Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 13 of 199
Found at i:4227228 original size:14 final size:15
Alignment explanation
Indices: 4227179--4227230 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
4227169 GTAAAATATA
4227179 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
4227194 TATTAAATATATTAT
1 AATTAAATATATTAT
4227209 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
4227222 AATTTAATA
1 AATTAAATA
4227231 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:4227366 original size:120 final size:120
Alignment explanation
Indices: 4226823--4227355 Score: 921
Period size: 120 Copynumber: 4.4 Consensus size: 120
4226813 ATCATATTTA
4226823 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
4226888 TATTCTTATATGAATTTACTCAAATCATAATATATGATATTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
4226943 AACATAATTATTATTAAATATATTATAATTAAAATGTATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
4227008 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
4227063 AACATAATTATTATTAAATATATTATAGTTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
4227128 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
4227183 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
4227248 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAAA-TT
* * * * *
4227303 GAA-ATAATTAATA-TATCATATATTTTATTTAAAATATATGATTTAATAAAATT
1 -AACATAATTATTATTA-AATATATTATAATTAAAATATATAATTTAATAAAATT
4227356 TAAAATAATT
Statistics
Matches: 398, Mismatches: 11, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
119 9 0.02
120 387 0.97
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:4227442 original size:24 final size:25
Alignment explanation
Indices: 4227396--4227443 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
4227386 TATGAATTTG
4227396 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
4227422 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
4227444 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:4227447 original size:92 final size:92
Alignment explanation
Indices: 4227351--4227579 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
4227341 TGATTTAATA
* * *
4227351 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
4227413 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
4227443 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
4227508 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
4227533 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
4227580 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:4237930 original size:16 final size:17
Alignment explanation
Indices: 4237899--4237931 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4237889 ATTAATTAAA
4237899 TTAACTAAATTAATTTT
1 TTAACTAAATTAATTTT
4237916 TTAACTAAA-TAATTTT
1 TTAACTAAATTAATTTT
4237932 CTAAACTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAACTAAATTAATTTT
Found at i:4237938 original size:17 final size:17
Alignment explanation
Indices: 4237901--4237943 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
4237891 TAATTAAATT
*
4237901 AACTAAATTAATTTTTT
1 AACTAAATTAATTTTTA
4237918 AACTAAA-TAATTTTCTA
1 AACTAAATTAATTTT-TA
*
4237935 AACTCAATT
1 AACTAAATT
4237944 TTAATTCCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 14 0.64
18 1 0.05
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (17 bp):
AACTAAATTAATTTTTA
Found at i:4239062 original size:11 final size:11
Alignment explanation
Indices: 4239046--4239073 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4239036 TATTGTTTAG
4239046 TATTAGTTAAA
1 TATTAGTTAAA
4239057 TATTAGTTAAA
1 TATTAGTTAAA
4239068 TATTAG
1 TATTAG
4239074 ATAACTAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (11 bp):
TATTAGTTAAA
Found at i:4239485 original size:111 final size:111
Alignment explanation
Indices: 4239291--4239513 Score: 374
Period size: 111 Copynumber: 2.0 Consensus size: 111
4239281 ACATGCATGA
*
4239291 TTTTGGTTAAGAGTTTATTGTTATAAATATTACAAAGCTCGATTTTAAGAAACTTTTTAAACTTT
1 TTTTGGTTAAGAGTTTATTGTTATAAATATCACAAAGCTCGATTTTAAGAAACTTTTTAAACTTT
* * * *
4239356 CACTGTGCTTAAAAATACTATTTTGTAAACCGATTTTTCCAACAGT
66 CACCGTGCTTAAAAATACTATTTTATAAACCAATATTTCCAACAGT
*
4239402 TTTTGGTTAAGAGTTTATTGTTATAAATATCACAATGCTCGATTTTAAGAAACTTTTTAAACTTT
1 TTTTGGTTAAGAGTTTATTGTTATAAATATCACAAAGCTCGATTTTAAGAAACTTTTTAAACTTT
* *
4239467 TACCGTGCTTAAAAATACTATTTTATAAACTAATATTTCCAACAGT
66 CACCGTGCTTAAAAATACTATTTTATAAACCAATATTTCCAACAGT
4239513 T
1 T
4239514 AGGTCCATTC
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (111 bp):
TTTTGGTTAAGAGTTTATTGTTATAAATATCACAAAGCTCGATTTTAAGAAACTTTTTAAACTTT
CACCGTGCTTAAAAATACTATTTTATAAACCAATATTTCCAACAGT
Found at i:4245247 original size:3 final size:3
Alignment explanation
Indices: 4245223--4245293 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
4245213 AATATCCTTG
* * * *
4245223 TTA TTT TTA -TA TTA TTA GTA TTA TTA CTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
4245270 TGTA TTA GTA TATA TTT TTA TTA T
1 T-TA TTA TTA T-TA TTA TTA TTA T
4245294 GTACGCGTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:4245290 original size:23 final size:22
Alignment explanation
Indices: 4245235--4245296 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
4245225 ATTTTTATAT
* *
4245235 TATTAGTATTATTA-CTATTAC
1 TATTATTATTATTATGTATTAC
*
4245256 TATTATTATTATTATGTATTAG
1 TATTATTATTATTATGTATTAC
*
4245278 TATATATTTTTATTATGTA
1 TAT-TATTATTATTATGTA
4245297 CGCGTATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.37
22 8 0.23
23 14 0.40
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (22 bp):
TATTATTATTATTATGTATTAC
Found at i:4245303 original size:23 final size:23
Alignment explanation
Indices: 4245259--4245304 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4245249 CTATTACTAT
**
4245259 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTACGAGTATA
* *
4245282 TATTTTTATTATGTACGCGTATA
1 TATTATTATTATGTACGAGTATA
4245305 CATATATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (23 bp):
TATTATTATTATGTACGAGTATA
Found at i:4245366 original size:22 final size:22
Alignment explanation
Indices: 4245323--4245366 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4245313 TATTTTCATA
* *
4245323 TTTAATATTTTTTTCACTTTAT
1 TTTAATATTTTATTCAATTTAT
4245345 TTTAATATTTTATT-AATGTTAT
1 TTTAATATTTTATTCAAT-TTAT
4245367 GTTTGTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTAATATTTTATTCAATTTAT
Found at i:4264391 original size:120 final size:120
Alignment explanation
Indices: 4264178--4264536 Score: 675
Period size: 120 Copynumber: 3.0 Consensus size: 120
4264168 GTTTTATGAG
* *
4264178 TCAAAGTGGTGGTTCCTTTGCTTTTTTAATTATTAATTTTTGGCTGTATCAACAGTCACAAGAAA
1 TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATTAAATTTTGGCTGTATCAACAGTCACAAGAAA
*
4264243 CTTTGACAAGAATTTTGGGAGCTTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
66 CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
4264298 TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATTAAATTTTGGCTGTATCAACAGTCACAAGAAA
1 TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATTAAATTTTGGCTGTATCAACAGTCACAAGAAA
4264363 CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
66 CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
4264418 TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATT-AATTTTGGCTGTATCAACAGTCACAAGAAA
1 TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATTAAATTTTGGCTGTATCAACAGTCACAAGAAA
*
4264482 CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTAAGTTTTATGCTTGTT
66 CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
4264537 GTATACGTGC
Statistics
Matches: 235, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
119 84 0.36
120 151 0.64
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (120 bp):
TCAAAGTGGTGGTTCCTTTTCTTTTTTAATTATTAAATTTTGGCTGTATCAACAGTCACAAGAAA
CTTTGACAAGAATTTTGGGAACTTTTGAAAGTTCAGTCTATGTTTTATGCTTGTT
Found at i:4266412 original size:20 final size:20
Alignment explanation
Indices: 4266392--4266429 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4266382 ATAAAAAACT
4266392 TTTCATTAT-TTTATTTTAC
1 TTTCATTATATTTATTTTAC
*
4266411 TTTCATTTTATTTATTTTA
1 TTTCATTATATTTATTTTA
4266430 TTTACTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTCATTATATTTATTTTAC
Found at i:4266420 original size:11 final size:9
Alignment explanation
Indices: 4266401--4266443 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
4266391 TTTTCATTAT
4266401 TTTATTTTA
1 TTTATTTTA
4266410 CTTTCATTTTA
1 -TTT-ATTTTA
4266421 TTTATTTTA
1 TTTATTTTA
*
4266430 TTTACTTTTG
1 TTTA-TTTTA
4266440 TTTA
1 TTTA
4266444 GTTAAAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 10 0.33
10 14 0.47
11 6 0.20
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTATTTTA
Found at i:4272233 original size:16 final size:15
Alignment explanation
Indices: 4272205--4272241 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
4272195 AAGGTATCAA
*
4272205 TTTTTTTGGCTTTTC
1 TTTTTTTGCCTTTTC
4272220 TTTTCTTTGCCTTTTC
1 TTTT-TTTGCCTTTTC
4272236 TTTTTT
1 TTTTTT
4272242 GTTTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (15 bp):
TTTTTTTGCCTTTTC
Found at i:4278932 original size:3 final size:3
Alignment explanation
Indices: 4278924--4278959 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4278914 AAGCATAAAC
4278924 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4278960 CATTGGAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4279098 original size:3 final size:3
Alignment explanation
Indices: 4279084--4279134 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
4279074 ACACTAGTAC
* * * * *
4279084 ATA ATT ATA ATA ATA GTA ATA CTA ATA ATA CTA ATA AT- ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4279131 ATA A
1 ATA A
4279135 GGATATTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4280872 original size:44 final size:44
Alignment explanation
Indices: 4280744--4281365 Score: 425
Period size: 44 Copynumber: 14.1 Consensus size: 44
4280734 CGCCATCGTC
* *
4280744 GATCTGCTT-TCTTCGATCTACTTCACCACCAGTATGGGAAGACAA
1 GATCTG-TTATCTTCGATCTACTTCA-CACCAATATAGGAAGACAA
* ** * * * * * *
4280789 GATTTG-CGTCGTCGATCCACTTC-CAATCATTATAGGAAGATAG
1 GATCTGTTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
* * * * *
4280832 GACCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGTTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* *
4280876 GATCTGCTT-TCTGT-GATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTG-TTATCT-TCGATCTACTTC-ACACCAATATAGGAAGACAA
* * * * *
4280921 GATCTG-TATCTTGGATCCACTTC-CTATCAATATAGGAAGATAG
1 GATCTGTTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
* * * * *
4280964 GACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGTTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* * *
4281008 GATCTGCTT-TCTTCGATCTACTTCGCCGCCAATATGGGAAGACAA
1 GATCTG-TTATCTTCGATCTACTTC-ACACCAATATAGGAAGACAA
* * * * *
4281053 GATCTG-TATCTTGGATCCACTTC-CTATCAATATAGGAAGATAG
1 GATCTGTTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
* * * * *
4281096 GACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGTTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* *
4281140 GATCTGCTT-TCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTG-TTATCTTCGATCTACTTC-ACACCAATATAGGAAGACAA
* * * * *
4281185 TATCTG-TATCTT-GAATCCACTTC-CTATCAATATAGGAAGATAG
1 GATCTGTTATCTTCG-ATCTACTTCAC-ACCAATATAGGAAGACAA
* * * * *
4281228 GACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGTTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* *
4281272 GATCTGCTT-TCTTCGATCTACTTCGC-CGCTAATATGGGAAGACAA
1 GATCTG-TTATCTTCGATCTACTTCACAC-C-AATATAGGAAGACAA
* * * *
4281317 GATCTG-CATCTTCGATCCACTTC-CTACCAATATAGGAAGATAG
1 GATCTGTTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
4281360 GATCTG
1 GATCTG
4281366 CTCCTTTGAC
Statistics
Matches: 447, Mismatches: 98, Indels: 66
0.73 0.16 0.11
Matches are distributed among these distances:
42 4 0.01
43 97 0.22
44 248 0.55
45 98 0.22
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (44 bp):
GATCTGTTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
Found at i:4280931 original size:88 final size:88
Alignment explanation
Indices: 4280744--4281367 Score: 501
Period size: 88 Copynumber: 7.1 Consensus size: 88
4280734 CGCCATCGTC
* * * ** * * * *
4280744 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATTTGC-GTCGTCGATCCA
1 GATCTGCTATCTTCGATCTACTTCA-CGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * * *
4280808 CTTCCAATCATTATAGGAAGATAG
65 CTTCCCACCAATATAGGAAGACAA
* * * * *
4280832 GACCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGT-GATCTA
1 GATCTGCTATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCT-TCGATCTA
*
4280896 CTTCGCCACCAATATGGGAAGACAA
65 CTTC-CCACCAATATAGGAAGACAA
* * ** * * * *
4280921 GATCTG-TATCTTGGATCCACTTC-CTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTA
1 GATCTGCTATCTTCGATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
4280984 CTTCACGCCAATACATGAAGACAA
65 CTTCCCACCAATATAGGAAGACAA
* * ** * *
4281008 GATCTGCTTTCTTCGATCTACTTCGCCGCCAATATGGGAAGACAAGATCTG-TATCTTGGATCCA
1 GATCTGCTATCTTCGATCTACTTC-ACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * *
4281072 CTTCCTATCAATATAGGAAGATAG
65 CTTCCCACCAATATAGGAAGACAA
* * *
4281096 GACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
1 GATCTGCTATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
*
4281161 TTCGCCACCAATATGGGAAGACAA
66 TTC-CCACCAATATAGGAAGACAA
* * ** * * * *
4281185 TATCTG-TATCTT-GAATCCACTTC-CTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCT
1 GATCTGCTATCTTCG-ATCTACTTCAC-GCCAATACAGGAAGACAAGATCTGCTATCTTCGATCT
* * * *
4281247 ACTTCACGCCAATACATGAAGACAA
64 ACTTCCCACCAATATAGGAAGACAA
* * * ** *
4281272 GATCTGCTTTCTTCGATCTACTTCGCCGCTAATATGGGAAGACAAGATCTGC-ATCTTCGATCCA
1 GATCTGCTATCTTCGATCTACTTC-ACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTA
* * *
4281336 CTTCCTACCAATATAGGAAGATAG
65 CTTCCCACCAATATAGGAAGACAA
4281360 GATCTGCT
1 GATCTGCT
4281368 CCTTTGACCT
Statistics
Matches: 418, Mismatches: 102, Indels: 32
0.76 0.18 0.06
Matches are distributed among these distances:
87 87 0.21
88 253 0.61
89 76 0.18
90 2 0.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (88 bp):
GATCTGCTATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTAC
TTCCCACCAATATAGGAAGACAA
Found at i:4280982 original size:132 final size:132
Alignment explanation
Indices: 4280744--4281367 Score: 1052
Period size: 132 Copynumber: 4.7 Consensus size: 132
4280734 CGCCATCGTC
* * * ** * *
4280744 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATTTGCGTCGTCGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTGGATCCAC
* * * *
4280809 TTCCAATCATTATAGGAAGATAGGACCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
4280874 AA
131 AA
4280876 GATCTGCTTTCTGT-GATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTGGATCCA
1 GATCTGCTTTCT-TCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTGGATCCA
4280940 CTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
65 CTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGA
4281005 CAA
130 CAA
*
4281008 GATCTGCTTTCTTCGATCTACTTCGCCGCCAATATGGGAAGACAAGATCTGTATCTTGGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTGGATCCAC
4281073 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
4281138 AA
131 AA
* *
4281140 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAATATCTGTATCTTGAATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTGGATCCAC
4281205 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
4281270 AA
131 AA
* * * *
4281272 GATCTGCTTTCTTCGATCTACTTCGCCGCTAATATGGGAAGACAAGATCTGCATCTTCGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTGGATCCAC
* *
4281337 TTCCTACCAATATAGGAAGATAGGATCTGCT
66 TTCCTATCAATATAGGAAGATAGGACCTGCT
4281368 CCTTTGACCT
Statistics
Matches: 467, Mismatches: 23, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
131 1 0.00
132 465 1.00
133 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (132 bp):
GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTGGATCCAC
TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
AA
Found at i:4300052 original size:17 final size:16
Alignment explanation
Indices: 4300030--4300063 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4300020 ATAAGTACGC
*
4300030 ATATATACATATTATAA
1 ATATATAAATA-TATAA
4300047 ATATATAAATATATAA
1 ATATATAAATATATAA
4300063 A
1 A
4300064 AAAGCATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATATAAATATATAA
Found at i:4300053 original size:8 final size:8
Alignment explanation
Indices: 4300030--4300063 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4300020 ATAAGTACGC
*
4300030 ATATATAC
1 ATATATAA
4300038 ATATTATAA
1 ATA-TATAA
4300047 ATATATAA
1 ATATATAA
4300055 ATATATAA
1 ATATATAA
4300063 A
1 A
4300064 AAAGCATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAA
Found at i:4300083 original size:3 final size:3
Alignment explanation
Indices: 4300075--4300113 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4300065 AAGCATAAAC
4300075 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4300114 CATTGGAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4300252 original size:3 final size:3
Alignment explanation
Indices: 4300238--4300288 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
4300228 ACACTAGTAC
* * * * *
4300238 ATA ATT ATA ATA ATA GTA ATA CTA ATA ATA CTA ATA AT- ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4300285 ATA A
1 ATA A
4300289 GGATATTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4308106 original size:24 final size:24
Alignment explanation
Indices: 4308079--4308127 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4308069 AAAAGTTTTC
* *
4308079 TTAACAATAATTCTAAAAAAGAAA
1 TTAAAAATAAATCTAAAAAAGAAA
* *
4308103 TTAAAAATAAATCTTAAAAATAAA
1 TTAAAAATAAATCTAAAAAAGAAA
4308127 T
1 T
4308128 ACAAATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
TTAAAAATAAATCTAAAAAAGAAA
Found at i:4308119 original size:13 final size:13
Alignment explanation
Indices: 4308077--4308127 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
4308067 AAAAAAGTTT
* *
4308077 TCTTAACAATAAT
1 TCTTAAAAATAAA
* *
4308090 TCTAAAAAAGAAA
1 TCTTAAAAATAAA
4308103 --TTAAAAATAAA
1 TCTTAAAAATAAA
4308114 TCTTAAAAATAAA
1 TCTTAAAAATAAA
4308127 T
1 T
4308128 ACAAATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
11 9 0.30
13 21 0.70
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (13 bp):
TCTTAAAAATAAA
Found at i:4308157 original size:20 final size:19
Alignment explanation
Indices: 4308130--4308184 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
4308120 AAATAAATAC
*
4308130 AAATTA-TTAAAATTATTAA
1 AAATTATTTAAAA-AATTAA
4308149 AAATATATTTAAAAAATTAA
1 AAAT-TATTTAAAAAATTAA
*
4308169 AAATTACGTTAAAAAA
1 AAATTA-TTTAAAAAA
4308185 ATTTAAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 19 0.61
21 6 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATTATTTAAAAAATTAA
Found at i:4308443 original size:15 final size:15
Alignment explanation
Indices: 4308411--4308453 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
4308401 ATTTTGAATT
*
4308411 TTTAGAATTTTT-TA
1 TTTAAAATTTTTATA
*
4308425 TTTAAAATTTTTATG
1 TTTAAAATTTTTATA
4308440 TTTAAAATATTTTA
1 TTTAAAAT-TTTTA
4308454 ACCTAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TTTAAAATTTTTATA
Found at i:4308882 original size:9 final size:9
Alignment explanation
Indices: 4308863--4308899 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
4308853 TGAGTTTTCG
*
4308863 AATTTGAAT
1 AATTCGAAT
*
4308872 AACTCGAAT
1 AATTCGAAT
4308881 AATTCGAAT
1 AATTCGAAT
4308890 AATTCGAAT
1 AATTCGAAT
4308899 A
1 A
4308900 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:4309152 original size:30 final size:31
Alignment explanation
Indices: 4309118--4309177 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
4309108 AAACCTTTTA
*
4309118 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
4309148 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
4309178 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:4315686 original size:30 final size:28
Alignment explanation
Indices: 4315650--4315745 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 28
4315640 TATTTTTAAA
4315650 AAAAATTATAAAATATATAGAAAATTATTT
1 AAAAATTATAAAAT-TATA-AAAATTATTT
* *
4315680 AAAAATTATCAAGAATTATAATAATTTTTT
1 AAAAATTAT-AA-AATTATAAAAATTATTT
* *
4315710 AAAAAAGTATTAAAATTTAATAAAAGTTATTT
1 -AAAAATTA-TAAAA-TT-ATAAAAATTATTT
4315742 AAAA
1 AAAA
4315746 TTACATTAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
30 19 0.35
31 21 0.39
32 14 0.26
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (28 bp):
AAAAATTATAAAATTATAAAAATTATTT
Found at i:4315743 original size:21 final size:18
Alignment explanation
Indices: 4315707--4315747 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
4315697 ATAATAATTT
4315707 TTTAAAAAAGTATTAAAA
1 TTTAAAAAAGTATTAAAA
4315725 TTTAATAAAAGTTATTTAAAA
1 TTTAA-AAAAG-TA-TTAAAA
4315746 TT
1 TT
4315748 ACATTAGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 2 0.10
21 8 0.40
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TTTAAAAAAGTATTAAAA
Found at i:4316179 original size:19 final size:19
Alignment explanation
Indices: 4316135--4316186 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
4316125 TAATTAATTA
* * *
4316135 AATTTTTAATATTTTTATT
1 AATTTTTAATAATTTCAGT
*
4316154 AACTTTTAATAATTTCAGT
1 AATTTTTAATAATTTCAGT
*
4316173 AATTTTTTATAATT
1 AATTTTTAATAATT
4316187 ATTAATATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTTTTAATAATTTCAGT
Found at i:4316888 original size:19 final size:19
Alignment explanation
Indices: 4316864--4316941 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 19
4316854 ATTCCCAAAC
*
4316864 TAATTTTCGTCAGAAATGG
1 TAATTTTTGTCAGAAATGG
* *
4316883 TAATTTTTGTGAGAAATGAT
1 TAATTTTTGTCAGAAATG-G
* * *
4316903 TAGTTTTTGTCAAAAACGG
1 TAATTTTTGTCAGAAATGG
*
4316922 TAAATTTTGTCAGAAATGG
1 TAATTTTTGTCAGAAATGG
4316941 T
1 T
4316942 TGGAAACAAA
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
19 32 0.70
20 14 0.30
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (19 bp):
TAATTTTTGTCAGAAATGG
Found at i:4319832 original size:9 final size:9
Alignment explanation
Indices: 4319818--4319851 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
4319808 TTACTCACAT
4319818 TTTTAAAAC
1 TTTTAAAAC
4319827 TTTTAAAAC
1 TTTTAAAAC
*
4319836 TTGTAAAA-
1 TTTTAAAAC
4319844 TTTTAAAA
1 TTTTAAAA
4319852 AAGGGGCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (9 bp):
TTTTAAAAC
Found at i:4321364 original size:13 final size:13
Alignment explanation
Indices: 4321312--4321364 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
4321302 CAGTTCTCAT
*
4321312 TGCTTTTGAAAAG
1 TGCTTTTAAAAAG
* * *
4321325 TGCTATGAAAAAA
1 TGCTTTTAAAAAG
* *
4321338 TGCTTTTGAGAAG
1 TGCTTTTAAAAAG
4321351 TGCTTTTAAAAAG
1 TGCTTTTAAAAAG
4321364 T
1 T
4321365 TTGGTTTAAA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (13 bp):
TGCTTTTAAAAAG
Found at i:4323222 original size:98 final size:94
Alignment explanation
Indices: 4323111--4323292 Score: 258
Period size: 94 Copynumber: 1.9 Consensus size: 94
4323101 TAATAATAAA
*
4323111 GAATAAAAGATA-TTTCTATCAATTCATATGCATATCATATAATAATAAATTTTACATCCAATAA
1 GAATAAAAGATATTTTC-ATCAATTCATATGCATAT--TAT-ATAATAAA-TTTACATACAATAA
*
4323175 GTACTTCAATTATTTTATATAAAAGAACTCTAAT
61 GCACTTCAATTATTTTATATAAAAGAACTCTAAT
* * *
4323209 GAATAAAATATATTTTCATCAATTCATATGCATATTATATAATAAATTTACATACAATGAGCATT
1 GAATAAAAGATATTTTCATCAATTCATATGCATATTATATAATAAATTTACATACAATAAGCACT
*
4323274 TTAATTATTTTATATAAAA
66 TCAATTATTTTATATAAAA
4323293 AATCCCTATT
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
94 33 0.43
95 8 0.10
96 3 0.04
98 29 0.38
99 4 0.05
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (94 bp):
GAATAAAAGATATTTTCATCAATTCATATGCATATTATATAATAAATTTACATACAATAAGCACT
TCAATTATTTTATATAAAAGAACTCTAAT
Found at i:4329609 original size:18 final size:20
Alignment explanation
Indices: 4329586--4329624 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
4329576 AAAACAACAA
4329586 TTTTTT-TCAAATTTT-TAT
1 TTTTTTCTCAAATTTTATAT
4329604 TTTTTTCTCAAATTTTATAT
1 TTTTTTCTCAAATTTTATAT
4329624 T
1 T
4329625 AAAAATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTTCTCAAATTTTATAT
Found at i:4329775 original size:19 final size:20
Alignment explanation
Indices: 4329731--4329775 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
4329721 TTTTTTTCAT
* *
4329731 ATATTTTTTTAAATTTTTAG
1 ATATTTTATGAAATTTTTAG
4329751 AT-TTTTATGAAATTTTTA-
1 ATATTTTATGAAATTTTTAG
4329769 ATATTTT
1 ATATTTT
4329776 GGAAATTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 18 0.82
20 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
ATATTTTATGAAATTTTTAG
Found at i:4329780 original size:18 final size:19
Alignment explanation
Indices: 4329741--4329782 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4329731 ATATTTTTTT
*
4329741 AAATTTTTAGATTTTTATG
1 AAATTTTTAGATTTTTAGG
4329760 AAATTTTTA-ATATTTT-GG
1 AAATTTTTAGAT-TTTTAGG
4329778 AAATT
1 AAATT
4329783 CTTATAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (19 bp):
AAATTTTTAGATTTTTAGG
Found at i:4333920 original size:22 final size:22
Alignment explanation
Indices: 4333861--4333957 Score: 63
Period size: 21 Copynumber: 4.3 Consensus size: 22
4333851 TCATTCTATG
* *
4333861 TTAAAAATACATAA-TTATAAA
1 TTAATAATAAATAATTTATAAA
* * *
4333882 TTAATAATATATGATTTATAAT
1 TTAATAATAAATAATTTATAAA
* *
4333904 TTACTAATAAATAATTTTGTTTATAAT
1 TTAATAATAAATAA-----TTTATAAA
*
4333931 TTAAAAATAAATAA-TTATAAA
1 TTAATAATAAATAATTTATAAA
4333952 TTAATA
1 TTAATA
4333958 GTATTGAAGG
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
21 22 0.37
22 17 0.29
27 20 0.34
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAATAATAAATAATTTATAAA
Found at i:4341299 original size:17 final size:20
Alignment explanation
Indices: 4341259--4341305 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 20
4341249 AAATTAAAAA
4341259 TAATAAT-ATAACTTTTAAG
1 TAATAATAATAACTTTTAAG
4341278 TAATAATAATAAC-TTT-AG
1 TAATAATAATAACTTTTAAG
4341296 -AATAATAATA
1 TAATAATAATA
4341306 CACAATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.37
18 2 0.07
19 10 0.37
20 5 0.19
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
TAATAATAATAACTTTTAAG
Found at i:4342233 original size:28 final size:28
Alignment explanation
Indices: 4342201--4342268 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
4342191 TTTATTTTTA
4342201 TTTTTAATTTTAAAACTTTTAAAAT-AT
1 TTTTTAATTTTAAAACTTTTAAAATAAT
* *** *
4342228 TTTTTTATTTTTTTATTTTTAAAATAAT
1 TTTTTAATTTTAAAACTTTTAAAATAAT
4342256 TTTTTAATGTTTA
1 TTTTTAAT-TTTA
4342269 TTAAAAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
27 20 0.62
28 9 0.28
29 3 0.09
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (28 bp):
TTTTTAATTTTAAAACTTTTAAAATAAT
Found at i:4344476 original size:19 final size:20
Alignment explanation
Indices: 4344454--4344502 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
4344444 TTTAATTTTT
*
4344454 TCTTT-ATGTTTTAAGTAAC
1 TCTTTCATGTTTTAAATAAC
* *
4344473 TCTTTCATCTTTTAAATAAT
1 TCTTTCATGTTTTAAATAAC
4344493 TCTTTCATGT
1 TCTTTCATGT
4344503 ATTACTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.55
Consensus pattern (20 bp):
TCTTTCATGTTTTAAATAAC
Found at i:4346465 original size:3 final size:3
Alignment explanation
Indices: 4346423--4346572 Score: 81
Period size: 3 Copynumber: 50.0 Consensus size: 3
4346413 ATTTCGATAG
* * * * * ** *
4346423 TAT TAT CAT TAT TGT TAC TAT TAT TTT TAA TAT TGC TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
4346471 TGT GCTAT TAT TAT TAT TACT TAC T-T TAT TAT TAT CAT TAT CAT TAT
1 TAT --TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
4346518 T-T T-T TAT TAT TAC TAA TAT TAT TAT TTT TAT TTT TAC TAC TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4346564 TAT TAT TAT
1 TAT TAT TAT
4346573 ACATTGTTAT
Statistics
Matches: 107, Mismatches: 35, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
2 5 0.05
3 97 0.91
4 3 0.03
5 2 0.02
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:4346529 original size:25 final size:25
Alignment explanation
Indices: 4346495--4346556 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
4346485 TATTACTTAC
*
4346495 TTTATTATTA-TCATTATCATTATTT
1 TTTATTATTACT-AATATCATTATTT
*
4346520 TTTATTATTACTAATATTATTA-TT
1 TTTATTATTACTAATATCATTATTT
*
4346544 TTTATTTTTACTA
1 TTTATTATTACTA
4346557 CTATTGTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.42
25 18 0.55
26 1 0.03
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTATTATTACTAATATCATTATTT
Found at i:4346580 original size:16 final size:18
Alignment explanation
Indices: 4346540--4346583 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
4346530 CTAATATTAT
* *
4346540 TATTTTTATTTTTACTAC
1 TATTGTTATTATTACTAC
4346558 TATTGTTATTATTA-TAC
1 TATTGTTATTATTACTAC
4346575 -ATTGTTATT
1 TATTGTTATT
4346584 TTTAAACTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 9 0.38
17 3 0.12
18 12 0.50
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (18 bp):
TATTGTTATTATTACTAC
Found at i:4346756 original size:24 final size:23
Alignment explanation
Indices: 4346706--4346759 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
4346696 TATCTTACTA
4346706 TTTTATTATTTCATCATTTTTGC
1 TTTTATTATTTCATCATTTTTGC
*
4346729 TTTTATTATTT-ATCTTATTTTTGT
1 TTTTATTATTTCATC--ATTTTTGC
4346753 TTTTATT
1 TTTTATT
4346760 CTTATTATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 3 0.11
23 11 0.39
24 14 0.50
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTTATTATTTCATCATTTTTGC
Found at i:4351179 original size:17 final size:16
Alignment explanation
Indices: 4351147--4351182 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
4351137 GAACCGACTG
*
4351147 TTCTTTTTCTTTTTCT
1 TTCTTTTTCTTCTTCT
4351163 TTCTTTTTCCTTCTTCT
1 TTCTTTTT-CTTCTTCT
4351180 TTC
1 TTC
4351183 AACTCAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTCTTTTTCTTCTTCT
Found at i:4351286 original size:16 final size:16
Alignment explanation
Indices: 4351267--4351331 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
4351257 GCCCTTCATA
4351267 TCTTTTCTCCTCTTTC
1 TCTTTTCTCCTCTTTC
* *
4351283 TCTTCTCTCTTCTTTC
1 TCTTTTCTCCTCTTTC
* **
4351299 TCTTTTTTTTTCTTTTC
1 TCTTTTCTCCTC-TTTC
4351316 TCTTTTCTTCCTCTTT
1 TCTTTTC-TCCTCTTT
4351332 TTTCTCTTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
16 23 0.59
17 13 0.33
18 3 0.08
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TCTTTTCTCCTCTTTC
Found at i:4351300 original size:9 final size:9
Alignment explanation
Indices: 4351270--4351342 Score: 55
Period size: 9 Copynumber: 8.2 Consensus size: 9
4351260 CTTCATATCT
*
4351270 TTTCTCCTC
1 TTTCTCTTC
4351279 TTTCTCTTC
1 TTTCTCTTC
4351288 --TCTCTTC
1 TTTCTCTTC
4351295 TTTCTCTT-
1 TTTCTCTTC
*
4351303 TTT-TTTTC
1 TTTCTCTTC
4351311 TTTTCTCTTTTC
1 -TTTCTC--TTC
* *
4351323 TTCCTCTTT
1 TTTCTCTTC
4351332 TTTCTCTTC
1 TTTCTCTTC
4351341 TT
1 TT
4351343 GTTTTGCTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
7 10 0.20
8 3 0.06
9 28 0.56
10 1 0.02
11 5 0.10
12 3 0.06
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTCTCTTC
Found at i:4351316 original size:28 final size:28
Alignment explanation
Indices: 4351279--4351334 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
4351269 TTTTCTCCTC
*
4351279 TTTCTCTTCTCTCTTCTTTCTCTTTTTT
1 TTTCTCTTCTCTCTTCTTCCTCTTTTTT
* *
4351307 TTTCTTTTCTCTTTTCTTCCTCTTTTTT
1 TTTCTCTTCTCTCTTCTTCCTCTTTTTT
4351335 CTCTTCTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTCTCTTCTCTCTTCTTCCTCTTTTTT
Found at i:4351933 original size:30 final size:31
Alignment explanation
Indices: 4351859--4351980 Score: 153
Period size: 31 Copynumber: 4.1 Consensus size: 31
4351849 CAAAACTTTC
* * * *
4351859 AGGGTCAAAATGTAATTTTAGAAAAATTTAG
1 AGGGTTAAAATGTAATTTTAGGAAAAGTTGG
4351890 AGGGTTAAAATGTAATTTTAGGAAAAGTTGG
1 AGGGTTAAAATGTAATTTTAGGAAAAGTTGG
* * *
4351921 AGGG-TCAAATGTAATTTTAGGATAA-TT-T
1 AGGGTTAAAATGTAATTTTAGGAAAAGTTGG
4351949 AGGGTTAAAATGTAATTTTAGG-AAAGTTGG
1 AGGGTTAAAATGTAATTTTAGGAAAAGTTGG
4351979 AG
1 AG
4351981 ACCAAAATGT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.08
29 20 0.26
30 21 0.27
31 31 0.40
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (31 bp):
AGGGTTAAAATGTAATTTTAGGAAAAGTTGG
Found at i:4351969 original size:59 final size:60
Alignment explanation
Indices: 4351859--4351994 Score: 197
Period size: 59 Copynumber: 2.3 Consensus size: 60
4351849 CAAAACTTTC
4351859 AGGGTCAAAATGTAATTTTAGAAAAATTTAGAGGGTTAAAATGTAATTTTAGGAAAAGTTGG
1 AGGGTCAAAATGTAATTTTAGAAAAATTTA-AGGGTTAAAATGTAATTTTAGG-AAAGTTGG
* *
4351921 AGGGTC-AAATGTAATTTTAGGATAATTT-AGGGTTAAAATGTAATTTTAGGAAAGTTGG
1 AGGGTCAAAATGTAATTTTAGAAAAATTTAAGGGTTAAAATGTAATTTTAGGAAAGTTGG
**
4351979 A-GACCAAAATGTAATT
1 AGGGTCAAAATGTAATT
4351995 AGTTAATTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
57 2 0.03
58 19 0.28
59 22 0.32
61 20 0.29
62 6 0.09
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (60 bp):
AGGGTCAAAATGTAATTTTAGAAAAATTTAAGGGTTAAAATGTAATTTTAGGAAAGTTGG
Found at i:4351987 original size:29 final size:28
Alignment explanation
Indices: 4351862--4351994 Score: 108
Period size: 29 Copynumber: 4.5 Consensus size: 28
4351852 AACTTTCAGG
* * *
4351862 GTCAAAATGTAATTTTAGAAAAATTTAGAGG
1 GTCAAAATGTAATTTTAG-GAAAGTT-G-GA
*
4351893 GTTAAAATGTAATTTTAGGAAAAGTTGGA
1 GTCAAAATGTAATTTTAGG-AAAGTTGGA
*
4351922 GGGTC-AAATGTAATTTTAGGATAATTTAGG-
1 --GTCAAAATGTAATTTTAGGA-AAGTT-GGA
*
4351952 GTTAAAATGTAATTTTAGGAAAGTTGGA
1 GTCAAAATGTAATTTTAGGAAAGTTGGA
*
4351980 GACCAAAATGTAATT
1 G-TCAAAATGTAATT
4351995 AGTTAATTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
27 2 0.02
28 7 0.08
29 29 0.35
30 20 0.24
31 26 0.31
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.34
Consensus pattern (28 bp):
GTCAAAATGTAATTTTAGGAAAGTTGGA
Found at i:4361570 original size:27 final size:27
Alignment explanation
Indices: 4361508--4361560 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
4361498 AACTAGAGTA
4361508 TGTTAAAATTTTGAATATTTTGAGTTG
1 TGTTAAAATTTTGAATATTTTGAGTTG
4361535 TGTTAAAATTTTGAATATTTTGAGTT
1 TGTTAAAATTTTGAATATTTTGAGTT
4361561 TTTTTGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (27 bp):
TGTTAAAATTTTGAATATTTTGAGTTG
Found at i:4363836 original size:28 final size:29
Alignment explanation
Indices: 4363796--4363853 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
4363786 CACTCGCTCA
4363796 CGAGTAGATGAAGATGAACAACTGT-GCG
1 CGAGTAGATGAAGATGAACAACTGTCGCG
4363824 CGAGTAGATGAAGATGAACAACTGTCGCG
1 CGAGTAGATGAAGATGAACAACTGTCGCG
4363853 C
1 C
4363854 AGGGTGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (29 bp):
CGAGTAGATGAAGATGAACAACTGTCGCG
Found at i:4367553 original size:5 final size:5
Alignment explanation
Indices: 4367545--4367571 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
4367535 AAATTAATTT
4367545 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
4367572 AAAATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:4372251 original size:22 final size:23
Alignment explanation
Indices: 4372207--4372251 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
4372197 ATATAAAAAA
4372207 ATAATATTATATTTTGTACTTTTCC
1 ATAATATTATA--TTGTACTTTTCC
*
4372232 ATAATATTATA-TGTATTTTT
1 ATAATATTATATTGTACTTTT
4372252 TTAGGTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
25 11 0.58
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (23 bp):
ATAATATTATATTGTACTTTTCC
Found at i:4373123 original size:27 final size:28
Alignment explanation
Indices: 4373077--4373140 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
4373067 AGACATTATC
*
4373077 ATAAATATAATAAATGTTTTATTATATT
1 ATAAATATAATAAATATTTTATTATATT
*
4373105 ATAAATA-AATAAATATTTTATTGTA-T
1 ATAAATATAATAAATATTTTATTATATT
4373131 -TAAATATAAT
1 ATAAATATAAT
4373141 TTTTAAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 6 0.18
26 4 0.12
27 16 0.48
28 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (28 bp):
ATAAATATAATAAATATTTTATTATATT
Found at i:4378399 original size:24 final size:26
Alignment explanation
Indices: 4378372--4378420 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
4378362 TATATTCGTA
*
4378372 AATGTTTAT-TCAT-ATATGCATTAG
1 AATGTTGATCTCATGATATGCATTAG
*
4378396 AATGTTGATCTCATGTTATGCATTA
1 AATGTTGATCTCATGATATGCATTA
4378421 CCCCTCTAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 4 0.19
26 9 0.43
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (26 bp):
AATGTTGATCTCATGATATGCATTAG
Found at i:4379352 original size:22 final size:23
Alignment explanation
Indices: 4379325--4379367 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4379315 TTATAATCAA
4379325 ATATAAACACATAATT-TTATTT
1 ATATAAACACATAATTATTATTT
* *
4379347 ATATAAATATATAATTATTAT
1 ATATAAACACATAATTATTAT
4379368 ATTTTATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAAACACATAATTATTATTT
Found at i:4390596 original size:4 final size:4
Alignment explanation
Indices: 4390587--4390699 Score: 63
Period size: 4 Copynumber: 27.8 Consensus size: 4
4390577 ACGGTTTCCT
* * *
4390587 TTTA TTTA TTTA TTTA -TTA TTCCT- TTTA TTTTA TTCA TTTA CTTA CTTA
1 TTTA TTTA TTTA TTTA TTTA TT--TA TTTA -TTTA TTTA TTTA TTTA TTTA
* * * **
4390636 CTTA TTTA TTTA TATA -TTA TTCA TTTA TTTA CTTT- TTTA TTCTAA TTCC
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TT-T-A TTTA
*
4390685 TTTA TTCA TTTA TTT
1 TTTA TTTA TTTA TTT
4390700 GTTATTCCTT
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
3 9 0.11
4 62 0.73
5 10 0.12
6 4 0.05
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:4410061 original size:30 final size:31
Alignment explanation
Indices: 4409994--4410061 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
4409984 ACATTCTCGT
* *
4409994 ATACAAA-ATCAGATGTATTTTCATAATCAG
1 ATACAAATATCAGATGCATATTCATAATCAG
4410024 ATACAAATA-CAGATGCATATTCA-AATTCAG
1 ATACAAATATCAGATGCATATTCATAA-TCAG
4410054 ATACAAAT
1 ATACAAAT
4410062 GTAGACACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 31 0.91
31 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (31 bp):
ATACAAATATCAGATGCATATTCATAATCAG
Found at i:4410914 original size:23 final size:23
Alignment explanation
Indices: 4410877--4410949 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
4410867 CATCAACAGT
* *
4410877 GTAATATCCCGAAAATTACTACT
1 GTAATACCCCGAAAATTACTACA
*
4410900 GTAATACCCCAAAAATTACTACA
1 GTAATACCCCGAAAATTACTACA
4410923 GTAATACCCCGAAAATTACTACA
1 GTAATACCCCGAAAATTACTACA
4410946 GTAA
1 GTAA
4410950 GGAAGTAGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (23 bp):
GTAATACCCCGAAAATTACTACA
Found at i:4421420 original size:17 final size:18
Alignment explanation
Indices: 4421388--4421434 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
4421378 TATTAAACCA
4421388 ATAATT-TATATTTAAA-T
1 ATAATTATAT-TTTAAACT
*
4421405 ATTATTATATTTTAAACT
1 ATAATTATATTTTAAACT
4421423 ATAATTCATATT
1 ATAATT-ATATT
4421435 AAAAGTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 11 0.44
18 9 0.36
19 5 0.20
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAATTATATTTTAAACT
Found at i:4421436 original size:17 final size:18
Alignment explanation
Indices: 4421378--4421449 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 18
4421368 TATTTTTATG
* * *
4421378 TATTAAACCAATAATTTA
1 TATTAAAACTATAATTCA
* *
4421396 TATTTAAA-TATTATT-A
1 TATTAAAACTATAATTCA
*
4421412 TATTTTAAACTATAATTCA
1 TA-TTAAAACTATAATTCA
*
4421431 TATTAAAAGTATAATTCA
1 TATTAAAACTATAATTCA
4421449 T
1 T
4421450 GAAAATATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
16 3 0.07
17 11 0.25
18 27 0.61
19 3 0.07
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (18 bp):
TATTAAAACTATAATTCA
Found at i:4424765 original size:28 final size:28
Alignment explanation
Indices: 4424733--4424826 Score: 134
Period size: 28 Copynumber: 3.4 Consensus size: 28
4424723 TAATGAGATT
*
4424733 AGCACTAAGTATGTGAGTTTAATTGTAA
1 AGCACTAAGTATGCGAGTTTAATTGTAA
* *
4424761 AGCACTAAGTGTGCGAGTTTAATGGTAA
1 AGCACTAAGTATGCGAGTTTAATTGTAA
* * *
4424789 AGCACTAAGTATGCGAGTTTGATTATTA
1 AGCACTAAGTATGCGAGTTTAATTGTAA
4424817 AGCACTAAGT
1 AGCACTAAGT
4424827 GTGTGAACTT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTATGCGAGTTTAATTGTAA
Found at i:4426077 original size:46 final size:46
Alignment explanation
Indices: 4426010--4426194 Score: 302
Period size: 46 Copynumber: 4.0 Consensus size: 46
4426000 ACATTGCTAT
4426010 AACTCAGTATGGTTTTCTTCAC-GAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTG-AAATACCATACCTACTTTTCAC
*
4426056 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
*
4426102 AACTCAGTATGGTTTTCTTTA-TCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
* *
4426148 AACTCAGTATGGTTTTCTTCACTGAAATACCATACATACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
4426194 A
1 A
4426195 CTTTGCCATG
Statistics
Matches: 130, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
45 1 0.01
46 127 0.98
47 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:4428393 original size:113 final size:111
Alignment explanation
Indices: 4428032--4428648 Score: 806
Period size: 113 Copynumber: 5.6 Consensus size: 111
4428022 ACGAAAAAGA
* *
4428032 AAAAAAACAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAA
1 AAAAAAATAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAA
*****
4428097 -AAATTTTTTTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATAC
66 GAAAAAAAATTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATAC
* * *
4428142 GAAAAAATAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAATACAAA
1 AAAAAAATAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAA
4428207 GAAAAAAAATTTATTTTTTTTCGTGTCAGAATCAGATAAAAAAAT--
66 GAAAAAAAA-TTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATAC
* *
4428252 -----AA-AAAAAAAAA--TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACACAGTATAAA
1 AAAAAAATAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAA
*
4428309 GAAAAAAAATTA-TTTTTTTCGTGTCAGAATCAGATAAATAAATAC
66 GAAAAAAAATTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATAC
* * *
4428354 AAAAAAATTAAAAAAAAAGTTTTTGGATGCTGGCCTGTCAATGGCCGGCACCCAATACGCAGTAC
1 AAAAAAA-TAAAAAAAAA--TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTAC
4428419 AAAGAAAAAAAA--A-----TTTCGTGTCAGAATCAGAT-AAAAAATAC
63 AAAGAAAAAAAATTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATAC
4428460 GAAAAAAATAAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTA
1 -AAAAAAAT--A-AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTA
* *
4428525 CAAAGATAAAAAAATTATTTTTTTTCATGTCAGAATCAGATAAAAAAATATG
62 CAAAGA-AAAAAAATTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATA-C
* * * *
4428577 AAAAAAATTAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGTCGGCACCTAGTACGCAGTACAAA
1 AAAAAAATAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAA
4428642 GAAAAAA
66 GAAAAAA
4428649 TTTTTTTTTA
Statistics
Matches: 451, Mismatches: 27, Indels: 56
0.84 0.05 0.10
Matches are distributed among these distances:
100 30 0.07
101 3 0.01
102 52 0.12
104 9 0.02
105 2 0.00
106 9 0.02
107 75 0.17
108 8 0.02
109 17 0.04
110 63 0.14
111 4 0.01
112 40 0.09
113 105 0.23
115 18 0.04
116 16 0.04
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (111 bp):
AAAAAAATAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAA
GAAAAAAAATTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATAC
Found at i:4428524 original size:220 final size:214
Alignment explanation
Indices: 4428025--4428648 Score: 834
Period size: 220 Copynumber: 2.9 Consensus size: 214
4428015 CGGATATACG
4428025 AAAAA-GAAAAAAA-ACAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACA
1 AAAAATGAAAAAAATA-AAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACA
***** *
4428088 CAGTACAAA-AAATTTTTTTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATACGAAAAAA-TA
65 CAGTACAAAGAAAAAAAATTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATACAAAAAAATTA
* * *
4428151 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAATACAAAGAAAAAAAA
130 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACGCAGTACAAAGAAAAAAAA
** * **
4428216 TTTATTTTTTTTCGTGTCAGAA
195 --TATTTCGTGTCGAATCAGAA
** * *
4428238 TCAGAT-AAAAAAATAAAAAAAAAAA-TTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAC
1 AAAAATGAAAAAAATAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAC
* *
4428301 AGTATAAAGAAAAAAAATTA-TTTTTTTCGTGTCAGAATCAGATAAATAAATACAAAAAAATTAA
66 AGTACAAAGAAAAAAAATTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATACAAAAAAATTAA
* *
4428365 AAAAAAAGTTTTTGGATGCTGGCCTGTCAATGGCCGGCACCCAATACGCAGTACAAAGAAAAAAA
131 AAAAAAA--TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACGCAGTACAAAGAAAAAAA
4428430 A-ATTTCGTGTCAGAATCAGATA
194 ATATTTCGTGTC-GAATCAGA-A
4428452 AAAAATACGAAAAAAATAAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGT
1 AAAAAT--GAAAAAAATAAA-AAAAAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGT
* *
4428517 ACACAGTACAAAGATAAAAAAATTATTTTTTTTCATGTCAGAATCAGATAAAAAAATATGAAAAA
62 ACACAGTACAAAGA-AAAAAAATTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATA-CAAAAA
* *
4428582 AATT-AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGTCGGCACCTAGTACGCAGTACAAAGAAA
125 AATTAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACGCAGTACAAAGAAA
4428646 AAA
190 AAA
4428649 TTTTTTTTTA
Statistics
Matches: 360, Mismatches: 34, Indels: 27
0.86 0.08 0.06
Matches are distributed among these distances:
212 89 0.25
213 41 0.11
214 5 0.01
215 52 0.14
217 11 0.03
218 8 0.02
220 97 0.27
221 10 0.03
222 38 0.11
223 9 0.03
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (214 bp):
AAAAATGAAAAAAATAAAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAC
AGTACAAAGAAAAAAAATTATTTTTTTTCGTGTCAGAATCAGATAAAAAAATACAAAAAAATTAA
AAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACGCAGTACAAAGAAAAAAAAT
ATTTCGTGTCGAATCAGAA
Found at i:4428946 original size:115 final size:115
Alignment explanation
Indices: 4428645--4428955 Score: 512
Period size: 115 Copynumber: 2.8 Consensus size: 115
4428635 GTACAAAGAA
*
4428645 AAAATTTTTTTTT-ATTTTTTTCGTATTTTTTTATCTGATTCTGACACG-AAAAAAAATAA---T
1 AAAATTTTTTTTTAAATTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAATAATTTT
4428705 TTTTT-TTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC
66 TTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC
*
4428754 AAAA--TTTTTTTAAATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAGAAAATAATTT
1 AAAATTTTTTTTTAAA-TTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAATAATTT
*
4428817 TTTTTTCTTTGTACTGCGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC
65 TTTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC
* *
4428868 AAAATTTTTTTTTAAATTTTTTCCTATTTTTTTATCTGATTCTGACGCGAAAAAAAAATAATTTT
1 AAAATTTTTTTTTAAATTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAATAATTTT
4428933 TTTTTCTTTGTACTGTGTACTGG
66 TTTTTCTTTGTACTGTGTACTGG
4428956 AATTTTTTCC
Statistics
Matches: 186, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
107 7 0.04
108 1 0.01
109 37 0.20
110 10 0.05
113 6 0.03
114 47 0.25
115 68 0.37
116 10 0.05
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (115 bp):
AAAATTTTTTTTTAAATTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAATAATTTT
TTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC
Found at i:4429007 original size:73 final size:74
Alignment explanation
Indices: 4428882--4429028 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 74
4428872 TTTTTTTTTA
*
4428882 AATTTTTTCCTATTTTTTTATCTGATTCTGACGCGAAAAAAAAATAATTTTTTTTTCTTTGTACT
1 AATTTTTTCCTATTTTTTTATCTGATTCTGACGCGAAAAAAAAATAAATTTTTTTTCTTTGTACT
4428947 GTGTACTGG
66 GTGTACTGG
4428956 AATTTTTTCCTA-TTTTTTATCTGATTCTGACGCGAAAAAAAAATAAATTTTTTTTCTTTGTACT
1 AATTTTTTCCTATTTTTTTATCTGATTCTGACGCGAAAAAAAAATAAATTTTTTTTCTTTGTACT
4429020 GTGTACTGG
66 GTGTACTGG
4429029 GTTCCGGCCA
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
73 60 0.83
74 12 0.17
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (74 bp):
AATTTTTTCCTATTTTTTTATCTGATTCTGACGCGAAAAAAAAATAAATTTTTTTTCTTTGTACT
GTGTACTGG
Found at i:4429028 original size:188 final size:191
Alignment explanation
Indices: 4428769--4429118 Score: 580
Period size: 188 Copynumber: 1.8 Consensus size: 191
4428759 TTTTTTAAAT
* * *
4428769 TTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAGAAAATAATTTTTTTTTCTTTGTACTGC
1 TTTTTTCCTATTTTTTTATCTGATTCTGACACGAAAAAAAAATAAATTTTTTTTCTTTGTACTGC
4428834 GTACTGGGTGCCGGCCATTGACAGGCCAGCACCC-AAAATTTTTTTTTAA-ATTTTTTCCTATTT
66 GTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTTTAATATTTTTTCCTATTT
*
4428897 TTTTATCTGATTCTGACGCGAAAAAAAAATAATTTTTTTTTCTTTGTACTGTGTACTGGAA
131 TTTTATCTGATTCTGACACGAAAAAAAAATAATTTTTTTTTCTTTGTACTGTGTACTGGAA
* *
4428958 TTTTTTCCTA-TTTTTTATCTGATTCTGACGCGAAAAAAAAATAAATTTTTTTTCTTTGTACTGT
1 TTTTTTCCTATTTTTTTATCTGATTCTGACACGAAAAAAAAATAAATTTTTTTTCTTTGTACTGC
* * *
4429022 GTACTGGGTTCCGGCCATTGACAGGCCAGCACCCAAAAAAATTTTTTTTTAATTTTTTTTCGTAT
66 GTACTGGGTGCCGGCCATTGACAGGCCAGCACCC--AAAAATTTTTTTTTAATATTTTTTCCTAT
4429087 TTTTTTATCTGATTCTGACACGAAAAAAAAAT
129 TTTTTTATCTGATTCTGACACGAAAAAAAAAT
4429119 TGTACTGTGT
Statistics
Matches: 148, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
188 83 0.56
189 9 0.06
191 15 0.10
192 41 0.28
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (191 bp):
TTTTTTCCTATTTTTTTATCTGATTCTGACACGAAAAAAAAATAAATTTTTTTTCTTTGTACTGC
GTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTTTAATATTTTTTCCTATTT
TTTTATCTGATTCTGACACGAAAAAAAAATAATTTTTTTTTCTTTGTACTGTGTACTGGAA
Found at i:4442538 original size:17 final size:17
Alignment explanation
Indices: 4442516--4442550 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4442506 CAAATGAGTT
* *
4442516 TAATATATGTTTATATA
1 TAATATATATATATATA
4442533 TAATATATATATATATA
1 TAATATATATATATATA
4442550 T
1 T
4442551 CACTACAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TAATATATATATATATA
Found at i:4442941 original size:20 final size:20
Alignment explanation
Indices: 4442898--4442941 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
4442888 CAGAAAAATT
** *
4442898 AAAAAAATCTTTAAAATCTA
1 AAAAAAATAATTAAAATATA
4442918 AAAAAAATAATTAAAATATGA
1 AAAAAAATAATTAAAATAT-A
4442939 AAA
1 AAA
4442942 CCCCAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAAATAATTAAAATATA
Found at i:4443369 original size:15 final size:15
Alignment explanation
Indices: 4443346--4443379 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4443336 ACTTATATCT
* *
4443346 ATGTCTGAAATTATA
1 ATGTATGAAATTAAA
4443361 ATGTATGAAATTAAA
1 ATGTATGAAATTAAA
4443376 ATGT
1 ATGT
4443380 CAAAAGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (15 bp):
ATGTATGAAATTAAA
Found at i:4443824 original size:21 final size:21
Alignment explanation
Indices: 4443790--4443845 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
4443780 GGTCCATATT
* *
4443790 TTTTTTATGATTTTTT-TATA
1 TTTTTAATGATTTTTTAAATA
4443810 TTTTTAATGATTTTTTAAATA
1 TTTTTAATGATTTTTTAAATA
4443831 TTTTTAAAT-ATTTTT
1 TTTTT-AATGATTTTT
4443846 AATGTCCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 15 0.47
21 14 0.44
22 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTAATGATTTTTTAAATA
Found at i:4443826 original size:11 final size:10
Alignment explanation
Indices: 4443789--4443845 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
4443779 GGGTCCATAT
*
4443789 TTTTTTTATGA
1 TTTTTTAAT-A
*
4443800 TTTTTTTATA
1 TTTTTTAATA
4443810 -TTTTTAATGA
1 TTTTTTAAT-A
4443820 TTTTTTAAATA
1 TTTTTT-AATA
*
4443831 TTTTTAAATA
1 TTTTTTAATA
4443841 TTTTT
1 TTTTT
4443846 AATGTCCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 7 0.17
10 11 0.27
11 20 0.49
12 3 0.07
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (10 bp):
TTTTTTAATA
Found at i:4443834 original size:10 final size:10
Alignment explanation
Indices: 4443807--4443847 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
4443797 TGATTTTTTT
4443807 ATATTTTT-A
1 ATATTTTTAA
4443816 ATGATTTTTTAA
1 AT-A-TTTTTAA
4443828 ATATTTTTAA
1 ATATTTTTAA
4443838 ATATTTTTAA
1 ATATTTTTAA
4443848 TGTCCAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.07
10 18 0.62
11 6 0.21
12 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
ATATTTTTAA
Found at i:4447577 original size:3 final size:3
Alignment explanation
Indices: 4447569--4447593 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4447559 GCAGTCCCTA
4447569 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
4447594 CGAACAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:4449072 original size:22 final size:23
Alignment explanation
Indices: 4449041--4449083 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4449031 AAAAATATAT
*
4449041 TAAATTTATAAATTT-ATTATCA
1 TAAATATATAAATTTAATTATCA
*
4449063 TAAATATATAAGTTTAATTAT
1 TAAATATATAAATTTAATTAT
4449084 TATTTAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAATATATAAATTTAATTATCA
Found at i:4450314 original size:13 final size:13
Alignment explanation
Indices: 4450296--4450323 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4450286 TAAGTTTAAA
4450296 TTAATTTAAATTT
1 TTAATTTAAATTT
4450309 TTAATTTAAATTT
1 TTAATTTAAATTT
4450322 TT
1 TT
4450324 GGATTGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAATTTAAATTT
Found at i:4455611 original size:22 final size:22
Alignment explanation
Indices: 4455563--4455613 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
4455553 TTTTTCTTGC
* * *
4455563 TATTTTTCTACTATTTTGTTAT
1 TATTTTACTACTATGTTGCTAT
* *
4455585 CATTTTACTATTATGTTGCTAT
1 TATTTTACTACTATGTTGCTAT
4455607 TATTTTA
1 TATTTTA
4455614 TTGTTATTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.63
Consensus pattern (22 bp):
TATTTTACTACTATGTTGCTAT
Found at i:4461865 original size:4 final size:4
Alignment explanation
Indices: 4461856--4461881 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4461846 ATCTACTTCA
4461856 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
4461882 ATCTAGCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:4467153 original size:46 final size:45
Alignment explanation
Indices: 4467069--4467320 Score: 158
Period size: 46 Copynumber: 5.2 Consensus size: 45
4467059 TTTGAGTACT
* *
4467069 TCTGATCAAGTGACAAAGT-GATAAGTGGT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGGA-AAGTGATAAG-TATAGCTACACTTA
* *
4467115 TCTAATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAGTGGAAAGTGATAAGT-ATA------GCTACACTTA
*
4467167 TCTGATCAAGTGACAAAGT-GATAAGTGAT-AGCT-TCGGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGGA-AAGTGATAAG-TAT-AGCTACACTTA
* *
4467213 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAGTGGAAAGTGATAAGT-ATA------GCTACACTTA
* *
4467265 TCTGATCAAGAGACAAAGT-GATAAGTGAT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGGA-AAGTGATAAG-TATAGCTACACTTA
4467311 TCTGATCAAG
1 TCTGATCAAG
4467321 AAACAAAGTG
Statistics
Matches: 166, Mismatches: 14, Indels: 52
0.72 0.06 0.22
Matches are distributed among these distances:
45 23 0.14
46 64 0.39
47 1 0.01
51 1 0.01
52 53 0.32
53 24 0.14
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAGTGGAAAGTGATAAGTATAGCTACACTTA
Found at i:4467154 original size:52 final size:46
Alignment explanation
Indices: 4467135--4467333 Score: 272
Period size: 46 Copynumber: 4.2 Consensus size: 46
4467125 TGACAAGTGG
* *
4467135 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
4467181 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
* *
4467227 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
** **
4467279 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
4467325 AAAGTGATA
1 AAAGTGATA
4467334 GGTGGCTACA
Statistics
Matches: 139, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
46 95 0.68
52 44 0.32
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
Found at i:4467238 original size:98 final size:98
Alignment explanation
Indices: 4467069--4467320 Score: 441
Period size: 98 Copynumber: 2.6 Consensus size: 98
4467059 TTTGAGTACT
* *
4467069 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
4467134 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
4467167 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
4467232 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
4467265 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG
4467321 AAACAAAGTG
Statistics
Matches: 145, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 145 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:4470966 original size:30 final size:29
Alignment explanation
Indices: 4470932--4470991 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
4470922 AAAATAGATA
* *
4470932 AATATTAAATTTATACATAAATTTTGATTT
1 AATATGAAATTGATACATAAATTTT-ATTT
* *
4470962 AATATGCAATTGATACATAACTTTTATTT
1 AATATGAAATTGATACATAAATTTTATTT
4470991 A
1 A
4470992 GTGTAATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (29 bp):
AATATGAAATTGATACATAAATTTTATTT
Found at i:4512196 original size:46 final size:45
Alignment explanation
Indices: 4512112--4512363 Score: 158
Period size: 46 Copynumber: 5.2 Consensus size: 45
4512102 TTTGAGTACT
* *
4512112 TCTGATCAAGTGACAAAGT-GATAAGTGGT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGGA-AAGTGATAAG-TATAGCTACACTTA
* *
4512158 TCTAATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAGTGGAAAGTGATAAGT-ATA------GCTACACTTA
*
4512210 TCTGATCAAGTGACAAAGT-GATAAGTGAT-AGCT-TCGGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGGA-AAGTGATAAG-TAT-AGCTACACTTA
* *
4512256 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAGTGGAAAGTGATAAGT-ATA------GCTACACTTA
* *
4512308 TCTGATCAAGAGACAAAGT-GATAAGTGAT-AGCTTTAGCTACACTTA
1 TCTGATCAAGTGAC-AAGTGGA-AAGTGATAAG-TATAGCTACACTTA
4512354 TCTGATCAAG
1 TCTGATCAAG
4512364 AAACAAAGTG
Statistics
Matches: 166, Mismatches: 14, Indels: 52
0.72 0.06 0.22
Matches are distributed among these distances:
45 23 0.14
46 64 0.39
47 1 0.01
51 1 0.01
52 53 0.32
53 24 0.14
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAGTGGAAAGTGATAAGTATAGCTACACTTA
Found at i:4512197 original size:52 final size:46
Alignment explanation
Indices: 4512178--4512376 Score: 272
Period size: 46 Copynumber: 4.2 Consensus size: 46
4512168 TGACAAGTGG
* *
4512178 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
4512224 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
* *
4512270 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
** **
4512322 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
4512368 AAAGTGATA
1 AAAGTGATA
4512377 GGTGGCTACA
Statistics
Matches: 139, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
46 95 0.68
52 44 0.32
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
Found at i:4512281 original size:98 final size:98
Alignment explanation
Indices: 4512112--4512363 Score: 441
Period size: 98 Copynumber: 2.6 Consensus size: 98
4512102 TTTGAGTACT
* *
4512112 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
4512177 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
4512210 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
4512275 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
4512308 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG
4512364 AAACAAAGTG
Statistics
Matches: 145, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 145 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:4515466 original size:65 final size:65
Alignment explanation
Indices: 4515391--4515520 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
4515381 TCTATAATTT
*
4515391 TAATTTTTAAAAAATAAATTTATTGTTTGTTAATATTTACTAATTATGTATATATATCTCTTTTG
1 TAATTTTTAAAAAATAAAATTATTGTTTGTTAATATTTACTAATTATGTATATATATCTCTTTTG
4515456 TAATTTTTAAAAAATAAAATTATTGTTTGTTAATATTTACTAATTATGTATATATATCTCTTTTG
1 TAATTTTTAAAAAATAAAATTATTGTTTGTTAATATTTACTAATTATGTATATATATCTCTTTTG
4515521 CTATCATTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (65 bp):
TAATTTTTAAAAAATAAAATTATTGTTTGTTAATATTTACTAATTATGTATATATATCTCTTTTG
Found at i:4546107 original size:19 final size:19
Alignment explanation
Indices: 4546083--4546125 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
4546073 CCTTTTTTTG
* *
4546083 TAATTTTATTAAATATATT
1 TAATTTTATTAAAAAAATT
*
4546102 TAATTTTTTTAAAAAAATT
1 TAATTTTATTAAAAAAATT
4546121 TAATT
1 TAATT
4546126 GCATGGATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATTTTATTAAAAAAATT
Found at i:4555582 original size:21 final size:22
Alignment explanation
Indices: 4555558--4555607 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
4555548 TTTTCCCCTA
4555558 CTGTTTTACTG-CTTTATGTTG
1 CTGTTTTACTGTCTTTATGTTG
* *
4555579 CTGTTTTATTGTTTTTATGTTG
1 CTGTTTTACTGTCTTTATGTTG
*
4555601 TTGTTTT
1 CTGTTTT
4555608 GTTACCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.66
Consensus pattern (22 bp):
CTGTTTTACTGTCTTTATGTTG
Found at i:4562752 original size:15 final size:16
Alignment explanation
Indices: 4562722--4562754 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4562712 TAATGTCTCT
4562722 TTTTTTAAAATATTTA
1 TTTTTTAAAATATTTA
*
4562738 TTTTTTAATAT-TTTA
1 TTTTTTAAAATATTTA
4562753 TT
1 TT
4562755 ATACCCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTAAAATATTTA
Found at i:4567767 original size:20 final size:20
Alignment explanation
Indices: 4567742--4567779 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4567732 TTAATGTACC
4567742 AAATAATTAAAAAA-AATTTA
1 AAATAA-TAAAAAAGAATTTA
4567762 AAATAATAAAAAAGAATT
1 AAATAATAAAAAAGAATT
4567780 GAATTTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AAATAATAAAAAAGAATTTA
Found at i:4573195 original size:19 final size:19
Alignment explanation
Indices: 4573157--4573205 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
4573147 ATTACTAAAC
*
4573157 CAGCCCAAACATTAAACCCT
1 CAGCCCAAA-TTTAAACCCT
*
4573177 CAGCCCAAATTTTAACCCT
1 CAGCCCAAATTTAAACCCT
*
4573196 AAGCCCAAAT
1 CAGCCCAAAT
4573206 GGCCCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.39, C:0.37, G:0.06, T:0.18
Consensus pattern (19 bp):
CAGCCCAAATTTAAACCCT
Found at i:4574481 original size:20 final size:20
Alignment explanation
Indices: 4574450--4574499 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
4574440 GCTTACATTA
4574450 TTATTA-TTTATTTCATTT-C
1 TTATTATTTTATTT-ATTTGC
4574469 ATT-TTATTTTATTTATTTGC
1 -TTATTATTTTATTTATTTGC
4574489 TTATTATTTTA
1 TTATTATTTTA
4574500 GTATCGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (20 bp):
TTATTATTTTATTTATTTGC
Found at i:4574643 original size:15 final size:15
Alignment explanation
Indices: 4574623--4574656 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4574613 TTATCGTTGA
4574623 TTATTATTATTGTT-T
1 TTATTA-TATTGTTAT
4574638 TTATTATATTGTTAT
1 TTATTATATTGTTAT
4574653 TTAT
1 TTAT
4574657 ATCATTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (15 bp):
TTATTATATTGTTAT
Found at i:4575006 original size:107 final size:108
Alignment explanation
Indices: 4574877--4575319 Score: 606
Period size: 109 Copynumber: 4.1 Consensus size: 108
4574867 TATCCAAATA
* * *
4574877 AAAATTTCAAAATAAGGTAATATTTTGCGTTTGGAAGTTCGAGAAAACGTGCCCTAACTTGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTGG
*
4574942 GTCTCGA-TTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
66 GTTTCGATTTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
* *
4574984 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTTGAGAAAATGTGCCCTAACGTGCTGG
1 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTGG
4575049 GTTTCGATTTTTTTCGTTCGACCAAATAGCTAAAAATATCCTTTT
66 GTTTCGA-TTTTTTCGTTCGACCAAATAGCT-AAAATATCCTTTT
* * *
4575094 AAAATTTCAAAATAAGGCAATATTTCACGTTTGGAAGTTCGA-AAAACGTGCCCTAACGTGTTAG
1 AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTGG
*
4575158 GTTTCGATTTTTTTCGTTCGACCAAATAGCTAAAATATCCTTCT
66 GTTTCGA-TTTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
* * * * * * **
4575202 AAAATTTCATAATAAAGGTAATATTTTGCATTTGAAAATTCGAGAAAGTGTGCCCTAACGTGCTG
1 AAAATTTCAAAAT-AAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTG
* * * * *
4575267 GGTTTTGA-TTTCTCGTTTGACCAAATAGC-CAAATATCCTCTT
65 GGTTTCGATTTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
*
4575309 AAAACTTCAAA
1 AAAATTTCAAA
4575320 GTATGTTTTT
Statistics
Matches: 300, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
107 85 0.28
108 43 0.14
109 95 0.32
110 77 0.26
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (108 bp):
AAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTGG
GTTTCGATTTTTTCGTTCGACCAAATAGCTAAAATATCCTTTT
Found at i:4576536 original size:21 final size:22
Alignment explanation
Indices: 4576511--4576554 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4576501 GGATTTATAT
4576511 TATTCGGG-GTGTGTT-GTTGGA
1 TATTCGGGTGTGT-TTGGTTGGA
*
4576532 TATTCTGGTGTGTTTGGTTGGA
1 TATTCGGGTGTGTTTGGTTGGA
4576554 T
1 T
4576555 CCATATATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.09, C:0.05, G:0.39, T:0.48
Consensus pattern (22 bp):
TATTCGGGTGTGTTTGGTTGGA
Found at i:4580657 original size:11 final size:11
Alignment explanation
Indices: 4580643--4580708 Score: 60
Period size: 11 Copynumber: 6.0 Consensus size: 11
4580633 ATATCAAAAC
4580643 AATAACAACAA
1 AATAACAACAA
*
4580654 AATAATAACAA
1 AATAACAACAA
* * *
4580665 TATAATAGCAA
1 AATAACAACAA
** *
4580676 AATGTCATCAA
1 AATAACAACAA
*
4580687 AACAACAACAA
1 AATAACAACAA
4580698 AATAACAACAA
1 AATAACAACAA
4580709 GAAAAAGAAT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 42 1.00
ACGTcount: A:0.65, C:0.17, G:0.03, T:0.15
Consensus pattern (11 bp):
AATAACAACAA
Found at i:4583625 original size:474 final size:474
Alignment explanation
Indices: 4582738--4583689 Score: 1886
Period size: 474 Copynumber: 2.0 Consensus size: 474
4582728 TCAAACCAAC
4582738 ATTTAGCACTTATTTCACTTATCAACTATTCGATTCTTATACAAGATCATTTAATTGCACATAAC
1 ATTTAGCACTTATTTCACTTATCAACTATTCGATTCTTATACAAGATCATTTAATTGCACATAAC
4582803 ATTATACTTTTGATTATTATTCTATTTAGTACCTTAAAGCTTACATGTAAATTTAATTACATCAT
66 ATTATACTTTTGATTATTATTCTATTTAGTACCTTAAAGCTTACATGTAAATTTAATTACATCAT
4582868 CACTTCACATACTATAATTCATATATCACAAATAGTGATGGATCAATGACAATGCCTGTCATCAT
131 CACTTCACATACTATAATTCATATATCACAAATAGTGATGGATCAATGACAATGCCTGTCATCAT
4582933 TGAAACTCCACTGGCTACCAGCAACTTTTTTAGAAAGCGGATGACTCTTCGTCAATTTCTGTTTT
196 TGAAACTCCACTGGCTACCAGCAACTTTTTTAGAAAGCGGATGACTCTTCGTCAATTTCTGTTTT
4582998 GAGAGTATTTCAGAATAATAAATGATTTCACGAATAGGTTTGGACCATTCGGAGCTGATTTCCTT
261 GAGAGTATTTCAGAATAATAAATGATTTCACGAATAGGTTTGGACCATTCGGAGCTGATTTCCTT
*
4583063 ATTATATTAAATGCTTGCAACCACTCTAGATATATCGTATTTAAGTTGTGACAGAGCAAATTGTC
326 ATTATATTAAATGCTTGCAACCACTCTAGATATATCGTATTTAAATTGTGACAGAGCAAATTGTC
4583128 AATGTATCATAATGTTATATTTATGCTGAGACTGAAACCTTTATCATGTTGATGAAATTTACCTT
391 AATGTATCATAATGTTATATTTATGCTGAGACTGAAACCTTTATCATGTTGATGAAATTTACCTT
4583193 TTACCGCCTTTATTATTAA
456 TTACCGCCTTTATTATTAA
4583212 ATTTAGCACTTATTTCACTTATCAACTATTCGATTCTTATACAAGATCATTTAATTGCACATAAC
1 ATTTAGCACTTATTTCACTTATCAACTATTCGATTCTTATACAAGATCATTTAATTGCACATAAC
4583277 ATTATACTTTTGATTATTATTCTATTTAGTACCTTAAAGCTTACATGTAAATTTAATTACATCAT
66 ATTATACTTTTGATTATTATTCTATTTAGTACCTTAAAGCTTACATGTAAATTTAATTACATCAT
4583342 CACTTCACATACTATAATTCATATATCACAAATAGTGATGGATCAATGACAATGCCTGTCATCAT
131 CACTTCACATACTATAATTCATATATCACAAATAGTGATGGATCAATGACAATGCCTGTCATCAT
4583407 TGAAACTCCACTGGCTACCAGCAACTTTTTTAGAAAGCGGATGACTCTTCGTCAATTTCTGTTTT
196 TGAAACTCCACTGGCTACCAGCAACTTTTTTAGAAAGCGGATGACTCTTCGTCAATTTCTGTTTT
*
4583472 GAGAGTATTTCAGAATAATAAATTATTTCACGAATAGGTTTGGACCATTCGGAGCTGATTTCCTT
261 GAGAGTATTTCAGAATAATAAATGATTTCACGAATAGGTTTGGACCATTCGGAGCTGATTTCCTT
4583537 ATTATATTAAATGCTTGCAACCACTCTAGATATATCGTATTTAAATTGTGACAGAGCAAATTGTC
326 ATTATATTAAATGCTTGCAACCACTCTAGATATATCGTATTTAAATTGTGACAGAGCAAATTGTC
4583602 AATGTATCATAATGTTATATTTATGCTGAGACTGAAACCTTTATCATGTTGATGAAATTTACCTT
391 AATGTATCATAATGTTATATTTATGCTGAGACTGAAACCTTTATCATGTTGATGAAATTTACCTT
4583667 TTACCGCCTTTATTATTAA
456 TTACCGCCTTTATTATTAA
4583686 ATTT
1 ATTT
4583690 TCTCAAATTG
Statistics
Matches: 476, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
474 476 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.38
Consensus pattern (474 bp):
ATTTAGCACTTATTTCACTTATCAACTATTCGATTCTTATACAAGATCATTTAATTGCACATAAC
ATTATACTTTTGATTATTATTCTATTTAGTACCTTAAAGCTTACATGTAAATTTAATTACATCAT
CACTTCACATACTATAATTCATATATCACAAATAGTGATGGATCAATGACAATGCCTGTCATCAT
TGAAACTCCACTGGCTACCAGCAACTTTTTTAGAAAGCGGATGACTCTTCGTCAATTTCTGTTTT
GAGAGTATTTCAGAATAATAAATGATTTCACGAATAGGTTTGGACCATTCGGAGCTGATTTCCTT
ATTATATTAAATGCTTGCAACCACTCTAGATATATCGTATTTAAATTGTGACAGAGCAAATTGTC
AATGTATCATAATGTTATATTTATGCTGAGACTGAAACCTTTATCATGTTGATGAAATTTACCTT
TTACCGCCTTTATTATTAA
Found at i:4599203 original size:16 final size:18
Alignment explanation
Indices: 4599164--4599197 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4599154 TAAGTTTATA
4599164 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
4599181 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
4599198 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:4599812 original size:16 final size:16
Alignment explanation
Indices: 4599776--4599820 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
4599766 ATGTGGGTAA
4599776 ATAAAAATAT-TTTAT
1 ATAAAAATATATTTAT
4599791 ATTAAAAATATATATT-T
1 A-TAAAAATATAT-TTAT
4599808 ATAAAAATATATT
1 ATAAAAATATATT
4599821 AATAAATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.07
16 20 0.74
17 3 0.11
18 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:4604203 original size:3 final size:3
Alignment explanation
Indices: 4604197--4604225 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4604187 ACAACACAGT
4604197 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
4604226 GTAGGCATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4604706 original size:17 final size:16
Alignment explanation
Indices: 4604679--4604711 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
4604669 TTTTTATTTG
4604679 TAACTTTTAATTTATT
1 TAACTTTTAATTTATT
4604695 TAACTATTTAATTTATT
1 TAACT-TTTAATTTATT
4604712 ACTTATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TAACTTTTAATTTATT
Found at i:4606047 original size:24 final size:24
Alignment explanation
Indices: 4606015--4606067 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
4606005 TTTCTAGAAG
*
4606015 ATTTAGCATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
4606039 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
4606063 ATTTA
1 ATTTA
4606068 ACTTTGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:4606077 original size:24 final size:24
Alignment explanation
Indices: 4606015--4606078 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
4606005 TTTCTAGAAG
* * *
4606015 ATTTAGCATTTATGAGTATAATAT
1 ATTTAACATTTATTAGCATAATAT
*
4606039 ATTTAGCATTTATTAGCATAATAT
1 ATTTAACATTTATTAGCATAATAT
4606063 ATTTAAC-TTTGATTAG
1 ATTTAACATTT-ATTAG
4606079 AATTAGGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 3 0.08
24 33 0.92
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (24 bp):
ATTTAACATTTATTAGCATAATAT
Found at i:4610497 original size:24 final size:24
Alignment explanation
Indices: 4610469--4610520 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
4610459 TTTCTAGAAG
* *
4610469 ATTTAATATTTATGAGTATAATAT
1 ATTTAACATTTATGAGCATAATAT
* *
4610493 ATTTAGCATTTATTAGCATAATAT
1 ATTTAACATTTATGAGCATAATAT
4610517 ATTT
1 ATTT
4610521 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAACATTTATGAGCATAATAT
Found at i:4618428 original size:9 final size:8
Alignment explanation
Indices: 4618407--4618470 Score: 60
Period size: 8 Copynumber: 7.8 Consensus size: 8
4618397 TCAGACTCAA
4618407 AAAAAATTC
1 AAAAAA-TC
*
4618416 AAAAAGTC
1 AAAAAATC
4618424 AAAAAATC
1 AAAAAATC
4618432 AAAAAA--
1 AAAAAATC
*
4618438 AAAATCATC
1 AAAA-AATC
4618447 AAAAAAATC
1 -AAAAAATC
4618456 AAAAAAATC
1 -AAAAAATC
4618465 AAAAAA
1 AAAAAA
4618471 AATCAAAGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
6 4 0.09
7 1 0.02
8 21 0.45
9 17 0.36
10 4 0.09
ACGTcount: A:0.75, C:0.11, G:0.02, T:0.12
Consensus pattern (8 bp):
AAAAAATC
Found at i:4618452 original size:32 final size:30
Alignment explanation
Indices: 4618405--4618472 Score: 93
Period size: 33 Copynumber: 2.2 Consensus size: 30
4618395 GTTCAGACTC
*
4618405 AAAAAAAATTCAAAAAGTC-AAAAAATCAA
1 AAAAAAAATTCAAAAAATCAAAAAAATCAA
4618434 AAAAAAAATCATCAAAAAAATCAAAAAAATCAA
1 AAAAAAAAT--TC-AAAAAATCAAAAAAATCAA
4618467 AAAAAA
1 AAAAAA
4618473 TCAAAGTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.26
31 2 0.06
32 7 0.21
33 16 0.47
ACGTcount: A:0.76, C:0.10, G:0.01, T:0.12
Consensus pattern (30 bp):
AAAAAAAATTCAAAAAATCAAAAAAATCAA
Found at i:4618471 original size:9 final size:9
Alignment explanation
Indices: 4618406--4618477 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 9
4618396 TTCAGACTCA
4618406 AAAAAAATTC
1 AAAAAAA-TC
*
4618416 -AAAAAGTC
1 AAAAAAATC
4618424 -AAAAAATC
1 AAAAAAATC
4618432 -AAAAAA--
1 AAAAAAATC
**
4618438 AAAATCATC
1 AAAAAAATC
4618447 AAAAAAATC
1 AAAAAAATC
4618456 AAAAAAATC
1 AAAAAAATC
4618465 AAAAAAAATC
1 -AAAAAAATC
4618475 AAA
1 AAA
4618478 GTCAAAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
7 4 0.08
8 15 0.29
9 24 0.46
10 9 0.17
ACGTcount: A:0.75, C:0.11, G:0.01, T:0.12
Consensus pattern (9 bp):
AAAAAAATC
Found at i:4618472 original size:12 final size:12
Alignment explanation
Indices: 4618424--4618462 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
4618414 TCAAAAAGTC
4618424 AAAAAATCAAAA
1 AAAAAATCAAAA
**
4618436 AAAAAATCATCA
1 AAAAAATCAAAA
4618448 AAAAAATCAAAA
1 AAAAAATCAAAA
4618460 AAA
1 AAA
4618463 TCAAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAATCAAAA
Found at i:4618473 original size:31 final size:29
Alignment explanation
Indices: 4618403--4618475 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 29
4618393 GAGTTCAGAC
*
4618403 TCAAAAAAAAT--TCAAAAAGTCAAAAAA
1 TCAAAAAAAATCATCAAAAAATCAAAAAA
4618430 TCAAAAAAAAAATCATCAAAAAAATCAAAAAAA
1 TC--AAAAAAAATCATC-AAAAAATC-AAAAAA
4618463 TCAAAAAAAATCA
1 TCAAAAAAAATCA
4618476 AAGTCAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 2 0.05
29 9 0.23
31 13 0.33
32 7 0.18
33 8 0.21
ACGTcount: A:0.73, C:0.12, G:0.01, T:0.14
Consensus pattern (29 bp):
TCAAAAAAAATCATCAAAAAATCAAAAAA
Found at i:4619334 original size:7 final size:7
Alignment explanation
Indices: 4619322--4619378 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
4619312 TTGAGTCAAA
4619322 AAAAAAG
1 AAAAAAG
4619329 AAAAAAG
1 AAAAAAG
*
4619336 AAGAAATG
1 AA-AAAAG
*
4619344 AGAAAAAT
1 A-AAAAAG
*
4619352 AAAAATG
1 AAAAAAG
*
4619359 AAAAATG
1 AAAAAAG
4619366 AAAAAATG
1 AAAAAA-G
4619374 AAAAA
1 AAAAA
4619379 GTAAAAATGG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
7 25 0.61
8 15 0.37
9 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (7 bp):
AAAAAAG
Found at i:4619334 original size:8 final size:8
Alignment explanation
Indices: 4619321--4619378 Score: 61
Period size: 8 Copynumber: 7.6 Consensus size: 8
4619311 TTTGAGTCAA
*
4619321 AAAAAAAG
1 AAAAAATG
4619329 AAAAAA-G
1 AAAAAATG
*
4619336 AAGAAATG
1 AAAAAATG
4619344 AGAAAAAT-
1 A-AAAAATG
4619352 -AAAAATG
1 AAAAAATG
4619359 -AAAAATG
1 AAAAAATG
4619366 AAAAAATG
1 AAAAAATG
4619374 AAAAA
1 AAAAA
4619379 GTAAAAATGG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 6 0.14
7 13 0.30
8 20 0.45
9 5 0.11
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:4619349 original size:22 final size:22
Alignment explanation
Indices: 4619322--4619387 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
4619312 TTGAGTCAAA
4619322 AAAAAAGAAAAAA-GAAGAAATG
1 AAAAAAGAAAAAATGAA-AAATG
*
4619344 AGAAAAA-TAAAAATGAAAAATG
1 A-AAAAAGAAAAAATGAAAAATG
*
4619366 AAAAAATGAAAAAGT-AAAAATG
1 AAAAAA-GAAAAAATGAAAAATG
4619388 GAGAGGCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
21 5 0.14
22 19 0.51
23 13 0.35
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (22 bp):
AAAAAAGAAAAAATGAAAAATG
Done.