATTTTAGTGTTGTCC
1 ATT-CTTGACTTTCTCGTGAAGAGA-AGTCAATCTTTCAGTATT-TCC
* * * * *
414506 -TTCTTGACTTTCACGCGAAGAGGAGCCAATCTTTCAGTGTGTT-C
1 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTAT-TTCC
* * * * *
414550 -TTCCTTGACTTTCTCGTGAAAAGGAGTCAAT-TTTTAGTGTTGTTC
1 ATT-CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATT-TCC
* * * * * * *
414595 -TTATTAACTTTTTCGCGAAGAGGAGTCAAATCTTTTAGTGTTGTCC
1 ATTCTTGACTTTCTCGTGAAGAGAAGTC-AATCTTTCAGTATT-TCC
* *
414641 -TTCTTGACTTTCTCGCG-A-AGAAGATACAATCTTTCAGTGTTATCC
1 ATTCTTGACTTTCTCGTGAAGAGAAG-T-CAATCTTTCAGTATT-TCC
* * * *
414686 -TCCTTGACTTTCTCATGAAGATG-AGTCAATATTTCAGTGTTGTCC
1 ATTCTTGACTTTCTCGTGAAGA-GAAGTCAATCTTTCAGTATT-TCC
* * * *
414731 -TTCTTAACTTTCTCGTGAAGATG-AGTCAATCTTTTATTATTGTTC
1 ATTCTTGACTTTCTCGTGAAGA-GAAGTCAATCTTTCAGTATT-TCC
414776 -TTCTTGACTTT
1 ATTCTTGACTTT
414787 ATCACAAAGA
Statistics
Matches: 459, Mismatches: 72, Indels: 38
0.81 0.13 0.07
Matches are distributed among these distances:
41 12 0.03
42 25 0.05
43 3 0.01
44 39 0.08
45 342 0.75
46 34 0.07
47 3 0.01
48 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (45 bp):
ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTCC
Found at i:414514 original size:90 final size:90
Alignment explanation
Indices: 414195--414786 Score: 474
Period size: 90 Copynumber: 6.6 Consensus size: 90
414185 ATCTTTGTTA
* * * * * * *
414195 TTCTTGAC-TCCTCGTGAAGAGGAATCAATTTTTCAGT-AT-T-ATTCTTGACTTCCTCGTGAAG
1 TTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGAAG
414256 AGAAGTCAATATTTCAGTATT-TCC
66 AGAAGTCAATATTTCAGTATTGTCC
** * * * *
414280 ATTCTTGACTTTCTTATGAAG-AGAAATCAATCTCTCAGT-ATGGCCATTCTTGACTTTCTCGTG
1 -TTCTTGACTTTCTCGTGAAGAAG-AGTCAATCTTTCAGTGTTGTCC-TTCTTGACTTTCTCGTG
* * * *
414343 AAGAGAAGTCAATCTCTCAGTATTTTCA
63 AAGAGAAGTCAATATTTCAGTATTGTCC
* * * * *** *
414371 TTCTTGACTTTCTCATGAAG-AGAAGTCAACCTCTCAGTATTGGAATTCCTGACTTTCTCGTGAA
1 TTCTTGACTTTCTCGTGAAGAAG-AGTCAATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGAA
* *
414435 AAGAAGTCAATTTTTCAGTATTGT-C
65 GAGAAGTCAATATTTCAGTATTGTCC
* * * * *
414460 TTCCTTGATTTTCTCGTGAAGAAGAGTCAATATTTTAGTGTTGTCCTTCTTGACTTTCACGCGAA
1 TT-CTTGACTTTCTCGTGAAGAAGAGTCAATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGAA
* * * * *
414525 GAGGAGCCAATCTTTCAGT-GTGTTC
65 GAGAAGTCAATATTTCAGTATTGTCC
* * * * * *
414550 TTCCTTGACTTTCTCGTGAA-AAGGAGTCAAT-TTTTAGTGTTGTTCTTATTAACTTTTTCGCGA
1 TT-CTTGACTTTCTCGTGAAGAA-GAGTCAATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGA
* * * *
414613 AGAGGAGTCAAATCTTTTAGTGTTGTCC
64 AGAGAAGTC-AATATTTCAGTATTGTCC
* * * *
414641 TTCTTGACTTTCTCGCGAAGAAGA-TACAATCTTTCAGTGTTATCCTCCTTGACTTTCTCATGAA
1 TTCTTGACTTTCTCGTGAAGAAGAGT-CAATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGAA
*
414705 GATG-AGTCAATATTTCAGTGTTGTCC
65 GA-GAAGTCAATATTTCAGTATTGTCC
* * * * * *
414731 TTCTTAACTTTCTCGTGAAGATGAGTCAATCTTTTATTATTGTTCTTCTTGACTTT
1 TTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTTCAGTGTTGTCCTTCTTGACTTT
414787 ATCACAAAGA
Statistics
Matches: 415, Mismatches: 73, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
86 9 0.02
87 23 0.06
89 43 0.10
90 293 0.71
91 46 0.11
92 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (90 bp):
TTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGAAG
AGAAGTCAATATTTCAGTATTGTCC
Found at i:414581 original size:135 final size:134
Alignment explanation
Indices: 414416--414786 Score: 471
Period size: 135 Copynumber: 2.8 Consensus size: 134
414406 AGTATTGGAA
* * *
414416 TTCC-TGACTTTCTCGTGAAAAGAAGTCAATTTTTCAGTATTGTCTTCCTTGATTTTCTCGTGAA
1 TTCCTTGACTTTCTCGTGAAAAGGAGTCAATTTTTCAGTGTTGTCTT-CTTAATTTTCTCGTGAA
* * *
414480 GAAGAGTCAATATTTTAGTGTTGTCCTTCTTGACTTTCACGCGAAGAGGAGCCAATCTTTCAGTG
65 GAAGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCACGCGAAGAAGAGACAATCTTTCAGTG
414545 TGT-TC
130 T-TATC
* *
414550 TTCCTTGACTTTCTCGTGAAAAGGAGTCAATTTTT-AGTGTTGTTCTTATTAACTTTT-TCGCGA
1 TTCCTTGACTTTCTCGTGAAAAGGAGTCAATTTTTCAGTGTTG-TCTTCTTAA-TTTTCTCGTGA
* * *
414613 AGAGGAGTCAAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCGCGAAGAAGATACAATCTTTCAG
64 AGAAGAGTC-AATCTTTTAGTGTTGTCCTTCTTGACTTTCACGCGAAGAAGAGACAATCTTTCAG
414678 TGTTATC
128 TGTTATC
* * * * * *
414685 CTCCTTGACTTTCTCATGAAGATGAGTCAATATTTCAGTGTTGTCCTTCTTAACTTTCTCGTGAA
1 TTCCTTGACTTTCTCGTGAAAAGGAGTCAATTTTTCAGTGTTGT-CTTCTTAATTTTCTCGTGAA
* * * *
414750 GATGAGTCAATCTTTTATTATTGTTCTTCTTGACTTT
65 GAAGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTT
414787 ATCACAAAGA
Statistics
Matches: 206, Mismatches: 23, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
134 27 0.13
135 152 0.74
136 27 0.13
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (134 bp):
TTCCTTGACTTTCTCGTGAAAAGGAGTCAATTTTTCAGTGTTGTCTTCTTAATTTTCTCGTGAAG
AAGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCACGCGAAGAAGAGACAATCTTTCAGTGT
TATC
Found at i:414809 original size:135 final size:131
Alignment explanation
Indices: 414236--414849 Score: 450
Period size: 135 Copynumber: 4.5 Consensus size: 131
414226 TTCAGTATTA
** * * * * *
414236 TTCTTGACTTCCTCGTGAAGAGAAGTCAATATTTCAGTATTTCCATTCTTGACTTTCTTATGAAG
1 TTCTTGACTTTATCGCGAAGA-AAGTCAATCTTTCAGTGTTTCC-TCCTTGACTTTCTCATGAAG
* * * * * * * *
414301 -AGAAATCAATCTCTCAGTATGGCCATTCTTGACTTTCTCGTGAAG-AGAAGTCAATCTCTCAGT
64 AAG-AGTCAAT-TTTCAGTGTTGTC-TTCTTAACTTTCTCGTGAAGAAG-AGTCAATCTTTTAGT
* * *
414364 ATTTTCA
125 GTTGTCC
* ** * * * *** *
414371 TTCTTGACTTTCTCATGAAGAGAAGTCAACCTCTCAGTATTGGAATTCC-TGACTTTCTCGTGAA
1 TTCTTGACTTTATCGCGAAGA-AAGTCAATCTTTCAGTGTT--TCCTCCTTGACTTTCTCATGAA
* * * *
414435 -AAGAAGTCAATTTTTCAGTATTGTCTTCCTTGATTTTCTCGTGAAGAAGAGTCAATATTTTAGT
63 GAAG-AGTCAA-TTTTCAGTGTTGTCTT-CTTAACTTTCTCGTGAAGAAGAGTCAATCTTTTAGT
414499 GTTGTCC
125 GTTGTCC
* * * *
414506 TTCTTGACTTTCA-CGCGAAGAGGAGCCAATCTTTCAGTGTGTTCTTCCTTGACTTTCTCGTGAA
1 TTCTTGACTTT-ATCGCGAAGA-AAGTCAATCTTTCAGTGT-TTCCTCCTTGACTTTCTCATGAA
* * * * *
414570 -AAGGAGTCAATTTTTAGTGTTGTTCTTATTAACTTTTTCGCGAAGAGGAGTCAAATCTTTTAGT
63 GAA-GAGTCAATTTTCAGTGTTG-TCTTCTTAACTTTCTCGTGAAGAAGAGTC-AATCTTTTAGT
414634 GTTGTCC
125 GTTGTCC
*
414641 TTCTTGACTTTCTCGCGAAG-AAGATACAATCTTTCAGTGTTATCCTCCTTGACTTTCTCATGAA
1 TTCTTGACTTTATCGCGAAGAAAG-T-CAATCTTTCAGTGTT-TCCTCCTTGACTTTCTCATGAA
* * * *
414705 GATGAGTCAATATTTCAGTGTTGTCCTTCTTAACTTTCTCGTGAAGATGAGTCAATCTTTTATTA
63 GAAGAGTCAAT-TTTCAGTGTTGT-CTTCTTAACTTTCTCGTGAAGAAGAGTCAATCTTTTAGTG
*
414770 TTGTTC
126 TTGTCC
* * ** * ** * *
414776 TTCTTGACTTTATCACAAAGACAAGTCGGTCTTTTAGTGTTTTCCTTTTTTACTTTCTCACGAAG
1 TTCTTGACTTTATCGCGAAGA-AAGTCAATCTTTCAGTG-TTTCCTCCTTGACTTTCTCATGAAG
414841 AAGAGTCAA
64 AAGAGTCAA
414850 CCTTTTAATA
Statistics
Matches: 391, Mismatches: 66, Indels: 44
0.78 0.13 0.09
Matches are distributed among these distances:
133 2 0.01
134 36 0.09
135 305 0.78
136 45 0.12
137 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (131 bp):
TTCTTGACTTTATCGCGAAGAAAGTCAATCTTTCAGTGTTTCCTCCTTGACTTTCTCATGAAGAA
GAGTCAATTTTCAGTGTTGTCTTCTTAACTTTCTCGTGAAGAAGAGTCAATCTTTTAGTGTTGTC
C
Found at i:414815 original size:90 final size:90
Alignment explanation
Indices: 414252--414856 Score: 420
Period size: 90 Copynumber: 6.7 Consensus size: 90
414242 ACTTCCTCGT
* * * ** * *
414252 GAAGAGAAGTCAATATTTCAGTATT-TCCATTCTTGACTTTCTTATGAAG-AGAAATCAATCTCT
1 GAAGAGGAGTCAATCTTTCAGTGTTGTCC-TTCTTGACTTTCTCGTGAAGAAG-AGTCAATCTTT
* * * * **
414315 CAGT-ATGGCCATTCTTGACTTTCTCGT
64 TAGTGTTGTCC-TTCTTGACTTTATCAC
* * * * * * * * *
414342 GAAGAGAAGTCAATCTCTCAGTATTTTCATTCTTGACTTTCTCATGAAG-AGAAGTCAACCTCTC
1 GAAGAGGAGTCAATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGAAGAAG-AGTCAATCTTTT
* *** * * **
414406 AGTATTGGAATTCCTGACTTTCTCGT
65 AGTGTTGTCCTTCTTGACTTTATCAC
* * * * * *
414432 GAAAAGAAGTCAATTTTTCAGTATTGT-CTTCCTTGATTTTCTCGTGAAGAAGAGTCAATATTTT
1 GAAGAGGAGTCAATCTTTCAGTGTTGTCCTT-CTTGACTTTCTCGTGAAGAAGAGTCAATCTTTT
*
414496 AGTGTTGTCCTTCTTGACTTTCA-CGC
65 AGTGTTGTCCTTCTTGACTTT-ATCAC
* *
414522 GAAGAGGAGCCAATCTTTCAGTG-TGTTCTTCCTTGACTTTCTCGTGAA-AAGGAGTCAAT-TTT
1 GAAGAGGAGTCAATCTTTCAGTGTTGTCCTT-CTTGACTTTCTCGTGAAGAA-GAGTCAATCTTT
* * * * *
414584 TAGTGTTGTTCTTATTAACTTTTTCGC
64 TAGTGTTGTCCTTCTTGACTTTATCAC
* *
414611 GAAGAGGAGTCAAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCGCGAAGAAGA-TACAATCTTT
1 GAAGAGGAGTC-AATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGAAGAAGAGT-CAATCTTT
* * * * *
414675 CAGTGTTATCCTCCTTGACTTTCTCAT
64 TAGTGTTGTCCTTCTTGACTTTATCAC
* * * *
414702 GAAGATGAGTCAATATTTCAGTGTTGTCCTTCTTAACTTTCTCGTGAAGATGAGTCAATCTTTTA
1 GAAGAGGAGTCAATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTTTA
* * *
414767 TTATTGTTCTTCTTGACTTTATCAC
66 GTGTTGTCCTTCTTGACTTTATCAC
* ** ** * * * * ** *
414792 AAAGACAAGTCGGTCTTTTAGTGTTTTCCTTTTTTACTTTCTCACGAAGAAGAGTCAACCTTTTA
1 GAAGAGGAGTCAATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTTTA
414857 ATATTATCTT
Statistics
Matches: 422, Mismatches: 79, Indels: 28
0.80 0.15 0.05
Matches are distributed among these distances:
89 43 0.10
90 332 0.79
91 47 0.11
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (90 bp):
GAAGAGGAGTCAATCTTTCAGTGTTGTCCTTCTTGACTTTCTCGTGAAGAAGAGTCAATCTTTTA
GTGTTGTCCTTCTTGACTTTATCAC
Found at i:414855 original size:45 final size:45
Alignment explanation
Indices: 414326--414856 Score: 357
Period size: 45 Copynumber: 11.8 Consensus size: 45
414316 AGTATGGCCA
* * * * *
414326 TTCTTGACTTTCTCGTGAAG-AGAAGTCAATCTCTCAGTATTTTCA
1 TTCTTGACTTTCTCGCGAAGAAG-AGTCAATCTTTTAGTGTTTTCC
** * * * * ****
414371 TTCTTGACTTTCTCATGAAG-AGAAGTCAACCTCTCAGTATTGGAA
1 TTCTTGACTTTCTCGCGAAGAAG-AGTCAATCTTTTAGTGTTTTCC
* * * *
414416 TTCCTGACTTTCTCGTGAA-AAGAAGTCAAT-TTTTCAGTATTGT-C
1 TTCTTGACTTTCTCGCGAAGAAG-AGTCAATCTTTT-AGTGTTTTCC
* * * *
414460 TTCCTTGATTTTCTCGTGAAGAAGAGTCAATATTTTAGTGTTGTCC
1 TT-CTTGACTTTCTCGCGAAGAAGAGTCAATCTTTTAGTGTTTTCC
* * * * *
414506 TTCTTGACTTTCACGCGAAGAGGAGCCAATCTTTCAGTGTGTT-C
1 TTCTTGACTTTCTCGCGAAGAAGAGTCAATCTTTTAGTGTTTTCC
*
414550 TTCCTTGACTTTCTCGTGAA-AAGGAGTCAAT-TTTTAGTGTTGTT-C
1 TT-CTTGACTTTCTCGCGAAGAA-GAGTCAATCTTTTAGTGTT-TTCC
* * * * *
414595 TTATTAACTTTTTCGCGAAGAGGAGTCAAATCTTTTAGTGTTGTCC
1 TTCTTGACTTTCTCGCGAAGAAGAGTC-AATCTTTTAGTGTTTTCC
* *
414641 TTCTTGACTTTCTCGCGAAGAAGA-TACAATCTTTCAGTGTTATCC
1 TTCTTGACTTTCTCGCGAAGAAGAGT-CAATCTTTTAGTGTTTTCC
* ** * * * *
414686 TCCTTGACTTTCTCATGAAGATGAGTCAATATTTCAGTGTTGTCC
1 TTCTTGACTTTCTCGCGAAGAAGAGTCAATCTTTTAGTGTTTTCC
* * * * *
414731 TTCTTAACTTTCTCGTGAAGATGAGTCAATCTTTTATTATTGTT-C
1 TTCTTGACTTTCTCGCGAAGAAGAGTCAATCTTTTAGTGTT-TTCC
* * * **
414776 TTCTTGACTTTATCACAAAGACA-AGTCGGTCTTTTAGTGTTTTCC
1 TTCTTGACTTTCTCGCGAAGA-AGAGTCAATCTTTTAGTGTTTTCC
* * * *
414821 TTTTTTACTTTCTCACGAAGAAGAGTCAACCTTTTA
1 TTCTTGACTTTCTCGCGAAGAAGAGTCAATCTTTTA
414857 ATATTATCTT
Statistics
Matches: 394, Mismatches: 73, Indels: 38
0.78 0.14 0.08
Matches are distributed among these distances:
44 37 0.09
45 313 0.79
46 44 0.11
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (45 bp):
TTCTTGACTTTCTCGCGAAGAAGAGTCAATCTTTTAGTGTTTTCC
Found at i:415880 original size:134 final size:135
Alignment explanation
Indices: 415467--416000 Score: 709
Period size: 134 Copynumber: 4.0 Consensus size: 135
415457 GAATCAATTA
* * * *
415467 TCCTAAAAAGCAGTGAAGCAAATCAATTCTGAGTCAATCTTCCCTGAAGAGCAGTGAAGTGGATC
1 TCCTAAAGAGCAGTGAAGCAAATCAATTATGATTCAATCTTCCCTGAAGAACAGTGAAGTGGATC
* * * **
415532 AAAGATTTCTCGATTCT-GATCTCCCCTAAAGAGTACTGGAATAGATTCTTCTTCTTCTTTCAGA
66 AAAGTTTTCTCGAGTCTAGATCTCCCCTAAAGAGTAGTGGAGCAGA---TTCTTCTTCTTTCAGA
415596 TTTGGTCT
128 TTTGGTCT
* * * * * *
415604 TCCTGAAGAACAGTAAAGCAAATCGATTATGATTCAATCTTCCATGAAGAATAGTGAAGTGGATC
1 TCCTAAAGAGCAGTGAAGCAAATCAATTATGATTCAATCTTCCCTGAAGAACAGTGAAGTGGATC
* *
415669 AAAG-TTTCTCGAGTCTA-ATCTCCCCTAAAGAGTAGTGGAGCATATTCTTATTCTTTCAGATTT
66 AAAGTTTTCTCGAGTCTAGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTT
415732 GGTCT
131 GGTCT
* * * * * *
415737 TCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTTAATCTTCCCTGAAGAGCAGTGAAGTAGATC
1 TCCTAAAGAGCAGTGAAGCAAATCAATTATGATTCAATCTTCCCTGAAGAACAGTGAAGTGGATC
* * *
415802 AAAGTTTTCTCGAGTCTAG-TCTACCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTGATATTT
66 AAAGTTTTCTCGAGTCTAGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTT
415866 GGTCT
131 GGTCT
415871 TCCTAAAGAGCAGTGAAGCAAATCAATTATGATTCAATCTTCCCTGAAGAACAGTGAAGTGGATC
1 TCCTAAAGAGCAGTGAAGCAAATCAATTATGATTCAATCTTCCCTGAAGAACAGTGAAGTGGATC
* * * * * * *
415936 AAAGTTTTCTCAAGT-TTGATCTCCCCTAAAGATTAATGGAGCAGATTATTCTTCTTCCATATTT
66 AAAGTTTTCTCGAGTCTAGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTT
416000 G
131 G
416001 ATATTCCCTG
Statistics
Matches: 350, Mismatches: 43, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
133 86 0.25
134 171 0.49
136 34 0.10
137 59 0.17
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (135 bp):
TCCTAAAGAGCAGTGAAGCAAATCAATTATGATTCAATCTTCCCTGAAGAACAGTGAAGTGGATC
AAAGTTTTCTCGAGTCTAGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTT
GGTCT
Found at i:417823 original size:19 final size:19
Alignment explanation
Indices: 417784--417841 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
417774 TTAATATCCC
*
417784 CTAATTATTCAATTAAATCA
1 CTAATTA-TCCATTAAATCA
*
417804 CTAATTATCCATTCAATCA
1 CTAATTATCCATTAAATCA
*
417823 CTAATTATCCATTTAATCA
1 CTAATTATCCATTAAATCA
417842 ATGTATCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 28 0.80
20 7 0.20
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.40
Consensus pattern (19 bp):
CTAATTATCCATTAAATCA
Found at i:417888 original size:2 final size:2
Alignment explanation
Indices: 417883--417909 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
417873 ATAAAAAATT
417883 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
417910 TATCTCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:422335 original size:15 final size:15
Alignment explanation
Indices: 422261--422336 Score: 57
Period size: 15 Copynumber: 5.0 Consensus size: 15
422251 TAGTTAGATT
422261 ATAAAATAAAATATATA
1 ATAAAAT-AAATA-ATA
* *
422278 TATATAA-AAAGAATA
1 -ATAAAATAAATAATA
* * *
422293 ATAGAAGAAAAAATA
1 ATAAAATAAATAATA
*
422308 ATATAAT-AATAATA
1 ATAAAATAAATAATA
422322 ATAAAATAAATAATA
1 ATAAAATAAATAATA
422337 TAGATAAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
14 17 0.35
15 22 0.46
16 4 0.08
18 5 0.10
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (15 bp):
ATAAAATAAATAATA
Found at i:422343 original size:18 final size:18
Alignment explanation
Indices: 422261--422344 Score: 53
Period size: 20 Copynumber: 4.3 Consensus size: 18
422251 TAGTTAGATT
*
422261 ATAAAATAAAATATATATAT
1 ATAAAAT-AAATA-ATATAG
*
422281 ATAAAA-AGAATAATAGAAG
1 ATAAAATA-AATAATA-TAG
* *
422300 AAAAAATAATATAATAATAATA
1 ATAAAATAA-ATAAT-AT-A-G
422322 ATAAAATAAATAATATAG
1 ATAAAATAAATAATATAG
422340 ATAAA
1 ATAAA
422345 TAAGGATAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
18 9 0.18
19 12 0.24
20 14 0.28
21 7 0.14
22 8 0.16
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
ATAAAATAAATAATATAG
Found at i:422386 original size:17 final size:16
Alignment explanation
Indices: 422366--422398 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
422356 AAAAATGAGT
422366 AAAAAGAAAAATAATAA
1 AAAAAGAAAAA-AATAA
422383 AAAAAGAAAAAAATAA
1 AAAAAGAAAAAAATAA
422399 TTATGAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (16 bp):
AAAAAGAAAAAAATAA
Found at i:423616 original size:124 final size:124
Alignment explanation
Indices: 423385--423914 Score: 407
Period size: 124 Copynumber: 4.3 Consensus size: 124
423375 AAAGTCGATC
* * * * * * *
423385 TGTGGAGCACAATATCTTTCGTTGTGAAATTGAAATCATGGATGACTCATTCGTTGTGAAGTTAA
1 TGTGGA-CACAATATCCTTCGTCGTGAAGTTGAAATCGTAGATGACCCATTCGTTGTGAAGTTGA
* * *
423450 ACCTTGAATTGGATATCTTTTGTCGTGAAATTGAAATCCAATCTAAAGAAGAATATTG-T
65 GCCTTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGAAGAATATTGCT
*
423509 TGGTGGACACGATATCCTTCGTCGTGAAGTTGAAATCGTAGAT-AGCCCATTCGTTGTGAAGTTG
1 T-GTGGACACAATATCCTTCGTCGTGAAGTTGAAATCGTAGATGA-CCCATTCGTTGTGAAGTTG
* * * * * *
423573 AGTCTCGAATTTGATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
64 AGCCTTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGAAGAATATTGCT
* * * *
423634 TCG-AGTC-TAATATCCTTCG-CAGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCAT
1 T-GTGGACACAATATCCTTCGTC-GTGAAGTTGAAA-----TC-G--T-AGA-T--G-A-CCCAT
** * * *
423696 TCGCCGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCT-----A
50 TCGTTGTGAAGTTGAGCCTTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGAA
423756 G---A--G--
115 GAATATTGCT
* * * * * *
423759 T-TGG-CACGATAGCCTTCGTCGTGAAGTTGAAATCGTGGATGTCCCCTTCGTTATGAAGTTGAG
1 TGTGGACACAATATCCTTCGTCGTGAAGTTGAAATCGTAGATGACCCATTCGTTGTGAAGTTGAG
* *
423822 CCTTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
66 CCTTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGAAGAATATTGCT
*** *
423881 TCAAGTC-CAATATCCTTCGTCGTGAAGTTGAAAT
1 TGTGGACACAATATCCTTCGTCGTGAAGTTGAAAT
423915 TGGCTCTGAA
Statistics
Matches: 318, Mismatches: 53, Indels: 71
0.72 0.12 0.16
Matches are distributed among these distances:
110 57 0.18
112 1 0.00
114 1 0.00
115 2 0.01
116 1 0.00
118 1 0.00
119 2 0.01
120 1 0.00
122 2 0.01
123 50 0.16
124 123 0.39
125 10 0.03
127 1 0.00
128 2 0.01
129 1 0.00
131 1 0.00
132 3 0.01
133 1 0.00
137 58 0.18
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (124 bp):
TGTGGACACAATATCCTTCGTCGTGAAGTTGAAATCGTAGATGACCCATTCGTTGTGAAGTTGAG
CCTTGAATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGAAGAATATTGCT
Found at i:424090 original size:110 final size:110
Alignment explanation
Indices: 423970--424829 Score: 488
Period size: 110 Copynumber: 7.3 Consensus size: 110
423960 TTTGAATTAG
*
423970 ATATCCTTCGTCGAGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCCTTCGTCGTGAAGTTG
1 ATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCCTTCGTCGTGAAGTTG
*
424035 AAATTGTGGATAGCCCCTTCATTGTAAAGTTAAGCCCTGACTTGA
66 AAATTGTGGATAGCCCCTTCATTGTGAAGTTAAGCCCTGACTTGA
* * * *
424080 ATATCATTCGTCGTGAACTTGAAATCC-ATGCTTGTATTGTTTCGAGTC-CAATATCCTTCG-CT
1 ATATCCTTCGTCGTGAAGTTGAAATCCAAT-CTAG-A--G-TT-G-G-CACGATATCCTTCGTC-
* * * * ** *
424142 GTGAAGTTTAAATTGGCTCTAAATGAAACTGGGAAGCCCCTTCACTGTGAAGTTGAGCTTTGAAT
57 GTGAAGTTGAAATT-G-------TG-GA-T----AGCCCCTTCATTGTGAAGTTAAGCCCTGACT
*
424207 TGG
108 TGA
* *
424210 ATATCCTTCTTCTTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCCTTCGTCGTGAAGTTG
1 ATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCCTTCGTCGTGAAGTTG
* * *
424275 AAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCTGACTTGA
66 AAATTGTGGATAGCCCCTTCATTGTGAAGTTAAGCCCTGACTTGA
* * * * *
424320 ATATCCTTCGTCGTGAAGTTGAAATACAAGCTTGTATTGTTTCGAGTC-CAATATCCTTCGCCGT
1 ATATCCTTCGTCGTGAAGTTGAAATCCAATCTAG-A--G-TT-G-G-CACGATATCCTTCGTCGT
* * *** * ** *
424384 GAAGTTAAAATTAGCTTTGAATAAAACTGGGAAGCCCCTTCGCCGTGAAGTTGAGCTTTGAATTG
59 GAAGTTGAAATT-G---TG-----GA-T----AGCCCCTTCATTGTGAAGTTAAGCCCTGACTTG
*
424449 G
110 A
** * * * * * *
424450 ATATATTTCATCGTAAAGTTAAAATCCAATCTAGAGTTGACATGATATCCTTCGTCGTGAAGTTA
1 ATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCCTTCGTCGTGAAGTTG
* * *
424515 AAATCGTGGATGGCCCTTTCATTGTGAAGTTAAGCCCTGACTTGA
66 AAATTGTGGATAGCCCCTTCATTGTGAAGTTAAGCCCTGACTTGA
* ** * * * *
424560 ATATCCTTCATATTGAAGTTGAAATCCAAGCTTGTA-TTGTTTCAAGTCCAATATCCTTCGTCGT
1 ATATCCTTCGTCGTGAAGTTGAAATCCAATCTAG-AGTTG--GC-A---CGATATCCTTCGTCGT
* ** * ** *
424624 GAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCTCTTCACCGTGAAGTTGAGCTTTGAATTG
59 GAAGTTGAAATT-G---TG---G--A-T----AGCCCCTTCATTGTGAAGTTAAGCCCTGACTTG
*
424689 G
110 A
*
424690 ATATCATTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCCTTCGTCGTGAAGTTG
1 ATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCCTTCGTCGTGAAGTTG
* * *
424755 AAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCTGACTTGA
66 AAATTGTGGATAGCCCCTTCATTGTGAAGTTAAGCCCTGACTTGA
* * *
424800 ATATCCTTCTTCATGAAGTTAAAAATCCAA
1 ATATCCTTCGTCGTGAAGTT-GAAATCCAA
424830 GCTTGTATTG
Statistics
Matches: 560, Mismatches: 119, Indels: 141
0.68 0.15 0.17
Matches are distributed among these distances:
109 2 0.00
110 176 0.31
111 11 0.02
112 1 0.00
113 3 0.01
114 7 0.01
115 6 0.01
116 76 0.14
117 6 0.01
120 8 0.01
123 6 0.01
124 76 0.14
125 6 0.01
126 7 0.01
127 3 0.01
128 1 0.00
129 3 0.01
130 160 0.29
131 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (110 bp):
ATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCCTTCGTCGTGAAGTTG
AAATTGTGGATAGCCCCTTCATTGTGAAGTTAAGCCCTGACTTGA
Found at i:424230 original size:240 final size:240
Alignment explanation
Indices: 423516--424892 Score: 1934
Period size: 240 Copynumber: 5.7 Consensus size: 240
423506 TGTTGGTGGA
* * * * *
423516 CACGATATCCTTCGTCGTGAAGTTGAAATCGTAGATAGCCCATTCGTTGTGAAGTTGAG-TCTCG
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCT-G
* * * * * *
423580 AATTTG-ATATCATTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTTCGAGTCTAA
65 -ACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCT-----TG--TATTGTTTCGAGTCCAA
* * *
423644 TATCCTTCGCAGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCATTCGCCGTGAAGTT
122 TATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTT
*
423709 GAGCTTTGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGTTGG
187 GAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGG
* * * * *
423763 CACGATAGCCTTCGTCGTGAAGTTGAAATCGTGGATGTCCCCTTCGTTATGAAGTTGAGCCTTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCTGA
* * * * * * *
423828 ATTGGATATCTTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTTCAAGTCCAATA
66 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCT-----TG--TATTGTTTCGAGTCCAATA
* *
423893 TCCTTCG-TCGTGAAGTTGAAATTGGCTCTGAATGAAACTTGGAAGCCCCTTCACCGTAAAGTTG
124 TCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTTG
* *
423957 AGCTTTGAATTAGATATCCTTCGTCGAGAAGTTGAAATCCAATCTAGAGTTGG
188 AGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGG
* * * *
424010 CACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATAGCCCCTTCATTGTAAAGTTAAGCCCTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCTGA
* * *
424075 CTTGAATATCATTCGTCGTGAACTTGAAATCCATGCTTGTATTGTTTCGAGTCCAATATCCTTCG
66 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
* * *
424140 CTGTGAAGTTTAAATTGGCTCTAAATGAAACTGGGAAGCCCCTTCACTGTGAAGTTGAGCTTTGA
131 CTGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTTGAGCTTTGA
* *
424205 ATTGGATATCCTTCTTCTTGAAGTTGAAATCCAATCTAGAGTTGG
196 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGG
424250 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCTGA
*
424315 CTTGAATATCCTTCGTCGTGAAGTTGAAATACAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
66 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
* * * * * *
424380 CCGTGAAGTTAAAATTAGCTTTGAATAAAACTGGGAAGCCCCTTCGCCGTGAAGTTGAGCTTTGA
131 CTGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTTGAGCTTTGA
** * * * *
424445 ATTGGATATATTTCATCGTAAAGTTAAAATCCAATCTAGAGTTGA
196 ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGG
* * * *
424490 CATGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCCCTTTCATTGTGAAGTTAAGCCCTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCTGA
* ** *
424555 CTTGAATATCCTTCATATTGAAGTTGAAATCCAAGCTTGTATTGTTTCAAGTCCAATATCCTTCG
66 CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
*
424620 -TCGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCTCTTCACCGTGAAGTTGAGCTTTG
131 CT-GTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTTGAGCTTTG
*
424684 AATTGGATATCATTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGG
195 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGG
424730 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCTGA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCTGA
* * *
424795 CTTGAATATCCTTCTTCATGAAGTTAAAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTC
66 CTTGAATATCCTTCGTCGTGAAGTT-GAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTC
424860 GCTGTGAAGTTGAAATTGGCTCTGAATGAAACT
130 GCTGTGAAGTTGAAATTGGCTCTGAATGAAACT
424893 CGAAAAGTTG
Statistics
Matches: 1022, Mismatches: 101, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
240 639 0.63
241 69 0.07
242 3 0.00
246 4 0.00
247 306 0.30
248 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.33
Consensus pattern (240 bp):
CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTAAGCCCTGA
CTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCG
CTGTGAAGTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTTGAGCTTTGA
ATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGG
Found at i:425904 original size:95 final size:95
Alignment explanation
Indices: 425708--425964 Score: 318
Period size: 95 Copynumber: 2.7 Consensus size: 95
425698 TGGCTAGCTG
* * * * *
425708 TATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAGCTTAA-TATCATTGTATAGA
1 TATCCATAAAGCCGAGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTG--T--A
425772 TATTATAATCACCTTTATCAGGCTAGCTGAATAT
62 TATTATAATCACCTTTATCAGGCTAGCTGAATAT
* ***
425806 TATCCATAAAGCCGAGGCATTTAACCAATTGCTCTAAAAACACAACTCAAGTTTTATTGTATATT
1 TATCCATAAAGCCGAGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATATT
* *
425871 ATAATCACCTTTATCAGGCTAGTTGAATCT
66 ATAATCACCTTTATCAGGCTAGCTGAATAT
* * * * * *
425901 TATCCATAAAGTCGTGGCGTTTAACCAATTGTTTTAGAGGGACAACTCAAGATTTATTGTATAT
1 TATCCATAAAGCCGAGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATAT
425965 ACATAATATT
Statistics
Matches: 137, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
95 87 0.64
97 1 0.01
98 43 0.31
99 6 0.04
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (95 bp):
TATCCATAAAGCCGAGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGTTTTATTGTATATT
ATAATCACCTTTATCAGGCTAGCTGAATAT
Found at i:428669 original size:13 final size:14
Alignment explanation
Indices: 428651--428684 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
428641 TATAATAATA
428651 AAATAAATAA-GAT
1 AAATAAATAAGGAT
*
428664 AGATAAATAAGGAT
1 AAATAAATAAGGAT
428678 AAATAAA
1 AAATAAA
428685 ATTGATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.21
Consensus pattern (14 bp):
AAATAAATAAGGAT
Found at i:430659 original size:21 final size:20
Alignment explanation
Indices: 430621--430683 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
430611 GGTGTTGTAA
*
430621 TTTAGGATTTAG-GATTTGAG
1 TTTAGGGTTTAGAG-TTTGAG
* *
430641 TTTAGAGTTTTA-ATGTTTGAT
1 TTTAG-GGTTTAGA-GTTTGAG
430662 TTTAGGGTTTAGAGTTTGAG
1 TTTAGGGTTTAGAGTTTGAG
430682 TT
1 TT
430684 GAATTTTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 18 0.51
21 16 0.46
22 1 0.03
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (20 bp):
TTTAGGGTTTAGAGTTTGAG
Found at i:431307 original size:17 final size:18
Alignment explanation
Indices: 431263--431309 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
431253 TATTTATTTA
431263 TTAATATT-TATAATAAT
1 TTAATATTATATAATAAT
* *
431280 ATAA-ATAATATAAT-AT
1 TTAATATTATATAATAAT
431296 TTAATATTATATAA
1 TTAATATTATATAA
431310 AATAATCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATATTATATAATAAT
Found at i:431307 original size:26 final size:27
Alignment explanation
Indices: 431264--431315 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
431254 ATTTATTTAT
431264 TAATATTTATAATAATAT-AAATAATA
1 TAATATTTATAATAATATAAAATAATA
*
431290 TAATATTTA-ATATTATATAAAATAAT
1 TAATATTTATA-ATAATATAAAATAAT
431316 CAATTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 1 0.04
26 15 0.65
27 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TAATATTTATAATAATATAAAATAATA
Found at i:431339 original size:18 final size:18
Alignment explanation
Indices: 431299--431342 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
431289 ATAATATTTA
431299 ATATTATATAAAATAATC
1 ATATTATATAAAATAATC
*
431317 A-ATTATATAAAAATAA-G
1 ATATTATAT-AAAATAATC
431334 ATATTATAT
1 ATATTATAT
431343 TTTTATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
ATATTATATAAAATAATC
Found at i:431400 original size:26 final size:26
Alignment explanation
Indices: 431328--431412 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
431318 ATTATATAAA
* *
431328 AATAAGATATTATATT-TTTAT-TTT
1 AATAATATATAATATTATTTATATTT
**
431352 AATAATATATAA-AAAATTATATATTT
1 AATAATATATAATATTATT-TATATTT
431378 AATAATGA-ATAATATTATTTATATTT
1 AATAAT-ATATAATATTATTTATATTT
431404 AAATAATAT
1 -AATAATAT
431413 TTTAATAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
23 1 0.02
24 12 0.25
25 3 0.06
26 21 0.44
27 11 0.23
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
AATAATATATAATATTATTTATATTT
Found at i:431856 original size:21 final size:21
Alignment explanation
Indices: 431804--431857 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
431794 TAATTTATTT
*
431804 TTCAGAATTTAAATTCCAGTAA
1 TTCA-AATTTCAATTCCAGTAA
** *
431826 TTCATTTTTCAATTCTAGTAA
1 TTCAAATTTCAATTCCAGTAA
*
431847 TTTAAATTTCA
1 TTCAAATTTCA
431858 GTAATTTATT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
TTCAAATTTCAATTCCAGTAA
Found at i:437475 original size:15 final size:14
Alignment explanation
Indices: 437448--437499 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 14
437438 ATCCAATCAA
*
437448 AACAAAGAGAAAAT
1 AACAAAGAAAAAAT
437462 GAACAAAGAAAAAA-
1 -AACAAAGAAAAAAT
*
437476 ATCAAAGAAAAAAT
1 AACAAAGAAAAAAT
437490 --CAAAGAAAAA
1 AACAAAGAAAAA
437500 GAATAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 10 0.29
13 12 0.35
15 12 0.35
ACGTcount: A:0.75, C:0.08, G:0.12, T:0.06
Consensus pattern (14 bp):
AACAAAGAAAAAAT
Found at i:437498 original size:11 final size:12
Alignment explanation
Indices: 437465--437499 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
437455 AGAAAATGAA
437465 CAAAGAAAAAAAT
1 CAAAG-AAAAAAT
437478 CAAAGAAAAAAT
1 CAAAGAAAAAAT
437490 CAAAGAAAAA
1 CAAAGAAAAA
437500 GAATAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.06
Consensus pattern (12 bp):
CAAAGAAAAAAT
Found at i:437502 original size:18 final size:18
Alignment explanation
Indices: 437479--437517 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
437469 GAAAAAAATC
437479 AAAGAA-AAAATCAAAGAA
1 AAAGAATAAAA-CAAAGAA
*
437497 AAAGAATAAAAGAAAGAA
1 AAAGAATAAAACAAAGAA
437515 AAA
1 AAA
437518 AAAGATGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAGAATAAAACAAAGAA
Found at i:438605 original size:32 final size:32
Alignment explanation
Indices: 438569--438632 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
438559 AAGATACGAT
* *
438569 GAATGATGGGGCATCTTTGGAGATTCAACATC
1 GAATGATAGGGCATCTTTGGAGATTAAACATC
* *
438601 GAATGTTAGGGCATCTTTGGGGATTAAACATC
1 GAATGATAGGGCATCTTTGGAGATTAAACATC
438633 CTAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (32 bp):
GAATGATAGGGCATCTTTGGAGATTAAACATC
Found at i:439120 original size:37 final size:37
Alignment explanation
Indices: 439079--439189 Score: 89
Period size: 37 Copynumber: 3.2 Consensus size: 37
439069 TTTGAGTCTG
439079 TTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAA
**
439116 TTTCTTTTGAGAAA-AAAATATTTG--AGTC-T--G----
1 TTTC-TTTG-GAAACAAAAT-TTTGTCTCTCTTGAGACAA
* *
439146 TTACTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAA
1 TTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAA
439183 TTTCTTT
1 TTTCTTT
439190 TGAGAAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 26
0.62 0.08 0.30
Matches are distributed among these distances:
28 8 0.15
29 8 0.15
30 5 0.09
31 1 0.02
33 1 0.02
34 1 0.02
36 1 0.02
37 12 0.22
38 9 0.17
39 8 0.15
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (37 bp):
TTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAA
Found at i:439123 original size:131 final size:132
Alignment explanation
Indices: 438935--439200 Score: 448
Period size: 132 Copynumber: 2.0 Consensus size: 132
438925 CAAAATTTAT
438935 AATCTTTGAGTCTGTTTCTTTGGAAACAAATTTTGTCTCTCTTGAAACAATTTCTTTTGAG-AAA
1 AATCTTTGAGTCTGTTTCTTTGGAAACAAATTTTGTCTCTCTTGAAACAATTTCTTTTGAGAAAA
* *
438999 AAATATTTGAGTATGTTTCTTTGGAAAC-AAGATTTTG-TCTCTTGGGACAATTTCTTTTGAGAA
66 AAATATTTGAGTATGTTACTTTGGAAACAAAG-TTTTGCTCTCTTGAGACAATTTCTTTTGAGAA
439062 AAA
130 AAA
*
439065 AATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAA
1 AATCTTTGAGTCTGTTTCTTTGGAAAC-AAATTTTGTCTCTCTTGAAACAATTTCTTTTGAGAAA
*
439130 AAAATATTTGAGTCTGTTACTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAGA
65 AAAATATTTGAGTATGTTACTTTGGAAACAAAGTTTTG-CTCTCTTGAGACAATTTCTTTTGAGA
439195 AAAA
129 AAAA
439199 AA
1 AA
439201 ATCATCTTTG
Statistics
Matches: 127, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
130 27 0.21
131 33 0.26
132 34 0.27
133 3 0.02
134 30 0.24
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (132 bp):
AATCTTTGAGTCTGTTTCTTTGGAAACAAATTTTGTCTCTCTTGAAACAATTTCTTTTGAGAAAA
AAATATTTGAGTATGTTACTTTGGAAACAAAGTTTTGCTCTCTTGAGACAATTTCTTTTGAGAAA
AA
Found at i:439140 original size:67 final size:67
Alignment explanation
Indices: 438939--439200 Score: 433
Period size: 67 Copynumber: 4.0 Consensus size: 67
438929 ATTTATAATC
*
438939 TTTGAGTCTGTTTCTTTGGAAAC-AAATTTTGTCTCTCTTGAAACAATTTCTTTTGAG-AAAAAA
1 TTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAA
439002 TA
66 TA
* * *
439004 TTTGAGTATGTTTCTTTGGAAACAAGATTTTG--TCTCTTGGGACAATTTCTTTTGAGAAAAAAA
1 TTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAA
*
439067 TC
66 TA
439069 TTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAA
1 TTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAA
439134 TA
66 TA
* *
439136 TTTGAGTCTGTTACTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAA
1 TTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAA
439201 ATCATCTTTG
Statistics
Matches: 182, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
64 22 0.12
65 59 0.32
66 7 0.04
67 94 0.52
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.42
Consensus pattern (67 bp):
TTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAA
TA
Found at i:439410 original size:32 final size:31
Alignment explanation
Indices: 439342--439418 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
439332 CCTTGAGGTA
*
439342 ATTTCTTTTGAAACATAAAATCTTTGAGTCT
1 ATTTCTCTTGAAACATAAAATCTTTGAGTCT
439373 ATTTCTCTTGAAACA-AAACCATCTTTGAGATC-
1 ATTTCTCTTGAAACATAAA--ATCTTTGAG-TCT
*
439405 GTTTCTCTTGAAAC
1 ATTTCTCTTGAAAC
439419 GATTTTTGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
30 3 0.07
31 14 0.34
32 22 0.54
33 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (31 bp):
ATTTCTCTTGAAACATAAAATCTTTGAGTCT
Found at i:439412 original size:160 final size:162
Alignment explanation
Indices: 439154--439445 Score: 344
Period size: 160 Copynumber: 1.8 Consensus size: 162
439144 TGTTACTTTG
439154 GAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAAATCATCTTTGAGTAGTTT
1 GAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAAA-CATCTTTGAGTAGTTT
* * * *
439219 ATATTGAGACAAAAATCTTGGAAATTATTTCTCTTAAAAAAAGTTTTGTCT-TTTGAGACAGTTT
65 ATATTGAAACAAAAATCTTGGAAATCATTTCTCTTAAAAAAAGTTTTGTCTCCTTGAGACAGCTT
439283 CTATTAAAACCAACCTTTGAGATCGTTTCCATT
130 CTATTAAAACCAACCTTTGAGATCGTTTCCATT
** * *
439316 GAAACAAA-TTTTGTCTC-CTTGAGGTAATTTCTTTTGA-AACATAAA-ATCTTTGAGTCTA-TT
1 GAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAAACATCTTTGAG--TAGTT
* * * * * * ** *
439376 TCTCTTGAAACAAAACCATCTTTGAGATCGTTTCTCTTGAAACGATTTTTGTCTCCTTGAGACAG
64 TATATTGAAACAAAA--ATCTTGGAAATCATTTCTCTTAAAAAAAGTTTTGTCTCCTTGAGACAG
439441 CTTCT
127 CTTCT
439446 CTTGAAGCAT
Statistics
Matches: 108, Mismatches: 17, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
157 9 0.08
158 14 0.13
159 8 0.07
160 47 0.44
161 22 0.20
162 8 0.07
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (162 bp):
GAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAAACATCTTTGAGTAGTTTA
TATTGAAACAAAAATCTTGGAAATCATTTCTCTTAAAAAAAGTTTTGTCTCCTTGAGACAGCTTC
TATTAAAACCAACCTTTGAGATCGTTTCCATT
Found at i:439814 original size:133 final size:128
Alignment explanation
Indices: 439486--439866 Score: 390
Period size: 133 Copynumber: 2.9 Consensus size: 128
439476 TTGAGACATT
* ** * *
439486 ATCCCTAAAGATGGTATGCCATCCTCATCGCGTAGGAACCGTGTCATCCCTCGACCAGACCTCCT
1 ATCCCTAAAAATGACATGACATCCTCATCACGTA-GAACCGTGTCATCCCT-GACCAGACCTCCT
* ** * * * * *
439551 TATCATATAGGAGCCGCGTCAACCCTAGATAACCAGCCGTCCTTATCATGTAGGAACCGTGTTAT
64 CATCACGTAGGAGCCGTGTC-ACCCTAGATAACCAGCCGTCCTCATCACGTAAGAACCGCGTTAT
439616 C
128 C
* ** *
439617 ATCCCTAAAAATGACATGCCATCCTCATCACGTAGAAATTGTGTCATCTCCTAACCAGACCTCCT
1 ATCCCTAAAAATGACATGACATCCTCATCACGTAG-AACCGTGTCATC-CCTGACCAGACCTCCT
* *
439682 CATCACGTAGGAGCCGTGTCACCCTAGATAACCAGTCGTCCTCATCGCGTAAGAACCGCGTTATC
64 CATCACGTAGGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAAGAACCGCGTTATC
* * * *
439747 ATCCTTCCTAAAGATGAC-TAGA-ACTCTTCATCACGTATGAGCCGTGTCATCCACTGACCAGAT
1 AT-C--CCTAAAAATGACAT-GACA-TCCTCATCACGTA-GAACCGTGTCATCC-CTGACCAGAC
* *
439810 CTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATGACCAGACC-TCTTCATCACGTA
59 CTCCTCATCACGTAGGAGCCGTGTCACCC-TAGATAACCAG-CCGTCCTCATCACGTA
439867 TGAGCCATGT
Statistics
Matches: 210, Mismatches: 29, Indels: 19
0.81 0.11 0.07
Matches are distributed among these distances:
130 42 0.20
131 69 0.33
132 6 0.03
133 70 0.33
134 22 0.10
135 1 0.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (128 bp):
ATCCCTAAAAATGACATGACATCCTCATCACGTAGAACCGTGTCATCCCTGACCAGACCTCCTCA
TCACGTAGGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAAGAACCGCGTTATC
Found at i:439862 original size:43 final size:41
Alignment explanation
Indices: 439758--439877 Score: 143
Period size: 40 Copynumber: 2.9 Consensus size: 41
439748 TCCTTCCTAA
* *
439758 AGATGACTAGAACTCTTCATCACGTATGAGCCGTGTCATCC
1 AGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCACCC
* * * *
439799 A-CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCC
1 AGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCACCC
* *
439839 TTAGATGACCAGACCTCTTCATCACGTATGAGCCATGTC
1 --AGATGACCAGAACTCTTCATCACGTATGAGCCGTGTC
439878 GTCCCCCATC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
40 33 0.51
41 1 0.02
42 1 0.02
43 30 0.46
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (41 bp):
AGATGACCAGAACTCTTCATCACGTATGAGCCGTGTCACCC
Found at i:441303 original size:468 final size:470
Alignment explanation
Indices: 440425--441362 Score: 1792
Period size: 468 Copynumber: 2.0 Consensus size: 470
440415 TCAACACATC
440425 CATCAAACAGTGATAGAAAAATCAAATCAAAATCTAATACGAGATGATGACATATCTAACCAAAA
1 CATCAAACAGTGATAGAAAAATCAAATCAAAATCTAATACGAGATGATGACATATCTAACCAAAA
440490 TCCTGAGGGGATTTAGGGGGATGATATCAAACATGCTAGAAAAAAGGGAGAGGCAACATAAATGG
66 TCCTGAGGGGATTTAGGGGGATGATATCAAACATGCTAGAAAAAAGGGAGAGGCAACATAAATGG
* *
440555 TTTTTGGCCAGAGAGAAAAAGGGGGGACGATTTGGGGGTATAGGAGAGAAATCATAGAAGGGTAT
131 TTTTTGGCCAGAGAGAAAAAGGAGGGACGATTCGGGGGTATAGGAGAGAAATCATAGAAGGGTAT
440620 TCGGGGGAAATAAAAAATATATAAAGGAATCTGGGGTGTTTTCCAGAGAAAAATAGGGATAAAGA
196 TCGGGGGAAATAAAAAATATATAAAGGAATCTGGGGTGTTTTCCAGAGAAAAATAGGGATAAAGA
440685 TTCGGTTGGTTTAGAGAAAAAAAGATAGGGAAAATGAACCAAACAAGAACAAAAAGGGAGACACA
261 TTCGGTTGGTTTAGAGAAAAAAAGATAGGGAAAATGAACCAAACAAGAACAAAAAGGGAGACACA
*
440750 TACCTTAGTTCAAAGTCGTGGAAGCCGAGAGGTCATTGGATTTCGAAATCTTTTGAAGGTAACAA
326 TACCTTAGTTCAAAGTCGTGGAAGCCGAAAGGTCATTGGATTTCGAAATCTTTTGAAGGTAACAA
440815 TCTATATCTAGGGGTTTAGAGTTACTTTTAGGCCAAAGTGGTTCAAGATATGGGTTGAGGGTGAC
391 TCTATATCTAGGGGTTTAGAGTTACTTTTAGGCCAAAGTGGTTCAAGATATGGGTTGAGGGTGAC
440880 GAGGGGATATTTTTT
456 GAGGGGATATTTTTT
440895 CATCAAACAGTGATAGAAAAATCAAATCAAAATCTAATACGAGATGATGACATATCTAACCAAAA
1 CATCAAACAGTGATAGAAAAATCAAATCAAAATCTAATACGAGATGATGACATATCTAACCAAAA
*
440960 TCCTGAGGGGATTTAGGGGGATGATATC-AACATTCTAGGAAAAAA-GGAGAGGCAACATAAATG
66 TCCTGAGGGGATTTAGGGGGATGATATCAAACATGCTA-GAAAAAAGGGAGAGGCAACATAAATG
*
441023 GTTTTTGGCCAGAGAGAAAAA-GAGGGACGATTCGGGGGTATAGGAGAGAAATCGTAGAAGGGTA
130 GTTTTTGGCCAGAGAGAAAAAGGAGGGACGATTCGGGGGTATAGGAGAGAAATCATAGAAGGGTA
441087 TTCGGGGGAAATAAAAAATATATAAAGGAATCTGGGGTGTTTTCCAGAGAAAAATAGGGATAAAG
195 TTCGGGGGAAATAAAAAATATATAAAGGAATCTGGGGTGTTTTCCAGAGAAAAATAGGGATAAAG
441152 ATTCGGTTGGTTTAGAGAAAAAAAGATAGGGAAAATGAACCAAACAAGAACAAAAAGGGAGACAC
260 ATTCGGTTGGTTTAGAGAAAAAAAGATAGGGAAAATGAACCAAACAAGAACAAAAAGGGAGACAC
*
441217 ATACCTTAGTTCGAAGTCGTGGAAGCCGAAAGGTCATTGGATTTCGAAATCTTTTGAAGGTAACA
325 ATACCTTAGTTCAAAGTCGTGGAAGCCGAAAGGTCATTGGATTTCGAAATCTTTTGAAGGTAACA
441282 ATCTATATCTAGGGGTTTAGAGTTACTTTTAGGCCAAAGTGGTTCAAGATATGGGTTGAGGGTGA
390 ATCTATATCTAGGGGTTTAGAGTTACTTTTAGGCCAAAGTGGTTCAAGATATGGGTTGAGGGTGA
441347 CGAGGGGATATTTTTT
455 CGAGGGGATATTTTTT
441363 TTACCGTTTG
Statistics
Matches: 461, Mismatches: 6, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
468 314 0.68
469 47 0.10
470 100 0.22
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (470 bp):
CATCAAACAGTGATAGAAAAATCAAATCAAAATCTAATACGAGATGATGACATATCTAACCAAAA
TCCTGAGGGGATTTAGGGGGATGATATCAAACATGCTAGAAAAAAGGGAGAGGCAACATAAATGG
TTTTTGGCCAGAGAGAAAAAGGAGGGACGATTCGGGGGTATAGGAGAGAAATCATAGAAGGGTAT
TCGGGGGAAATAAAAAATATATAAAGGAATCTGGGGTGTTTTCCAGAGAAAAATAGGGATAAAGA
TTCGGTTGGTTTAGAGAAAAAAAGATAGGGAAAATGAACCAAACAAGAACAAAAAGGGAGACACA
TACCTTAGTTCAAAGTCGTGGAAGCCGAAAGGTCATTGGATTTCGAAATCTTTTGAAGGTAACAA
TCTATATCTAGGGGTTTAGAGTTACTTTTAGGCCAAAGTGGTTCAAGATATGGGTTGAGGGTGAC
GAGGGGATATTTTTT
Found at i:442446 original size:5 final size:5
Alignment explanation
Indices: 442436--442471 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
442426 TGTTTTTTCC
*
442436 TTTTA TTTTA TTTTA TTTTA TGTTA TTTTA TCTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA
442472 CTAAAATTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:442456 original size:15 final size:15
Alignment explanation
Indices: 442414--442471 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
442404 TTTATTTTGA
*
442414 TTATTTT-TTTAATG
1 TTATTTTATTTTATG
* *
442428 TT-TTTTCCTTTTATT
1 TTATTTT-ATTTTATG
442443 TTATTTTATTTTATG
1 TTATTTTATTTTATG
442458 TTATTTTATCTTTA
1 TTATTTTAT-TTTA
442472 CTAAAATTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 4 0.11
14 2 0.06
15 22 0.61
16 8 0.22
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.74
Consensus pattern (15 bp):
TTATTTTATTTTATG
Found at i:445853 original size:43 final size:41
Alignment explanation
Indices: 445800--446042 Score: 176
Period size: 43 Copynumber: 5.9 Consensus size: 41
445790 GTTTATTCAA
*
445800 AAAACGCCACTAAAGTATGAGTCTTTAGAGGCATTTTTTAATT
1 AAAACGCCACTAAAGTATGAGT-TTTAGCGGCATTTTTT-ATT
* * **
445843 AAAACACCACTAAAGTACT-ATGTTTTAGCGGCATTTGTT-GG
1 AAAACGCCACTAAAGTA-TGA-GTTTTAGCGGCATTTTTTATT
*
445884 AAAACGCCACTAAAGTACGAGTATTTAGCGGCATTTTTTACTT
1 AAAACGCCACTAAAGTATGAGT-TTTAGCGGCATTTTTTA-TT
* * * * ** *
445927 AAAAAGCCATTAATGTATTATGTTTTAGCGGTGTTTGTTGA--
1 AAAACGCCACTAAAGTATGA-GTTTTAGCGGCATTT-TTTATT
* * * * *
445968 AAAATGCCACTAAAGTATTAGTTTTAGCGGCGTTCTTGA--
1 AAAACGCCACTAAAGTATGAGTTTTAGCGGCATTTTTTATT
*
446007 AAAACGCCACTAAAGTTAT-AGGTTTTAGCAGCATTT
1 AAAACGCCACTAAAG-TATGA-GTTTTAGCGGCATTT
446043 GTCTAAAAAC
Statistics
Matches: 163, Mismatches: 27, Indels: 23
0.77 0.13 0.11
Matches are distributed among these distances:
39 19 0.12
40 30 0.18
41 49 0.30
43 57 0.35
44 8 0.05
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (41 bp):
AAAACGCCACTAAAGTATGAGTTTTAGCGGCATTTTTTATT
Found at i:445911 original size:84 final size:84
Alignment explanation
Indices: 445799--445984 Score: 257
Period size: 84 Copynumber: 2.2 Consensus size: 84
445789 TGTTTATTCA
* *
445799 AAAAACGCCACTAAAGTATGAGTCTTTAGAGGCATTTTTTAATTAAAACA-CCACTAAAGTACTA
1 AAAAACGCCACTAAAGTACGAGTATTTAGAGGCATTTTTTAATTAAAA-AGCCACTAAAGTACTA
445863 TGTTTTAGCGGCATTTGTTG
65 TGTTTTAGCGGCATTTGTTG
* * * * * *
445883 GAAAACGCCACTAAAGTACGAGTATTTAGCGGCATTTTTTACTTAAAAAGCCATTAATGTATTAT
1 AAAAACGCCACTAAAGTACGAGTATTTAGAGGCATTTTTTAATTAAAAAGCCACTAAAGTACTAT
**
445948 GTTTTAGCGGTGTTTGTTG
66 GTTTTAGCGGCATTTGTTG
*
445967 AAAAATGCCACTAAAGTA
1 AAAAACGCCACTAAAGTA
445985 TTAGTTTTAG
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
83 1 0.01
84 88 0.99
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (84 bp):
AAAAACGCCACTAAAGTACGAGTATTTAGAGGCATTTTTTAATTAAAAAGCCACTAAAGTACTAT
GTTTTAGCGGCATTTGTTG
Found at i:445992 original size:40 final size:41
Alignment explanation
Indices: 445799--446211 Score: 195
Period size: 41 Copynumber: 10.0 Consensus size: 41
445789 TGTTTATTCA
* * * * *
445799 AAAAACGCCACTAAAGTATGA-GTCTTTAGAGGCATTTTTTA
1 AAAAACGCCACTAAAGTATTATGT-TTTAGCGGCGTTTGTTG
* * *
445840 ATTAAAACACCACTAAAGTACTATGTTTTAGCGGCATTTGTTG
1 A--AAAACGCCACTAAAGTATTATGTTTTAGCGGCGTTTGTTG
* ** * *
445883 GAAAACGCCACTAAAGTACGA-GTATTTAGCGGCATTT-TTT
1 AAAAACGCCACTAAAGTATTATGT-TTTAGCGGCGTTTGTTG
* * * *
445923 ACTTAAAAAGCCATTAATGTATTATGTTTTAGCGGTGTTTGTTG
1 A---AAAACGCCACTAAAGTATTATGTTTTAGCGGCGTTTGTTG
* *
445967 AAAAATGCCACTAAAGTATTA-GTTTTAGCGGCG-TTCTTG
1 AAAAACGCCACTAAAGTATTATGTTTTAGCGGCGTTTGTTG
* * *
446006 AAAAACGCCACTAAAGT-TATAGGTTTTAGCAGCATTTGTCT-
1 AAAAACGCCACTAAAGTAT-TATGTTTTAGCGGCGTTTGT-TG
* * * ** * * *
446047 AAAAACGTCACGATA-TATGTACCATATT-GTGGCGTTTGTTT
1 AAAAACGCCACTAAAGTAT-TA-TGTTTTAGCGGCGTTTGTTG
* ** * * *
446088 AAAAACGCCACTAAAGAACGAT-TATATGGCGACGTTTGCTT-
1 AAAAACGCCACTAAAGTATTATGT-TTTAGCGGCGTTTG-TTG
* * * * **
446129 ACAAACGCCACTAAAGTACTAAT-CTTTAGAGGCGTTTGTCA
1 AAAAACGCCACTAAAGTA-TTATGTTTTAGCGGCGTTTGTTG
* **
446170 AATAAACGCCACGAAAGTACGA-GTTTTAGCGGCGTTTGTTG
1 AA-AAACGCCACTAAAGTATTATGTTTTAGCGGCGTTTGTTG
446211 A
1 A
446212 GAATCGCCGT
Statistics
Matches: 281, Mismatches: 67, Indels: 48
0.71 0.17 0.12
Matches are distributed among these distances:
38 1 0.00
39 24 0.09
40 29 0.10
41 139 0.49
42 24 0.09
43 57 0.20
44 7 0.02
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTATTATGTTTTAGCGGCGTTTGTTG
Found at i:446165 original size:41 final size:41
Alignment explanation
Indices: 446129--446208 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
446119 ACGTTTGCTT
* *
446129 ACAAACGCCACTAAAGTACTAATCTTTAGAGGCGTTTGTCAA
1 ACAAACGCCACGAAAGTACGAAT-TTTAGAGGCGTTTGTCAA
* * *
446171 ATAAACGCCACGAAAGTACGAGTTTTAGCGGCGTTTGT
1 ACAAACGCCACGAAAGTACGAATTTTAGAGGCGTTTGT
446209 TGAGAATCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 14 0.42
42 19 0.58
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (41 bp):
ACAAACGCCACGAAAGTACGAATTTTAGAGGCGTTTGTCAA
Found at i:447628 original size:148 final size:148
Alignment explanation
Indices: 447447--447740 Score: 330
Period size: 148 Copynumber: 2.0 Consensus size: 148
447437 CAAATATATT
* **
447447 AAAATAATTTTTATAACACTAAAGTAAATATATATAT-TTTTGGAGTTT-T-A-TAA-GCATTTA
1 AAAATAATTTTGATAACACTAAAACAAATATATATATATTTTGGAGTTTATAAGTAAGGCATTTA
* * *
447507 TTTATTTAAAAATATCAGAAAAGGACATCTAGTTACTTTAAGACAGTCTCTTTCTTTAATATTAA
66 TTTATTTAAAAATATCAGAAAAGGACATCTAGTTAATTTAAGACA-AC-CCTTC-TTAATATT--
447572 AAAAAATAAATAAATATTTAAGA
126 AAAAAATAAATAAATATTTAAGA
* * ** *
447595 AAAATAA-TTTGAGTAACACTAAAACAACTATATATATATTTTTGTTTTTATAAGTAAGGTATTT
1 AAAATAATTTTGA-TAACACTAAAACAAATATATATATATTTTGGAGTTTATAAGTAAGGCATTT
** * * * **
447659 ATTTATTTAAAAATATTGGAATATGACCTCTAGTTAATTTAAGACAACCCTTCTTAATATTTTAA
65 ATTTATTTAAAAATATCAGAAAAGGACATCTAGTTAATTTAAGACAACCCTTCTTAATATTAAAA
447724 AATAAATAAATATTTAA
130 AATAAATAAATATTTAA
447741 TATATATATA
Statistics
Matches: 122, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
147 4 0.03
148 47 0.39
149 8 0.07
150 9 0.07
151 5 0.04
152 4 0.03
153 45 0.37
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (148 bp):
AAAATAATTTTGATAACACTAAAACAAATATATATATATTTTGGAGTTTATAAGTAAGGCATTTA
TTTATTTAAAAATATCAGAAAAGGACATCTAGTTAATTTAAGACAACCCTTCTTAATATTAAAAA
ATAAATAAATATTTAAGA
Found at i:448746 original size:3 final size:3
Alignment explanation
Indices: 448738--448790 Score: 65
Period size: 3 Copynumber: 18.3 Consensus size: 3
448728 AATTATTTAT
* * *
448738 TAA TAA TAA T-A TAA TAA T-A TAA TAA TGA TAA TAT TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
448784 TAA TAA T
1 TAA TAA T
448791 TTTAAAATGG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:449272 original size:116 final size:116
Alignment explanation
Indices: 449044--449708 Score: 1010
Period size: 116 Copynumber: 5.7 Consensus size: 116
449034 CCTGCATTAG
* **** *
449044 AGGTCTTACAGATGACCCGAAGG-TCTTAAATATCAAAAAGATTTTAAAGGCTTTTTTTGAAAAT
1 AGGTCTTACAGATGACCCGAAGGCT-TTAAATATCAAAAAGCTCCCGAAGGC--TTTTTGAAAAC
* *
449108 ATCATGCAATGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGT
63 ATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGT
449162 AGGTCTTACAGATGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATC
1 AGGTCTTACAGATGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATC
* *
449227 CTGCACTGTAGGTATTATGGATGTCCCTGAGGTCTTATCATCTTGCACTGT
66 CTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGT
*
449278 AGGTCTTACAGACGACCC-AGAGGCTTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACA
1 AGGTCTTACAGATGACCCGA-AGGC-TTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACA
* * *
449342 TCCTGCACTGTAGGTCTTATGGATGACCTTGAGGTCTTATCATTTTGCACTGT
64 TCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGT
449395 AGGTCTTACAGATGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATC
1 AGGTCTTACAGATGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATC
* * *
449460 CTGCACTGTAGGTCTTATGAATGGCTCTGAGGTCTTATCATCTTGCAGTGT
66 CTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGT
* * * *
449511 AGGTCTTATAGATGACCCGGAGGCTTTAAATATAAAAAATCTCCCGAAGGCTTTTTGAAAACATC
1 AGGTCTTACAGATGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATC
* * *
449576 ATGCACTGTAGGTCTTATGGATAGCCCTGAGGTCTTATCATCATGCACTGT
66 CTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGT
* * * * *
449627 AGGCCTTACATATGACCCGGAGGCTTTAAATATAAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
1 AGGTCTTACAGATGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATC
449692 CTGCACTGTAGGTCTTA
66 CTGCACTGTAGGTCTTA
449709 CAGATGTGGG
Statistics
Matches: 505, Mismatches: 38, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
115 1 0.00
116 349 0.69
117 109 0.22
118 45 0.09
119 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (116 bp):
AGGTCTTACAGATGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATC
CTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGT
Found at i:449364 original size:233 final size:232
Alignment explanation
Indices: 449044--449704 Score: 1011
Period size: 233 Copynumber: 2.8 Consensus size: 232
449034 CCTGCATTAG
* * **** *
449044 AGGTCTTACAGATGACCCGAAGG-TCTTAAATATCAAAAAGATTTTAAAGGCTTTTTTTGAAAAT
1 AGGTCTTACAGATGACCCG-AGGCTTTTAAATATCAAAAAGCTCCCGAAGGC--TTTTTGAAAAC
*
449108 ATCATGCAATGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAG
63 ATCATGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAG
449173 ATGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAG
128 ATGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAG
* *
449238 GTATTATGGATGTCCCTGAGGTCTTATCATCTTGCACTGT
193 GTATTATGAATGGCCCTGAGGTCTTATCATCTTGCACTGT
*
449278 AGGTCTTACAGACGACCCAGAGGCTTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACAT
1 AGGTCTTACAGATGACCC-GAGGCTTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACAT
* * * *
449343 CCTGCACTGTAGGTCTTATGGATGACCTTGAGGTCTTATCATTTTGCACTGTAGGTCTTACAGAT
65 CATGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGAT
449408 GACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGT
130 GACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGT
* * *
449473 CTTATGAATGGCTCTGAGGTCTTATCATCTTGCAGTGT
195 ATTATGAATGGCCCTGAGGTCTTATCATCTTGCACTGT
* * *
449511 AGGTCTTATAGATGACCCGGAGGC-TTTAAATATAAAAAATCTCCCGAAGGCTTTTTGAAAACAT
1 AGGTCTTACAGATGACCC-GAGGCTTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACAT
* * * *
449575 CATGCACTGTAGGTCTTATGGATAGCCCTGAGGTCTTATCATCATGCACTGTAGGCCTTACATAT
65 CATGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGAT
* * *
449640 GACCCGGAGGCTTTAAATATAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCCTGCACTGTAGGT
130 GACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGT
449705 CTTACAGATG
Statistics
Matches: 391, Mismatches: 34, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
232 157 0.40
233 191 0.49
234 20 0.05
235 23 0.06
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (232 bp):
AGGTCTTACAGATGACCCGAGGCTTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATC
ATGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATG
ACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTA
TTATGAATGGCCCTGAGGTCTTATCATCTTGCACTGT
Found at i:449611 original size:349 final size:349
Alignment explanation
Indices: 449044--449708 Score: 1057
Period size: 349 Copynumber: 1.9 Consensus size: 349
449034 CCTGCATTAG
*** *
449044 AGGTCTTACAGATGACCCGAAGGTCTTAAATATCAAAAAGATTTTAAAGGCTTTTTTTGAAAATA
1 AGGTCTTACAGATGACCCGAAGGTCTTAAATATCAAAAAGATCCCAAAGGC-TTTTTTGAAAACA
*
449109 TCATGCAATGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGA
65 TCATGCAATGTAGGTCTTATGAATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGA
* *
449174 TGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGG
130 TGACCCGAAGGCTTTAAATATAAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
* *
449239 TATTATGGATGTCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGACGACCCAGAGGCTT
195 TATTATGGATGTCCCTGAGGTCTTATCATCATGCACTGTAGGCCTTACAGACGACCCAGAGGC-T
*
449304 TTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGAC
259 TTAAATATAAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGAC
449369 CTTGAGGTCTTATCATTTTGCACTGT
324 CTTGAGGTCTTATCATTTTGCACTGT
* *
449395 AGGTCTTACAGATGACCCGAAGG-CTTTAAATATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACA
1 AGGTCTTACAGATGACCCGAAGGTC-TTAAATATCAAAAAGATCCCAAAGGCTTTTTTGAAAACA
* * * * *
449458 TCCTGCACTGTAGGTCTTATGAATGGCTCTGAGGTCTTATCATCTTGCAGTGTAGGTCTTATAGA
65 TCATGCAATGTAGGTCTTATGAATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGA
* *
449523 TGACCCGGAGGCTTTAAATATAAAAAATCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
130 TGACCCGAAGGCTTTAAATATAAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
* * * *
449588 TCTTATGGATAG-CCCTGAGGTCTTATCATCATGCACTGTAGGCCTTACATATGACCCGGAGGCT
195 TATTATGGAT-GTCCCTGAGGTCTTATCATCATGCACTGTAGGCCTTACAGACGACCCAGAGGCT
*
449652 TTAAATATAAAAAAGCTCCCGAAGGCTTTTTGGAAACATCCTGCACTGTAGGTCTTA
259 TTAAATATAAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTA
449709 CAGATGTGGG
Statistics
Matches: 288, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
348 56 0.19
349 186 0.65
350 2 0.01
351 44 0.15
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (349 bp):
AGGTCTTACAGATGACCCGAAGGTCTTAAATATCAAAAAGATCCCAAAGGCTTTTTTGAAAACAT
CATGCAATGTAGGTCTTATGAATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGAT
GACCCGAAGGCTTTAAATATAAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGT
ATTATGGATGTCCCTGAGGTCTTATCATCATGCACTGTAGGCCTTACAGACGACCCAGAGGCTTT
AAATATAAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCT
TGAGGTCTTATCATTTTGCACTGT
Found at i:451385 original size:75 final size:75
Alignment explanation
Indices: 451063--451384 Score: 425
Period size: 75 Copynumber: 4.3 Consensus size: 75
451053 ATATGGGCCC
* * ** ** *
451063 TCAGCATGCCCCAACAATTGCTGATACGCACGTTCAAAATGCGTCAACATTCCTGATTCTGATTG
1 TCAGCATGCCCCATCATTTGCTGATACAAACGTTCAAAACACATCAACATTCCTGATTCTGATTG
451128 AAATGGGCTT
66 AAATGGGCTT
* *
451138 TCAACATGCCCCATCATTTGCTGATACAGACGTTCAAAACACATCAACATTCCT-ATTTCTGATT
1 TCAGCATGCCCCATCATTTGCTGATACAAACGTTCAAAACACATCAACATTCCTGA-TTCTGATT
*
451202 GAAATGGTCTT
65 GAAATGGGCTT
* *
451213 TCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAACACATCAACATTCTTGATTCTGATTG
1 TCAGCATGCCCCATCATTTGCTGATACAAACGTTCAAAACACATCAACATTCCTGATTCTGATTG
451278 AAATGGGCTT
66 AAATGGGCTT
* * * ** * *
451288 TCAGCATGCCCTAAT-ATTTGCTTATACAAACATTCAAAATGCGTCAACATTCGT-ATTTCTGAT
1 TCAGCATGCCC-CATCATTTGCTGATACAAACGTTCAAAACACATCAACATTCCTGA-TTCTGAT
451351 TGAAATGGGCTT
64 TGAAATGGGCTT
451363 TCAGCATGCCCCATCATTTGCT
1 TCAGCATGCCCCATCATTTGCT
451385 TCTTGTTGAT
Statistics
Matches: 219, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
74 4 0.02
75 213 0.97
76 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (75 bp):
TCAGCATGCCCCATCATTTGCTGATACAAACGTTCAAAACACATCAACATTCCTGATTCTGATTG
AAATGGGCTT
Found at i:451414 original size:40 final size:39
Alignment explanation
Indices: 451359--451454 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
451349 ATTGAAATGG
** * * **
451359 GCTTTCAGCATGCCCCATCATTTGCTTCTTGTTGATGTGA
1 GCTTTCAAAATGCCCCAACATTT-CTTCATACTGATGTGA
*
451399 GCTTTCAAAATGCCCCAACATTTTTTCATACTGATGTGA
1 GCTTTCAAAATGCCCCAACATTTCTTCATACTGATGTGA
*
451438 GCCTTCAAAATGCCCCA
1 GCTTTCAAAATGCCCCA
451455 CATGGATCTG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 28 0.58
40 20 0.42
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (39 bp):
GCTTTCAAAATGCCCCAACATTTCTTCATACTGATGTGA
Found at i:453621 original size:72 final size:72
Alignment explanation
Indices: 453503--453645 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
453493 ATATAATAGT
* * * *
453503 ATAACAGGATGGCTGAATATTATCCATAAAGCTGGGGCGATTAACCAATTGCTTTAGGGGGACAA
1 ATAACAGGATAGCTGAATATTATCCATAAAGCCGGGGCGATAAACCAATTACTTTAGGGGGACAA
453568 ATCAAGA
66 ATCAAGA
* * *
453575 ATAACAGGTTAGCTGAATATTATCCATAAAGCCGGGGCTATAAACCAATTACTTTAGGGGGATAA
1 ATAACAGGATAGCTGAATATTATCCATAAAGCCGGGGCGATAAACCAATTACTTTAGGGGGACAA
*
453640 CTCAAG
66 ATCAAG
453646 CTTTATTGTA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (72 bp):
ATAACAGGATAGCTGAATATTATCCATAAAGCCGGGGCGATAAACCAATTACTTTAGGGGGACAA
ATCAAGA
Found at i:454722 original size:16 final size:16
Alignment explanation
Indices: 454701--454735 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
454691 ATCGAGCTCT
454701 TGGATTAAGGGACAAC
1 TGGATTAAGGGACAAC
454717 TGGATTAAGGGACAAC
1 TGGATTAAGGGACAAC
454733 TGG
1 TGG
454736 TGCCATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.20
Consensus pattern (16 bp):
TGGATTAAGGGACAAC
Found at i:455369 original size:7 final size:7
Alignment explanation
Indices: 455335--455374 Score: 57
Period size: 6 Copynumber: 5.9 Consensus size: 7
455325 TAAAAGTACG
455335 AATGCAA
1 AATGCAA
455342 AATG-AA
1 AATGCAA
455348 AATGCAA
1 AATGCAA
455355 AGATGCAA
1 A-ATGCAA
455363 AATGC-A
1 AATGCAA
455369 AATGCA
1 AATGCA
455375 TGTATGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 12 0.40
7 11 0.37
8 7 0.23
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:461782 original size:3 final size:3
Alignment explanation
Indices: 461774--461838 Score: 80
Period size: 3 Copynumber: 22.3 Consensus size: 3
461764 AATTATTTAT
* * * *
461774 TAA TAA TAA TAA T-A TAA TAA TCA TAA T-A TAA TAA TGA TAA TAT TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
461820 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
461839 TTTAAAATGG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
2 4 0.08
3 48 0.92
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:462652 original size:49 final size:50
Alignment explanation
Indices: 462565--462681 Score: 152
Period size: 49 Copynumber: 2.4 Consensus size: 50
462555 ACTACTGAAT
*
462565 AAAATAATAATAAACTAAAGATAATTGTTTAGATTCTATCCTAATTACTA
1 AAAATAATAATAAACTAAAGATAATTGTTTAGACTCTATCCTAATTACTA
* *
462615 AAAATAATAATAAACTAAA-ATTAA-TGTTTTA-ACTCTATCTTAATTCCTA
1 AAAATAATAATAAACTAAAGA-TAATTG-TTTAGACTCTATCCTAATTACTA
462664 AAAA-AATAATAAATCTAA
1 AAAATAATAATAAA-CTAA
462682 TCCTAAAAGA
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
48 9 0.15
49 26 0.43
50 26 0.43
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.35
Consensus pattern (50 bp):
AAAATAATAATAAACTAAAGATAATTGTTTAGACTCTATCCTAATTACTA
Found at i:462668 original size:50 final size:51
Alignment explanation
Indices: 462565--462675 Score: 140
Period size: 50 Copynumber: 2.2 Consensus size: 51
462555 ACTACTGAAT
*
462565 AAAATAATAATAAACTAAAGATAATTGTTTAGATTCTATCCTAATTACT-A
1 AAAATAATAATAAACTAAAGATAATTGTTTAGACTCTATCCTAATTACTAA
* *
462615 AAAATAATAATAAACTAAA-ATTAA-TGTTTTA-ACTCTATCTTAATTCCTAAA
1 AAAATAATAATAAACTAAAGA-TAATTG-TTTAGACTCTATCCTAATTACT-AA
462666 AAAATAATAA
1 AAAATAATAA
462676 ATCTAATCCT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
49 17 0.31
50 26 0.48
51 11 0.20
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (51 bp):
AAAATAATAATAAACTAAAGATAATTGTTTAGACTCTATCCTAATTACTAA
Found at i:474602 original size:117 final size:117
Alignment explanation
Indices: 474385--474754 Score: 295
Period size: 117 Copynumber: 3.2 Consensus size: 117
474375 TCAACAAGAT
* *
474385 TTCATAATGAGAAGAACTCATCCAAAGAGGAAAATAAGTTCATAATGAGACAAACTTGTTCGACA
1 TTCATAATGAGAAGAACTCATCCAAAGAGGAAAAGAAGTTCATAATGAGACAAACTTGTTCAACA
* * ** * * * * *
474450 TTTTGCACAAACCCATTACAGAAGGATGTGGATCAATATTTTTAGTAT-GGAG
66 TTTTGCACAAACCCATCACAAAAAAAGGTGAATCAACATTTTCAAT-TGGGAG
** *
474502 TTCATAATGACG-AGAACTCAT-TTAAGAGGGAGAAGAAGTTCATAATGAGA-AGAACATT-TTC
1 TTCATAATGA-GAAGAACTCATCCAAAGA-GGAAAAGAAGTTCATAATGAGACA-AAC-TTGTTC
* * *
474563 AACCTTTTGCTCAAATCCATCACAAAAAAAGGTGAATCAACATTTTCAATTGGGAG
62 AACATTTTGCACAAACCCATCACAAAAAAAGGTGAATCAACATTTTCAATTGGGAG
* * * * * **
474619 TTCATAATAAGAAGAACCCATCCAAAAAGGAAAAAGAAATTCATAATTAGA-AGAACTTGTTTGA
1 TTCATAATGAGAAGAACTCATCCAAAGAGG-AAAAGAAGTTCATAATGAGACA-AACTTGTTCAA
* * * * * ** * * ***
474683 CTTTTTTCTCAAATCCATCACAGAAGGAGGTGGATCAACCTTTTCAA-CAAGAG
64 CATTTTGCACAAACCCATCACAAAAAAAGGTGAATCAACATTTTCAATTGGGAG
*
474736 TTCATAATGATAAGAACTC
1 TTCATAATGAGAAGAACTC
474755 GTCTATAGAG
Statistics
Matches: 204, Mismatches: 40, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
116 7 0.03
117 126 0.62
118 71 0.35
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.27
Consensus pattern (117 bp):
TTCATAATGAGAAGAACTCATCCAAAGAGGAAAAGAAGTTCATAATGAGACAAACTTGTTCAACA
TTTTGCACAAACCCATCACAAAAAAAGGTGAATCAACATTTTCAATTGGGAG
Found at i:480260 original size:15 final size:15
Alignment explanation
Indices: 480240--480269 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
480230 CTTTCTCATA
480240 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
480255 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
480270 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:481455 original size:30 final size:29
Alignment explanation
Indices: 481421--481492 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 29
481411 TGGTTTTCCA
481421 GAAAATGAATTATTGGAATTTGAATTACTG
1 GAAAATGAATTATTGGAATTTGAATT-CTG
481451 GAAAATGAATTATTGGAATTTGAATTCTG
1 GAAAATGAATTATTGGAATTTGAATTCTG
481480 GAAAAATGAATTA
1 G-AAAATGAATTA
481493 CATTTCTGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 4 0.10
30 37 0.90
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (29 bp):
GAAAATGAATTATTGGAATTTGAATTCTG
Found at i:481489 original size:15 final size:15
Alignment explanation
Indices: 481421--481493 Score: 76
Period size: 15 Copynumber: 4.9 Consensus size: 15
481411 TGGTTTTCCA
*
481421 GAAAATGAATTATTG
1 GAAAATGAATTACTG
**
481436 GAATTTGAATTACTG
1 GAAAATGAATTACTG
*
481451 GAAAATGAATTATTG
1 GAAAATGAATTACTG
**
481466 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
481480 GAAAAATGAATTAC
1 G-AAAATGAATTAC
481494 ATTTCTGGAA
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
14 3 0.07
15 41 0.91
16 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.34
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:481866 original size:23 final size:23
Alignment explanation
Indices: 481822--481894 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
481812 AGTGTTATAT
* *
481822 TATATTTTAAAAATAATAATTAG
1 TATATTTTAAAAATATTAATTAA
*
481845 TATATTTTAAAAATATTTATTAA
1 TATATTTTAAAAATATTAATTAA
* *
481868 AATATTATT-AAAATATATAAATAA
1 TATATT-TTAAAAATAT-TAATTAA
481892 TAT
1 TAT
481895 TATTCATTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 32 0.78
24 9 0.22
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAA
Found at i:481871 original size:12 final size:12
Alignment explanation
Indices: 481854--481883 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
481844 GTATATTTTA
481854 AAAATATTTATT
1 AAAATATTTATT
481866 AAAATA-TTATT
1 AAAATATTTATT
481877 AAAATAT
1 AAAATAT
481884 ATAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AAAATATTTATT
Found at i:481913 original size:19 final size:20
Alignment explanation
Indices: 481861--481913 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
481851 TTAAAAATAT
481861 TTATTAAA-ATATTATTAAA
1 TTATTAAATATATTATTAAA
* *
481880 ATATATAAATAATATTATT-CA
1 TTAT-TAAAT-ATATTATTAAA
481901 TTATTAAATATAT
1 TTATTAAATATAT
481914 AAAATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 4 0.14
22 8 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTAAATATATTATTAAA
Found at i:481960 original size:29 final size:29
Alignment explanation
Indices: 481869--481974 Score: 92
Period size: 29 Copynumber: 3.6 Consensus size: 29
481859 ATTTATTAAA
*
481869 ATATTATTAAAATATATAA-ATAATA-TT
1 ATATTATTAAAATATAAAATATAATATTT
* **
481896 ATTCATTATTAAATATATAAAATTTTTTATTAT
1 A-T-ATTATTAAA-ATATAAAATATAATATT-T
481929 ATATTATTAAAATA-AAAATATAATATCTT
1 ATATTATTAAAATATAAAATATAATAT-TT
* *
481958 ATATTAATATAATATAA
1 ATATTATTAAAATATAA
481975 TTGATTATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.02
28 1 0.02
29 31 0.50
30 13 0.21
31 12 0.19
32 2 0.03
33 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATTATTAAAATATAAAATATAATATTT
Found at i:481989 original size:57 final size:60
Alignment explanation
Indices: 481869--481999 Score: 137
Period size: 59 Copynumber: 2.2 Consensus size: 60
481859 ATTTATTAAA
* **
481869 ATATTATTAAAATATATAAATAATATTATTCATTATTAAATATATAAAATTTTTTATTAT
1 ATATTATTAAAATATATAAATAATAATATTCATTATTAAATATATAAAATTGATTATTAT
* *
481929 ATATTATTAAAATA-A-AAAT-ATAATA-TC-TTATATTAATATAATATAATTGATTATTTTAT
1 ATATTATTAAAATATATAAATAATAATATTCATTAT-TAAATAT-ATAAAATTGATTA--TTAT
*
481988 ATAATATTAAAA
1 ATATTATTAAAA
482000 ACATAATATT
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
55 4 0.07
56 8 0.13
57 15 0.25
58 4 0.07
59 16 0.26
60 14 0.23
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (60 bp):
ATATTATTAAAATATATAAATAATAATATTCATTATTAAATATATAAAATTGATTATTAT
Found at i:482046 original size:54 final size:53
Alignment explanation
Indices: 481941--482046 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 53
481931 ATTATTAAAA
* **
481941 TAAAAATATAATATCTTATATTAATATAATATAATTGATTATTTTATATAATAT
1 TAAAAACATAATA-CTTATATTAATATAATATAATAAATTATTTTATATAATAT
*
481995 TAAAAACATAATA-TTATATTATTATAAATATTAATAAATATATTTTA-ATAAT
1 TAAAAACATAATACTTATATTAATAT-AATA-TAATAAAT-TATTTTATATAAT
482047 TAATATTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
52 11 0.24
53 4 0.09
54 23 0.51
55 7 0.16
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (53 bp):
TAAAAACATAATACTTATATTAATATAATATAATAAATTATTTTATATAATAT
Found at i:482302 original size:42 final size:42
Alignment explanation
Indices: 482224--482341 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
482214 ATGAATTACA
*
482224 TTCCGAAAAACGAATTACGTGAAACAAACAC-GGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
482265 TTTCGGAAAACAAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
482307 TTCCGGAAAACGAATTACATGAAACAAACATGGGA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGA
482342 TTTCGGGGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 28 0.41
42 41 0.59
ACGTcount: A:0.47, C:0.18, G:0.17, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:482983 original size:42 final size:43
Alignment explanation
Indices: 482937--483026 Score: 146
Period size: 43 Copynumber: 2.1 Consensus size: 43
482927 ATAATAAAAT
* *
482937 AATATATTATCGATGAA-TTTTTATATAAATAATTTATATTTA
1 AATATATTACCAATGAATTTTTTATATAAATAATTTATATTTA
*
482979 AATATATTACCAATGAATTTTTTATATAAATAATTTTTATTTA
1 AATATATTACCAATGAATTTTTTATATAAATAATTTATATTTA
483022 AATAT
1 AATAT
483027 TTAAAATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 15 0.34
43 29 0.66
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (43 bp):
AATATATTACCAATGAATTTTTTATATAAATAATTTATATTTA
Found at i:483028 original size:14 final size:15
Alignment explanation
Indices: 482952--483025 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 15
482942 ATTATCGATG
482952 AATTTTTATATAAAT
1 AATTTTTATATAAAT
* *
482967 AATTTATATTTAAAT
1 AATTTTTATATAAAT
*** *
482982 ATATTACCA-ATGAAT
1 A-ATTTTTATATAAAT
482997 --TTTTTATATAAAT
1 AATTTTTATATAAAT
*
483010 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
483025 A
1 A
483026 TTTAAAATTT
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
12 3 0.07
13 5 0.12
15 31 0.72
16 4 0.09
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:484411 original size:29 final size:29
Alignment explanation
Indices: 484378--484450 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
484368 TTTATTATAT
484378 TTATTTACATTTCATCCTTTTACTTTTATG
1 TTATTTACATTTCATCCTTTT-CTTTTATG
* * * *
484408 -TATTTATATTTCTTTTCTTTTCTTTTTTG
1 TTATTTACATTTC-ATCCTTTTCTTTTATG
*
484437 TTATTTACTTTTCA
1 TTATTTACATTTCA
484451 GTACTTTAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.16, C:0.14, G:0.03, T:0.67
Consensus pattern (29 bp):
TTATTTACATTTCATCCTTTTCTTTTATG
Found at i:484591 original size:20 final size:20
Alignment explanation
Indices: 484566--484608 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
484556 ATATTTTATG
*
484566 TTATTTTA-ACATTTGTCATT
1 TTATTTTAGAAATTT-TCATT
484586 TTATTTTAGAAATTTTCATT
1 TTATTTTAGAAATTTTCATT
484606 TTA
1 TTA
484609 GTCCTTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (20 bp):
TTATTTTAGAAATTTTCATT
Found at i:485377 original size:46 final size:46
Alignment explanation
Indices: 485321--485411 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 46
485311 TTGATGTTCT
* ** *
485321 AAATTGATTATTTGATTTAATAAAAT-GATAAAATTAATTAGGTTTC
1 AAATTAATTATTCAATTTAAT-AAATGGATAAAATTAACTAGGTTTC
* *
485367 AAATTAATTATTCAATTTAATAATTGGTTAAAATTAACTAGGTTT
1 AAATTAATTATTCAATTTAATAAATGGATAAAATTAACTAGGTTT
485412 TAATATTAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 3 0.08
46 35 0.92
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (46 bp):
AAATTAATTATTCAATTTAATAAATGGATAAAATTAACTAGGTTTC
Found at i:486912 original size:17 final size:17
Alignment explanation
Indices: 486874--486914 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
486864 ATTTTTTAAA
486874 ATAAAAATATAAAAATT
1 ATAAAAATATAAAAATT
*
486891 ATAAATATATAAAAAATT
1 ATAAAAATAT-AAAAATT
486909 -TAAAAA
1 ATAAAAA
486915 CATTACCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAATATAAAAATT
Found at i:487332 original size:31 final size:32
Alignment explanation
Indices: 487257--487425 Score: 200
Period size: 33 Copynumber: 5.2 Consensus size: 32
487247 ACTTAAAGGC
* *
487257 AAAATATTATATAATATATATTATATAGCTTTG
1 AAAATAGTATAT-ATATATATTATATAGTTTTG
*
487290 AAATTAGTATATAT-TATA-TATATAGTTTTG
1 AAAATAGTATATATATATATTATATAGTTTTG
* *
487320 AAAAATAATATATAGTATATATTATATAGATTTG
1 -AAAATAGTATATA-TATATATTATATAGTTTTG
* *
487354 AAAATAGTATATA-GTATATTAAATAGTTTTG
1 AAAATAGTATATATATATATTATATAGTTTTG
* *
487385 AAAATGGTATATAATATATATTATATAGTTTTA
1 AAAATAGTATAT-ATATATATTATATAGTTTTG
487418 AAAATAGT
1 AAAATAGT
487426 TTTGAAAATA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
30 11 0.10
31 41 0.36
32 4 0.03
33 48 0.42
34 11 0.10
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (32 bp):
AAAATAGTATATATATATATTATATAGTTTTG
Found at i:487339 original size:64 final size:64
Alignment explanation
Indices: 487257--487425 Score: 232
Period size: 64 Copynumber: 2.6 Consensus size: 64
487247 ACTTAAAGGC
* * * * *
487257 AAAATATTATATAATATATATTATATAGCTTTGAAATTAGTATATATTATA-TATATAGTTTTG
1 AAAATAATATATAATATATATTATATAGATTTGAAAATAGTATATAGTATATTAAATAGTTTTG
*
487320 AAAAATAATATATAGTATATATTATATAGATTTGAAAATAGTATATAGTATATTAAATAGTTTTG
1 -AAAATAATATATAATATATATTATATAGATTTGAAAATAGTATATAGTATATTAAATAGTTTTG
** * *
487385 AAAATGGTATATAATATATATTATATAGTTTTAAAAATAGT
1 AAAATAATATATAATATATATTATATAGATTTGAAAATAGT
487426 TTTGAAAATA
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
64 82 0.88
65 11 0.12
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (64 bp):
AAAATAATATATAATATATATTATATAGATTTGAAAATAGTATATAGTATATTAAATAGTTTTG
Found at i:487363 original size:26 final size:26
Alignment explanation
Indices: 487331--487404 Score: 76
Period size: 31 Copynumber: 2.7 Consensus size: 26
487321 AAAATAATAT
487331 ATAGTATATATTATATAGATTTGAAA
1 ATAGTATATATTATATAGATTTGAAA
*
487357 ATAGTATATAGTATATTAAATAGTTTTGAAA
1 ATAGTATATA-T-TA-T--ATAGATTTGAAA
* *
487388 ATGGTATATAATATATA
1 ATAGTATATATTATATA
487405 TTATATAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
26 13 0.32
27 1 0.03
28 3 0.08
29 3 0.08
31 20 0.50
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (26 bp):
ATAGTATATATTATATAGATTTGAAA
Found at i:494432 original size:148 final size:145
Alignment explanation
Indices: 494086--494482 Score: 410
Period size: 148 Copynumber: 2.7 Consensus size: 145
494076 AAAATATTTA
*
494086 TATATAAATAAGATATTTATTTACTTAGAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACAG
1 TATATAAATAAGATATTTATTTATTTA-AAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACAG
* *
494151 CCTATTTCTTAATATTAAAAAATAAATAAATATTATTAAAACATTTCTCTAAAAATAATTAAAAT
65 CCCATTTCTTAATA-TAAAAAATAAATAAATATTATAAAAACATTTCTCTAAAAATAATTAAAAT
494216 AAATTAATATATATAATT
129 -AATTAATATATATAATT
* * * *
494234 TATAAAAATAGGATATATATTTATTTAAGAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAG
1 TATATAAATAAGATATTTATTTATTTAA-AATATCAGAAAAGGACTTCTAGGTGCTTTAAGACAG
* *
494299 CCCATTTCTTAATATAAAAAAATAAATAAATATTA-AAATATGATTATTTTTCTAAGAAAATAAT
65 CCCATTTCTTAATAT-AAAAAATAAATAAATATTATAAA-A--A-CATTTCTCT-A-AAAATAAT
* * * **
494363 T-TAAT-ATGT-AT-TTTCTGGTT
123 TAAAATAAT-TAATATATATAATT
* * * * * *
494383 TTTATAAGTAAGATATTTATTTATTTAAAATA-CTAGAATAGGACATCTAGTTGCTTTAAGACTG
1 TATATAAATAAGATATTTATTTATTTAAAATATC-AGAAAAGGACTTCTAGGTGCTTTAAGACAG
* * * *
494447 TCCTTTTCTTTGATATTAAAAATAAATAAATATTAT
65 CCCATTTC-TTAATATAAAAAATAAATAAATATTAT
494483 TATTTAAACA
Statistics
Matches: 209, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
147 5 0.02
148 144 0.69
149 34 0.16
150 5 0.02
151 8 0.04
152 4 0.02
153 9 0.04
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (145 bp):
TATATAAATAAGATATTTATTTATTTAAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACAGC
CCATTTCTTAATATAAAAAATAAATAAATATTATAAAAACATTTCTCTAAAAATAATTAAAATAA
TTAATATATATAATT
Found at i:494544 original size:12 final size:12
Alignment explanation
Indices: 494530--494570 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
494520 GAATAAGATA
494530 AAAATAATAA-T
1 AAAATAATAATT
494541 AAAATAATAATT
1 AAAATAATAATT
**
494553 AAAGCAATAATT
1 AAAATAATAATT
494565 AAAATA
1 AAAATA
494571 TAAAAGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:494585 original size:12 final size:11
Alignment explanation
Indices: 494530--494589 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
494520 GAATAAGATA
494530 AAAATAATAAT
1 AAAATAATAAT
494541 AAAATAATAATT
1 AAAATAATAA-T
**
494553 AAAGCAATAATT
1 AAAATAATAA-T
494565 AAAAT-AT-A-
1 AAAATAATAAT
*
494573 AAAGTAATAAT
1 AAAATAATAAT
494584 AAAATA
1 AAAATA
494590 CTATTGCAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 17 0.44
12 14 0.36
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:496294 original size:26 final size:26
Alignment explanation
Indices: 496254--496313 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
496244 CAGAGGCATC
* * * *
496254 GTGGCAGCAGCATCGGTGGCCGAGTG
1 GTGGCAGTAGAATCGGCGGACGAGTG
*
496280 GTGGCAGTAGAATCGGCGGACGTGTG
1 GTGGCAGTAGAATCGGCGGACGAGTG
*
496306 GTGACAGT
1 GTGGCAGT
496314 GGGCTCAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.45, T:0.18
Consensus pattern (26 bp):
GTGGCAGTAGAATCGGCGGACGAGTG
Found at i:496608 original size:18 final size:18
Alignment explanation
Indices: 496572--496627 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
496562 TATTATTATT
496572 AATAATAATAATAAAATAA
1 AATAATAATAAT-AAATAA
* *
496591 AATATTTATAATAAATAA
1 AATAATAATAATAAATAA
*
496609 ACTAATAATAA-AAATAA
1 AATAATAATAATAAATAA
496626 AA
1 AA
496628 ATAAATGGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 7 0.23
18 14 0.45
19 10 0.32
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAATAATAATAAATAA
Found at i:503099 original size:15 final size:15
Alignment explanation
Indices: 503081--503119 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
503071 ATAAAAGTAT
503081 AAATGCAAAAATAAA
1 AAATGCAAAAATAAA
* **
503096 AAATGCAAAGATGCA
1 AAATGCAAAAATAAA
503111 AAATGCAAA
1 AAATGCAAA
503120 TGTATGTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.64, C:0.10, G:0.13, T:0.13
Consensus pattern (15 bp):
AAATGCAAAAATAAA
Found at i:503263 original size:43 final size:44
Alignment explanation
Indices: 503201--503284 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 44
503191 TGCATCAAAC
*
503201 AAAACTTTTACATGCAGGGGACAACTTTCACTCCTAACTTCAAT
1 AAAACTTTTACATACAGGGGACAACTTTCACTCCTAACTTCAAT
* * *
503245 AAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AAAACTTTTACATACAGGGGACAACTTTCACTCCTAACTTC
503285 TCTAAAGCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 31 0.86
44 5 0.14
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (44 bp):
AAAACTTTTACATACAGGGGACAACTTTCACTCCTAACTTCAAT
Found at i:505602 original size:12 final size:12
Alignment explanation
Indices: 505588--505628 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
505578 GAATAAGATA
505588 AAAATAATAA-T
1 AAAATAATAATT
505599 AAAATAATAATT
1 AAAATAATAATT
**
505611 AAAGCAATAATT
1 AAAATAATAATT
505623 AAAATA
1 AAAATA
505629 TAAAAGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:505643 original size:12 final size:11
Alignment explanation
Indices: 505588--505647 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
505578 GAATAAGATA
505588 AAAATAATAAT
1 AAAATAATAAT
505599 AAAATAATAATT
1 AAAATAATAA-T
**
505611 AAAGCAATAATT
1 AAAATAATAA-T
505623 AAAAT-AT-A-
1 AAAATAATAAT
*
505631 AAAGTAATAAT
1 AAAATAATAAT
505642 AAAATA
1 AAAATA
505648 CTATTGCAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 17 0.44
12 14 0.36
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:507336 original size:26 final size:26
Alignment explanation
Indices: 507284--507338 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
507274 CAGAGGCATC
* * *
507284 GTGGCAGAAGCATCGGTGGCCGAGTG
1 GTGGCAGAAGAATCGGCGGACGAGTG
* *
507310 GTGGCAGCAGAATCGGCGGACGTGTG
1 GTGGCAGAAGAATCGGCGGACGAGTG
507336 GTG
1 GTG
507339 ACAGTGGGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.47, T:0.16
Consensus pattern (26 bp):
GTGGCAGAAGAATCGGCGGACGAGTG
Found at i:507601 original size:3 final size:3
Alignment explanation
Indices: 507595--507661 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
507585 TTTATTATAT
* *
507595 TAA TAA TAA TAA TAA TAA TAA -AA TAA -AA TAT TTA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* * *
507639 -AC TAA TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
507662 ATGGATAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
2 5 0.10
3 42 0.84
4 3 0.06
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:507638 original size:18 final size:18
Alignment explanation
Indices: 507596--507657 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
507586 TTATTATATT
507596 AATAATAATAATAATAATAA
1 AATAA-AATAATAATAAT-A
* *
507616 AATAAAATATTTATAATA
1 AATAAAATAATAATAATA
*
507634 AATAAACTAATAATAA-A
1 AATAAAATAATAATAATA
507651 AATAAAA
1 AATAAAA
507658 ATAAATGGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 7 0.19
18 14 0.39
19 10 0.28
20 5 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAAATAATAATAATA
Found at i:508185 original size:122 final size:115
Alignment explanation
Indices: 508021--508342 Score: 388
Period size: 122 Copynumber: 2.8 Consensus size: 115
508011 GAATTAATGC
* *
508021 AAGGTTGAACAAGTTTTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * * *
508086 GAACACTT-T-TGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTT-ATGCAA
66 GAAC-TTTATATGGAAATGTTGAT-C-GATCCA--T-C--CAGTGAT-GAATTCA-GCAA
* *
508143 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* * *
508208 GAACTTTCTCTGGAAA---TG-TCGATCCATCGAGTGATGAATTCGAGCAA
66 GAACTTTATATGGAAATGTTGATCGATCCATCCAGTGATGAATTC-AGCAA
508255 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTA
508320 TGAACTTTATATGGAAATGTTGA
65 TGAACTTTATATGGAAATGTTGA
508343 AAACATTCTG
Statistics
Matches: 178, Mismatches: 13, Indels: 23
0.83 0.06 0.11
Matches are distributed among these distances:
111 4 0.02
112 46 0.26
113 41 0.23
114 1 0.01
115 1 0.01
116 2 0.01
117 5 0.03
118 1 0.01
119 1 0.01
120 2 0.01
121 2 0.01
122 66 0.37
123 6 0.03
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (115 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTATATGGAAATGTTGATCGATCCATCCAGTGATGAATTCAGCAA
Found at i:509827 original size:26 final size:26
Alignment explanation
Indices: 509794--509852 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
509784 CAGAGGCATC
* *
509794 GTGGCAGCA-ACATCGGTGGCCGAGTG
1 GTGGCAGCAGA-ATCGGAGGACGAGTG
*
509820 GTGGCAGCAGAATCGGAGGACGTGTG
1 GTGGCAGCAGAATCGGAGGACGAGTG
509846 GTGGCAG
1 GTGGCAG
509853 TGGGCTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.20, C:0.19, G:0.46, T:0.15
Consensus pattern (26 bp):
GTGGCAGCAGAATCGGAGGACGAGTG
Found at i:514129 original size:30 final size:30
Alignment explanation
Indices: 514093--514170 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
514083 TAAACACCAT
*
514093 TTTTCAACACCAACACCTACCACC-CAATTG
1 TTTTCAACACCAACACCCACCACCAC-ATTG
* * *
514123 TTTTCAACACCAACACCCACCATCACTTTT
1 TTTTCAACACCAACACCCACCACCACATTG
514153 TTTTCAACACCAAC-CCCA
1 TTTTCAACACCAACACCCA
514171 TCATCCCTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 4 0.09
30 38 0.88
31 1 0.02
ACGTcount: A:0.32, C:0.41, G:0.01, T:0.26
Consensus pattern (30 bp):
TTTTCAACACCAACACCCACCACCACATTG
Found at i:517022 original size:16 final size:17
Alignment explanation
Indices: 516995--517042 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
516985 CTTAGAAGAA
516995 GAAAAGAAGGAAAAAAG
1 GAAAAGAAGGAAAAAAG
517012 GAAAA-AAGGAAAAAA-
1 GAAAAGAAGGAAAAAAG
* *
517027 GAAGAGAAAGAAAAAA
1 GAAAAGAAGGAAAAAA
517043 AAGAAATGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 4 0.14
16 19 0.68
17 5 0.18
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
GAAAAGAAGGAAAAAAG
Found at i:517024 original size:7 final size:8
Alignment explanation
Indices: 516995--517027 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
516985 CTTAGAAGAA
516995 GAAAAGAAG
1 GAAAA-AAG
517004 GAAAAAAG
1 GAAAAAAG
517012 GAAAAAAG
1 GAAAAAAG
517020 GAAAAAAG
1 GAAAAAAG
517028 AAGAGAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.79
9 5 0.21
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (8 bp):
GAAAAAAG
Found at i:517042 original size:18 final size:21
Alignment explanation
Indices: 517021--517061 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
517011 GGAAAAAAGG
517021 AAAAAAG-AA-GAGAAA-GAA
1 AAAAAAGAAATGAGAAATGAA
517039 AAAAAAGAAATGAGAAATGAA
1 AAAAAAGAAATGAGAAATGAA
517060 AA
1 AA
517062 TGAGGGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 6 0.30
21 5 0.25
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.05
Consensus pattern (21 bp):
AAAAAAGAAATGAGAAATGAA
Found at i:526894 original size:62 final size:62
Alignment explanation
Indices: 526819--526944 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
526809 CTTAACTTTC
526819 AAAATGTACATTTTGGTCACTATCTAAAATTTGGGGTATTATAATTCTATACCCCCAAATAA
1 AAAATGTACATTTTGGTCACTATCTAAAATTTGGGGTATTATAATTCTATACCCCCAAATAA
526881 AAAATGTACATTTTGGTCACTATCTAAAATTTGGGGTATTATAATTCTATACCCCCAAATAA
1 AAAATGTACATTTTGGTCACTATCTAAAATTTGGGGTATTATAATTCTATACCCCCAAATAA
526943 AA
1 AA
526945 TTTGTCATCG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (62 bp):
AAAATGTACATTTTGGTCACTATCTAAAATTTGGGGTATTATAATTCTATACCCCCAAATAA
Found at i:531326 original size:26 final size:26
Alignment explanation
Indices: 531290--531341 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
531280 CGAAGTGCTT
* * *
531290 ATACACATAAGGTCGTGCCTACCATA
1 ATACAAATAAGGTCGTACCCACCATA
531316 ATACAAATAAGGTCGTACCCACCATA
1 ATACAAATAAGGTCGTACCCACCATA
531342 TGTACTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (26 bp):
ATACAAATAAGGTCGTACCCACCATA
Found at i:532510 original size:145 final size:147
Alignment explanation
Indices: 532247--532538 Score: 570
Period size: 145 Copynumber: 2.0 Consensus size: 147
532237 GAAGAATACT
532247 TCCTACATCATTTCTTGCCCTTACATAATTTTTCTCATCCAAACAAGCCATTGTTGAATGCTCTA
1 TCCTACATCATTTCTTGCCCTTACATAATTTTTCTCATCCAAACAAGCCATTGTTGAATGCTCTA
532312 AAGCTCTAAAACTAGGGTTTTCATGGTTTTGCTCAATTTTGATTTGATTCAAGCATGAAATC-AC
66 AAGCTCTAAAACTAGGGTTTTCATGGTTTTGCTCAATTTTGATTTGATTCAAGCATGAAATCAAC
532376 CTCCATCC-ACTTTACA
131 CTCCATCCAACTTTACA
532392 TCCTACATCATTTCTTGCCCTTACATAATTTTTCTCATCCAAACAAGCCATTGTTGAATGCTCTA
1 TCCTACATCATTTCTTGCCCTTACATAATTTTTCTCATCCAAACAAGCCATTGTTGAATGCTCTA
532457 AAGCTCTAAAACTAGGGTTTTCATGGTTTTGCTCAATTTTGATTTGATTCAAGCATGAAATCAAC
66 AAGCTCTAAAACTAGGGTTTTCATGGTTTTGCTCAATTTTGATTTGATTCAAGCATGAAATCAAC
532522 CTCCATCCAACTTTACA
131 CTCCATCCAACTTTACA
532539 ACATATCTAC
Statistics
Matches: 145, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
145 127 0.88
146 10 0.07
147 8 0.06
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (147 bp):
TCCTACATCATTTCTTGCCCTTACATAATTTTTCTCATCCAAACAAGCCATTGTTGAATGCTCTA
AAGCTCTAAAACTAGGGTTTTCATGGTTTTGCTCAATTTTGATTTGATTCAAGCATGAAATCAAC
CTCCATCCAACTTTACA
Found at i:535684 original size:140 final size:140
Alignment explanation
Indices: 535425--535685 Score: 296
Period size: 140 Copynumber: 1.9 Consensus size: 140
535415 AAACTCTTTT
* * * *
535425 ATTTATGGAATAATTTGATTTGGCCTTCACATTAACATGCCCGAAGGTCCAAATTGATTATTCGG
1 ATTTAGGGAATAATTCGATTTGGCCTTCACATTAACATGCCAGAAGCTCCAAATTGATTATTCGG
* * * *
535490 TTTCATAATTGACATAATCAATTAGGGATAACAATTAGAGCCTTCATTTTAGATTTTTCGCACTT
66 ATTCATAATTGACAAAATAAATTAGGGATAACAATTAGAGCCTTCATTTCAGATTTTTCGCACTT
535555 TAGTCCTTAA
131 TAGTCCTTAA
* * * * * *
535565 ATTTAGGGAATAATTCGATTTGGCTTTCACATTAACATGTCATAAGCTCCAAGTTGGTTATT-TG
1 ATTTAGGGAATAATTCGATTTGGCCTTCACATTAACATGCCAGAAGCTCCAAATTGATTATTCGG
** * *
535629 ATTCAATAATTGGTTAAAATAAATTA-GGTTAA-TATTAGAG-CTTCCATTTACAGATTT
66 ATTC-ATAATT-GACAAAATAAATTAGGGATAACAATTAGAGCCTT-CATTT-CAGATTT
535686 AGTCCTCTAG
Statistics
Matches: 99, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
138 3 0.03
139 16 0.16
140 70 0.71
141 10 0.10
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (140 bp):
ATTTAGGGAATAATTCGATTTGGCCTTCACATTAACATGCCAGAAGCTCCAAATTGATTATTCGG
ATTCATAATTGACAAAATAAATTAGGGATAACAATTAGAGCCTTCATTTCAGATTTTTCGCACTT
TAGTCCTTAA
Found at i:542422 original size:15 final size:15
Alignment explanation
Indices: 542404--542436 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
542394 AAATTCTAAA
542404 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
542419 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
542434 TAT
1 TAT
542437 ATTTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:543440 original size:17 final size:17
Alignment explanation
Indices: 543418--543452 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
543408 AATGATCAGG
*
543418 TGAATCATTTGTCATTC
1 TGAATCAATTGTCATTC
543435 TGAATCAATTGTCATTC
1 TGAATCAATTGTCATTC
543452 T
1 T
543453 TTTAACTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (17 bp):
TGAATCAATTGTCATTC
Found at i:549145 original size:24 final size:25
Alignment explanation
Indices: 549091--549138 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
549081 AAAAATAGTG
* *
549091 ACAAGAGTACACGAATGTACTAAAT
1 ACAAGAGTACACAAATGCACTAAAT
*
549116 ACAAGAGTGCACAAATGCACTAA
1 ACAAGAGTACACAAATGCACTAA
549139 TATAAGATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.17
Consensus pattern (25 bp):
ACAAGAGTACACAAATGCACTAAAT
Found at i:553711 original size:21 final size:21
Alignment explanation
Indices: 553687--553726 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
553677 AATTTTATGT
553687 TTTTAATAA-ATAAATAATATA
1 TTTTAATAATATAAA-AATATA
553708 TTTTAATAATATAAAAATA
1 TTTTAATAATATAAAAATA
553727 AAAGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTTAATAATATAAAAATATA
Found at i:553735 original size:24 final size:24
Alignment explanation
Indices: 553685--553752 Score: 56
Period size: 25 Copynumber: 2.9 Consensus size: 24
553675 ATAATTTTAT
*
553685 GTTTTTAATAA-AT--AAATAATA
1 GTTTTTAATAATATAAAAATAAAA
553706 -TATTTTAATAATATAAAAATAAAA
1 GT-TTTTAATAATATAAAAATAAAA
*
553730 GTTTTTTAA-AATATTAAATATAA
1 G-TTTTTAATAATA-TAAAAATAA
553753 TATATATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 1 0.03
21 9 0.24
22 2 0.05
24 11 0.29
25 14 0.37
26 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (24 bp):
GTTTTTAATAATATAAAAATAAAA
Found at i:556843 original size:3 final size:3
Alignment explanation
Indices: 556835--556860 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
556825 TTCTTTTTAT
556835 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
556861 CTGCTATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:558643 original size:3 final size:3
Alignment explanation
Indices: 558631--558666 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
558621 TGTAAATATC
558631 ATA A-A ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
558667 TTTTTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:578222 original size:219 final size:215
Alignment explanation
Indices: 577777--578483 Score: 674
Period size: 219 Copynumber: 3.3 Consensus size: 215
577767 CCTTCCAGAA
* * *
577777 AAACCTTTTTGAAGTCAATTTCAACTCCACGACGGAGGATATTAAGTTC-AAAATCCAAATCG-T
1 AAACCTTTTCGAAGTCAATTTCAACTCCACGATGGAGGATATTGAGTTCGAAAA-CCAAATCGAT
* * * * * *
577840 CTACATTCTACCTTAACTCAGTGCGATGAGCTAGTTTCTAGTTAAAATTTTTAGGCCTAGTTTCA
65 -TGCATTCTAGCTTAACTCAGTGCGAGGAGCTAGTTTCTAATT-AAGTTTTCAGGCC-AGTTTCA
* * * * * * *
577905 ACTTCACGA-AGAAGGATACTTAACCTGGAAACACATCAAGAATCGACTGCATTTTGGCTTAACT
127 ACTTCATGACA-AAGGATACTT-GCCTGAAAATACACCAAGAATTGACTACATTTTGGCTTAACT
* * *
577969 CAATGGGGAGGAGCCACCTTCTAGTC
190 CAGTGGCGAGGAGCCACCTTTTAGTC
* * * *
577995 AGACCTTTTCGAAGTCAATTTCAAGTCCACGATGGAGGATGTTGAGTTCGAAAGCCAAATCGATT
1 AAACCTTTTCGAAGTCAATTTCAACTCCACGATGGAGGATATTGAGTTCGAAAACCAAATCGATT
* * *
578060 GCATTTTAGCTTAACTCGGTGACGAGGAACTAGTTT-TCAATTAATGTTTTCAGGCCAGGTTTCA
66 GCATTCTAGCTTAACTCAGTG-CGAGGAGCTAGTTTCT-AATTAA-GTTTTCAGGCCA-GTTTCA
* * *
578124 ACTTCATGACAAATGATACTTGGCCTGAAAATACACCAAGAATTGATTACATTTTGGCTTTACTC
127 ACTTCATGACAAAGGATACTT-GCCTGAAAATACACCAAGAATTGACTACATTTTGGCTTAACTC
* * ** *
578189 AGTAGCAAGGAGATACCTTTTATTC
191 AGTGGCGAGGAGCCACCTTTTAGTC
* * * *
578214 AAACCTTTT--AAGTCAATTTTAACTCCACGATGGAGGATATTGAGTTTGAAAACTAAATTGATT
1 AAACCTTTTCGAAGTCAATTTCAACTCCACGATGGAGGATATTGAGTTCGAAAACCAAATCGATT
* * *
578277 GTATTCTAGCTTAACTCAACG-GCGAGGAGCTGGTTTCTAATTGAAG-TTTCAGGCTAAGTTTCA
66 GCATTCTAGCTTAACTC-A-GTGCGAGGAGCTAGTTTCTAATT-AAGTTTTCAGGC-CAGTTTCA
* * * * *
578340 ACTTCATGACGAAGGATACTTGACTCGTAAGCATA-TCCAA-AACTGACTACATTTTGGCTTAAC
127 ACTTCATGACAAAGGATACTTGCCT-G-AA-AATACACCAAGAATTGACTACATTTTGGCTTAAC
*
578403 TCAAG-GGCGAGGAGCCACCTTTCAGTC
189 TC-AGTGGCGAGGAGCCACCTTTTAGTC
* * *
578430 AAACCTATTCGAAGTCAATTTCAA-T----GATGGAGGATATTGGGTTC-AAAATCAAAT
1 AAACCTTTTCGAAGTCAATTTCAACTCCACGATGGAGGATATTGAGTTCGAAAACCAAAT
578484 TCAGAATAAA
Statistics
Matches: 402, Mismatches: 69, Indels: 42
0.78 0.13 0.08
Matches are distributed among these distances:
212 8 0.02
213 17 0.04
215 3 0.01
216 80 0.20
217 89 0.22
218 92 0.23
219 112 0.28
220 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (215 bp):
AAACCTTTTCGAAGTCAATTTCAACTCCACGATGGAGGATATTGAGTTCGAAAACCAAATCGATT
GCATTCTAGCTTAACTCAGTGCGAGGAGCTAGTTTCTAATTAAGTTTTCAGGCCAGTTTCAACTT
CATGACAAAGGATACTTGCCTGAAAATACACCAAGAATTGACTACATTTTGGCTTAACTCAGTGG
CGAGGAGCCACCTTTTAGTC
Found at i:579493 original size:2 final size:2
Alignment explanation
Indices: 579421--579477 Score: 84
Period size: 2 Copynumber: 29.5 Consensus size: 2
579411 GTTTTAAAAG
579421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
579463 AT AT A- AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT A
579478 GTAGGTATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.06
2 47 0.92
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:580670 original size:17 final size:17
Alignment explanation
Indices: 580645--580683 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
580635 AGAGTTTGGA
*
580645 GGGTAAGATTTTTTATG
1 GGGTGAGATTTTTTATG
580662 GGGTGAGATTTTTTATG
1 GGGTGAGATTTTTTATG
580679 GGGTG
1 GGGTG
580684 TTACAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.38, T:0.44
Consensus pattern (17 bp):
GGGTGAGATTTTTTATG
Found at i:580960 original size:12 final size:12
Alignment explanation
Indices: 580943--580969 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
580933 TTTCATTAAC
580943 TATTTTATTTTT
1 TATTTTATTTTT
580955 TATTTTATTTTT
1 TATTTTATTTTT
580967 TAT
1 TAT
580970 CCTTTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TATTTTATTTTT
Found at i:588962 original size:15 final size:15
Alignment explanation
Indices: 588944--588977 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
588934 ATACTATGCT
* *
588944 TATATTTTTAGTATA
1 TATATTTTAAATATA
588959 TATATTTTAAATATA
1 TATATTTTAAATATA
588974 TATA
1 TATA
588978 CTTACGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TATATTTTAAATATA
Found at i:592994 original size:30 final size:30
Alignment explanation
Indices: 592960--593019 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
592950 CGCCAGGTGG
* *
592960 TCCGAATGACCTATACAGGTCGCCATGCAA
1 TCCGAACGACATATACAGGTCGCCATGCAA
* *
592990 TCCGAACGACATGTGCAGGTCGCCATGCAA
1 TCCGAACGACATATACAGGTCGCCATGCAA
593020 GCCATGCGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.18
Consensus pattern (30 bp):
TCCGAACGACATATACAGGTCGCCATGCAA
Found at i:593327 original size:17 final size:18
Alignment explanation
Indices: 593302--593335 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
593292 GAGGTAATTT
593302 TTTAATA-TTTAAATTAG
1 TTTAATATTTTAAATTAG
*
593319 TTTATTATTTTAAATTA
1 TTTAATATTTTAAATTA
593336 TTAGTTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAATATTTTAAATTAG
Found at i:593408 original size:23 final size:23
Alignment explanation
Indices: 593376--593430 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
593366 ACAAAAATTT
593376 AGTTA-ATTAGTTTGTTAGTTTA
1 AGTTATATTAGTTTGTTAGTTTA
*
593398 AGTTATATTAGTTTGTTAGTTTT
1 AGTTATATTAGTTTGTTAGTTTA
593421 AGTTATATTA
1 AGTTATATTA
593431 TACGTAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.56
Consensus pattern (23 bp):
AGTTATATTAGTTTGTTAGTTTA
Found at i:593459 original size:35 final size:34
Alignment explanation
Indices: 593435--593542 Score: 121
Period size: 35 Copynumber: 3.2 Consensus size: 34
593425 ATATTATACG
*
593435 TAAATAAAAA-ATTATTTAATTAGTTTGTTAGTTA
1 TAAATAAAAATATTATTTAATTAGTTTATTAG-TA
* *
593469 TATATAAAAATATTATTTAATTAGTTTGTTAGTTA
1 TAAATAAAAATATTATTTAATTAGTTTATTAG-TA
* * * *
593504 TATATAAAAAAAATATTTAATTAGTTTGTTAGT-
1 TAAATAAAAATATTATTTAATTAGTTTATTAGTA
593537 TAAATA
1 TAAATA
593543 GTTTAAGTTA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
33 5 0.07
34 10 0.14
35 54 0.78
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (34 bp):
TAAATAAAAATATTATTTAATTAGTTTATTAGTA
Found at i:596102 original size:18 final size:17
Alignment explanation
Indices: 596060--596106 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
596050 CAATTTAAAA
596060 TAAACTTAAATA-T-GT
1 TAAACTTAAATATTAGT
596075 TAAA-TTAAATATTAGT
1 TAAACTTAAATATTAGT
596091 TATAACTTAAATATTA
1 TA-AACTTAAATATTA
596107 TAATATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.25
15 5 0.18
16 4 0.14
17 2 0.07
18 10 0.36
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (17 bp):
TAAACTTAAATATTAGT
Found at i:597625 original size:31 final size:32
Alignment explanation
Indices: 597537--597631 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 32
597527 GAACCTCGGC
* *
597537 AACTGTCCATAGGTC-CCAAAGAACCTAGGTA
1 AACTGTCCATATGTCTCCAAAGAACATAGGTA
* **
597568 AACTATCCATATGT-TCCTTAGAACATAGGTA
1 AACTGTCCATATGTCTCCAAAGAACATAGGTA
* *
597599 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTCTCCAAAGAACATAGGTA
597630 AA
1 AA
597632 ACCCTCGACT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
31 47 0.92
32 4 0.08
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (32 bp):
AACTGTCCATATGTCTCCAAAGAACATAGGTA
Found at i:598340 original size:64 final size:64
Alignment explanation
Indices: 598229--598376 Score: 192
Period size: 64 Copynumber: 2.3 Consensus size: 64
598219 TCTTTCAATG
* * * * *
598229 AAGGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTAA
1 AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTT-A
* * *
598294 AAGG-ATGCATCGATGCATTAGC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTGTTTTA
1 AAGGAATGCATCGATGCACTA-CTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTA
598357 AAGGAATGCATCGATGCACT
1 AAGGAATGCATCGATGCACT
598377 TATGAATGTG
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
63 5 0.07
64 63 0.86
65 5 0.07
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (64 bp):
AAGGAATGCATCGATGCACTACTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTA
Found at i:601922 original size:15 final size:16
Alignment explanation
Indices: 601902--601934 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
601892 TCACGGGCAT
601902 GGAGCAGTGC-TGCAG
1 GGAGCAGTGCATGCAG
601917 GGAGCAGTGCATGCAG
1 GGAGCAGTGCATGCAG
601933 GG
1 GG
601935 TAGTCACGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.18, G:0.48, T:0.12
Consensus pattern (16 bp):
GGAGCAGTGCATGCAG
Found at i:602019 original size:26 final size:24
Alignment explanation
Indices: 601975--602073 Score: 76
Period size: 26 Copynumber: 3.9 Consensus size: 24
601965 TGCTTACTAA
* *
601975 TATTTTTAATAATTATTTAATAAT
1 TATTATTAATAATGATTTAATAAT
*
601999 TATTATTAATCTAATGATTTAATATT
1 TATTATTAA--TAATGATTTAATAAT
*
602025 TAATGATTTAATAATGATTATTAATAAT
1 T-ATTA-TTAATAATGA-T-TTAATAAT
602053 TATTTATT-ATAAAT-ATTTAAT
1 TA-TTATTAAT-AATGATTTAAT
602074 GATTTAGATT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
24 13 0.21
25 1 0.02
26 23 0.38
27 10 0.16
28 14 0.23
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (24 bp):
TATTATTAATAATGATTTAATAAT
Found at i:602041 original size:11 final size:11
Alignment explanation
Indices: 601979--602167 Score: 51
Period size: 11 Copynumber: 15.2 Consensus size: 11
601969 TACTAATATT
*
601979 TTTAATAATTA
1 TTTAATAATGA
*
601990 TTTAATAATTA
1 TTTAATAATGA
602001 TTATTAATCTAATGA
1 -T-TTAA--TAATGA
602016 TTTAATATTTAATGA
1 TTT-A-A--TAATGA
602031 TTTAATAATGA
1 TTTAATAATGA
*
602042 TTATTAATAATTA
1 -T-TTAATAATGA
602055 TTTATTATAAAT-A
1 TTTA--AT-AATGA
*
602068 TTTAATGATTTAGA
1 TTTAAT-A-AT-GA
*
602082 TTTGATACTACTGA
1 TTT-A-A-TAATGA
602096 TTTAATAATGA
1 TTTAATAATGA
*
602107 TTACTAATAATAAA
1 TT--TAATAAT-GA
*
602121 ATT-ATAA-GA
1 TTTAATAATGA
*
602130 TTTGATAATGA
1 TTTAATAATGA
*
602141 TTTGATAATAATGT
1 -TT--TAATAATGA
602155 TTTAATAATGA
1 TTTAATAATGA
602166 TT
1 TT
602168 AGTTTGATAA
Statistics
Matches: 139, Mismatches: 14, Indels: 50
0.68 0.07 0.25
Matches are distributed among these distances:
9 3 0.02
10 4 0.03
11 46 0.33
12 8 0.06
13 33 0.24
14 24 0.17
15 18 0.13
16 2 0.01
17 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.48
Consensus pattern (11 bp):
TTTAATAATGA
Done.