Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007782.1 Hibiscus syriacus cultivar Beakdansim tig00110065_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: 3900615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 19
Found at i:3102575 original size:177 final size:178
Alignment explanation
Indices: 3102271--3102643 Score: 694
Period size: 177 Copynumber: 2.1 Consensus size: 178
3102261 TTCAGTTACG
3102271 ATCAGAGGACCAAATTAAACAAAATACAAAGTTGAGGAACTAAATTGCAAAAAAAAAGGAAATTT
1 ATCAG-GGACCAAATTAAACAAAATACAAAGTTGAGGAACTAAATTGC-AAAAAAAAGGAAATTT
*
3102336 GTTGTCACAAAGAGAAATTGGAGGTACAAATATATTCTGCAATGGTTGAGGAGCATGTCGTTCGA
64 GTTGTCACAAAGAGAAATTGGAGGTACAAATATATTCTACAATGGTTGAGGAGCATGTCGTTCGA
*
3102401 ATTTGGTCAAAATGAACTTAAAATGGAGGAGTAATTGAAGAAACATGAAA
129 ATTTGGTCAAAATGAACTTAAAATGGAGGAGTAATTGAAGAAACAAGAAA
3102451 ATCAGGGACCAAATTAAACAAAATACAAAGTTGAGGAACTAAATTGC-AAAAAAAGGAAATTTGT
1 ATCAGGGACCAAATTAAACAAAATACAAAGTTGAGGAACTAAATTGCAAAAAAAAGGAAATTTGT
3102515 TGTCACAAAGAGAAATTGGAGGTACAAATATATTCTACAATGGTTGAGGAGCATGTCGTTCGAAT
66 TGTCACAAAGAGAAATTGGAGGTACAAATATATTCTACAATGGTTGAGGAGCATGTCGTTCGAAT
3102580 TTGGTCAAAATGAACTTAAAATGGAGGAGTAATTGAAGAAACAAGAAA
131 TTGGTCAAAATGAACTTAAAATGGAGGAGTAATTGAAGAAACAAGAAA
*
3102628 ATCAGGGACTAAATTA
1 ATCAGGGACCAAATTA
3102644 CAAAACAATA
Statistics
Matches: 190, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
177 143 0.75
179 42 0.22
180 5 0.03
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.23
Consensus pattern (178 bp):
ATCAGGGACCAAATTAAACAAAATACAAAGTTGAGGAACTAAATTGCAAAAAAAAGGAAATTTGT
TGTCACAAAGAGAAATTGGAGGTACAAATATATTCTACAATGGTTGAGGAGCATGTCGTTCGAAT
TTGGTCAAAATGAACTTAAAATGGAGGAGTAATTGAAGAAACAAGAAA
Found at i:3108656 original size:2 final size:2
Alignment explanation
Indices: 3108651--3108677 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3108641 TTATTATTAT
3108651 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
3108678 TAAATAAAAA
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:3110237 original size:20 final size:22
Alignment explanation
Indices: 3110149--3110237 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 22
3110139 TAATTCTTTC
*
3110149 ATTTTAATTATTA-TTAT-TTT
1 ATTTTAATTATTACTTATGATT
3110169 ATTTT-ATTATTACGTT-TGATAT
1 ATTTTAATTATTAC-TTATGAT-T
3110191 ATGTTTAAATTATTATCTTCATGATT
1 AT-TTT-AATTATTA-CTT-ATGATT
*
3110217 ATTTT-ATTATTA-TTATTATT
1 ATTTTAATTATTACTTATGATT
3110237 A
1 A
3110238 AGTTATATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 20
0.72 0.03 0.25
Matches are distributed among these distances:
19 7 0.12
20 12 0.21
21 5 0.09
22 3 0.05
23 10 0.18
25 12 0.21
26 4 0.07
27 4 0.07
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTTAATTATTACTTATGATT
Found at i:3110595 original size:16 final size:18
Alignment explanation
Indices: 3110574--3110606 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3110564 ATATTTCTAA
3110574 ATAAA-TAA-ATATTTTT
1 ATAAATTAATATATTTTT
3110590 ATAAATTAATATATTTT
1 ATAAATTAATATATTTT
3110607 CTTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATAAATTAATATATTTTT
Found at i:3112778 original size:19 final size:16
Alignment explanation
Indices: 3112735--3112767 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3112725 ACATTCACAC
3112735 TTTT-ATATTTGCATT
1 TTTTCATATTTGCATT
3112750 TTTTCATATTTGCATT
1 TTTTCATATTTGCATT
3112766 TT
1 TT
3112768 ACGTTCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTCATATTTGCATT
Found at i:3114163 original size:15 final size:15
Alignment explanation
Indices: 3114143--3114192 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3114133 ATCCATTAGT
3114143 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
3114158 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
3114172 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
3114188 TTTTA
1 TTTTA
3114193 TTTTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 1 0.04
17 4 0.14
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:3114611 original size:16 final size:18
Alignment explanation
Indices: 3114590--3114622 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3114580 ATATTTCTAA
3114590 ATAAA-TAA-ATATTTTT
1 ATAAATTAATATATTTTT
3114606 ATAAATTAATATATTTT
1 ATAAATTAATATATTTT
3114623 CTTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATAAATTAATATATTTTT
Found at i:3117625 original size:114 final size:114
Alignment explanation
Indices: 3117425--3117648 Score: 367
Period size: 114 Copynumber: 2.0 Consensus size: 114
3117415 GTTCCACGTT
*
3117425 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * * *
3117490 GTTTGGTATGAACCTCAAAACCAATCATTAGATTTGAAATATGAATTTG
66 GTTCGATAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
*
3117539 CTCATAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
3117604 GTTCGATAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
66 GTTCGATAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
3117649 CTGCATAATT
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTCGATAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
Found at i:3120228 original size:22 final size:22
Alignment explanation
Indices: 3120197--3120251 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
3120187 ATCTACACTC
*
3120197 TTCAAAGATGATAGATTCTTTT
1 TTCAAAGATGATAGATTCTCTT
*
3120219 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
3120241 TTCAAAGATGA
1 TTCAAAGATGA
3120252 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:3121023 original size:76 final size:76
Alignment explanation
Indices: 3120924--3121684 Score: 1285
Period size: 76 Copynumber: 10.0 Consensus size: 76
3120914 CTATTTCCCA
*
3120924 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTCCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
3120989 AGCCTTAGGGT
66 AGCCTTAGGGT
3121000 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
3121065 AACCTTAGGGT
66 AGCCTTAGGGT
3121076 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
3121141 AACCTTAGGGT
66 AGCCTTAGGGT
3121152 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
3121216 AGCCTTAGGGT
66 AGCCTTAGGGT
3121227 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
3121292 AACCTTAGGGT
66 AGCCTTAGGGT
3121303 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGATCTTTTTGATGTTTT-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGATCTTTTTGATGTTTTCA
*
3121367 AAGACTTAGGGT
65 AAGCCTTAGGGT
* *
3121379 CATCTGTAAGACCTTCAATGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
3121443 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
3121454 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
* *
3121519 ACCCTCAGGGT
66 AGCCTTAGGGT
* * *
3121530 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
* *
3121595 ACCCTCAGGGT
66 AGCCTTAGGGT
* * * * *
3121606 CATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
* *
3121671 ACCCTCAGGGT
66 AGCCTTAGGGT
3121682 CAT
1 CAT
3121685 TCATAAGACC
Statistics
Matches: 664, Mismatches: 18, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
75 174 0.26
76 460 0.69
77 30 0.05
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:3121320 original size:227 final size:227
Alignment explanation
Indices: 3120924--3121684 Score: 1303
Period size: 227 Copynumber: 3.3 Consensus size: 227
3120914 CTATTTCCCA
*
3120924 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTCCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
3120989 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
3121054 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
3121119 GGGATCTTTTTGATGTTTTCAAAACCTTAGGGT
196 GGGATCTTTTTGATGTTTT-AAAACCTTAGGGT
3121152 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
3121216 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
3121281 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTT
131 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTT
3121346 CGGGATCTTTTTGATGTTTTAAAGA-CTTAGGGT
195 CGGGATCTTTTTGATGTTTTAAA-ACCTTAGGGT
* *
3121379 CATCTGTAAGACCTTCAATGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
* *
3121443 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
* * *
3121508 GATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
* * *
3121573 GGGAGCTTTTTGATGTTTTTAAACCCTCAGGGT
196 GGGATCTTTTTGATG-TTTTAAAACCTTAGGGT
* * * * *
3121606 CATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
* *
3121671 ACCCTCAGGGTCAT
66 AGCCTTAGGGTCAT
3121685 TCATAAGACC
Statistics
Matches: 508, Mismatches: 19, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
226 25 0.05
227 377 0.74
228 106 0.21
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (227 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
GGGATCTTTTTGATGTTTTAAAACCTTAGGGT
Found at i:3121695 original size:303 final size:303
Alignment explanation
Indices: 3120924--3121684 Score: 1285
Period size: 303 Copynumber: 2.5 Consensus size: 303
3120914 CTATTTCCCA
*
3120924 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTCCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
3120989 AGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
66 AACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
* * *
3121054 GATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTTAAAACCTTAGGGTCATCTGTAAGACCTTCAATGCATGATGTTTCCAAAAAGCCTTC
*
3121119 GGGATCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
196 GGGATCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCC
* * *
3121184 AAAAAGCCTTCGGGATCTTTTGATGTTTTCAAAGCCTTAGGGT
261 AAAAAGCCTTCGGGAGCTTTTGATGTTTTCAAACCCTCAGGGT
3121227 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
3121292 AACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGATCTTTT
66 AACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGATCTTTT
3121357 TGATG-TTTTAAAGA-CTTAGGGTCATCTGTAAGACCTTCAATGCATGATGTTTCCAAAAAGCCT
130 TGATGTTTTTAAA-ACCTTAGGGTCATCTGTAAGACCTTCAATGCATGATGTTTCCAAAAAGCCT
*
3121420 TCGGGATCTTTTTGATGTTTT-AAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTT
194 TCGGGATCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTT
3121484 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCCTCAGGGT
259 CCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAAACCCTCAGGGT
* * *
3121530 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
* * * * * *
3121595 ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTT
66 AACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
* *
3121660 GATGTTTTTAAACCCTCAGGGTCAT
131 GATGTTTTTAAAACCTTAGGGTCAT
3121685 TCATAAGACC
Statistics
Matches: 432, Mismatches: 21, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
302 83 0.19
303 322 0.75
304 27 0.06
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (303 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AACCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTT
GATGTTTTTAAAACCTTAGGGTCATCTGTAAGACCTTCAATGCATGATGTTTCCAAAAAGCCTTC
GGGATCTTTTTGATGTTTTCAAAACCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCC
AAAAAGCCTTCGGGAGCTTTTGATGTTTTCAAACCCTCAGGGT
Found at i:3123338 original size:15 final size:15
Alignment explanation
Indices: 3123318--3123367 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3123308 ATCCATTAGT
3123318 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
3123333 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
3123347 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
3123363 TTTTA
1 TTTTA
3123368 TTTTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 1 0.04
17 4 0.14
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:3123466 original size:4 final size:4
Alignment explanation
Indices: 3123457--3123489 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
3123447 ATTTATATAA
3123457 TATT TATT TATT TATT TATT TATT TATT CTATT
1 TATT TATT TATT TATT TATT TATT TATT -TATT
3123490 CGTTTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:3123797 original size:16 final size:18
Alignment explanation
Indices: 3123776--3123808 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3123766 ATATTTCTAA
3123776 ATAAA-TAA-ATATTTTT
1 ATAAATTAATATATTTTT
3123792 ATAAATTAATATATTTT
1 ATAAATTAATATATTTT
3123809 CTTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATAAATTAATATATTTTT
Found at i:3125600 original size:2 final size:2
Alignment explanation
Indices: 3125589--3125618 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3125579 TGTTATAATT
3125589 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3125619 GTTCCTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3125613 original size:28 final size:28
Alignment explanation
Indices: 3125560--3125615 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
3125550 TCCACTTAAA
*
3125560 TTATAATATTATTATATAATGTTATAAT
1 TTATAATATTATTATATAATGATATAAT
3125588 TTATAATATATATATATATATAT-ATATA
1 TTATAATAT-TAT-TATATA-ATGATATA
3125616 TATGTTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 9 0.38
29 3 0.12
30 10 0.42
31 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
TTATAATATTATTATATAATGATATAAT
Found at i:3128907 original size:21 final size:21
Alignment explanation
Indices: 3128881--3128920 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3128871 CAGAACCCCA
*
3128881 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3128902 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3128921 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3128952 original size:21 final size:23
Alignment explanation
Indices: 3128901--3128952 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3128891 GATTCCCCTG
3128901 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTTCCCCTTCA
**
3128924 AAGGGGGAATCGGTT-CCC-TCA
1 TGGGGGGAATCGGTTCCCCTTCA
3128945 TGGGGGGA
1 TGGGGGGA
3128953 TCAATTCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCGGTTCCCCTTCA
Found at i:3139775 original size:20 final size:21
Alignment explanation
Indices: 3139746--3139801 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
3139736 TTTGTTCTTC
*
3139746 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
3139766 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
3139788 ATGCATCGATGCAT
1 ATGCATCGATGCAT
3139802 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:3141370 original size:21 final size:21
Alignment explanation
Indices: 3141328--3141371 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3141318 ACCCCGGGAG
*
3141328 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
3141349 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
3141370 CT
1 CT
3141372 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:3142425 original size:19 final size:19
Alignment explanation
Indices: 3142401--3142439 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3142391 TCAAATGCAT
3142401 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
3142420 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
3142439 T
1 T
3142440 GAATTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:3142456 original size:65 final size:63
Alignment explanation
Indices: 3142338--3142546 Score: 197
Period size: 65 Copynumber: 3.2 Consensus size: 63
3142328 TATTCAAAGG
** * *
3142338 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAATTAATT-GAACATCAAATGCAT
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC--TGAATTTTTTCAAACATCGAATGCAT
*
3142401 TC
62 TT
3142403 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATTTTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCTGAATTTTTTC-AAACATCGAATGCATTT
* ** *** * ** *
3142468 GATGCATAGATGCACAAGCCATGCATCGATGCATCAGGCTATTTCTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAAT-TTTTTCAAACATCGAATGCATTT
*
3142532 CATGCATCGATGCAC
1 CATGCACCGATGCAC
3142547 ACTTGGTGCA
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
63 8 0.07
64 50 0.41
65 62 0.51
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCTGAATTTTTTCAAACATCGAATGCATTT
Found at i:3145317 original size:18 final size:17
Alignment explanation
Indices: 3145281--3145324 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3145271 CGCCATGGTC
3145281 ATATTTACTATTTGTTTT
1 ATATTTA-TATTTGTTTT
*
3145299 ATATTTATATTTTTATTT
1 ATATTTATATTTGT-TTT
*
3145317 ATTTTTAT
1 ATATTTAT
3145325 TATAACTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
ATATTTATATTTGTTTT
Found at i:3149773 original size:95 final size:94
Alignment explanation
Indices: 3149609--3149793 Score: 273
Period size: 95 Copynumber: 2.0 Consensus size: 94
3149599 ATATTATTTA
* * * *
3149609 TATACAATAAAGTTTGAGTTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGACTTTATGGATGAT
1 TATACAATAAAGTTTGAGCTGTCCCTATAAAGCAATTGGTTAAATGCCCCGACTTTATGGATAAC
*
3149674 ATTCAGCTAGCCTGATAAAGGCTATTATAC
66 ATTCAGCTAACCTGATAAAGG-TATTATAC
* * *
3149704 TATACAATAAA-TCTTGAGCTGTCCCTATAAGGTAATTGGTTAAATGCCCCGGCTTTATGGATAA
1 TATACAATAAAGT-TTGAGCTGTCCCTATAAAGCAATTGGTTAAATGCCCCGACTTTATGGATAA
3149768 CATTCAGCTAACCTGATAAAGGTATT
65 CATTCAGCTAACCTGATAAAGGTATT
3149794 TACATATTGA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 5 0.06
95 76 0.94
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (94 bp):
TATACAATAAAGTTTGAGCTGTCCCTATAAAGCAATTGGTTAAATGCCCCGACTTTATGGATAAC
ATTCAGCTAACCTGATAAAGGTATTATAC
Found at i:3151262 original size:36 final size:36
Alignment explanation
Indices: 3151175--3151511 Score: 286
Period size: 36 Copynumber: 9.4 Consensus size: 36
3151165 TTGAATCTGT
* *
3151175 TTTCT-TTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
3151210 TTTCT-TTAAAACAAATTTTATCTCTCTTGAGACAT
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
*
3151245 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGAAAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * *
3151281 TTTCCCTTGAAACAAAATCTTTGAATCTATTTTCCTTGAGACAG
1 TTTCTCTTAAAAC-AAAT-TTTG--TC---TCT-CTTGAGACAG
*
3151325 TTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
3151361 TTTCCCTTGAAACAAA------ATCT-TTGA-ATCTG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGA-CAG
* * * *
3151390 TTT-TCCTTTAAATAAATTTCGTCTCCCTTGAGACAG
1 TTTCT-CTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
3151426 TTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAT
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
**
3151462 TTTCTCTT-AAA-ATGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
3151496 TTTCCCTTGAAACAAA
1 TTTCTCTTAAAACAAA
3151512 ATCTTTGAAT
Statistics
Matches: 241, Mismatches: 39, Indels: 43
0.75 0.12 0.13
Matches are distributed among these distances:
28 1 0.00
29 18 0.07
30 3 0.01
34 27 0.11
35 44 0.18
36 103 0.43
37 8 0.03
38 4 0.02
40 4 0.02
42 4 0.02
43 6 0.02
44 19 0.08
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (36 bp):
TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:3151336 original size:80 final size:80
Alignment explanation
Indices: 3151235--3151397 Score: 290
Period size: 80 Copynumber: 2.0 Consensus size: 80
3151225 TTTTATCTCT
*
3151235 CTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTGAAACAAAATC
1 CTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTGAAACAAAATC
3151300 TTTGAATCTATTTTC
66 TTTGAATCTATTTTC
* *
3151315 CTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC
1 CTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTGAAACAAAATC
*
3151380 TTTGAATCTGTTTTC
66 TTTGAATCTATTTTC
3151395 CTT
1 CTT
3151398 TAAATAAATT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (80 bp):
CTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGAAAGTTTCCCTTGAAACAAAATC
TTTGAATCTATTTTC
Found at i:3151338 original size:44 final size:43
Alignment explanation
Indices: 3151271--3151397 Score: 142
Period size: 44 Copynumber: 3.1 Consensus size: 43
3151261 TTTTGTCTCT
*
3151271 CTTGAGAAAGTTTCCCTTGAAACAAAATCTTTGAATCTATTTTC
1 CTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT-TTTTC
** * *
3151315 CTTGAGACAGTTTCTTTTAAAAC-AAAT-TTTG--TC--TCT-
1 CTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTTTTTC
3151351 CTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTC
1 CTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT-TTTTC
3151395 CTT
1 CTT
3151398 TAAATAAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
36 20 0.30
37 6 0.09
38 4 0.06
40 4 0.06
42 4 0.06
43 6 0.09
44 22 0.33
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (43 bp):
CTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTTTTTC
Found at i:3151408 original size:65 final size:63
Alignment explanation
Indices: 3151338--3151564 Score: 224
Period size: 65 Copynumber: 3.4 Consensus size: 63
3151328 CTTTTAAAAC
*
3151338 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTTAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTT-CTTTAAA
* ** * * *
3151402 TAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGA-C-ATTTT
1 -AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAA------ATCT-TTGA-ATCTGTTTT
3151465 CTCTTAAA
57 CT-TTAAA
** * *
3151473 ATGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTTCTTGAAA
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTG-TTTTCTTTAAA
3151537 CAAATTTTGTCTCCCTTGAGACAGTTTC
1 -AAATTTTGTCTCCCTTGAGACAGTTTC
3151565 TTTTAAAACA
Statistics
Matches: 129, Mismatches: 20, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 7 0.05
65 64 0.50
70 34 0.26
71 12 0.09
72 5 0.04
73 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (63 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCTTTAAA
Found at i:3151559 original size:135 final size:134
Alignment explanation
Indices: 3151341--3151712 Score: 541
Period size: 135 Copynumber: 2.7 Consensus size: 134
3151331 TTAAAACAAA
* *
3151341 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTTAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTAAAACAAA
*
3151406 TTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTA
66 TTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTT-
3151471 AAATG
130 AAATG
* *
3151476 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTAAAACAAA
3151541 TTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTA
66 TTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTA
* *
3151606 ATTT
131 AATG
* * *
3151610 TTTTGTCTCTCTTGAGACAGTCTCTCTTGAAGCACAAAATCTTTTAA-CT-TATTTCCCTTAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAA--ACAAAATCTTTGAATCTGT-TTT-CCTTAAAA
* * * **
3151673 CAAAATTTTGTTTACCTTGAGACCGTTTCTCATAAAACAA
62 C-AAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAA
3151713 CAAATATCTT
Statistics
Matches: 216, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
134 33 0.15
135 130 0.60
136 20 0.09
137 33 0.15
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.43
Consensus pattern (134 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTAAAACAAA
TTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTA
AATG
Found at i:3151575 original size:36 final size:36
Alignment explanation
Indices: 3151524--3151606 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
3151514 CTTTGAATCT
* *
3151524 GTTTTTCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACA
* *
3151560 GTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACA
*
3151596 TTTTCTCTTAA
1 GTTTCTCTTAA
3151607 TTTTTTTGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.46
Consensus pattern (36 bp):
GTTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACA
Found at i:3152226 original size:2 final size:2
Alignment explanation
Indices: 3152217--3152262 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3152207 TATATAATGT
3152217 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3152258 TA TA T
1 TA TA T
3152263 GTTCCTTTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3153507 original size:13 final size:13
Alignment explanation
Indices: 3153489--3153546 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
3153479 TATTATTTTC
3153489 TTTTCTATTTTAA
1 TTTTCTATTTTAA
3153502 TTTTCTATTTT-A
1 TTTTCTATTTTAA
* *
3153514 TTTACTCATTTTTA
1 TTTTCT-ATTTTAA
* * *
3153528 CTTTCTTTTTTAT
1 TTTTCTATTTTAA
3153541 TTTTCT
1 TTTTCT
3153547 TTTATTTCTA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
12 6 0.17
13 25 0.69
14 5 0.14
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTCTATTTTAA
Found at i:3153515 original size:18 final size:17
Alignment explanation
Indices: 3153466--3153516 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
3153456 TCTTTTATTA
3153466 TTTCTATTGTTATTATTAT
1 TTTCTATT-TTATT-TTAT
3153485 TTTCT-TTTCTATTTTAAT
1 TTTCTATTT-TATTTT-AT
3153503 TTTCTATTTTATTT
1 TTTCTATTTTATTT
3153517 ACTCATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.10
18 18 0.62
19 8 0.28
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTCTATTTTATTTTAT
Found at i:3153685 original size:9 final size:9
Alignment explanation
Indices: 3153671--3153709 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
3153661 CTTTCCTTCG
3153671 TTTTATTTA
1 TTTTATTTA
*
3153680 TTTTATCTA
1 TTTTATTTA
3153689 TTTTATTTA
1 TTTTATTTA
3153698 -TTTATTTA
1 TTTTATTTA
3153706 TTTT
1 TTTT
3153710 TCTCTCTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTATTTA
Found at i:3153703 original size:26 final size:26
Alignment explanation
Indices: 3153672--3153722 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3153662 TTTCCTTCGT
3153672 TTTATTTATTTTATCTAT-TTTATTTA
1 TTTATTTATTTT-TCTATCTTTATTTA
*
3153698 TTTATTTATTTTTCTCTCTTTATTT
1 TTTATTTATTTTTCTATCTTTATTT
3153723 GTATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTATTTATTTTTCTATCTTTATTTA
Found at i:3153710 original size:18 final size:18
Alignment explanation
Indices: 3153671--3153709 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
3153661 CTTTCCTTCG
3153671 TTTTATTTATTTTATCTA
1 TTTTATTTATTTTATCTA
*
3153689 TTTTATTTA-TTTATTTA
1 TTTTATTTATTTTATCTA
3153706 TTTT
1 TTTT
3153710 TCTCTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATTTATTTTATCTA
Found at i:3156319 original size:53 final size:53
Alignment explanation
Indices: 3156234--3156353 Score: 177
Period size: 53 Copynumber: 2.3 Consensus size: 53
3156224 GGGCACGTGC
*
3156234 CCACCCTGGAATTCGAATTTCTTTATACTAGTTCCTCATTTTACTGAAGGTGT
1 CCACCCTGGAATTTGAATTTCTTTATACTAGTTCCTCATTTTACTGAAGGTGT
* ** *
3156287 CCACCCTGGAATTTGAATTTCTTTATATTAGTTGTTCATTTTACTTAAGGTGT
1 CCACCCTGGAATTTGAATTTCTTTATACTAGTTCCTCATTTTACTGAAGGTGT
* *
3156340 CCATCCTGAAATTT
1 CCACCCTGGAATTT
3156354 TATCCCATAC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.42
Consensus pattern (53 bp):
CCACCCTGGAATTTGAATTTCTTTATACTAGTTCCTCATTTTACTGAAGGTGT
Found at i:3157694 original size:14 final size:14
Alignment explanation
Indices: 3157675--3157705 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3157665 GAAGGGTTAG
3157675 GGTAGTAGATGATA
1 GGTAGTAGATGATA
3157689 GGTAGTAGATGATA
1 GGTAGTAGATGATA
3157703 GGT
1 GGT
3157706 TATAGTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (14 bp):
GGTAGTAGATGATA
Found at i:3160179 original size:23 final size:23
Alignment explanation
Indices: 3160149--3160249 Score: 125
Period size: 23 Copynumber: 4.3 Consensus size: 23
3160139 AGTCGAGGGT
*
3160149 TCTATGTGGTCATTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
*
3160172 TCTATGTGGTCCTTTGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
*
3160195 TCTATG-GGATCTTTCAGGG-CAAA
1 TCTATGTGG-TCCTTC-GGGACAAA
*
3160218 CCTATGTGGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
3160241 TTCTATGTG
1 -TCTATGTG
3160250 ACACTTCGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
22 5 0.08
23 49 0.74
24 12 0.18
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACAAA
Found at i:3160270 original size:46 final size:45
Alignment explanation
Indices: 3160168--3160271 Score: 113
Period size: 46 Copynumber: 2.2 Consensus size: 45
3160158 TCATTCGGGA
* *
3160168 CAAATCTATGTGGTCCTTTGGGACAAATCTATGGGATCTTTCAGGG
1 CAAAT-TATGTGGTCCTTCGGGACAAATCTATGGGATCCTTCAGGG
* *
3160214 CAAACCTATGTGGTCCTTCGGGACAAATTCTATGTGA-CACTTC-GGTG
1 CAAA-TTATGTGGTCCTTCGGGACAAA-TCTATGGGATC-CTTCAGG-G
3160261 CAAATTATGTG
1 CAAATTATGTG
3160272 AGCAGTTGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
46 33 0.67
47 16 0.33
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (45 bp):
CAAATTATGTGGTCCTTCGGGACAAATCTATGGGATCCTTCAGGG
Found at i:3163802 original size:45 final size:44
Alignment explanation
Indices: 3163700--3164007 Score: 277
Period size: 45 Copynumber: 6.9 Consensus size: 44
3163690 TCTAACTTAA
* *
3163700 CTTAAACCCGCGAAGGGGAGTCAT-CGAA-AGT-ATTCTTCACATGG
1 CTTAAACCCGCGAAGGGGAGTCATCCGAAGAATCA-T-TTCACCT-G
* * * *
3163744 CTTAAACCCGCGAAGGAGAGTCGTCTGATGAATCATTTCACCTG
1 CTTAAACCCGCGAAGGGGAGTCATCCGAAGAATCATTTCACCTG
* * * *
3163788 ACTTAAACCTGCGAAGGGGAGTCATCCAAAGAATTC-CTTCACATGG
1 -CTTAAACCCGCGAAGGGGAGTCATCCGAAGAA-TCATTTCACCT-G
*
3163834 CTTGAAA-CCGCGAAGGGGAGTCATCCGAAGAATCATTTCAACTTG
1 CTT-AAACCCGCGAAGGGGAGTCATCCGAAGAATCATTTC-ACCTG
* * *
3163879 TTTAAACCCGCGAAGGGGAGTCATCCAAAGAATCATGTCACCTTG
1 CTTAAACCCGCGAAGGGGAGTCATCCGAAGAATCATTTCACC-TG
* * * ** * *
3163924 CTTAAACCCGTGAAGAGGAGTCGTTTGAATAATCATTTCACCTCA
1 CTTAAACCCGCGAAGGGGAGTCATCCGAAGAATCATTTCACCT-G
* *
3163969 CTTAAACCCGTGAAGGGGAGTCATCCAAAGAAT-ATTTCA
1 CTTAAACCCGCGAAGGGGAGTCATCCGAAGAATCATTTCA
3164008 TCGAGCTTAA
Statistics
Matches: 214, Mismatches: 38, Indels: 24
0.78 0.14 0.09
Matches are distributed among these distances:
44 37 0.17
45 164 0.77
46 12 0.06
47 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (44 bp):
CTTAAACCCGCGAAGGGGAGTCATCCGAAGAATCATTTCACCTG
Found at i:3163855 original size:90 final size:90
Alignment explanation
Indices: 3163699--3164001 Score: 382
Period size: 90 Copynumber: 3.4 Consensus size: 90
3163689 ATCTAACTTA
* * *
3163699 ACTTAAACCCGCGAAGGGGAGTCATCGAAAGTATT-CTTCACATGGCTTAAACCCGCGAAGGAGA
1 ACTTAAACCCGCGAAGGGGAGTCATCCAAAGAATTCCTTCACATGGCTTAAACCCGCGAAGGGGA
3163763 GTCGTCTGATGAATCATTTCACCTG
66 GTCGTCTGATGAATCATTTCACCTG
*
3163788 ACTTAAACCTGCGAAGGGGAGTCATCCAAAGAATTCCTTCACATGGCTTGAAA-CCGCGAAGGGG
1 ACTTAAACCCGCGAAGGGGAGTCATCCAAAGAATTCCTTCACATGGCTT-AAACCCGCGAAGGGG
* * * *
3163852 AGTCATCCGAAGAATCATTTCAACTTG
65 AGTCGTCTGATGAATCATTTC-ACCTG
* * * * * *
3163879 -TTTAAACCCGCGAAGGGGAGTCATCCAAAGAA-TCATGTCACCTTGCTTAAACCCGTGAAGAGG
1 ACTTAAACCCGCGAAGGGGAGTCATCCAAAGAATTCCT-TCACATGGCTTAAACCCGCGAAGGGG
* *
3163942 AGTCGTTTGAAT-AATCATTTCACCTC
65 AGTCGTCTG-ATGAATCATTTCACCTG
*
3163968 ACTTAAACCCGTGAAGGGGAGTCATCCAAAGAAT
1 ACTTAAACCCGCGAAGGGGAGTCATCCAAAGAAT
3164002 ATTTCATCGA
Statistics
Matches: 183, Mismatches: 23, Indels: 14
0.83 0.10 0.06
Matches are distributed among these distances:
89 41 0.22
90 134 0.73
91 8 0.04
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (90 bp):
ACTTAAACCCGCGAAGGGGAGTCATCCAAAGAATTCCTTCACATGGCTTAAACCCGCGAAGGGGA
GTCGTCTGATGAATCATTTCACCTG
Found at i:3164256 original size:9 final size:8
Alignment explanation
Indices: 3164229--3164289 Score: 54
Period size: 9 Copynumber: 7.2 Consensus size: 8
3164219 ACTTCAAGGG
3164229 TTTATATA
1 TTTATATA
3164237 -TTATATA
1 TTTATATA
3164244 -TTATAGTA
1 TTTATA-TA
3164252 TTTATATTA
1 TTTATA-TA
*
3164261 TATATAGTA
1 TTTATA-TA
3164270 TTATATATA
1 TT-TATATA
3164279 TTATATATA
1 TT-TATATA
3164288 TT
1 TT
3164290 ATAATTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
7 12 0.26
8 2 0.04
9 28 0.61
10 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (8 bp):
TTTATATA
Found at i:3164287 original size:21 final size:20
Alignment explanation
Indices: 3164231--3164288 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
3164221 TTCAAGGGTT
3164231 TATATATTATATATTATAGTA
1 TATATATTATATA-TATAGTA
* *
3164252 TTTATATTATATATAGTATTA
1 TATATATTATATATA-TAGTA
3164273 TATATATTATATATAT
1 TATATATTATATATAT
3164289 TATAATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.09
21 30 0.91
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TATATATTATATATATAGTA
Found at i:3164290 original size:9 final size:9
Alignment explanation
Indices: 3164238--3164292 Score: 71
Period size: 9 Copynumber: 6.2 Consensus size: 9
3164228 GTTTATATAT
3164238 TATATATTA
1 TATATATTA
3164247 TAGTAT-TTA
1 TA-TATATTA
3164256 TAT-TA-TA
1 TATATATTA
3164263 TATAGTATTA
1 TATA-TATTA
3164273 TATATATTA
1 TATATATTA
3164282 TATATATTA
1 TATATATTA
3164291 TA
1 TA
3164293 ATTTTTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 6 0.15
8 1 0.02
9 25 0.61
10 9 0.22
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (9 bp):
TATATATTA
Found at i:3164292 original size:7 final size:7
Alignment explanation
Indices: 3164230--3164286 Score: 66
Period size: 7 Copynumber: 8.1 Consensus size: 7
3164220 CTTCAAGGGT
3164230 TTATATA
1 TTATATA
3164237 TTATATA
1 TTATATA
3164244 TTATAGTA
1 TTATA-TA
3164252 TT-TATA
1 TTATATA
3164258 TTATATA
1 TTATATA
3164265 -TAGTAT-
1 TTA-TATA
3164271 TATATATA
1 T-TATATA
3164279 TTATATA
1 TTATATA
3164286 T
1 T
3164287 ATTATAATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.14
7 31 0.70
8 7 0.16
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (7 bp):
TTATATA
Found at i:3164367 original size:21 final size:21
Alignment explanation
Indices: 3164335--3164385 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3164325 TTTTTTGGAA
3164335 AATATA-TA-TTATAATATAT
1 AATATATTATTTATAATATAT
*
3164354 AATATATTATTTATATTATAT
1 AATATATTATTTATAATATAT
* *
3164375 TATTTATTATT
1 AATATATTATT
3164386 AATACTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 6 0.22
20 2 0.07
21 19 0.70
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATATATTATTTATAATATAT
Found at i:3164368 original size:14 final size:14
Alignment explanation
Indices: 3164351--3164381 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3164341 TATTATAATA
3164351 TATAATATATTATT
1 TATAATATATTATT
*
3164365 TATATTATATTATT
1 TATAATATATTATT
3164379 TAT
1 TAT
3164382 TATTAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATAATATATTATT
Found at i:3165795 original size:17 final size:17
Alignment explanation
Indices: 3165773--3165812 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3165763 TTTGGTCCTT
*
3165773 TTTTATTTATTTATTTA
1 TTTTATTTACTTATTTA
*
3165790 TTTTATTTACTTATTTT
1 TTTTATTTACTTATTTA
3165807 TTTTAT
1 TTTTAT
3165813 CTAAATTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTACTTATTTA
Found at i:3165796 original size:13 final size:13
Alignment explanation
Indices: 3165774--3165812 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3165764 TTGGTCCTTT
3165774 TTTA-TTTATTTA
1 TTTATTTTATTTA
3165786 TTTATTTTATTTA
1 TTTATTTTATTTA
* *
3165799 CTTATTTTTTTTA
1 TTTATTTTATTTA
3165812 T
1 T
3165813 CTAAATTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:3174596 original size:54 final size:54
Alignment explanation
Indices: 3174532--3174639 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
3174522 CTAGTTACAT
* *
3174532 TATATAAAACTCTTTAGTTTTACACTGATTTAGGATCATTGATGAATGTAAATC
1 TATATAAAACTCATTAATTTTACACTGATTTAGGATCATTGATGAATGTAAATC
3174586 TATATAAAACTCATTAATTTTACACTGATTTAGGATCATTGATGAATGTAAATC
1 TATATAAAACTCATTAATTTTACACTGATTTAGGATCATTGATGAATGTAAATC
3174640 AATGACCGAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (54 bp):
TATATAAAACTCATTAATTTTACACTGATTTAGGATCATTGATGAATGTAAATC
Found at i:3180375 original size:21 final size:21
Alignment explanation
Indices: 3180350--3180418 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
3180340 ATATCGTTAA
3180350 TATACTATGAATCATGAATAT
1 TATACTATGAATCATGAATAT
* * *
3180371 TATACATAT-AAACAT-ACTAG
1 TATAC-TATGAATCATGAATAT
*
3180391 TAGTATGTATGAATCATGAATAT
1 TA-TA-CTATGAATCATGAATAT
3180414 TATAC
1 TATAC
3180419 ATATAAACAT
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
20 5 0.14
21 15 0.43
22 10 0.29
23 5 0.14
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
TATACTATGAATCATGAATAT
Found at i:3180404 original size:43 final size:43
Alignment explanation
Indices: 3180355--3180439 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
3180345 GTTAATATAC
3180355 TATGAATCATGAATATTATACATATAAACATACTAGTAGTATG
1 TATGAATCATGAATATTATACATATAAACATACTAGTAGTATG
3180398 TATGAATCATGAATATTATACATATAAACATACTAGTAGTAT
1 TATGAATCATGAATATTATACATATAAACATACTAGTAGTAT
3180440 TAGAGTATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (43 bp):
TATGAATCATGAATATTATACATATAAACATACTAGTAGTATG
Found at i:3181614 original size:88 final size:90
Alignment explanation
Indices: 3181440--3181602 Score: 287
Period size: 88 Copynumber: 1.8 Consensus size: 90
3181430 TAATCCCAAA
* *
3181440 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
3181505 TAGGGTAACTTAGATATAAGAGGAT
66 TAGGGTAACTTAGATATAAGAGGAT
3181530 TATTAAATTCCAATTAATT-AA-ATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
3181592 TAGGGTAACTT
66 TAGGGTAACTT
3181603 GGCTATAAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
87 23 0.32
88 29 0.41
89 2 0.03
90 17 0.24
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.39
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
TAGGGTAACTTAGATATAAGAGGAT
Found at i:3187882 original size:2 final size:2
Alignment explanation
Indices: 3187875--3187918 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3187865 TATGAAGGGA
*
3187875 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3187917 AT
1 AT
3187919 CAGTCACCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3192710 original size:143 final size:142
Alignment explanation
Indices: 3192444--3192728 Score: 507
Period size: 143 Copynumber: 2.0 Consensus size: 142
3192434 TGATTTGGAG
* *
3192444 GAGCAAAAAATAGAACGTTGTGGCTAGATCAAGTACAAAAGTTGAGTTTAGGGTAATGGCACTTG
1 GAGCAAAAAACAAAACGTTGTGGCTAGATCAAGTACAAAAGTTGAGTTTAGGGTAATGGCACTTG
3192509 GGATTGTGAGTTATTATGGCTGAAAATTATCTTTGAAGACTTGAAGGTCAAGTGGGAAGGTCCAA
66 GGATTGTGAGTTATTATGGCTGAAAATTATCTTTGAAGACTTGAAGGTCAAGTGGGAAGGTCCAA
*
3192574 TGAAACTGTATT
131 TGAAACTATATT
* *
3192586 GAGCAAAAAACAAAATGTTGTGGCTAGATCAAGTACAGAAGTTGAGTTTAGGGTAATGGCACTTG
1 GAGCAAAAAACAAAACGTTGTGGCTAGATCAAGTACAAAAGTTGAGTTTAGGGTAATGGCACTTG
*
3192651 GGATTTGTGAGTTATTATGGCTGAAAATTATCTTTGAATACTTGAAGGTCAAGTGGGAAGGTCCA
66 GGA-TTGTGAGTTATTATGGCTGAAAATTATCTTTGAAGACTTGAAGGTCAAGTGGGAAGGTCCA
3192716 ATGAAACTATATT
130 ATGAAACTATATT
3192729 TTTGATAATA
Statistics
Matches: 136, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
142 64 0.47
143 72 0.53
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (142 bp):
GAGCAAAAAACAAAACGTTGTGGCTAGATCAAGTACAAAAGTTGAGTTTAGGGTAATGGCACTTG
GGATTGTGAGTTATTATGGCTGAAAATTATCTTTGAAGACTTGAAGGTCAAGTGGGAAGGTCCAA
TGAAACTATATT
Found at i:3197317 original size:147 final size:147
Alignment explanation
Indices: 3197110--3197404 Score: 468
Period size: 147 Copynumber: 2.0 Consensus size: 147
3197100 TTATTTAAAT
* * * *
3197110 ACTAAACGTATAATTTACTCAAAAATTATTTTTTAGTTAATTCTTTTTAGTCAC-TTTTTTTTAA
1 ACTAAACGCATAATTTACTCAAAAATTAATTTTTACTTAATTCATTTTAGTCACTTTTTTTTTAA
3197174 TTTGGAAGCTAAAAATA-TTTTTAATAGTAAAAATACTTTTTTATAATTTCCAAAATGAATTTTT
66 TTTGGAAGCTAAAAATATTTTTTAATAGTAAAAATACTTTTTTATAATTTCCAAAATG-ATTTTT
* *
3197238 TTTGGTTTGCAATAAGGAA
130 TTT-GTGTGCAACAAGGAA
* * *
3197257 ACTAAACGCATAATTTACTCAAAAATTAATTTTTACTTCATTCATTTTAGTCGCTTTTTTTTTAT
1 ACTAAACGCATAATTTACTCAAAAATTAATTTTTACTTAATTCATTTTAGTCACTTTTTTTTTAA
*
3197322 TTTTGAAGCTAAAAATATTTTTTAATAGTAAAAATACTTTTTTATAATTTCCAAAATGATTTTTT
66 TTTGGAAGCTAAAAATATTTTTTAATAGTAAAAATACTTTTTTATAATTTCCAAAATGATTTTTT
3197387 TTGTGTGCAACAAGGAA
131 TTGTGTGCAACAAGGAA
3197404 A
1 A
3197405 TTCTATAATG
Statistics
Matches: 136, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
147 62 0.46
148 34 0.25
149 40 0.29
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.46
Consensus pattern (147 bp):
ACTAAACGCATAATTTACTCAAAAATTAATTTTTACTTAATTCATTTTAGTCACTTTTTTTTTAA
TTTGGAAGCTAAAAATATTTTTTAATAGTAAAAATACTTTTTTATAATTTCCAAAATGATTTTTT
TTGTGTGCAACAAGGAA
Found at i:3199265 original size:19 final size:18
Alignment explanation
Indices: 3199243--3199285 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3199233 TATTTATTTC
*
3199243 ATATTATGTAATTTTATAT
1 ATATTACGT-ATTTTATAT
*
3199262 ATATATACGTATTTTTTAT
1 ATAT-TACGTATTTTATAT
3199281 ATATT
1 ATATT
3199286 TTATCTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.76
20 4 0.19
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (18 bp):
ATATTACGTATTTTATAT
Found at i:3202266 original size:60 final size:59
Alignment explanation
Indices: 3202192--3202342 Score: 180
Period size: 60 Copynumber: 2.5 Consensus size: 59
3202182 AATAAAATAT
** *
3202192 ATTTAAAAAATATATTTTGTTATTA-ATTTATGTTCAAATAATATATTTTATTTTTTTATTA
1 ATTT-AAAAATATATTTTGTTATTATA-TTAACTTCAAAT-ATATATTTTATTCTTTTATTA
*
3202253 ATTTAAAATTATATTTTGTTATTATATTAACTTCAAATATATATTTTATTCTTTTATTA
1 ATTTAAAAATATATTTTGTTATTATATTAACTTCAAATATATATTTTATTCTTTTATTA
* * *
3202312 ACTTAAAAGATCA-ATTTTATTATTATCTTAA
1 ATTTAAAA-AT-ATATTTTGTTATTATATTAA
3202343 GTTAATAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
59 27 0.34
60 46 0.58
61 6 0.08
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (59 bp):
ATTTAAAAATATATTTTGTTATTATATTAACTTCAAATATATATTTTATTCTTTTATTA
Found at i:3202298 original size:30 final size:30
Alignment explanation
Indices: 3202194--3202347 Score: 125
Period size: 30 Copynumber: 5.1 Consensus size: 30
3202184 TAAAATATAT
* * **
3202194 TTAAAAAATATATTTTGTTATTA-ATTTATG
1 TTAAAATATATATTTTATTATTATA-TTAAC
* * * *
3202224 TTCAAATAATATATTTTATTTTTTTATTAAT
1 TTAAAAT-ATATATTTTATTATTATATTAAC
*
3202255 TTAAAAT-TATATTTTGTTATTATATTAAC
1 TTAAAATATATATTTTATTATTATATTAAC
* * *
3202284 TTCAAATATATATTTTATTCTTTTATTAAC
1 TTAAAATATATATTTTATTATTATATTAAC
* * *
3202314 TTAAAAGATCA-ATTTTATTATTATCTTAAG
1 TTAAAATAT-ATATTTTATTATTATATTAAC
3202344 TTAA
1 TTAA
3202348 TAAATAAAGA
Statistics
Matches: 98, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
29 24 0.24
30 50 0.51
31 23 0.23
32 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (30 bp):
TTAAAATATATATTTTATTATTATATTAAC
Found at i:3203826 original size:20 final size:20
Alignment explanation
Indices: 3203801--3203840 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3203791 TTTGGTTCAC
* *
3203801 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTACCAGTG
3203821 GGAATAAAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
3203841 AATATGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.25
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:3212428 original size:17 final size:17
Alignment explanation
Indices: 3212403--3212435 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
3212393 ACGTGTGTTG
3212403 AACAGAAGTTGGTGTTTA
1 AACAGAAG-TGGTGTTTA
3212421 AACA-AAGTGGTGTTT
1 AACAGAAGTGGTGTTT
3212436 GCAGTAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 3 0.20
18 4 0.27
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (17 bp):
AACAGAAGTGGTGTTTA
Found at i:3213509 original size:22 final size:22
Alignment explanation
Indices: 3213484--3213537 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
3213474 AGTTAAAATA
3213484 AGAATAAAATATATTTTGAATT
1 AGAATAAAATATATTTTGAATT
*
3213506 AGAATAAAATATATTTTGAGTT
1 AGAATAAAATATATTTTGAATT
*
3213528 AAAATAAAAT
1 AGAATAAAAT
3213538 TAAAATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (22 bp):
AGAATAAAATATATTTTGAATT
Found at i:3226919 original size:18 final size:20
Alignment explanation
Indices: 3226874--3226923 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3226864 CTCATGTGGG
3226874 GAGTATCGATACTCTAACATT
1 GAGTATCGATACTCT-ACATT
3226895 G-GTATCGATACTCT-CA-T
1 GAGTATCGATACTCTACATT
3226912 GAGTATCGATAC
1 GAGTATCGATAC
3226924 CAAAATTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.07
18 12 0.43
20 13 0.46
21 1 0.04
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (20 bp):
GAGTATCGATACTCTACATT
Found at i:3226989 original size:20 final size:19
Alignment explanation
Indices: 3226960--3227012 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
3226950 TTACCACCCA
3226960 TATCGATACTACCCTCTGAG
1 TATCGATACTACCC-CTGAG
* *
3226980 TATTGATACTAGACCCTGAG
1 TATCGATACTA-CCCCTGAG
*
3227000 TATCGATATTACC
1 TATCGATACTACC
3227013 TTTATAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (19 bp):
TATCGATACTACCCCTGAG
Found at i:3231571 original size:2 final size:2
Alignment explanation
Indices: 3231564--3231588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3231554 CCTCTCCTTA
3231564 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3231589 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3233066 original size:46 final size:47
Alignment explanation
Indices: 3233004--3233097 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
3232994 GAGAATTACC
* *
3233004 TAATATTAAATAAATAAATAAT-ATAATATTTGATCTTTTAATGCCA
1 TAATATTAAATAAATAAATAATAATAATATTTAATCTTTGAATGCCA
* * **
3233050 TAATTTTAAATTAATAAATAATAATTTTATTTAATCTTTGAATGCCA
1 TAATATTAAATAAATAAATAATAATAATATTTAATCTTTGAATGCCA
3233097 T
1 T
3233098 TTCCTGAAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
46 20 0.49
47 21 0.51
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (47 bp):
TAATATTAAATAAATAAATAATAATAATATTTAATCTTTGAATGCCA
Found at i:3233998 original size:43 final size:43
Alignment explanation
Indices: 3233945--3234047 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
3233935 TGGATAAGAT
* *
3233945 AAAATAAAAGAAAGACAAAGAAAAGAATAAT-AGTAAATTAAATA
1 AAAAT-AAAGAAAGACAAAGAAAAGAAAAATAAATAAA-TAAATA
* *
3233989 AAAATAAAGAAACAAAAAGAAAAGAAAAATAAATAAATAAATA
1 AAAATAAAGAAAGACAAAGAAAAGAAAAATAAATAAATAAATA
*
3234032 AATA-AAAGAAAAGACA
1 AAAATAAAG-AAAGACA
3234048 TAAAAAAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
42 4 0.08
43 36 0.72
44 10 0.20
ACGTcount: A:0.75, C:0.03, G:0.10, T:0.13
Consensus pattern (43 bp):
AAAATAAAGAAAGACAAAGAAAAGAAAAATAAATAAATAAATA
Found at i:3234240 original size:19 final size:20
Alignment explanation
Indices: 3234218--3234267 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 20
3234208 GATAATATAT
3234218 ATATATATAATAAATA-AAA
1 ATATATATAATAAATAGAAA
*
3234237 ATATA-A-AA-AAATAGTAA
1 ATATATATAATAAATAGAAA
3234254 ATATATAT-ATAAAT
1 ATATATATAATAAAT
3234268 TAATAAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
16 5 0.19
17 9 0.35
18 3 0.12
19 9 0.35
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
ATATATATAATAAATAGAAA
Found at i:3234272 original size:23 final size:22
Alignment explanation
Indices: 3234211--3234273 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
3234201 ACGAAATGAT
*
3234211 AATATATATATATATAATAAATA
1 AATATATATATAAATAAT-AATA
* *
3234234 AA-A-ATATA-AAAAAATAGTA
1 AATATATATATAAATAATAATA
3234253 AATATATATATAAATTAATAA
1 AATATATATATAAA-TAATAA
3234274 AACAAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 10 0.32
22 4 0.13
23 6 0.19
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AATATATATATAAATAATAATA
Found at i:3234298 original size:40 final size:39
Alignment explanation
Indices: 3234204--3234303 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 39
3234194 AAGATAAACG
*
3234204 AAATGATAATATATATATATATAATAAATAAAAATATAAAA
1 AAAT-ATAA-ATATATATATATAATAAATAAAAAAATAAAA
* *
3234245 AAATAGTAAATATATATATA-AATTAATAAAACAAATAATGA
1 AAATA-TAAATATATATATATAATAAATAAAA-AAATAA-AA
3234286 AAAT-TAACATATATATAT
1 AAATATAA-ATATATATAT
3234304 GTGTAATCTA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
39 13 0.25
40 27 0.52
41 12 0.23
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (39 bp):
AAATATAAATATATATATATAATAAATAAAAAAATAAAA
Found at i:3235396 original size:84 final size:85
Alignment explanation
Indices: 3235289--3235446 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 85
3235279 ATAATTTTAT
* * * *
3235289 TGATAGATAACCCTTATTGCCTTGAGCTATGCTATAAATAATGTG-CCTTAGAGCTGAGCATAGT
1 TGATAGATAACCCTTATAGCCTTGAGCTAGGCTATAAATAATGTGCCCTTAAAGCTGAGCATAAT
3235353 CGAACTCGAAGGTCTTTTGG
66 CGAACTCGAAGGTCTTTTGG
* * * * **
3235373 TGATAGATAACCCTTCTAGCCTTGAGTTAGGCTGTAAATGATGTGCCCTTAAAGCTGAGTGTAAT
1 TGATAGATAACCCTTATAGCCTTGAGCTAGGCTATAAATAATGTGCCCTTAAAGCTGAGCATAAT
3235438 CGAACTCGA
66 CGAACTCGA
3235447 GGGTTTGGTG
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
84 39 0.62
85 24 0.38
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (85 bp):
TGATAGATAACCCTTATAGCCTTGAGCTAGGCTATAAATAATGTGCCCTTAAAGCTGAGCATAAT
CGAACTCGAAGGTCTTTTGG
Found at i:3235526 original size:33 final size:34
Alignment explanation
Indices: 3235454--3235538 Score: 136
Period size: 36 Copynumber: 2.5 Consensus size: 34
3235444 CGAGGGTTTG
*
3235454 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGG--TTTTTTT
3235490 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
3235523 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
3235539 TGCATTCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 22 0.46
36 26 0.54
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (34 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
Found at i:3235700 original size:30 final size:30
Alignment explanation
Indices: 3235664--3235722 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3235654 GTAAAACATA
*
3235664 TTCAAAGATTT-TGTTTCAA-AGGAAACTGTT
1 TTCAAAG-TTTATGCTTCAAGA-GAAACTGTT
3235694 TTCAAAGTTTATGCTTCAAGAGAAACTGT
1 TTCAAAGTTTATGCTTCAAGAGAAACTGT
3235723 CTCAAGGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 22 0.85
31 1 0.04
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (30 bp):
TTCAAAGTTTATGCTTCAAGAGAAACTGTT
Found at i:3235753 original size:34 final size:35
Alignment explanation
Indices: 3235708--3235788 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
3235698 AAGTTTATGC
* * * *
3235708 TTCAAGAGAAACTGTCTCAAGGGAGACAAAGTT-T
1 TTCAAGGGAAACTATCTCAAGAGAGACAAAATTAT
* *
3235742 TTCAAGGGAAACTATCTCATGAGTGACAAAATTCAT
1 TTCAAGGGAAACTATCTCAAGAGAGACAAAATT-AT
3235778 TTCAAGGGAAA
1 TTCAAGGGAAA
3235789 TGTTTATGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 27 0.69
36 12 0.31
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (35 bp):
TTCAAGGGAAACTATCTCAAGAGAGACAAAATTAT
Found at i:3235888 original size:89 final size:90
Alignment explanation
Indices: 3235700--3235880 Score: 262
Period size: 89 Copynumber: 2.0 Consensus size: 90
3235690 TGTTTTCAAA
* * *
3235700 GTTTATGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAGTTTTTCAAGGGAAACTATCTCATGAG
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAGTTTTTCAAGGGAAACTATCGCAAGAG
*
3235765 TGACAAAATTCATTTCAAGGGAAAT
66 AGACAAAATTCATTTCAAGGGAAAT
* * *
3235790 GTTTATGTTTCAAGAG-AACTGTCTCAAGGGAGACAAATTTGTTTCAATGGAACCTAT-GCAAGA
1 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAGTT-TTTCAAGGGAAACTATCGCAAGA
3235853 GAGAC-AAATTCATTTC-AGGGAAAT
65 GAGACAAAATTCATTTCAAGGGAAAT
3235877 GTTT
1 GTTT
3235881 TAATGTTTAT
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
87 12 0.14
88 11 0.13
89 31 0.37
90 29 0.35
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (90 bp):
GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAGTTTTTCAAGGGAAACTATCGCAAGAG
AGACAAAATTCATTTCAAGGGAAAT
Found at i:3236039 original size:65 final size:65
Alignment explanation
Indices: 3235965--3236086 Score: 176
Period size: 65 Copynumber: 1.9 Consensus size: 65
3235955 ACGAAATTTG
*
3235965 TTTCAAGGGAAACAT-ATTCAAAGATTT-TGTTTCAAGAGAAACTATCTTAAGAGAGACAAAATT
1 TTTCAAGGGAAA-ATGATTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
3236028 CA
64 CA
* * *
3236030 TTTCAAGGGAAAATGTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTTCAAGGGAAAATGATTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
3236087 GAAACTTAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
64 5 0.10
65 46 0.90
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (65 bp):
TTTCAAGGGAAAATGATTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:3236141 original size:19 final size:21
Alignment explanation
Indices: 3236113--3236162 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3236103 AGAAAATGTC
*
3236113 TCAAGGGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
3236134 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
3236155 TCAAGAGA
1 TCAAGAGA
3236163 AACCATCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:3236212 original size:73 final size:72
Alignment explanation
Indices: 3236135--3236314 Score: 211
Period size: 73 Copynumber: 2.5 Consensus size: 72
3236125 AAATTTGTTT
* * * *
3236135 CAAGAGAGACAAAATTTGTTTCAAGAGAAACCATCTTGACTGAAATAAATCTTCTTTCGAGTGAA
1 CAAGAGAGACAAAACTGGTTTCAAGAAAAACAATCTTGACTGAAATAAATCTTCTTTCGAGT-AA
** *
3236200 AATGGTTC
65 AACAGTCC
* * *
3236208 CAAGAGAGACAAAACTGGTTTTAAGAAAAACAATCTTGAGTGGAATAAATCTTCTTTCGAGTAAA
1 CAAGAGAGACAAAACTGGTTTCAAGAAAAACAATCTTGACTGAAATAAATCTTCTTTCGAGTAAA
3236273 ACAGTCC
66 ACAGTCC
* *
3236280 CAAGTGAGACAAAGTA-TGCTTT-AAGAAAAACAATC
1 CAAGAGAGACAAA--ACTGGTTTCAAGAAAAACAATC
3236315 ACAAGTGAGA
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
72 32 0.34
73 60 0.65
74 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (72 bp):
CAAGAGAGACAAAACTGGTTTCAAGAAAAACAATCTTGACTGAAATAAATCTTCTTTCGAGTAAA
ACAGTCC
Found at i:3241857 original size:9 final size:9
Alignment explanation
Indices: 3241839--3241910 Score: 60
Period size: 9 Copynumber: 8.1 Consensus size: 9
3241829 AAGAAAAGAA
3241839 AAAT-AAAT
1 AAATAAAAT
3241847 AAATAAAAT
1 AAATAAAAT
*
3241856 AAA-AGACAT
1 AAATA-AAAT
3241865 AAA-AAAAT
1 AAATAAAAT
3241873 AAATAAAAT
1 AAATAAAAT
** *
3241882 CCATAAAAGC
1 AAATAAAA-T
*
3241892 AAATGAAAT
1 AAATAAAAT
3241901 AAATAAAAT
1 AAATAAAAT
3241910 A
1 A
3241911 CTAGAAAATA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
8 11 0.22
9 34 0.68
10 5 0.10
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.18
Consensus pattern (9 bp):
AAATAAAAT
Found at i:3241888 original size:30 final size:29
Alignment explanation
Indices: 3241827--3241910 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 29
3241817 TAAAGAAACG
*
3241827 AAAAGAAAAGAAAAATAAAT-AAATAAAAT
1 AAAAGCAAA-AAAAATAAATAAAATAAAAT
**
3241856 AAAAGACATAAAAAAATAAATAAAAT-CCAT
1 AAAAG-CA-AAAAAAATAAATAAAATAAAAT
**
3241886 AAAAGCAAATGAAATAAATAAAATA
1 AAAAGCAAAAAAAATAAATAAAATA
3241911 CTAGAAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
28 15 0.33
29 7 0.15
30 18 0.39
31 6 0.13
ACGTcount: A:0.74, C:0.05, G:0.06, T:0.15
Consensus pattern (29 bp):
AAAAGCAAAAAAAATAAATAAAATAAAAT
Found at i:3243264 original size:32 final size:34
Alignment explanation
Indices: 3243224--3243298 Score: 118
Period size: 32 Copynumber: 2.2 Consensus size: 34
3243214 CTGAGACATA
*
3243224 AAATAAAATAATAAAAGAAAAC-AAAT-TAAAAT
1 AAATAAAATAATAAAACAAAACGAAATATAAAAT
3243256 AAATAAAATAATAAAACAAAACGAAATAATAAAAT
1 AAATAAAATAATAAAACAAAACGAAAT-ATAAAAT
3243291 AAATAAAA
1 AAATAAAA
3243299 ACAAAAAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 21 0.54
33 4 0.10
35 14 0.36
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (34 bp):
AAATAAAATAATAAAACAAAACGAAATATAAAAT
Found at i:3243271 original size:27 final size:27
Alignment explanation
Indices: 3243221--3243304 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 27
3243211 TGGCTGAGAC
*
3243221 ATAAAATAAAATAATAA-AAGAAAACAAA
1 ATAAAAT-AAATAA-AATAATAAAACAAA
*
3243249 TTAAAATAAATAAAATAATAAAACAAA
1 ATAAAATAAATAAAATAATAAAACAAA
**
3243276 ACGAAAT-AATAAAATAAATAAAAACAAA
1 ATAAAATAAATAAAAT-AAT-AAAACAAA
3243304 A
1 A
3243305 AGAATGGAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
26 10 0.21
27 23 0.48
28 15 0.31
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (27 bp):
ATAAAATAAATAAAATAATAAAACAAA
Found at i:3243284 original size:18 final size:17
Alignment explanation
Indices: 3243229--3243289 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 17
3243219 ACATAAAATA
*
3243229 AAATAATAAAAGAAAAC
1 AAATAATAAAACAAAAC
*
3243246 AAAT--TAAAATAAATA-
1 AAATAATAAAACAAA-AC
3243261 AAATAATAAAACAAAAC
1 AAATAATAAAACAAAAC
3243278 GAAATAATAAAA
1 -AAATAATAAAA
3243290 TAAATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 12 0.32
16 2 0.05
17 12 0.32
18 11 0.30
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.16
Consensus pattern (17 bp):
AAATAATAAAACAAAAC
Found at i:3243418 original size:17 final size:18
Alignment explanation
Indices: 3243388--3243422 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3243378 GATGAAAAAC
*
3243388 AAAAAGAAAGAAAATAAG
1 AAAAAGAAACAAAATAAG
3243406 AAAAA-AAACAAAATAAG
1 AAAAAGAAACAAAATAAG
3243423 GGGCCTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.80, C:0.03, G:0.11, T:0.06
Consensus pattern (18 bp):
AAAAAGAAACAAAATAAG
Found at i:3243705 original size:2 final size:2
Alignment explanation
Indices: 3243700--3243732 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3243690 AATAGAAATA
3243700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3243733 CCAACGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3243933 original size:21 final size:21
Alignment explanation
Indices: 3243907--3243968 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
3243897 AAATAACCAA
3243907 AAATAGATAAATATAGTAAAT
1 AAATAGATAAATATAGTAAAT
*
3243928 AAATAG-TAAA-ATA-TAATT
1 AAATAGATAAATATAGTAAAT
* * * *
3243946 AAATATATATATAGAGAAAAT
1 AAATAGATAAATATAGTAAAT
3243967 AA
1 AA
3243969 CTTCAGTGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 9 0.28
19 6 0.19
20 6 0.19
21 11 0.34
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (21 bp):
AAATAGATAAATATAGTAAAT
Found at i:3243956 original size:35 final size:35
Alignment explanation
Indices: 3243840--3243956 Score: 84
Period size: 35 Copynumber: 3.3 Consensus size: 35
3243830 AATAATGGTA
* *
3243840 TAAA-ATACATAGATAAAAAAATAGT--AATATAAT
1 TAAATATATATAG-TAAATAAATAGTAAAATATAAT
* *
3243873 TTAATATAATATAGGTAAATAAATAAATAACCAA-A-AA-
1 TAAATAT-ATATA-GTAAATAAAT-AGTAA--AATATAAT
* *
3243910 TAGATAAATATAGTAAATAAATAGTAAAATATAAT
1 TAAATATATATAGTAAATAAATAGTAAAATATAAT
3243945 TAAATATATATA
1 TAAATATATATA
3243957 TAGAGAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 20
0.68 0.11 0.22
Matches are distributed among these distances:
32 2 0.03
33 4 0.06
34 8 0.13
35 32 0.51
36 8 0.13
37 4 0.06
38 2 0.03
39 1 0.02
40 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.30
Consensus pattern (35 bp):
TAAATATATATAGTAAATAAATAGTAAAATATAAT
Found at i:3244134 original size:21 final size:21
Alignment explanation
Indices: 3244105--3244148 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3244095 AATATGTAAA
*
3244105 TCGCATTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
3244126 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
3244147 TC
1 TC
3244149 ACAACGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:3244187 original size:20 final size:20
Alignment explanation
Indices: 3244164--3244212 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
3244154 GTGAATCTAT
* *
3244164 AATTCGCAACATAGAAGTCA
1 AATTCGCAACACAAAAGTCA
3244184 AATTCGCAACACAAAAGTCA
1 AATTCGCAACACAAAAGTCA
3244204 AATTCGCAA
1 AATTCGCAA
3244213 TGCGATTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.22, G:0.12, T:0.18
Consensus pattern (20 bp):
AATTCGCAACACAAAAGTCA
Found at i:3244260 original size:41 final size:40
Alignment explanation
Indices: 3244182--3244335 Score: 123
Period size: 41 Copynumber: 3.8 Consensus size: 40
3244172 ACATAGAAGT
* **
3244182 CAAATTCGCAACACAAAAGTCAAATTCGCAA-TGCGATTTC
1 CAAATTCGCAACACGAATTTCAAATTCGCAACT-CGATTTC
*
3244222 CAAATTCGCAACACTGAATTTCAAATTCGAAACTCGATTTC
1 CAAATTCGCAACAC-GAATTTCAAATTCGCAACTCGATTTC
** ** * * *
3244263 TGAATTCATAACGCGAATTTGGAAAATT-GCAACTCGATTTT
1 CAAATTCGCAACACGAATTT--CAAATTCGCAACTCGATTTC
* * * *
3244304 CGAATTCGCAACATGAATTTTAATTTCGCAAC
1 CAAATTCGCAACACGAATTTCAAATTCGCAAC
3244336 AGGTTTATTT
Statistics
Matches: 90, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
39 4 0.04
40 25 0.28
41 55 0.61
42 6 0.07
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (40 bp):
CAAATTCGCAACACGAATTTCAAATTCGCAACTCGATTTC
Found at i:3244314 original size:20 final size:20
Alignment explanation
Indices: 3244224--3244315 Score: 62
Period size: 21 Copynumber: 4.5 Consensus size: 20
3244214 GCGATTTCCA
* *
3244224 AATTCGCAACACTGAATTTCA
1 AATTCGCAACTC-GAATTTCG
*
3244245 AATTCGAAACTCG-ATTTCTG
1 AATTCGCAACTCGAATTTC-G
** * *
3244265 AATTCATAACGCGAATTTGG
1 AATTCGCAACTCGAATTTCG
*
3244285 AAAATT-GCAACTCGATTTTCG
1 --AATTCGCAACTCGAATTTCG
3244306 AATTCGCAAC
1 AATTCGCAAC
3244316 ATGAATTTTA
Statistics
Matches: 54, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
19 9 0.17
20 17 0.31
21 24 0.44
22 4 0.07
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
AATTCGCAACTCGAATTTCG
Found at i:3247612 original size:18 final size:18
Alignment explanation
Indices: 3247589--3247624 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3247579 AAGCAAAAGG
*
3247589 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
3247607 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
3247625 CAACCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:3249472 original size:21 final size:21
Alignment explanation
Indices: 3249448--3249518 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
3249438 GTGAATCGGG
3249448 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* * *
3249469 CTCTTGAACGATGAGATGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
3249490 CTCTTGAACGGTTGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
3249511 CTATTGAA
1 CTCTTGAA
3249519 AGATAGGGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:3249507 original size:42 final size:40
Alignment explanation
Indices: 3249448--3249539 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 40
3249438 GTGAATCGGG
* *
3249448 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGATGGG-C
1 CTCTTGAACGGTGGGAGGGGCCTATTGAAAGAT-AG--GGGAC
*
3249490 CTCTTGAACGGTTGGAGGGGCCTATTGAAAGATAGGGGAC
1 CTCTTGAACGGTGGGAGGGGCCTATTGAAAGATAGGGGAC
3249530 CTCTTGAACG
1 CTCTTGAACG
3249540 ATGACAGGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 3 0.07
40 11 0.24
41 2 0.04
42 30 0.65
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (40 bp):
CTCTTGAACGGTGGGAGGGGCCTATTGAAAGATAGGGGAC
Found at i:3249849 original size:21 final size:21
Alignment explanation
Indices: 3249825--3249875 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3249815 TGCAATAATC
*
3249825 TCACGTAGAGT-GACTACCTCA
1 TCACGTAAAGTAGA-TACCTCA
3249846 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGTAGATACCTCA
*
3249867 CCACGTAAA
1 TCACGTAAA
3249876 ACACCATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGTAGATACCTCA
Found at i:3250196 original size:41 final size:42
Alignment explanation
Indices: 3250115--3250210 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 42
3250105 GTGATGGAAT
* * * *
3250115 AGGTGATTGCTCTCGTTGTAGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTAGTTGTAGAGATGTAGAATCGGCTCGATC
*
3250157 AGGTGATGGCTCTAG-TGTCGAGATGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTAGTTGTAGAGATGTAGAATCGGCTCGATC
3250198 AGGTGATGGCTCT
1 AGGTGATGGCTCT
3250211 CGAAGTGGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 36 0.73
42 13 0.27
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (42 bp):
AGGTGATGGCTCTAGTTGTAGAGATGTAGAATCGGCTCGATC
Found at i:3251721 original size:19 final size:19
Alignment explanation
Indices: 3251670--3251723 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
3251660 AGTAGTTTCT
*
3251670 GAAACTTAAAATCGCAATGC
1 GAAAC-TAAAATCGCAACGC
*
3251690 GAAATTGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
3251710 GAAACTAAAATCGC
1 GAAACTAAAATCGC
3251724 GTTACGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:3251745 original size:20 final size:20
Alignment explanation
Indices: 3251720--3251782 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
3251710 GAAACTAAAA
3251720 TCGCGTTACGATTTTCATTT
1 TCGCGTTACGATTTTCATTT
3251740 TCGCGTTACGATTTTCATTT
1 TCGCGTTACGATTTTCATTT
3251760 TCGCGTTACGATTTTCATTT
1 TCGCGTTACGATTTTCATTT
3251780 TCG
1 TCG
3251783 TGTTGCAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.14, C:0.21, G:0.16, T:0.49
Consensus pattern (20 bp):
TCGCGTTACGATTTTCATTT
Found at i:3252160 original size:22 final size:22
Alignment explanation
Indices: 3252135--3252182 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
3252125 GGAGATAGAA
3252135 GGATTTCGTCGAAGATGGGGAT
1 GGATTTCGTCGAAGATGGGGAT
*
3252157 GGATTTCGTCGGAGATGGGGAT
1 GGATTTCGTCGAAGATGGGGAT
3252179 GGAT
1 GGAT
3252183 GTCACCGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.08, G:0.44, T:0.27
Consensus pattern (22 bp):
GGATTTCGTCGAAGATGGGGAT
Found at i:3252194 original size:22 final size:22
Alignment explanation
Indices: 3252147--3252194 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3252137 ATTTCGTCGA
* **
3252147 AGATGGGGATGGATTTCGTCGG
1 AGATGGGGATGGATGTCACCGG
*
3252169 AGATGGGGATGGATGTCACCGT
1 AGATGGGGATGGATGTCACCGG
3252191 AGAT
1 AGAT
3252195 AGTGAGAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.42, T:0.25
Consensus pattern (22 bp):
AGATGGGGATGGATGTCACCGG
Found at i:3252363 original size:20 final size:19
Alignment explanation
Indices: 3252338--3252407 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
3252328 ACGCGTTTGA
3252338 CGAATTTAAATTATGTGTTG
1 CGAATTTAAATT-TGTGTTG
* *
3252358 CGAATTTGACTTCTGTGTTG
1 CGAATTTAAATT-TGTGTTG
*
3252378 CG-ATTTACAGATTCGTGTTG
1 CGAATTTA-A-ATTTGTGTTG
3252398 CGAATTTAAA
1 CGAATTTAAA
3252408 AATCGCAACG
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 5 0.12
20 29 0.71
21 7 0.17
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.41
Consensus pattern (19 bp):
CGAATTTAAATTTGTGTTG
Found at i:3252431 original size:21 final size:20
Alignment explanation
Indices: 3252396--3252483 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 20
3252386 AGATTCGTGT
**
3252396 TGCGAATTTAAAAATCGCAA
1 TGCGAATTCGAAAATCGCAA
* * *
3252416 CGTGAATTCAGAAAATCACAA
1 TGCGAATTC-GAAAATCGCAA
3252437 TGCGAATTCGAAAAATCGCAA
1 TGCGAATTCG-AAAATCGCAA
3252458 TGCGAATTCGGAAAATCGCAA
1 TGCGAATTC-GAAAATCGCAA
3252479 TGCGA
1 TGCGA
3252484 TTTACATATT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
20 7 0.12
21 49 0.86
22 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (20 bp):
TGCGAATTCGAAAATCGCAA
Found at i:3252454 original size:42 final size:41
Alignment explanation
Indices: 3252396--3252483 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
3252386 AGATTCGTGT
* *
3252396 TGCGAATTTAAAAATCGCAACGTGAATTCAGAAAATCACAA
1 TGCGAATTGAAAAATCGCAACGCGAATTCAGAAAATCACAA
* * *
3252437 TGCGAATTCGAAAAATCGCAATGCGAATTCGGAAAATCGCAA
1 TGCGAATT-GAAAAATCGCAACGCGAATTCAGAAAATCACAA
3252479 TGCGA
1 TGCGA
3252484 TTTACATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 8 0.20
42 33 0.80
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (41 bp):
TGCGAATTGAAAAATCGCAACGCGAATTCAGAAAATCACAA
Found at i:3252635 original size:2 final size:2
Alignment explanation
Indices: 3252630--3252654 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3252620 TTATTTTTTC
3252630 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3252655 ATAAGGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3253860 original size:7 final size:7
Alignment explanation
Indices: 3253819--3253861 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
3253809 CATTGTACGC
3253819 ATATACT
1 ATATACT
*
3253826 ATATAAT
1 ATATACT
3253833 ATATA-T
1 ATATACT
3253839 ATATA-T
1 ATATACT
3253845 ATATACT
1 ATATACT
*
3253852 ATATGCT
1 ATATACT
3253859 ATA
1 ATA
3253862 AATAATAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (7 bp):
ATATACT
Found at i:3254588 original size:84 final size:83
Alignment explanation
Indices: 3254498--3255059 Score: 476
Period size: 84 Copynumber: 6.8 Consensus size: 83
3254488 AATCGAATTG
* * * * * *
3254498 GAAGGTCTTCAGTTGGTAGATAGCCCTTCTCGACTTAAGCTATACAGCAAAAGATGTTCCTTGGA
1 GAAGGTCTT-TGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTTCCTTGGA
*
3254563 GCTGAACGTAGTCAAACTC
65 GCTGAACGTAGTCGAACTC
* ** * * * * * * * *
3254582 GAAGGTCTTTTGGTGAAAGATAACCCTTCTAGTCTTGAGTTATGTTGTAAATGATGTTCCCTCGA
1 GAAGGTC-TTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTT-CCTTGG
* *
3254647 AGCT-AAGTGTAATCGAACTC
64 AGCTGAA-CGTAGTCGAACTC
* * *
3254667 GAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATCTGT-CTTGGA
1 GAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT-TCCTTGGA
*
3254728 GCTGAGCGTAGTCGAACTC
65 GCTGAACGTAGTCGAACTC
* * *
3254747 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGA
1 GAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTTCCTTGGA
*
3254812 GCTGAGCGTAGTCGAACTC
65 GCTGAACGTAGTCGAACTC
* ** * * * * * * * * * * *
3254831 GAAGGTCTTTCGGTAACAGATAACCTTTTTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGA
1 GAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT-TCCTTGG
** *
3254896 AGCTGAGTGTAATCGAACTC
64 AGCTGAACGTAGTCGAACTC
* * * * * *
3254916 CAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAG
1 GAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTTCCTTGGAG
*
3254978 CTGAGCGTAGTCGAACTC
66 CTGAACGTAGTCGAACTC
* * * *
3254996 GAAGGTCTTTGGTTGGCAGATAATCCTTCTCGACTTAAG-TTTGCTGCAAATGATATGCCTTGGA
1 GAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTTCCTTGGA
3255060 AATACCCTTC
Statistics
Matches: 381, Mismatches: 82, Indels: 31
0.77 0.17 0.06
Matches are distributed among these distances:
80 51 0.13
81 70 0.18
82 4 0.01
83 23 0.06
84 180 0.47
85 53 0.14
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (83 bp):
GAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTTCCTTGGAG
CTGAACGTAGTCGAACTC
Found at i:3254705 original size:165 final size:169
Alignment explanation
Indices: 3254424--3254801 Score: 441
Period size: 165 Copynumber: 2.3 Consensus size: 169
3254414 GACACTTTTA
* * * * *
3254424 TTGACAGATAACCCTTCTAGCCTTGAGTTATGCTT-TAAAT-TTGGTTTGCCTCTGAGCTGAGTG
1 TTGAAAGATAACCCTTCTAGACTTGAGTTATG-TTGTAAATGATGGTTTCCCTCTGAGCTAAGTG
* * *
3254487 TAATCGAATTGGAAGGTCTTCAGTTGGTAGATAGCCCTTCTCGACTTAAGCTATACAGCAAAAGA
65 TAATCGAACTCGAAGGTCTT-A-TTGGCAGATAGCCCTTCTCGACTTAAGCTATACAGCAAAAGA
*
3254552 TGT-TCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTTGG
128 TCTGT-CTTGGAGCTGAACGTAGTCAAACTCGAAGGTC-TTTGG
*
3254595 -TGAAAGATAACCCTTCTAGTCTTGAGTTATGTTGTAAATGAT-G-TTCCCTC-GAAGCTAAGTG
1 TTGAAAGATAACCCTTCTAGACTTGAGTTATGTTGTAAATGATGGTTTCCCTCTG-AGCTAAGTG
* * * *
3254656 TAATCGAACTCGAGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATC
65 TAATCGAACTCGAAGGTCTTATTGGCAGATAGCCCTTCTCGACTTAAGCTATACAGCAAAAGATC
* *
3254719 TGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
130 TGTCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTGG
** * * * *
3254759 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
1 TTGAAAGATAACCCTTCTAGACTTGAGTTATGTTGTAAATGAT
3254802 ATGCCTTGGA
Statistics
Matches: 180, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
164 5 0.03
165 105 0.58
166 1 0.01
168 2 0.01
169 31 0.17
170 35 0.19
171 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (169 bp):
TTGAAAGATAACCCTTCTAGACTTGAGTTATGTTGTAAATGATGGTTTCCCTCTGAGCTAAGTGT
AATCGAACTCGAAGGTCTTATTGGCAGATAGCCCTTCTCGACTTAAGCTATACAGCAAAAGATCT
GTCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTGG
Found at i:3254915 original size:249 final size:249
Alignment explanation
Indices: 3254477--3255059 Score: 882
Period size: 249 Copynumber: 2.3 Consensus size: 249
3254467 GTTTGCCTCT
* * * * ** * * * *
3254477 GAGCTGAGTGTAATCGAATTGGAAGGTCTTCAGTTGGTAGATAGCCCTTCTCGACTTAAGCTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * * * *
3254542 CAGCAAAAGATGTTCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTTGGTGAAAGATAACC
66 CTGCAAATGATATGCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTCGGTGAAAGATAACC
* * * *
3254607 CTTCTAGTCTTGAGTTATGTTGTAAATGATGTTCCCTCGAAGCTAAGTGTAATCGAACTCGAGGG
131 CTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAACTCCAGGG
*
3254672 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATCTGTCTTG
196 TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATCTGCCTTG
3254726 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
3254791 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTCGGT-AACAGATAAC
66 CTGCAAATGATATGCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTCGGTGAA-AGATAAC
* * *
3254855 CTTTTTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCCAGG
130 CCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAACTCCAGG
* * *
3254920 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTG
195 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATCTGCCTTG
*
3254975 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAATCCTTCTCGACTTAAGTT-TG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
3255039 CTGCAAATGATATGCCTTGGA
66 CTGCAAATGATATGCCTTGGA
3255060 AATACCCTTC
Statistics
Matches: 304, Mismatches: 29, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
248 25 0.08
249 279 0.92
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (249 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATATGCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTCGGTGAAAGATAACC
CTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAACTCCAGGG
TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATCTGCCTTG
Found at i:3255165 original size:129 final size:130
Alignment explanation
Indices: 3254935--3255190 Score: 505
Period size: 129 Copynumber: 2.0 Consensus size: 130
3254925 TGGCAGATAG
3254935 CCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
3255000 GTCTTTGGTTGGCAGATAATCCTTCTCGACTTAAGTT-TGCTGCAAATGATATGCCTTGGAAATA
66 GTCTTTGGTTGGCAGATAATCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAAATA
3255064 CCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
3255129 GTCTTTGGTTGGCAGATAATCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAA
66 GTCTTTGGTTGGCAGATAATCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAA
3255191 CTGAGCATAG
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 102 0.81
130 24 0.19
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (130 bp):
CCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTGGTTGGCAGATAATCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAAATA
Found at i:3255206 original size:84 final size:84
Alignment explanation
Indices: 3255063--3255268 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
3255053 CCTTGGAAAT
* *
3255063 ACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
1 ACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAACTGAGCATAGTCGAACTCGAA
*
3255128 GGT-CTTTGGTTGGCAGATA
66 GGTACTTTGG-TGACAGATA
* * *
3255147 ATCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAACTGAGCATAGTCGAACTCGAA
1 ACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAACTGAGCATAGTCGAACTCGAA
* *
3255212 GGTATTTTGGTGATAGATA
66 GGTACTTTGGTGACAGATA
* * * *
3255231 ACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCC
1 ACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCC
3255269 CTCGAAGCTG
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 101 0.95
85 5 0.05
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (84 bp):
ACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAACTGAGCATAGTCGAACTCGAA
GGTACTTTGGTGACAGATA
Found at i:3255594 original size:100 final size:105
Alignment explanation
Indices: 3255427--3255629 Score: 290
Period size: 100 Copynumber: 2.0 Consensus size: 105
3255417 GGCCCATTCT
* * *
3255427 TTGTGAAGTTGAAATTGACTCTGAAACTAGAAAGTAGTTTGTTGGCAGCCAGTCGCCTCTTCGCT
1 TTGTGAAGTTGAAATTGACTCTGAAACTAGAAAG-ACTTTGTTGACAGCCAGTCGCCCCTTCGCT
** * *
3255492 GTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCTTCG
65 GTGAAGTTGAGCTTGCATTATCTCGAGTCCAATATCCTTCG
*
3255533 TTGTGAAGTTGAAATTGACTCTG-AA-T-G-AA-ACTTTGTTGACAGTCAGTCGCCCCTTCGCTG
1 TTGTGAAGTTGAAATTGACTCTGAAACTAGAAAGACTTTGTTGACAGCCAGTCGCCCCTTCGCTG
3255593 TGAAGTTGAGCTTGCATTATCTCGAGTCCAATATCCT
66 TGAAGTTGAGCTTGCATTATCTCGAGTCCAATATCCT
3255630 AAAAACTTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
100 60 0.67
102 2 0.02
103 1 0.01
104 1 0.01
105 2 0.02
106 23 0.26
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (105 bp):
TTGTGAAGTTGAAATTGACTCTGAAACTAGAAAGACTTTGTTGACAGCCAGTCGCCCCTTCGCTG
TGAAGTTGAGCTTGCATTATCTCGAGTCCAATATCCTTCG
Found at i:3256614 original size:95 final size:96
Alignment explanation
Indices: 3256417--3256615 Score: 262
Period size: 95 Copynumber: 2.1 Consensus size: 96
3256407 CGACAACTTA
* * ** * *
3256417 ATATATAAACACCTTTTTCAGGTTAGCTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAATTA
1 ATATATAATCACCTTTATCAGGCAAGCTGAATATTATCCATAAAGCTAGGGCGTTTAACCAATTA
*
3256482 CCTTAGAAGGACATCTCAAGCTTTATTGTAT
66 CCTTAGAAGGACAACTCAAGCTTTATTGTAT
* *
3256513 A-GTATAATCACCTTTATCAGGCAAGCTGAATATTATCCATAAAGAC-AGGGCTTTTAACCAATT
1 ATATATAATCACCTTTATCAGGCAAGCTGAATATTATCCATAAAG-CTAGGGCGTTTAACCAATT
*
3256576 --CTCTAGAGGGACAACTCAAGCTTTATTGTAT
65 ACCT-TAGAAGGACAACTCAAGCTTTATTGTAT
3256607 ATATATAAT
1 ATATATAAT
3256616 ATTATAATAT
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
93 2 0.02
94 27 0.30
95 58 0.65
96 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (96 bp):
ATATATAATCACCTTTATCAGGCAAGCTGAATATTATCCATAAAGCTAGGGCGTTTAACCAATTA
CCTTAGAAGGACAACTCAAGCTTTATTGTAT
Found at i:3257014 original size:90 final size:91
Alignment explanation
Indices: 3256908--3257088 Score: 337
Period size: 90 Copynumber: 2.0 Consensus size: 91
3256898 TTCTTAAAAG
*
3256908 AAAATGGTATGGTGTTCAAACGCATATTTTGGGGAAAAACCAAGTGTCGTTATTTGATCA-TTAT
1 AAAATGGTATGGTGTTCAAAAGCATATTTTGGGGAAAAACCAAGTGTCGTTATTTGATCACTTAT
3256972 CAAAGATCTGTAACTCGGATCATTTA
66 CAAAGATCTGTAACTCGGATCATTTA
*
3256998 AAAATGGTATGGTGTTCAAAAGCATATTTTGGGGTAAAACCAAGTGTCGTTATTTGATCACTTAT
1 AAAATGGTATGGTGTTCAAAAGCATATTTTGGGGAAAAACCAAGTGTCGTTATTTGATCACTTAT
3257063 CAAAGATCTGTAACTCGGATCATTTA
66 CAAAGATCTGTAACTCGGATCATTTA
3257089 GAGAGTTTTT
Statistics
Matches: 88, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
90 58 0.66
91 30 0.34
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (91 bp):
AAAATGGTATGGTGTTCAAAAGCATATTTTGGGGAAAAACCAAGTGTCGTTATTTGATCACTTAT
CAAAGATCTGTAACTCGGATCATTTA
Found at i:3260783 original size:46 final size:47
Alignment explanation
Indices: 3260703--3260830 Score: 115
Period size: 46 Copynumber: 2.7 Consensus size: 47
3260693 AGTGAGTAAA
*
3260703 ATAAATATAAAAAATATAAAAAATAAAGAAAT-AAAGAAAAAATTAT
1 ATAAATATAAAAAATATAAAAAATAAAGAAATAAAAGAAAAAATAAT
* *
3260749 ATAAATA-AAACAAATA-AATAAAATAATA-ATATAAAAGTAAAAATAAT
1 ATAAATATAAA-AAATATAA-AAAATAA-AGAAATAAAAGAAAAAATAAT
*
3260796 ATATATATATATAATAAATA-AAAATATAAA-AAATA
1 ATA-A-ATATA-AA-AAATATAAAAAATAAAGAAATA
3260831 GTAAATATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
45 5 0.07
46 22 0.32
47 16 0.24
48 1 0.01
49 8 0.12
50 7 0.10
51 9 0.13
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (47 bp):
ATAAATATAAAAAATATAAAAAATAAAGAAATAAAAGAAAAAATAAT
Found at i:3260792 original size:25 final size:27
Alignment explanation
Indices: 3260731--3260830 Score: 75
Period size: 26 Copynumber: 3.7 Consensus size: 27
3260721 AAAAATAAAG
* *
3260731 AAATAAAGAA-AAAATTATATAAATAA-
1 AAATAAA-AATAAAATAATATATATAAT
3260757 AACA-AATAAATAAAATAATA-ATATAA-
1 AA-ATAA-AAATAAAATAATATATATAAT
* *
3260783 AAGTAAAAATAATATATATATATATAAT
1 AAATAAAAATAAAATA-ATATATATAAT
*
3260811 AAATAAAAATATAAAAAATA
1 AAATAAAAATA-AAATAATA
3260831 GTAAATATAT
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
25 9 0.15
26 18 0.31
27 16 0.27
28 13 0.22
29 3 0.05
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (27 bp):
AAATAAAAATAAAATAATATATATAAT
Found at i:3260792 original size:29 final size:28
Alignment explanation
Indices: 3260709--3260870 Score: 81
Period size: 28 Copynumber: 5.8 Consensus size: 28
3260699 TAAAATAAAT
* *
3260709 ATAAAAAAT-ATAAAAAATAAAGAAATAA
1 ATAAAAAATAATATAAAAT-AACAAATAA
* * *
3260737 AGAAAAAATTATATAAATAAAACAAATAA
1 ATAAAAAATAATATAAA-ATAACAAATAA
3260766 ATAAAATAATAATATAAAAGTAA-AAAT-A
1 ATAAAA-AATAATATAAAA-TAACAAATAA
* *
3260794 AT-ATATATATATATAATAAATAA-AAAT--
1 ATAAAAAATA-ATAT-A-AAATAACAAATAA
* * *
3260821 ATAAAAAATAGTA-AATATATA-AAATTA
1 ATAAAAAATAATATAAAATA-ACAAATAA
* *
3260848 ATAAAAGATAATAAAAAATAACA
1 ATAAAAAATAATATAAAATAACA
3260871 TATATATATA
Statistics
Matches: 105, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
24 4 0.04
25 6 0.06
26 3 0.03
27 22 0.21
28 30 0.29
29 27 0.26
30 13 0.12
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (28 bp):
ATAAAAAATAATATAAAATAACAAATAA
Found at i:3260839 original size:35 final size:34
Alignment explanation
Indices: 3260753--3260906 Score: 118
Period size: 35 Copynumber: 4.4 Consensus size: 34
3260743 AATTATATAA
* *
3260753 ATAAAACAA-ATAAATA-AAATAATAATATAAAAGT
1 ATAAAA-AATATAAATATATATAATAA-ATAAAAAT
*
3260787 A-AAAATAATATATATATATATAATAAATAAAAAT
1 ATAAAA-AATATAAATATATATAATAAATAAAAAT
* *
3260821 ATAAAAAATAGTAAATATATAAAATTAATAAAAGAT
1 ATAAAAAATA-TAAATATATATAATAAATAAAA-AT
* * *
3260857 AATAAAAAATA-ACATATATATATATAATCTAAAAAAA
1 -ATAAAAAATATAAATATATATA-ATAA-AT-AAAAAT
3260894 ATAAAAATATATA
1 ATAAAAA-ATATA
3260907 CTAAAGTAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 18
0.76 0.09 0.14
Matches are distributed among these distances:
33 6 0.06
34 19 0.20
35 40 0.41
36 12 0.12
37 15 0.15
38 5 0.05
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (34 bp):
ATAAAAAATATAAATATATATAATAAATAAAAAT
Found at i:3260839 original size:39 final size:38
Alignment explanation
Indices: 3260787--3260906 Score: 103
Period size: 37 Copynumber: 3.2 Consensus size: 38
3260777 ATATAAAAGT
*
3260787 AAAAATA-ATATATATATATATAATAAATAAAAATATA
1 AAAAATATAAATATATATATATAATAAATAAAAATATA
*
3260824 AAAAATAGT-AA-ATATATA-A-AATTAATAAAAGATAATA
1 AAAAATA-TAAATATATATATATAATAAATAAAA-AT-ATA
*
3260861 AAAAATA-ACATATATATATATAATCTAAA-AAAAATA-A
1 AAAAATATAAATATATATATATAA--TAAATAAAAATATA
*
3260898 AAATATATA
1 AAAAATATA
3260907 CTAAAGTAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
35 10 0.15
36 4 0.06
37 38 0.57
38 4 0.06
39 4 0.06
40 4 0.06
41 3 0.04
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (38 bp):
AAAAATATAAATATATATATATAATAAATAAAAATATA
Done.