Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009625.1 Hibiscus syriacus cultivar Beakdansim tig00117017_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: 6938204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 25
Found at i:5680731 original size:22 final size:22
Alignment explanation
Indices: 5680642--5680779 Score: 93
Period size: 22 Copynumber: 6.0 Consensus size: 22
5680632 ATAATATAAT
*
5680642 TTATTTAATATTAATATTTAAATTA
1 TTATTT-ATATT-AT-TTTATATTA
* *
5680667 ATATTTAATATTAATTTAATATTA
1 TTATTT-ATATT-ATTTTATATTA
*
5680691 TTAATTACTATTATTTTTTATATTA
1 TTATTTA-TATTA--TTTTATATTA
* * *
5680716 TTTTTTATATTATTTTTTTTTA
1 TTATTTATATTATTTTATATTA
*
5680738 TTATTTATA-TATTCTT-TTTTA
1 TTATTTATATTATT-TTATATTA
5680759 CTTATTTATA-TATTTTATATT
1 -TTATTTATATTATTTTATATT
5680780 TCTATTTCAT
Statistics
Matches: 95, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
21 11 0.12
22 34 0.36
23 2 0.02
24 20 0.21
25 28 0.29
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTTATATTATTTTATATTA
Found at i:5680732 original size:25 final size:25
Alignment explanation
Indices: 5680685--5680757 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
5680675 TATTAATTTA
**
5680685 ATATTATTAATTACTATTA-TTTTTT
1 ATATTATTTTTTA-TATTATTTTTTT
5680710 ATATTATTTTTTATATTATTTTTTT
1 ATATTATTTTTTATATTATTTTTTT
* * *
5680735 TTATTA-TTTATATATTCTTTTTT
1 ATATTATTTTTTATATTATTTTTT
5680758 ACTTATTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 20 0.48
25 22 0.52
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (25 bp):
ATATTATTTTTTATATTATTTTTTT
Found at i:5682669 original size:16 final size:15
Alignment explanation
Indices: 5682639--5682674 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
5682629 TTGTCTTGTC
5682639 TATATTTTTTATAGA
1 TATATTTTTTATAGA
*
5682654 TATATTTTTATCTAGA
1 TATATTTTT-TATAGA
5682670 TATAT
1 TATAT
5682675 CTTAAATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (15 bp):
TATATTTTTTATAGA
Found at i:5682690 original size:14 final size:14
Alignment explanation
Indices: 5682673--5682701 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5682663 ATCTAGATAT
5682673 ATCTTAAATACAAA
1 ATCTTAAATACAAA
5682687 ATCTTAAATACAAA
1 ATCTTAAATACAAA
5682701 A
1 A
5682702 ATAAAAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
ATCTTAAATACAAA
Found at i:5687195 original size:40 final size:40
Alignment explanation
Indices: 5687163--5687243 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
5687153 GTTTCGATAT
5687163 TTTCA-CAATAGCTTCAAAACTTTCATCAAAGTTTCAAAAC
1 TTTCATCAA-AGCTTCAAAACTTTCATCAAAGTTTCAAAAC
* * * *
5687203 TTTCATCAAAGTTTCAAAACTTTC-CCAAGGTTTCGAAAC
1 TTTCATCAAAGCTTCAAAACTTTCATCAAAGTTTCAAAAC
5687242 TT
1 TT
5687244 CATGTGTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 14 0.39
40 19 0.53
41 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (40 bp):
TTTCATCAAAGCTTCAAAACTTTCATCAAAGTTTCAAAAC
Found at i:5687206 original size:9 final size:9
Alignment explanation
Indices: 5687175--5687226 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
5687165 TCACAATAGC
5687175 TTCAAAACT
1 TTCAAAACT
*
5687184 TTCATCAAAGT
1 TTCA--AAACT
5687195 TTCAAAACT
1 TTCAAAACT
*
5687204 TTCATCAAAGT
1 TTCA--AAACT
5687215 TTCAAAACT
1 TTCAAAACT
5687224 TTC
1 TTC
5687227 CCAAGGTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 19 0.54
11 16 0.46
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (9 bp):
TTCAAAACT
Found at i:5687243 original size:19 final size:20
Alignment explanation
Indices: 5687175--5687226 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
5687165 TCACAATAGC
5687175 TTCAAAACTTTCATCAAAGT
1 TTCAAAACTTTCATCAAAGT
5687195 TTCAAAACTTTCATCAAAGT
1 TTCAAAACTTTCATCAAAGT
5687215 TTCAAAACTTTC
1 TTCAAAACTTTC
5687227 CCAAGGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37
Consensus pattern (20 bp):
TTCAAAACTTTCATCAAAGT
Found at i:5693317 original size:25 final size:25
Alignment explanation
Indices: 5693289--5693340 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5693279 AATTTTATAA
*
5693289 AAAAAATGGTCTTATT-GGATTTTTT
1 AAAAAAT-ATCTTATTGGGATTTTTT
*
5693314 AAAACATATCTTATTGGGATTTTTT
1 AAAAAATATCTTATTGGGATTTTTT
5693339 AA
1 AA
5693341 GTACAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (25 bp):
AAAAAATATCTTATTGGGATTTTTT
Found at i:5696858 original size:14 final size:14
Alignment explanation
Indices: 5696839--5696866 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5696829 CCCCTCAGAC
5696839 CGATGCGGGTAACT
1 CGATGCGGGTAACT
5696853 CGATGCGGGTAACT
1 CGATGCGGGTAACT
5696867 TGATCCGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (14 bp):
CGATGCGGGTAACT
Found at i:5697630 original size:24 final size:24
Alignment explanation
Indices: 5697603--5697689 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
5697593 AAACATATTT
5697603 CAGGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* *
5697627 CAGGTCATGTATCAGATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* *
5697651 AATGTCAA-TATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
5697674 CAGGTCAGGTATCATA
1 CAGGTCAAGTATCATA
5697690 ACAAAATTCA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 19 0.36
24 34 0.64
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:5699388 original size:23 final size:22
Alignment explanation
Indices: 5699362--5699404 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5699352 TTTTCAAAGT
*
5699362 TATTAATTAATAGAATATATACA
1 TATTAATGAATA-AATATATACA
*
5699385 TATTAATGACTAAATATATA
1 TATTAATGAATAAATATATA
5699405 ATTATACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (22 bp):
TATTAATGAATAAATATATACA
Found at i:5701171 original size:5 final size:5
Alignment explanation
Indices: 5701161--5701196 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
5701151 GGTTTTCTTC
5701161 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT T
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT T
5701197 TCATTTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TCCTT
Found at i:5701209 original size:3 final size:3
Alignment explanation
Indices: 5701201--5701241 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5701191 TCCTTTTCAT
5701201 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5701242 TTGTTTTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5702624 original size:18 final size:18
Alignment explanation
Indices: 5702601--5702636 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5702591 TGTTTGGGTT
5702601 ATAAACAACCATATGTTC
1 ATAAACAACCATATGTTC
*
5702619 ATAAACAATCATATGTTC
1 ATAAACAACCATATGTTC
5702637 GATGTCGTTT
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:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAAACAACCATATGTTC
Found at i:5704335 original size:30 final size:30
Alignment explanation
Indices: 5704300--5704361 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
5704290 AAATGAGTTT
* *
5704300 TTTTTTTATAAATAA-ATTTTAACTTTATTTA
1 TTTTTTTA-ATATAATATTATAA-TTTATTTA
*
5704331 TTTTTTTAATATAATATTATAATTTTTTTA
1 TTTTTTTAATATAATATTATAATTTATTTA
5704361 T
1 T
5704362 GAATCTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTTTTTAATATAATATTATAATTTATTTA
Found at i:5707328 original size:236 final size:236
Alignment explanation
Indices: 5706908--5707363 Score: 644
Period size: 236 Copynumber: 1.9 Consensus size: 236
5706898 CATTTTAAGG
* * * *
5706908 TCTTACAACCTCTTGAGATGATCCTTGAAGAAGCTTTATCAATTCCCAACGCAACTAACAAGATG
1 TCTTACAACCTCTTGAGACGATCCTTGAAGAAGCTTTATCAATTCCCAAAGAAACGAACAAGATG
** * * *
5706973 ACTTCCACATCCGGCTATTACGATCTTGAGGAATCCCACTCCATCACAAGGTCATCCTACTTCAA
66 ACTTCCACATCCAACTATTACGATCTTGACGAATCCCACTCCATCACAAGGCCATCATACTTCAA
* * * * *
5707038 TGGAGAAAATTATTCATATTGGAAGAATATGATGCTGTTTTTCATCCAAGCCACCGACCTTATGG
131 CGAAGAAAATTATTCATATTGGAAGAATATGATGATGTTGTTCATCCAAGCCACCGACCTTACGG
*
5707103 TTTGGGATGCCATTGTCGACGATTCTCCCACCTCTCAAAGA
196 TTTGGGATGCCATCGTCGACGATTCTCCCACCTCTCAAAGA
** * *
5707144 TCTTACAACCTCTTGAGACGATTTTTGAAGAAGCTTTATCAATTTCCAAAGAAACCGAA-TAGAT
1 TCTTACAACCTCTTGAGACGATCCTTGAAGAAGCTTTATCAATTCCCAAAGAAA-CGAACAAGAT
* * * *
5707208 GACTTCCACATCCAACTATTACTATCTTGACGACTCCCACTCCATCGCAAGGCCTTCATACTTCA
65 GACTTCCACATCCAACTATTACGATCTTGACGAATCCCACTCCATCACAAGGCCATCATACTTCA
* * *
5707273 ACGAAGAAAATTATTCTTATTGGAAGAATATGATGATGTTGTTCATCCTAGCCACCGATCTTACG
130 ACGAAGAAAATTATTCATATTGGAAGAATATGATGATGTTGTTCATCCAAGCCACCGACCTTACG
* *
5707338 GTTTGGGTTGTCATCGTCGACGATTC
195 GTTTGGGATGCCATCGTCGACGATTC
5707364 CTCCACCCTT
Statistics
Matches: 191, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
236 188 0.98
237 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (236 bp):
TCTTACAACCTCTTGAGACGATCCTTGAAGAAGCTTTATCAATTCCCAAAGAAACGAACAAGATG
ACTTCCACATCCAACTATTACGATCTTGACGAATCCCACTCCATCACAAGGCCATCATACTTCAA
CGAAGAAAATTATTCATATTGGAAGAATATGATGATGTTGTTCATCCAAGCCACCGACCTTACGG
TTTGGGATGCCATCGTCGACGATTCTCCCACCTCTCAAAGA
Found at i:5708218 original size:33 final size:33
Alignment explanation
Indices: 5708176--5708240 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
5708166 ATGTCTCATG
5708176 GCCATCAAAGAAGATTCAAGGGTAACTTCTAAA
1 GCCATCAAAGAAGATTCAAGGGTAACTTCTAAA
5708209 GCCATCAAAGAAGATTCAAGGGTAACTTCTAA
1 GCCATCAAAGAAGATTCAAGGGTAACTTCTAA
5708241 CTCTTGTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (33 bp):
GCCATCAAAGAAGATTCAAGGGTAACTTCTAAA
Found at i:5708402 original size:20 final size:21
Alignment explanation
Indices: 5708372--5708420 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5708362 AATGATTTGG
*
5708372 TTTTG-AAAGC-AAATTTGAT
1 TTTTGAAAAGCAAAATTTGAA
*
5708391 TTTTGAAAAGCAAAATTTTAA
1 TTTTGAAAAGCAAAATTTGAA
5708412 TTTTGAAAA
1 TTTTGAAAA
5708421 ATGATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 16 0.62
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (21 bp):
TTTTGAAAAGCAAAATTTGAA
Found at i:5715045 original size:21 final size:24
Alignment explanation
Indices: 5715013--5715055 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
5715003 GGTTTTATAA
5715013 AAATGAAACAAA-TA-ATGTGGTT
1 AAATGAAACAAAGTACATGTGGTT
5715035 AAATG-AACAAAGTACATGTGG
1 AAATGAAACAAAGTACATGTGG
5715056 GTGGGGCAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (24 bp):
AAATGAAACAAAGTACATGTGGTT
Found at i:5716303 original size:6 final size:6
Alignment explanation
Indices: 5716292--5716350 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
5716282 GGGTACCTAA
* * * *
5716292 AAAAAT AAAAAT AAAAAT AAATAAAT AAATAG AAAAAT AACAAT AAGAAT
1 AAAAAT AAAAAT AAAAAT -AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT
*
5716342 AAAAGT AAA
1 AAAAAT AAA
5716351 GAAAATTGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 35 0.81
7 4 0.09
8 4 0.09
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:5716317 original size:20 final size:20
Alignment explanation
Indices: 5716289--5716331 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5716279 TTTGGGTACC
*
5716289 TAAAAAAATAAAAATAAAAA
1 TAAAAAAATAAAAAGAAAAA
* *
5716309 TAAATAAATAAATAGAAAAA
1 TAAAAAAATAAAAAGAAAAA
5716329 TAA
1 TAA
5716332 CAATAAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (20 bp):
TAAAAAAATAAAAAGAAAAA
Found at i:5725256 original size:14 final size:13
Alignment explanation
Indices: 5725223--5725277 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 13
5725213 ATGCAACCCA
5725223 TTTTATTATTTATT
1 TTTTATTATTT-TT
*
5725237 ATTTATTATTTTT
1 TTTTATTATTTTT
5725250 TTGTTATTTATTTTT
1 TT-TTA-TTATTTTT
*
5725265 CTTTA-TATTTTT
1 TTTTATTATTTTT
5725277 T
1 T
5725278 AGGTACATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 7 0.20
13 3 0.09
14 16 0.46
15 9 0.26
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTATTATTTTT
Found at i:5725270 original size:25 final size:26
Alignment explanation
Indices: 5725223--5725278 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
5725213 ATGCAACCCA
5725223 TTTTATTATTTATTATTTATTAT-TT
1 TTTTATTATTTATTATTTATTATATT
* *
5725248 TTTTGTTATTTATT-TTTCTTTATATT
1 TTTTATTATTTATTATTT-ATTATATT
5725274 TTTTA
1 TTTTA
5725279 GGTACATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 3 0.12
25 17 0.65
26 6 0.23
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTATTATTTATTATTTATTATATT
Found at i:5725834 original size:20 final size:21
Alignment explanation
Indices: 5725811--5725854 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
5725801 AAAAAAGAAG
5725811 AAATTAAAAAAAT-AAAGGAA
1 AAATTAAAAAAATGAAAGGAA
* *
5725831 AAA-TCAAAAAATGAGAGGAA
1 AAATTAAAAAAATGAAAGGAA
5725851 AAAT
1 AAAT
5725855 AAGCCCTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.70, C:0.02, G:0.14, T:0.14
Consensus pattern (21 bp):
AAATTAAAAAAATGAAAGGAA
Found at i:5726716 original size:13 final size:13
Alignment explanation
Indices: 5726700--5726732 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5726690 TCCATCTTTC
*
5726700 TTTCTTTCTTTAT
1 TTTCTTTCATTAT
5726713 TTTCTTTCATTAT
1 TTTCTTTCATTAT
5726726 TTTCTTT
1 TTTCTTT
5726733 TCAAAATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTCATTAT
Found at i:5732364 original size:27 final size:27
Alignment explanation
Indices: 5732328--5732388 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
5732318 CTCGAAACTT
5732328 CCCAACATCTCTGGCTCCACATTGATC
1 CCCAACATCTCTGGCTCCACATTGATC
5732355 CCCAACATCTCTGGCTCCACATTGATC
1 CCCAACATCTCTGGCTCCACATTGATC
5732382 CCCAACA
1 CCCAACA
5732389 AGCACTCGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.43, G:0.10, T:0.23
Consensus pattern (27 bp):
CCCAACATCTCTGGCTCCACATTGATC
Found at i:5735661 original size:32 final size:32
Alignment explanation
Indices: 5735625--5735692 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
5735615 TTGTGTTTTA
* *
5735625 TGAATGACGCATCCTATGGAACGCACCTCTCT
1 TGAATGACGCATACTATGGAACGCACCTCCCT
* *
5735657 TGAATGGCGCATACTATGGAACGCGCCTCCCT
1 TGAATGACGCATACTATGGAACGCACCTCCCT
5735689 TGAA
1 TGAA
5735693 AGGCGTGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (32 bp):
TGAATGACGCATACTATGGAACGCACCTCCCT
Found at i:5738940 original size:8 final size:8
Alignment explanation
Indices: 5738888--5738944 Score: 62
Period size: 8 Copynumber: 7.1 Consensus size: 8
5738878 GAATTTTCTT
5738888 AGTTTGAG
1 AGTTTGAG
*
5738896 AGTTTAAG
1 AGTTTGAG
*
5738904 AGTTTGAA
1 AGTTTGAG
*
5738912 AGTTTGAA
1 AGTTTGAG
*
5738920 AGTTT-AC
1 AGTTTGAG
5738927 ACGTTTGAG
1 A-GTTTGAG
5738936 AGTTTGAG
1 AGTTTGAG
5738944 A
1 A
5738945 TTTCAAAGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
7 2 0.05
8 38 0.90
9 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.37
Consensus pattern (8 bp):
AGTTTGAG
Found at i:5739318 original size:83 final size:83
Alignment explanation
Indices: 5739056--5739690 Score: 778
Period size: 83 Copynumber: 7.7 Consensus size: 83
5739046 AGTGGAACAT
* * * * *
5739056 GCGCCTTTCA-TTCAGATGAGATGGAACACTATGACACGACATAGATTCTCTGAATAATAATGGA
1 GCGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGA
* * *
5739120 AAATGTTTCCCCTAGAAT
66 AAACGCTTCCCCTAGAAC
*
5739138 GCGCCTTTCATTTCGGATGGGATGGAACACTATGACATGTCAGAGA---T-TGAATAATAATGGA
1 GCGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGA
* *
5739199 AAACGCTTCCCCTGGAAT
66 AAACGCTTCCCCTAGAAC
* *
5739217 GCGCCTTTCATTTCGGATGGGATCGAACACTATGACATGACAGAGATTCTCTGAATAATAATGGA
1 GCGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGA
* *
5739282 AAATGCTTCCACTAGAAC
66 AAACGCTTCCCCTAGAAC
* * * * *
5739300 GCACCTTTCATTTTGGATGGGATGAAACACTATGGCATGGCATAGATTCTCTGAATAATAATGGA
1 GCGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGA
* *
5739365 AAACACTTCCCCTGGAAC
66 AAACGCTTCCCCTAGAAC
* * * *
5739383 GCGCCTTTCATTTCGGATGAGATGGAACACTATGACATGGAAGAGATTCTTTGAATAATAATAGA
1 GCGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGA
* *
5739448 AAACTCTTCCCCTATAAC
66 AAACGCTTCCCCTAGAAC
* * * * * * *
5739466 -CTGCCTTTTATTTCAGATGGGATTGAACAATATGACATGGCAAAGTTTCTCTGAATAATAATAG
1 GC-GCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGG
**
5739530 AAAACATTTCCCCTAGAAC
65 AAAACGCTTCCCCTAGAAC
* * * * *
5739549 ACGCCTCTCATTTCGGATGGGATGAAACACTATGACATGGTAGAGATTCTCTGAATAATAATGAA
1 GCGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGA
* *
5739614 AAACGCTTCCCCTGGAAT
66 AAACGCTTCCCCTAGAAC
* * * * *
5739632 ACGCCTTTCATTTTGGATGGGATGGAACACTATGACATGGTAGAGATTTTTTGAATAAT
1 GCGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAAT
5739691 GTAAAACACT
Statistics
Matches: 477, Mismatches: 69, Indels: 13
0.85 0.12 0.02
Matches are distributed among these distances:
79 73 0.15
80 1 0.00
82 12 0.03
83 390 0.82
84 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (83 bp):
GCGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGA
AAACGCTTCCCCTAGAAC
Found at i:5740716 original size:32 final size:32
Alignment explanation
Indices: 5740671--5740745 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
5740661 TTTTTCACAG
* * *
5740671 ACCTTAAACAGTAAATAAAATCATACACATAC
1 ACCTAAAATAGTAAATAAAAGCATACACATAC
5740703 ACCTAAAATAGTAAATAAAAGCATACACATAC
1 ACCTAAAATAGTAAATAAAAGCATACACATAC
5740735 ACCTAAAATAG
1 ACCTAAAATAG
5740746 ACTTTTTGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (32 bp):
ACCTAAAATAGTAAATAAAAGCATACACATAC
Found at i:5741967 original size:57 final size:57
Alignment explanation
Indices: 5741876--5741991 Score: 189
Period size: 57 Copynumber: 2.0 Consensus size: 57
5741866 AGTACACGAT
* *
5741876 CAGTCAGATGCCACTCAACAATAGCATAACAAATAAGGGGTACAACCGCCACTCATA
1 CAGTCAGATGCCACTCAACAATAGCATAACAAATAAGGGGCACAACCGCCACCCATA
*
5741933 CAGTCGGATGCCACTCAACAATAGCATTAA-AAATAAGGGGCACAACCGCCACCCATA
1 CAGTCAGATGCCACTCAACAATAGCA-TAACAAATAAGGGGCACAACCGCCACCCATA
5741990 CA
1 CA
5741992 TCCAATATCC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 52 0.95
58 3 0.05
ACGTcount: A:0.40, C:0.29, G:0.16, T:0.15
Consensus pattern (57 bp):
CAGTCAGATGCCACTCAACAATAGCATAACAAATAAGGGGCACAACCGCCACCCATA
Found at i:5742258 original size:2 final size:2
Alignment explanation
Indices: 5742251--5742284 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5742241 CACCTATTTA
5742251 AT AT AT AT AT A- AT -T 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
5742285 CATTCTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5742269 original size:12 final size:12
Alignment explanation
Indices: 5742252--5742298 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
5742242 ACCTATTTAA
5742252 TATATATATAAT
1 TATATATATAAT
5742264 TATATATAT-AT
1 TATATATATAAT
*
5742275 ATATATATATCAT
1 -TATATATATAAT
*
5742288 TCTATA-ATAAT
1 TATATATATAAT
5742299 CAAAAACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 6 0.19
12 23 0.74
13 2 0.06
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (12 bp):
TATATATATAAT
Found at i:5743134 original size:19 final size:19
Alignment explanation
Indices: 5743112--5743161 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
5743102 AAATAAATTC
5743112 TAAT-AATTTAAATAATAT
1 TAATAAATTTAAATAATAT
* *
5743130 ATAATCAATTT-CATAATAT
1 -TAATAAATTTAAATAATAT
*
5743149 TCATAAATTTAAA
1 TAATAAATTTAAA
5743162 AGGAATATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.32
19 12 0.48
20 5 0.20
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATAAATTTAAATAATAT
Found at i:5745368 original size:14 final size:13
Alignment explanation
Indices: 5745351--5745381 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
5745341 CTTAATTGTA
5745351 AAAATTTAAAATTT
1 AAAATTT-AAATTT
5745365 AAAATTTAAATTT
1 AAAATTTAAATTT
5745378 AAAA
1 AAAA
5745382 GCATCGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATTTAAATTT
Found at i:5745377 original size:6 final size:7
Alignment explanation
Indices: 5745351--5745381 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5745341 CTTAATTGTA
5745351 AAAATTT
1 AAAATTT
5745358 AAAATTT
1 AAAATTT
5745365 AAAATTT
1 AAAATTT
5745372 -AAATTT
1 AAAATTT
5745378 AAAA
1 AAAA
5745382 GCATCGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:5745606 original size:2 final size:2
Alignment explanation
Indices: 5745594--5745669 Score: 131
Period size: 2 Copynumber: 39.5 Consensus size: 2
5745584 AATAGAAGTA
5745594 AT AT A- AT AT AT AT AT AT AT AT AT -T 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
5745634 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5745670 AAACATAGAA
Statistics
Matches: 71, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
1 3 0.04
2 68 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5745760 original size:39 final size:39
Alignment explanation
Indices: 5745690--5745766 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
5745680 AGAAAGATGT
*
5745690 AAAAATAAATAGAAAATACAAACATAAAATAAATCAAAG
1 AAAAATAAATAGAAAATACAAACAAAAAATAAATCAAAG
5745729 AAAAAT-AATAGAAAA-ACAAACTAAAATAATAAATCAAA
1 AAAAATAAATAGAAAATACAAAC-AAAA-AATAAATCAAA
5745767 TTAAAAAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
37 6 0.17
38 12 0.34
39 17 0.49
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.16
Consensus pattern (39 bp):
AAAAATAAATAGAAAATACAAACAAAAAATAAATCAAAG
Found at i:5745793 original size:2 final size:2
Alignment explanation
Indices: 5745786--5745839 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
5745776 GAAGACACAA
*
5745786 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5745827 AT GT AT GT AT AT A
1 AT AT AT AT AT AT A
5745840 AATTAAAGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5746968 original size:24 final size:24
Alignment explanation
Indices: 5746931--5746982 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
5746921 GAAAAAAAAC
*
5746931 AAAATAAATAAAAAACGAATAATA
1 AAAATAAATAAAAAACAAATAATA
5746955 AAAATAAGAT-AAAAACAAATAATA
1 AAAATAA-ATAAAAAACAAATAATA
5746979 AAAA
1 AAAA
5746983 AATATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (24 bp):
AAAATAAATAAAAAACAAATAATA
Found at i:5747057 original size:12 final size:12
Alignment explanation
Indices: 5747040--5747081 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
5747030 TCAGACTATA
*
5747040 AAAAATGTTTTT
1 AAAAATATTTTT
5747052 AAAAATATTTTCT
1 AAAAATATTTT-T
5747065 AAAAATATTTTT
1 AAAAATATTTTT
5747077 AAAAA
1 AAAAA
5747082 CTATATAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 16 0.57
13 12 0.43
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:5747136 original size:36 final size:36
Alignment explanation
Indices: 5747091--5747258 Score: 189
Period size: 36 Copynumber: 4.6 Consensus size: 36
5747081 ACTATATAGG
*
5747091 TTTTCAAAAATGTTTTAATAGATATATATTATATTTA
1 TTTTCAAAAATGTTTTAA-AAATATATATTATATTTA
* * *
5747128 TTTT-AAAAATATTTTAAAAAT-TATATAATATATA
1 TTTTCAAAAATGTTTTAAAAATATATATTATATTTA
5747162 TTTTCAAAAATGTTTTAAAAACTATATATTATATTTA
1 TTTTCAAAAATGTTTTAAAAA-TATATATTATATTTA
** *
5747199 TTTTC-AAAATGTTTTAAAAACTATATAATATATAAATG
1 TTTTCAAAAATGTTTTAAAAA-TATAT-AT-TATATTTA
*
5747237 TTTTCAAACATGTTTTCAAAAA
1 TTTTCAAAAATGTTTT-AAAAA
5747259 AATGTTTTTA
Statistics
Matches: 113, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
34 15 0.13
35 18 0.16
36 34 0.30
37 22 0.19
38 10 0.09
39 9 0.08
40 5 0.04
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTTCAAAAATGTTTTAAAAATATATATTATATTTA
Found at i:5747142 original size:11 final size:11
Alignment explanation
Indices: 5747126--5747182 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
5747116 ATATTATATT
5747126 TATTTTAAAAA
1 TATTTTAAAAA
5747137 TATTTTAAAAA
1 TATTTTAAAAA
* *
5747148 T-TATATAATATA
1 TAT-TTTAA-AAA
5747160 TATTTTCAAAAA
1 TATTTT-AAAAA
*
5747172 TGTTTTAAAAA
1 TATTTTAAAAA
5747183 CTATATATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
10 1 0.03
11 21 0.57
12 12 0.32
13 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:5747171 original size:71 final size:71
Alignment explanation
Indices: 5747091--5747232 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 71
5747081 ACTATATAGG
* *
5747091 TTTTCAAAAATGTTTTAATAGA-TATATATTATATTTATTTTAAAAATATTTTAAAAATTATATA
1 TTTTCAAAAATGTTTTAA-AAACTATATATTATATTTATTTTAAAAATATTTTAAAAACTATATA
5747155 ATATATA
65 ATATATA
* *
5747162 TTTTCAAAAATGTTTTAAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAAACTATATAA
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATTTATTTTAAAAATATTTTAAAAACTATATAA
5747227 TATATA
66 TATATA
5747233 AATGTTTTCA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
70 2 0.03
71 64 0.97
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (71 bp):
TTTTCAAAAATGTTTTAAAAACTATATATTATATTTATTTTAAAAATATTTTAAAAACTATATAA
TATATA
Found at i:5747285 original size:2 final size:2
Alignment explanation
Indices: 5747274--5747306 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5747264 TTTTAAACTG
5747274 TA TA -A 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
5747307 AACAAATGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5747934 original size:84 final size:84
Alignment explanation
Indices: 5747839--5749056 Score: 1302
Period size: 84 Copynumber: 14.6 Consensus size: 84
5747829 AATCGAATTT
* * * *
5747839 GAAGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCTTGGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
5747904 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
* * * * * * * * * *
5747923 GAAGGTATTCGG-TGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGTCCTCGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGG
* *
5747987 AGCTGAGTGTAATCGAACTC
65 AGCTGAGCGTAGTCGAACTC
*
5748007 GAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
*
5748068 GCTGAGAGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
* * * *
5748087 GAAGGTCTTTGGTTGACAGATAACTCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
*
5748152 GCTGAGCGTAGTCGAACTT
66 GCTGAGCGTAGTCGAACTC
* * * * * * * * *
5748171 GAAGGTCTTTTGG-TGACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAAGGACGTGCCCTCG
1 GAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTG
* * * *
5748235 AAGCTGAGTGTAATCAAACTC
64 GAGCTGAGCGTAGTCGAACTC
* * *
5748256 -AAGGGTC--T--TTGGCAAATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGG
1 GAA-GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGG
*
5748316 AGCTGAGTGTAGTCGAACTC
65 AGCTGAGCGTAGTCGAACTC
* * *
5748336 GAAGGTCTTTGGTTGGCAGATAACACTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
*
5748401 GCTGAGTGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
* * * * * *
5748420 GAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAGGATGTGGCCTTG
1 GAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT-GCCTTG
* * * *
5748484 AAGCTGAGTGTATTCAAACTC
64 GAGCTGAGCGTAGTCGAACTC
* * * *
5748505 GAGGGTC--T--TTAGAAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
5748566 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
* * * *
5748585 GAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATGCAAATGATATGCCTTTGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
5748650 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
* * * * *** * * *
5748669 GAAGGTCTTT-GTTGGAAAATATCCCTTATTTCCTTGAGTTATGTTGCAAATGATGTTCCTTGGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
5748733 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
** * * *** * * *
5748752 GAAGGTCTTTTATTGGAAAATAACCCTTCTTTCCTTGAGCTATGTTGCAAATGATGTGCCTTGGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
5748817 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
* * * * * **
5748836 AAAGGTCTTTTGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTCAA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GG
* * *
5748901 AGCTGAGTGTAATCGAACTT
65 AGCTGAGCGTAGTCGAACTC
* * * * * * *
5748921 GAACGTGTTTGGTTGGAAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTTGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
5748986 GCTGAGCGTAGTCGAACTC
66 GCTGAGCGTAGTCGAACTC
* * * * * *
5749005 AAAGGTCTTT-ATTGGCAGATAACCCGTCTAGCCTTGAGTTATGCTGCAAATG
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
5749057 TTGTCTTTAA
Statistics
Matches: 946, Mismatches: 164, Indels: 49
0.82 0.14 0.04
Matches are distributed among these distances:
80 82 0.09
81 110 0.12
82 5 0.01
83 141 0.15
84 474 0.50
85 134 0.14
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (84 bp):
GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
GCTGAGCGTAGTCGAACTC
Found at i:5748277 original size:249 final size:249
Alignment explanation
Indices: 5747839--5748897 Score: 1491
Period size: 249 Copynumber: 4.2 Consensus size: 249
5747829 AATCGAATTT
* * * * *
5747839 GAAGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCTTGGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGA
* * * *
5747904 GCTGAGCGTAGTCGAACTCGAAGGT-ATTCGGTGACAGATAACCCTTCTAGCCTTGAGTTATACT
66 GCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCT
* * * *
5747968 GTAAATGATGTGTCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCT
131 GTAAAGGATGTGTCCTCGAAGCTGAGTGTAATCAAACTCAAGGGTCTTTGGCAAATAACCCTTCT
* *
5748033 CGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGAGTAGTCGAACTC
196 CGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
5748087 GAAGGTCTTTGGTTGACAGATAACTCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGA
*
5748152 GCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCT
66 GCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCT
* *
5748217 GTAAAGGACGTGCCCTCGAAGCTGAGTGTAATCAAACTCAAGGGTCTTTGGCAAATAACCCTTCT
131 GTAAAGGATGTGTCCTCGAAGCTGAGTGTAATCAAACTCAAGGGTCTTTGGCAAATAACCCTTCT
* *
5748282 CGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTC
196 CGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* *
5748336 GAAGGTCTTTGGTTGGCAGATAACACTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGA
* *
5748401 GCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
66 GCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCT
* * * * *
5748466 GTAAAGGATGTGGCCTTGAAGCTGAGTGTATTCAAACTCGAGGGTCTTTAG-AAGATAACCCTTC
131 GTAAAGGATGTGTCCTCGAAGCTGAGTGTAATCAAACTCAAGGGTCTTTGGCAA-ATAACCCTTC
5748530 TCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
195 TCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
5748585 GAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATGCAAATGATATGCCTTTGA
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGA
* * * ** *
5748650 GCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGA-AAATATCCCTTATTTCCTTGAGTTATGT
66 GCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGT-GACAGATAACCCTTATAGCCTTGAGTTATGC
* * * * * * * *
5748713 TGCAAATGATGT-TCCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTTATTGGAAAATAAC
130 TGTAAAGGATGTGTCCTCGAAGCTGAGTGTAATCAAACTC-AAGGGTC---T-TTGGCAAATAAC
*** * *
5748776 CCTTCTTTCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
190 CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * *
5748836 AAAGGTCTTTTGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTT
1 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT
5748898 CAAAGCTGAG
Statistics
Matches: 734, Mismatches: 68, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
247 26 0.04
248 121 0.16
249 465 0.63
250 1 0.00
251 119 0.16
252 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (249 bp):
GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGA
GCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCT
GTAAAGGATGTGTCCTCGAAGCTGAGTGTAATCAAACTCAAGGGTCTTTGGCAAATAACCCTTCT
CGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
Found at i:5748305 original size:165 final size:164
Alignment explanation
Indices: 5747839--5749056 Score: 1151
Period size: 165 Copynumber: 7.3 Consensus size: 164
5747829 AATCGAATTT
* * * * *
5747839 GAAGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCTTGGA
1 GAAGGTCTTTGG-TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
* * * * * * * * *
5747904 GCTGAGCGTAGTCGAACTCGAAGGTATTCGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTG
65 GCTGAGTGTAGTCGAACTCGAAGGT-CT-GTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTG
* * * * *
5747969 TAAATGATGTGTCCTCGAAGCTGAGTGTAATCGAACTC
128 CAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTC
*
5748007 GAGGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
1 GAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
* * * * *
5748069 CTGAGAGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACTCTTCTCGACTTAAGTTATGCTA
66 CTGAGTGTAGTCGAACTCGAAGGTC--T-GTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTG
* *
5748134 CAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTT
128 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * * * * *
5748171 GAAGGTCTTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAAGGACGTGCCCTCGA
1 GAAGGTC-TTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGG
* * * *
5748236 AGCTGAGTGTAATCAAACTC-AAGGGTCT-TTGGCAAATAACCCTTCTCGACTTAAGCTATACTG
64 AGCTGAGTGTAGTCGAACTCGAA-GGTCTGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTG
*
5748299 CAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTC
128 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * *
5748336 GAAGGTCTTTGGTTGGCAGATAACACTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGA
1 GAAGGTCTTTGG-TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
* * * * *
5748401 GCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
65 GCTGAGTGTAGTCGAACTCGAAGGTCTGTT-G-G-CAAATAACCCTTCTCGACTTAAGTTATGCT
* * * * * *
5748466 GTAAAGGATGTGGCCTTGAAGCTGAGTGTATTCAAACTC
127 GCAAATGATGT-GCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
5748505 GAGGGTCTTT--AGA-AGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAG
1 GAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
* * * *
5748567 CTGAGCGTAGTCGAACTCGAAGGTATTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATG
66 CTGAGTGTAGTCGAACTCGAAGG--TCT-GTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTG
* *
5748632 CAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTC
128 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * *** * * *
5748669 GAAGGTCTTTGTTGGA-AAATATCCCTTATTTCCTTGAGTTATGTTGCAAATGATGTTCCTTGGA
1 GAAGGTCTTTGGT-GACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGA
* * * *** * * *
5748733 GCTGAGCGTAGTCGAACTCGAAGGTCTTTTATTGGAAAATAACCCTTCTTTCCTTGAGCTATGTT
65 GCTGAGTGTAGTCGAACTCGAAGGTC---TGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCT
5748798 GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
127 GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * * * * * **
5748836 AAAGGTCTTTTGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTCAA
1 GAAGGTC-TTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GG
* * * * *
5748901 AGCTGAGTGTAATCGAACTTGAACGTGTTTGGTTGG-AAGATAGCCCTTCTCGACTTAAGCTATG
64 AGCTGAGTGTAGTCGAACTCGAA-G-GTCT-GTTGGCAA-ATAACCCTTCTCGACTTAAGTTATG
* *
5748965 CTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTC
125 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* ** * * * * *
5749005 AAAGGTCTTTATTGGCAGATAACCCGTCTAGCCTTGAGTTATGCTGCAAATG
1 GAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
5749057 TTGTCTTTAA
Statistics
Matches: 869, Mismatches: 150, Indels: 62
0.80 0.14 0.06
Matches are distributed among these distances:
164 160 0.18
165 253 0.29
166 4 0.00
167 140 0.16
168 163 0.19
169 146 0.17
170 1 0.00
171 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (164 bp):
GAAGGTCTTTGGTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
CTGAGTGTAGTCGAACTCGAAGGTCTGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAA
ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
Found at i:5752257 original size:47 final size:47
Alignment explanation
Indices: 5752188--5752283 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
5752178 ACCCTTACTT
5752188 AAAAGGGTTCGGAGCTCGGGTATAGAGCCAGAGATGAAAACTTTGAA
1 AAAAGGGTTCGGAGCTCGGGTATAGAGCCAGAGATGAAAACTTTGAA
5752235 AAAAGGGTTCGGAGCTCGGGTATAGAGCCAGAGATGAAAACTTTGAA
1 AAAAGGGTTCGGAGCTCGGGTATAGAGCCAGAGATGAAAACTTTGAA
5752282 AA
1 AA
5752284 TCTGAAATCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.38, C:0.12, G:0.31, T:0.19
Consensus pattern (47 bp):
AAAAGGGTTCGGAGCTCGGGTATAGAGCCAGAGATGAAAACTTTGAA
Found at i:5752834 original size:23 final size:23
Alignment explanation
Indices: 5752808--5752870 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
5752798 AATAACTACT
5752808 AAATAAATCAAAAGAAAGAAAAA
1 AAATAAATCAAAAGAAAGAAAAA
* * *
5752831 AAATGAAA--ATAAGTAAATAACAA
1 AAAT-AAATCAAAAG-AAAGAAAAA
*
5752854 AAATAAATCAAAGGAAA
1 AAATAAATCAAAAGAAA
5752871 AATTAAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
22 7 0.23
23 18 0.58
24 6 0.19
ACGTcount: A:0.73, C:0.05, G:0.10, T:0.13
Consensus pattern (23 bp):
AAATAAATCAAAAGAAAGAAAAA
Found at i:5752919 original size:28 final size:26
Alignment explanation
Indices: 5752868--5752949 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 26
5752858 AAATCAAAGG
5752868 AAAAATTAAATAAAAAATACAAATAATA
1 AAAAATTAAATAAAAAA-A-AAATAATA
5752896 AAAAATTAAATAAACCAAAAAAAT-ATA
1 AAAAATTAAATAAA--AAAAAAATAATA
*
5752923 AGAAA--AAATAAAAGAAAAATATAATA
1 AAAAATTAAATAAAA-AAAAA-ATAATA
5752949 A
1 A
5752950 GAAGTAATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
23 1 0.02
24 5 0.10
25 9 0.19
26 4 0.08
27 7 0.15
28 18 0.38
29 1 0.02
30 3 0.06
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (26 bp):
AAAAATTAAATAAAAAAAAAATAATA
Found at i:5752940 original size:11 final size:12
Alignment explanation
Indices: 5752913--5752952 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5752903 AAATAAACCA
*
5752913 AAAAAATATAAG
1 AAAAAATAAAAG
5752925 AAAAAATAAAAG
1 AAAAAATAAAAG
5752937 AAAAATATAATAAG
1 AAAAA-ATAA-AAG
5752951 AA
1 AA
5752953 GTAATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 16 0.64
13 4 0.16
14 5 0.20
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAAATAAAAG
Found at i:5754665 original size:30 final size:30
Alignment explanation
Indices: 5754631--5754694 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
5754621 CCCGAATGAC
5754631 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5754661 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5754691 CTAT
1 CTAT
5754695 TCATAGGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:5754809 original size:32 final size:32
Alignment explanation
Indices: 5754708--5754813 Score: 121
Period size: 31 Copynumber: 3.4 Consensus size: 32
5754698 TAGGTTCTGA
* *
5754708 AGAACCTAGGTAA-ACTGTCCATATGTTCCTT
1 AGAACATAGGTAATACTGTCCATATGTTCCGT
5754739 AGAACATAGGT-ATACTGTCCATATG-TCTCG-
1 AGAACATAGGTAATACTGTCCATATGTTC-CGT
* * *
5754769 AAAGACATAGGTAATTCTATCCATATGTTCCGT
1 AGA-ACATAGGTAATACTGTCCATATGTTCCGT
5754802 AGAACATAGGTA
1 AGAACATAGGTA
5754814 TACCCTCGAC
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
30 5 0.08
31 31 0.49
32 23 0.37
33 4 0.06
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (32 bp):
AGAACATAGGTAATACTGTCCATATGTTCCGT
Found at i:5755482 original size:52 final size:53
Alignment explanation
Indices: 5755419--5755525 Score: 207
Period size: 52 Copynumber: 2.0 Consensus size: 53
5755409 ATAGTCACTT
5755419 ATCACTTATCACATAGTTTACATCCTATGATCAT-GAATCATATCAATAACAC
1 ATCACTTATCACATAGTTTACATCCTATGATCATAGAATCATATCAATAACAC
5755471 ATCACTTATCACATAGTTTACATCCTATGATCATAGAATCATATCAATAACAC
1 ATCACTTATCACATAGTTTACATCCTATGATCATAGAATCATATCAATAACAC
5755524 AT
1 AT
5755526 ATAAATAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 34 0.63
53 20 0.37
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (53 bp):
ATCACTTATCACATAGTTTACATCCTATGATCATAGAATCATATCAATAACAC
Found at i:5755845 original size:19 final size:19
Alignment explanation
Indices: 5755821--5755860 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5755811 GGTGCATAAA
5755821 ATACATTCGATGTTGTATT
1 ATACATTCGATGTTGTATT
5755840 ATACATTCGATGTTGTATT
1 ATACATTCGATGTTGTATT
5755859 AT
1 AT
5755861 TATTGGATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (19 bp):
ATACATTCGATGTTGTATT
Found at i:5757013 original size:11 final size:11
Alignment explanation
Indices: 5756993--5757039 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
5756983 AAAACAAAAC
5756993 AAAATAAATAA
1 AAAATAAATAA
*
5757004 AAAATGAATAA
1 AAAATAAATAA
5757015 TAAAA-AAAT-A
1 -AAAATAAATAA
5757025 AAAATAAAATAA
1 AAAAT-AAATAA
5757037 AAA
1 AAA
5757040 CAAATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
9 4 0.13
10 1 0.03
11 17 0.57
12 8 0.27
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:5757025 original size:22 final size:19
Alignment explanation
Indices: 5756983--5757039 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
5756973 AAACCTTGAT
* *
5756983 AAAACAAAACAAAATAAATAA
1 AAAATAAAATAAAA-AAAT-A
5757004 AAAATGAATAATAAAAAAATA
1 AAAAT-AA-AATAAAAAAATA
5757025 AAAATAAAATAAAAA
1 AAAATAAAATAAAAA
5757040 CAAATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 8 0.25
20 2 0.06
21 10 0.31
22 6 0.19
23 6 0.19
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.14
Consensus pattern (19 bp):
AAAATAAAATAAAAAAATA
Found at i:5757118 original size:13 final size:13
Alignment explanation
Indices: 5757102--5757137 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5757092 TCATACTATA
*
5757102 AAAAATGTTTT-T
1 AAAAATATTTTCT
5757114 AAAAATATTTTCT
1 AAAAATATTTTCT
5757127 AAAAATATTTT
1 AAAAATATTTT
5757138 TATAAACTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (13 bp):
AAAAATATTTTCT
Found at i:5757119 original size:12 final size:12
Alignment explanation
Indices: 5757102--5757177 Score: 62
Period size: 12 Copynumber: 5.7 Consensus size: 12
5757092 TCATACTATA
*
5757102 AAAAATGTTTTT
1 AAAAATATTTTT
5757114 AAAAATATTTTCT
1 AAAAATATTTT-T
5757127 AAAAATATTTTT
1 AAAAATATTTTT
5757139 ATAAACTATATAAGTTTT
1 A-AAA--ATAT---TTTT
*
5757157 CAAAAATATTTTA
1 -AAAAATATTTTT
5757170 AAAAATAT
1 AAAAATAT
5757178 ATATTATATT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
12 20 0.37
13 18 0.33
15 4 0.07
16 4 0.07
18 7 0.13
19 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:5757179 original size:30 final size:32
Alignment explanation
Indices: 5757121--5757180 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
5757111 TTTAAAAATA
* *
5757121 TTTTCTAAAAATATTTTTATAAACTATATAAG
1 TTTTCTAAAAATATTTTTAAAAAATATATAAG
5757153 TTTTC-AAAAATA-TTTTAAAAAATATATA
1 TTTTCTAAAAATATTTTTAAAAAATATATA
5757181 TTATATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 14 0.54
31 7 0.27
32 5 0.19
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (32 bp):
TTTTCTAAAAATATTTTTAAAAAATATATAAG
Found at i:5757206 original size:36 final size:37
Alignment explanation
Indices: 5757153--5757293 Score: 200
Period size: 36 Copynumber: 3.9 Consensus size: 37
5757143 ACTATATAAG
5757153 TTTTCAAAAATATTTTAAAAAATATATATTATATTTA
1 TTTTCAAAAATATTTTAAAAAATATATATTATATTTA
* *
5757190 TTTTC-AAAATATTTT-AAAAAT-TATATAATATATA
1 TTTTCAAAAATATTTTAAAAAATATATATTATATTTA
* *
5757224 TATTCAAAAATATTTTAAAAATTATATATTATATTTA
1 TTTTCAAAAATATTTTAAAAAATATATATTATATTTA
* *
5757261 TTTTC-AAAATATTTTAAAAATTATATAATATAT
1 TTTTCAAAAATATTTTAAAAAATATATATTATAT
5757294 AAATGTTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
34 15 0.16
35 16 0.17
36 42 0.45
37 20 0.22
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (37 bp):
TTTTCAAAAATATTTTAAAAAATATATATTATATTTA
Found at i:5757235 original size:71 final size:71
Alignment explanation
Indices: 5757155--5757294 Score: 271
Period size: 71 Copynumber: 2.0 Consensus size: 71
5757145 TATATAAGTT
5757155 TTCAAAAATATTTTAAAAAATATATATTATATTTATTTTCAAAATATTTTAAAAATTATATAATA
1 TTCAAAAATATTTTAAAAAATATATATTATATTTATTTTCAAAATATTTTAAAAATTATATAATA
5757220 TATATA
66 TATATA
*
5757226 TTCAAAAATATTTTAAAAATTATATATTATATTTATTTTCAAAATATTTTAAAAATTATATAATA
1 TTCAAAAATATTTTAAAAAATATATATTATATTTATTTTCAAAATATTTTAAAAATTATATAATA
5757291 TATA
66 TATA
5757295 AATGTTTTAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (71 bp):
TTCAAAAATATTTTAAAAAATATATATTATATTTATTTTCAAAATATTTTAAAAATTATATAATA
TATATA
Found at i:5779753 original size:20 final size:20
Alignment explanation
Indices: 5779707--5779746 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5779697 GTCAACGTCA
*
5779707 ATCAACGATCAACGGTGGTG
1 ATCAACGATCAACGGTAGTG
*
5779727 ATCAACGATCAGCGGTAGTG
1 ATCAACGATCAACGGTAGTG
5779747 GTTAACGGTC
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:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (20 bp):
ATCAACGATCAACGGTAGTG
Found at i:5782002 original size:23 final size:23
Alignment explanation
Indices: 5781964--5782031 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
5781954 AAAAATTATG
* *
5781964 ACAT-ATATATATATATATGCAT
1 ACATCATAAATATATATATACAT
5781986 -CATACATAAATATATATATACAT
1 ACAT-CATAAATATATATATACAT
* * *
5782009 ACATCATACATATGTACATACAT
1 ACATCATAAATATATATATACAT
5782032 CATTGATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.08
23 32 0.84
24 3 0.08
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (23 bp):
ACATCATAAATATATATATACAT
Found at i:5782013 original size:27 final size:27
Alignment explanation
Indices: 5781968--5782020 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5781958 ATTATGACAT
* *
5781968 ATATATATATATATGCATCATACATAA
1 ATATATATATACATACATCATACATAA
5781995 ATATATATATACATACATCATACATA
1 ATATATATATACATACATCATACATA
5782021 TGTACATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (27 bp):
ATATATATATACATACATCATACATAA
Found at i:5782060 original size:2 final size:2
Alignment explanation
Indices: 5782053--5782286 Score: 159
Period size: 2 Copynumber: 117.5 Consensus size: 2
5782043 CTTAATTACT
*
5782053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA CT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
5782095 TA TA CA TA TA TA -A GTA TA -A TA TA TA -A GTA TA TG TA TA TA CA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
5782136 TCA TA TA TA TA CT- TA TA AA GTA TA CA CA T- TA TA TA TG TA -A
1 T-A TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
5782176 GTA TA -A GTA TA TA TA -A GTA TA TA TA TA CA TA TA CA CA CT- TA
1 -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
5782217 TG CA TA CA TA CT- TA TA TA TA TA TA TA TA TA TA TA T- 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
5782258 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5782287 TTAAGGGCAA
Statistics
Matches: 185, Mismatches: 24, Indels: 46
0.73 0.09 0.18
Matches are distributed among these distances:
1 12 0.06
2 163 0.88
3 10 0.05
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:5782118 original size:13 final size:14
Alignment explanation
Indices: 5782095--5782125 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
5782085 TAAACTTATA
5782095 TATACATATATAAG
1 TATACATATATAAG
5782109 TATA-ATATATAAG
1 TATACATATATAAG
5782122 TATA
1 TATA
5782126 TGTATATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (14 bp):
TATACATATATAAG
Found at i:5783518 original size:26 final size:26
Alignment explanation
Indices: 5783482--5783535 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
5783472 GAATTTGGAC
*
5783482 TCCTATGTGAGTTGAGATCCCAATGA
1 TCCTATGTGAGTTGACATCCCAATGA
*
5783508 TCCTGTGTGAGTTGACATCCCAATGA
1 TCCTATGTGAGTTGACATCCCAATGA
5783534 TC
1 TC
5783536 TTTTTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (26 bp):
TCCTATGTGAGTTGACATCCCAATGA
Found at i:5783990 original size:17 final size:17
Alignment explanation
Indices: 5783956--5783989 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5783946 CTTATCCATT
5783956 ATCAAACCAACAACAAA
1 ATCAAACCAACAACAAA
5783973 ATCAAACCAAC-ACAAA
1 ATCAAACCAACAACAAA
5783989 A
1 A
5783990 ACCACATCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.65, C:0.29, G:0.00, T:0.06
Consensus pattern (17 bp):
ATCAAACCAACAACAAA
Found at i:5784736 original size:20 final size:20
Alignment explanation
Indices: 5784711--5784763 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
5784701 GACCAACAAA
5784711 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
5784731 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
5784751 TTCGCAACGCGAA
1 TTCGCAACGCGAA
5784764 TATGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:5784846 original size:20 final size:20
Alignment explanation
Indices: 5784817--5784860 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5784807 TCCAAATTCA
*
5784817 CAACGTGAATCTGTAAATCG
1 CAACGCGAATCTGTAAATCG
*
5784837 CAACGCGAATTTGTAAATCG
1 CAACGCGAATCTGTAAATCG
5784857 CAAC
1 CAAC
5784861 ACATAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
CAACGCGAATCTGTAAATCG
Found at i:5784877 original size:20 final size:20
Alignment explanation
Indices: 5784854--5784960 Score: 132
Period size: 20 Copynumber: 5.5 Consensus size: 20
5784844 AATTTGTAAA
5784854 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
5784874 TCGCAACGC-TATAGTCAAAT
1 TCGCAACACATA-AGTCAAAT
*
5784894 TCGCAACACAAAAG-CAAAT
1 TCGCAACACATAAGTCAAAT
*
5784913 TCACAACACA-AAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
5784932 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
5784952 TCGCAACAC
1 TCGCAACAC
5784961 TGATTTGTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
18 3 0.04
19 28 0.37
20 43 0.57
21 1 0.01
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:5784933 original size:38 final size:40
Alignment explanation
Indices: 5784854--5784961 Score: 130
Period size: 39 Copynumber: 2.8 Consensus size: 40
5784844 AATTTGTAAA
* * * *
5784854 TCGCAACACATAAGTCAAATTCGCAACGCTATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCACAACACTAAAGTCAAAT
5784894 TCGCAACACAAAAG-CAAATTCACAACAC-AAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCACAACACTAAAGTCAAAT
* * * *
5784932 TCGCAACGCGATAGTCAAATTCGCAACACT
1 TCGCAACACAAAAGTCAAATTCACAACACT
5784962 GATTTGTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 20 0.34
39 25 0.43
40 13 0.22
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.19
Consensus pattern (40 bp):
TCGCAACACAAAAGTCAAATTCACAACACTAAAGTCAAAT
Found at i:5784975 original size:20 final size:20
Alignment explanation
Indices: 5784952--5784999 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
5784942 ATAGTCAAAT
5784952 TCGCAACACTG-ATTTGTAAA
1 TCGCAACAC-GAATTTGTAAA
**
5784972 TCGCAATGCGAATTTGTAAA
1 TCGCAACACGAATTTGTAAA
5784992 TCGCAACA
1 TCGCAACA
5785000 TAGAAAATCC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (20 bp):
TCGCAACACGAATTTGTAAA
Found at i:5785061 original size:20 final size:20
Alignment explanation
Indices: 5785032--5785075 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5785022 TCCAAATTCA
*
5785032 CAACGTGAATCTGTAAATCG
1 CAACGCGAATCTGTAAATCG
*
5785052 CAACGCGAATTTGTAAATCG
1 CAACGCGAATCTGTAAATCG
5785072 CAAC
1 CAAC
5785076 ACATAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
CAACGCGAATCTGTAAATCG
Found at i:5785083 original size:215 final size:217
Alignment explanation
Indices: 5784789--5785221 Score: 852
Period size: 215 Copynumber: 2.0 Consensus size: 217
5784779 ACGATTTTCC
5784789 AAATCCACGTTGCGATTTTCCAAATTCACAACGTGAATCTGTAAATCGCAACGCGAATTTGTAAA
1 AAATCCACGTTGCGATTTTCCAAATTCACAACGTGAATCTGTAAATCGCAACGCGAATTTGTAAA
5784854 TCGCAACACATAAGTCAAATTCGCAACGCTATAGTCAAATTCGCAACACAAAAG-CAAATTCACA
66 TCGCAACACATAAGTCAAATTCGCAACGCTATAGTCAAATTCGCAACACAAAAGTCAAATTCACA
5784918 ACAC-AAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGATTTGTAAATCGCAATGCG
131 ACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGATTTGTAAATCGCAATGCG
5784982 AATTTGTAAATCGCAACATAGA
196 AATTTGTAAATCGCAACATAGA
5785004 AAATCCACGTTGCGATTTTCCAAATTCACAACGTGAATCTGTAAATCGCAACGCGAATTTGTAAA
1 AAATCCACGTTGCGATTTTCCAAATTCACAACGTGAATCTGTAAATCGCAACGCGAATTTGTAAA
5785069 TCGCAACACATAAGTCAAATTCGCAACGCTATAGTCAAATTCGCAACACAAAAGTCAAATTCACA
66 TCGCAACACATAAGTCAAATTCGCAACGCTATAGTCAAATTCGCAACACAAAAGTCAAATTCACA
5785134 ACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGATTTGTAAATCGCAATGCG
131 ACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGATTTGTAAATCGCAATGCG
5785199 AATTTGTAAATCGCAACATAGA
196 AATTTGTAAATCGCAACATAGA
5785221 A
1 A
5785222 GTCAAATTCG
Statistics
Matches: 216, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
215 119 0.55
216 14 0.06
217 83 0.38
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (217 bp):
AAATCCACGTTGCGATTTTCCAAATTCACAACGTGAATCTGTAAATCGCAACGCGAATTTGTAAA
TCGCAACACATAAGTCAAATTCGCAACGCTATAGTCAAATTCGCAACACAAAAGTCAAATTCACA
ACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGATTTGTAAATCGCAATGCG
AATTTGTAAATCGCAACATAGA
Found at i:5785092 original size:20 final size:20
Alignment explanation
Indices: 5785069--5785274 Score: 149
Period size: 20 Copynumber: 10.3 Consensus size: 20
5785059 AATTTGTAAA
5785069 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
5785089 TCGCAACGC-TATAGTCAAAT
1 TCGCAACACATA-AGTCAAAT
*
5785109 TCGCAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
* *
5785129 TCACAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
5785149 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
**
5785169 TCGCAACACTGATTTGT-AAA-
1 TCGCAACAC--ATAAGTCAAAT
**
5785189 TCGCAATGCGA-ATTTGT-AAA-
1 TCGCAA--C-ACATAAGTCAAAT
* *
5785209 TCGCAACATAGAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
5785229 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
* *
5785249 TCACAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
5785269 TTGCAA
1 TCGCAA
5785275 TGCAGAATTT
Statistics
Matches: 153, Mismatches: 20, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.01
18 4 0.03
19 6 0.04
20 129 0.84
21 9 0.06
22 3 0.02
23 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:5785113 original size:60 final size:60
Alignment explanation
Indices: 5785049--5785194 Score: 190
Period size: 60 Copynumber: 2.4 Consensus size: 60
5785039 AATCTGTAAA
* * *
5785049 TCGCAACGCGAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACGCTATAGTCAAAT
1 TCGCAACACGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
** *
5785109 TCGCAACAC-AA-AAGTCAAATTCACAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACGAATTTGT-AAA-TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
5785169 TCGCAACACTG-ATTTGTAAATCGCAA
1 TCGCAACAC-GAATTTGTAAATCGCAA
5785195 TGCGAATTTG
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
58 2 0.03
59 5 0.07
60 59 0.82
61 4 0.06
62 2 0.03
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (60 bp):
TCGCAACACGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:5785289 original size:21 final size:19
Alignment explanation
Indices: 5785263--5785394 Score: 140
Period size: 19 Copynumber: 6.8 Consensus size: 19
5785253 AACACAAAAG
*
5785263 TCAAATTTGCAATGCAGAATT
1 TCAAATTCGCAA--CAGAATT
*
5785284 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACAGAATT
* *
5785303 TCAAATTCGTAACTGAATT
1 TCAAATTCGCAACAGAATT
*
5785322 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACAGAATT
* *
5785341 TCGAATTCGCAACTAGATTT
1 TCAAATTCGCAAC-AGAATT
5785361 TCAAATTCGCAACATGAATT
1 TCAAATTCGCAACA-GAATT
* *
5785381 T-AATTTCACAACAG
1 TCAAATTCGCAACAG
5785395 GTTTTAGTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
18 1 0.01
19 65 0.66
20 21 0.21
21 11 0.11
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (19 bp):
TCAAATTCGCAACAGAATT
Found at i:5785303 original size:19 final size:19
Alignment explanation
Indices: 5785279--5785381 Score: 161
Period size: 19 Copynumber: 5.3 Consensus size: 19
5785269 TTGCAATGCA
5785279 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
*
5785298 GAATTTCAAATTCGTAACT
1 GAATTTCAAATTCGCAACT
5785317 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
*
5785336 GAATTTCGAATTCGCAACT
1 GAATTTCAAATTCGCAACT
*
5785355 AGATTTTCAAATTCGCAACAT
1 -GAATTTCAAATTCGCAAC-T
5785376 GAATTT
1 GAATTT
5785382 AATTTCACAA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 54 0.71
20 21 0.28
21 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (19 bp):
GAATTTCAAATTCGCAACT
Found at i:5785311 original size:80 final size:79
Alignment explanation
Indices: 5785140--5785296 Score: 201
Period size: 80 Copynumber: 1.9 Consensus size: 79
5785130 CACAACACAA
* ***
5785140 AAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACTGATTTGTAAATCGCAATGCGAATTTG
1 AAGTCAAATTCGCAACGCGATAGTCAAATTCACAACAC-GAAAAGTAAATCGCAATGCGAATTTG
*
5785205 TAAATCGCAACATAG
65 CAAATCGCAACATAG
*
5785220 AAGTCAAATTCGCAACGCGATAGTCAAATTCACAACAC-AAAAGTCAAATTTGCAATGCAGAATT
1 AAGTCAAATTCGCAACGCGATAGTCAAATTCACAACACGAAAAGT-AAA-TCGCAATGC-GAATT
5785284 T-CAAATTCGCAAC
63 TGCAAA-TCGCAAC
5785297 TGAATTTCAA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
78 3 0.04
79 3 0.04
80 48 0.72
81 13 0.19
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (79 bp):
AAGTCAAATTCGCAACGCGATAGTCAAATTCACAACACGAAAAGTAAATCGCAATGCGAATTTGC
AAATCGCAACATAG
Found at i:5785410 original size:57 final size:57
Alignment explanation
Indices: 5785277--5785394 Score: 141
Period size: 58 Copynumber: 2.1 Consensus size: 57
5785267 ATTTGCAATG
* *
5785277 CAGAATTTCA-AATTCGCAACTGAATTTCAAATTCGTAACTGAATTTCAAATTCGCAA
1 CAGAATTT-AGAATTCGCAACTGAATTTCAAATTCGCAACTGAATTTCAAATTCACAA
* * * *
5785334 CTGAATTTCGAATTCGCAACTAGATTTTCAAATTCGCAACATGAATTT-AATTTCACAA
1 CAGAATTTAGAATTCGCAACT-GAATTTCAAATTCGCAAC-TGAATTTCAAATTCACAA
5785392 CAG
1 CAG
5785395 GTTTTAGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
57 18 0.35
58 26 0.51
59 7 0.14
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (57 bp):
CAGAATTTAGAATTCGCAACTGAATTTCAAATTCGCAACTGAATTTCAAATTCACAA
Found at i:5785569 original size:14 final size:16
Alignment explanation
Indices: 5785550--5785587 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5785540 TCCCCATCTC
5785550 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
5785564 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
5785580 TAATTTTA
1 TAATTTTA
5785588 CAATGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 3 0.14
16 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:5786203 original size:12 final size:12
Alignment explanation
Indices: 5786182--5786215 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5786172 ACCACATTTC
*
5786182 CAATACCAAACA
1 CAATATCAAACA
5786194 CAATATCAAACA
1 CAATATCAAACA
*
5786206 CAATCTCAAA
1 CAATATCAAA
5786216 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:5786269 original size:20 final size:20
Alignment explanation
Indices: 5786244--5786401 Score: 126
Period size: 20 Copynumber: 7.9 Consensus size: 20
5786234 TTTGAAATTC
5786244 CGCGTTGCGAATTTGACTAT
1 CGCGTTGCGAATTTGACTAT
*
5786264 CGCGTTGCGAATTTGACTTT
1 CGCGTTGCGAATTTGACTAT
* * *
5786284 TGTGTTGCG-ATTT-ACAAATT
1 CGCGTTGCGAATTTGAC-TA-T
* *
5786304 CGCATTGCG-ATTT-ACAAAT
1 CGCGTTGCGAATTTGAC-TAT
*
5786323 CAGTGTTGCGAATTTGACTAT
1 C-GCGTTGCGAATTTGACTAT
* *
5786344 CTCGTTGCGAATTTGACTTT
1 CGCGTTGCGAATTTGACTAT
*** *
5786364 TTTGTTGCGAATTTGGCTAT
1 CGCGTTGCGAATTTGACTAT
*
5786384 CGCGTTGCAAATTTGACT
1 CGCGTTGCGAATTTGACT
5786402 TATGTGTTGC
Statistics
Matches: 110, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
18 2 0.02
19 6 0.05
20 93 0.85
21 7 0.06
22 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
CGCGTTGCGAATTTGACTAT
Found at i:5786293 original size:40 final size:40
Alignment explanation
Indices: 5786247--5786413 Score: 180
Period size: 40 Copynumber: 4.2 Consensus size: 40
5786237 GAAATTCCGC
5786247 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* * * **
5786287 GTTGCG-ATTT-ACAAATTCGCATTGCG-ATTT-ACAAATCAGT
1 GTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGAC--TTTTGT
* *
5786327 GTTGCGAATTTGACTATCTCGTTGCGAATTTGACTTTTTT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
* * *
5786367 GTTGCGAATTTGGCTATCGCGTTGCAAATTTGACTTATGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
5786407 GTTGCGA
1 GTTGCGA
5786414 TTTACAAATT
Statistics
Matches: 102, Mismatches: 17, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
38 4 0.04
39 9 0.09
40 76 0.75
41 9 0.09
42 4 0.04
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.41
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
Found at i:5786428 original size:20 final size:20
Alignment explanation
Indices: 5786405--5786445 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5786395 TTTGACTTAT
5786405 GTGTTGCGATTTACAAATTC
1 GTGTTGCGATTTACAAATTC
*
5786425 GTGTTGCGATTTACAGATTC
1 GTGTTGCGATTTACAAATTC
5786445 G
1 G
5786446 CATTGCGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (20 bp):
GTGTTGCGATTTACAAATTC
Found at i:5786451 original size:20 final size:20
Alignment explanation
Indices: 5786408--5786453 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5786398 GACTTATGTG
**
5786408 TTGCGATTTACAAATTCGTG
1 TTGCGATTTACAAATTCGCA
*
5786428 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAAATTCGCA
5786448 TTGCGA
1 TTGCGA
5786454 ATTTGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACAAATTCGCA
Found at i:5786457 original size:60 final size:60
Alignment explanation
Indices: 5786263--5786458 Score: 179
Period size: 60 Copynumber: 3.3 Consensus size: 60
5786253 AATTTGACTA
* ** *
5786263 TCGCGTTGCGAATTTGACTTTTGTGTTGCGATTTACAAATTCGCATTGCGATTTACA-AA
1 TCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGTGTTGCGATTTACAGAT
* * * ** * *
5786322 TCAGTGTTGCGAATTTGAC-TATCTCGTTGCGAATTTGAC--TTTTTTGTTGCGAATTT--GGCT
1 TC-GCGTTGCGAATTTGACTTATGT-GTTGCG-ATTT-ACAAATTCGTGTTGCG-ATTTACAGAT
*
5786382 ATCGCGTTGCAAATTTGACTTATGTGTTGCGATTTACAAATTCGTGTTGCGATTTACAGAT
1 -TCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGTGTTGCGATTTACAGAT
*
5786443 TCGCATTGCGAATTTG
1 TCGCGTTGCGAATTTG
5786459 GAAAATCGCA
Statistics
Matches: 104, Mismatches: 21, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
58 2 0.02
59 13 0.12
60 71 0.68
61 16 0.15
62 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (60 bp):
TCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATTCGTGTTGCGATTTACAGAT
Found at i:5789533 original size:19 final size:19
Alignment explanation
Indices: 5789509--5789546 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5789499 GGAAAACACT
5789509 GATCTGGTTGTAATCCCAA
1 GATCTGGTTGTAATCCCAA
5789528 GATCTGGTTGTAATCCCAA
1 GATCTGGTTGTAATCCCAA
5789547 CTCCAAGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (19 bp):
GATCTGGTTGTAATCCCAA
Found at i:5791316 original size:24 final size:24
Alignment explanation
Indices: 5791289--5791335 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5791279 TCCCCCATCG
* *
5791289 TACGGAGGTGGCAGTCCTCCAACT
1 TACGGAGGTGGAAGCCCTCCAACT
*
5791313 TACGGTGGTGGAAGCCCTCCAAC
1 TACGGAGGTGGAAGCCCTCCAAC
5791336 ACCAGTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.19
Consensus pattern (24 bp):
TACGGAGGTGGAAGCCCTCCAACT
Found at i:5791428 original size:93 final size:93
Alignment explanation
Indices: 5791319--5791496 Score: 302
Period size: 93 Copynumber: 1.9 Consensus size: 93
5791309 AACTTACGGT
* *
5791319 GGTGGAAGCCCTCCAACACCAGTAATTGTAAGCCCGCCAACTCCCATTATCGATCCAGGAACTCC
1 GGTGGAAGCCCGCCAACACCAGTAACTGTAAGCCCGCCAACTCCCATTATCGATCCAGGAACTCC
*
5791384 AAGCACTCCCACATCTCCATCATATGGA
66 AAGCACTCCCACACCTCCATCATATGGA
* *
5791412 GGTGGAAGTCCGCCAACACCAGTAACTGTGAGCCCGCCAACTCCCATTATCGATCCAGGAACTCC
1 GGTGGAAGCCCGCCAACACCAGTAACTGTAAGCCCGCCAACTCCCATTATCGATCCAGGAACTCC
*
5791477 AAGCATTCCCACACCTCCAT
66 AAGCACTCCCACACCTCCAT
5791497 TCTTTCCTGC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.19
Consensus pattern (93 bp):
GGTGGAAGCCCGCCAACACCAGTAACTGTAAGCCCGCCAACTCCCATTATCGATCCAGGAACTCC
AAGCACTCCCACACCTCCATCATATGGA
Found at i:5799233 original size:19 final size:18
Alignment explanation
Indices: 5799205--5799241 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
5799195 ATACGCGTGT
5799205 GTATATAATACACCATTA
1 GTATATAATACACCATTA
*
5799223 GTATCATAATATACCATTA
1 GTAT-ATAATACACCATTA
5799242 AAATAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.35
Consensus pattern (18 bp):
GTATATAATACACCATTA
Found at i:5803647 original size:20 final size:20
Alignment explanation
Indices: 5803622--5803673 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
5803612 TCATGTAATG
* *
5803622 GGTATCGATATTATAGCTAA
1 GGTATCGATACTATAACTAA
5803642 GGTATCGATACTATAACTAA
1 GGTATCGATACTATAACTAA
5803662 GGTATCGATACT
1 GGTATCGATACT
5803674 CGTAGGGTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
GGTATCGATACTATAACTAA
Found at i:5804487 original size:16 final size:16
Alignment explanation
Indices: 5804449--5804488 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
5804439 TCTTTAGAGG
5804449 AAAAATAAATATATTA
1 AAAAATAAATATATTA
5804465 AATAAATAAATA-ATTA
1 AA-AAATAAATATATTA
5804481 AGAAAATA
1 A-AAAATA
5804489 TCATCCAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAAATAAATATATTA
Found at i:5805526 original size:17 final size:18
Alignment explanation
Indices: 5805501--5805534 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5805491 ATTTGTGTTT
5805501 GGTACCGATACT-CATGG
1 GGTACCGATACTACATGG
*
5805518 GGTATCGATACTACATG
1 GGTACCGATACTACATG
5805535 TAGGATACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (18 bp):
GGTACCGATACTACATGG
Found at i:5816523 original size:44 final size:42
Alignment explanation
Indices: 5816451--5816671 Score: 156
Period size: 44 Copynumber: 5.0 Consensus size: 42
5816441 TATTGATCTG
* * * *
5816451 CCTCCTTCTATGATTGAGTCTAGAAAAAGTTTGATGTTGATCCA
1 CCTCCTTATATGATGGAATCAAG-AAAAG-TTGATGTTGATCCA
* * * *
5816495 CCTACTTATATGATGAAATCAAGTAAAAGGGTGATGCTGATCCA
1 CCTCCTTATATGATGGAATCAAG-AAAA-GTTGATGTTGATCCA
* * * * * *
5816539 ACTCCTTGTTTGATGGAATCAAACAAAAGGGTT-AGGTTGATCTA
1 CCTCCTTATATGATGGAATC-AAGAAAA--GTTGATGTTGATCCA
* ***
5816583 ACTCCTTATATGATGGAATCAAGAAAAAAGACAATGTTGATCCA
1 CCTCCTTATATGATGGAATCAAG--AAAAGTTGATGTTGATCCA
* *
5816627 CCTCCTTATGTGATGGAATCAAACGAAATGTTGATGTTGATCCA
1 CCTCCTTATATGATGGAATC-AA-GAAAAGTTGATGTTGATCCA
5816671 C
1 C
5816672 TTCATTCAGT
Statistics
Matches: 137, Mismatches: 32, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
43 3 0.02
44 121 0.88
45 12 0.09
46 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (42 bp):
CCTCCTTATATGATGGAATCAAGAAAAGTTGATGTTGATCCA
Found at i:5816666 original size:88 final size:89
Alignment explanation
Indices: 5816481--5816670 Score: 222
Period size: 88 Copynumber: 2.2 Consensus size: 89
5816471 TAGAAAAAGT
* * * ***
5816481 TTGATGTTGATCCACCTACTTATATGATGAAATCAAGTAAAAGGGTGATGCTGATCCAACTCCTT
1 TTGATGTTGATCCAACTACTTATATGATGAAATCAAGAAAAAAGACAATGCTGATCCAACTCCTT
* *
5816546 GTTTGATGGAATCAAACAAAAGGG
66 ATGTGATGGAATCAAACAAAAGGG
* * * * * *
5816570 TT-AGGTTGATCTAACTCCTTATATGATGGAATCAAGAAAAAAGACAATGTTGATCCACCTCCTT
1 TTGATGTTGATCCAACTACTTATATGATGAAATCAAGAAAAAAGACAATGCTGATCCAACTCCTT
* *
5816634 ATGTGATGGAATCAAACGAAA-TG
66 ATGTGATGGAATCAAACAAAAGGG
5816657 TTGATGTTGATCCA
1 TTGATGTTGATCCA
5816671 CTTCATTCAG
Statistics
Matches: 82, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
87 3 0.04
88 77 0.94
89 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (89 bp):
TTGATGTTGATCCAACTACTTATATGATGAAATCAAGAAAAAAGACAATGCTGATCCAACTCCTT
ATGTGATGGAATCAAACAAAAGGG
Found at i:5825662 original size:61 final size:61
Alignment explanation
Indices: 5825537--5825667 Score: 158
Period size: 61 Copynumber: 2.1 Consensus size: 61
5825527 AATGACACTA
***
5825537 AGTGCAGGTGGAGGGCACAACCTTATGTGTCATATTTGGATTAGCACTAGACTGTAAACCT
1 AGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAGATTAGCACTAGACTGTAAACCT
* * * * *
5825598 AGTGTAGGTGGTA-GGCACGACCTTATGTGTCATATCCATATTAGCACTAGAGC-GTAAGCTT
1 AGTGCAGGTGG-AGGGCACAACCTTATGTGTCATATCCAGATTAGCACTAGA-CTGTAAACCT
5825659 AGTGCAGGT
1 AGTGCAGGT
5825668 TTAGTACTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
61 57 0.97
62 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (61 bp):
AGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAGATTAGCACTAGACTGTAAACCT
Found at i:5828618 original size:20 final size:20
Alignment explanation
Indices: 5828558--5828618 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
5828548 TGATTATTTG
*
5828558 GTAAGGGTTGTATCGATAACT
1 GTAAGGGTAGTATCGAT-ACT
* * * *
5828579 GTTGAGAGTGGTATCAATACT
1 G-TAAGGGTAGTATCGATACT
5828600 GTAAGGGTAGTATCGATAC
1 GTAAGGGTAGTATCGATAC
5828619 CTTAAAGATG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 14 0.45
21 5 0.16
22 12 0.39
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.31
Consensus pattern (20 bp):
GTAAGGGTAGTATCGATACT
Found at i:5829080 original size:21 final size:21
Alignment explanation
Indices: 5829056--5829106 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5829046 TGATTATGAA
* *
5829056 AATGTGAACTTTGAATAAGTG
1 AATGTGAACCTTGAACAAGTG
* *
5829077 AATGTGACCCTTGAACCAGTG
1 AATGTGAACCTTGAACAAGTG
5829098 AATGTGAAC
1 AATGTGAAC
5829107 AAACTCTATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (21 bp):
AATGTGAACCTTGAACAAGTG
Found at i:5829281 original size:21 final size:21
Alignment explanation
Indices: 5829257--5829347 Score: 69
Period size: 21 Copynumber: 4.2 Consensus size: 21
5829247 TCCTTCTGGA
*
5829257 CAAATATGTGGCACTTTGGTG
1 CAAATATGTGGCACTTCGGTG
**
5829278 CAAACCTGTGGCACTTCGGTG
1 CAAATATGTGGCACTTCGGTG
*
5829299 TAAATCTATGTGGTCA-TTCGG-G
1 CAAA--TATGTGG-CACTTCGGTG
* * *
5829321 ACAATTATGTGGCGCTTCAGTG
1 -CAAATATGTGGCACTTCGGTG
5829343 CAAAT
1 CAAAT
5829348 TACGAGTTGT
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
20 1 0.02
21 36 0.68
22 2 0.04
23 12 0.23
24 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (21 bp):
CAAATATGTGGCACTTCGGTG
Found at i:5835383 original size:20 final size:21
Alignment explanation
Indices: 5835360--5835402 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
5835350 TCAATACTGA
*
5835360 AAGGGTAGTATCGATA-CCTT
1 AAGGATAGTATCGATACCCTT
*
5835380 AAGGATGGTATCGATACCCTT
1 AAGGATAGTATCGATACCCTT
5835401 AA
1 AA
5835403 AACATCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (21 bp):
AAGGATAGTATCGATACCCTT
Found at i:5836066 original size:23 final size:23
Alignment explanation
Indices: 5836036--5836132 Score: 158
Period size: 23 Copynumber: 4.2 Consensus size: 23
5836026 GGGACAAATA
*
5836036 TGTGGCACTTAGGTTAAAACCTT
1 TGTGGCACTTAGGTGAAAACCTT
5836059 TGTGGCACTTAGGTGAAAACCTT
1 TGTGGCACTTAGGTGAAAACCTT
5836082 TGTGGCACTTAGGTGAAAACCTT
1 TGTGGCACTTAGGTGAAAACCTT
* * *
5836105 TGTGGCACTTCGGTGCAAACCTA
1 TGTGGCACTTAGGTGAAAACCTT
5836128 TGTGG
1 TGTGG
5836133 TCCTTCGGGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (23 bp):
TGTGGCACTTAGGTGAAAACCTT
Found at i:5842114 original size:16 final size:18
Alignment explanation
Indices: 5842093--5842130 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5842083 TATTTCATTT
5842093 AAGCATG-A-GTTTATTA
1 AAGCATGTAGGTTTATTA
*
5842109 AAGCATGTAGGTTTTTTA
1 AAGCATGTAGGTTTATTA
5842127 AAGC
1 AAGC
5842131 TACTTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (18 bp):
AAGCATGTAGGTTTATTA
Found at i:5854185 original size:23 final size:23
Alignment explanation
Indices: 5854159--5854205 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
5854149 TAAGAATAAT
*
5854159 TTTGTCTTTCTGGCACGTTTATC
1 TTTGTCTTTCTGGCACCTTTATC
*
5854182 TTTGTCTTTGTGGCACCTTTATC
1 TTTGTCTTTCTGGCACCTTTATC
5854205 T
1 T
5854206 ATGCCATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.09, C:0.21, G:0.17, T:0.53
Consensus pattern (23 bp):
TTTGTCTTTCTGGCACCTTTATC
Found at i:5854215 original size:23 final size:23
Alignment explanation
Indices: 5854169--5854216 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5854159 TTTGTCTTTC
* * * *
5854169 TGGCACGTTTATCTTTGTCTTTG
1 TGGCACCTTTATCTATGCCATTG
5854192 TGGCACCTTTATCTATGCCATTG
1 TGGCACCTTTATCTATGCCATTG
5854215 TG
1 TG
5854217 ACTCGTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (23 bp):
TGGCACCTTTATCTATGCCATTG
Found at i:5858010 original size:20 final size:20
Alignment explanation
Indices: 5857985--5858034 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
5857975 AAGCTATTTA
**
5857985 GTATCGATATTGGCCTCTAG
1 GTATCGATATTAACCTCTAG
* *
5858005 GTATCGATACTAACCTCTGG
1 GTATCGATATTAACCTCTAG
5858025 GTATCGATAT
1 GTATCGATAT
5858035 CACTGACTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (20 bp):
GTATCGATATTAACCTCTAG
Found at i:5858215 original size:18 final size:19
Alignment explanation
Indices: 5858170--5858219 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
5858160 CCCCTATGGG
*
5858170 GAGTATCGATACTCTACCCTT
1 GAGTATCGATACTCT--CCAT
5858191 G-GTATCGATACTCT-CAT
1 GAGTATCGATACTCTCCAT
5858208 GAGTATCGATAC
1 GAGTATCGATAC
5858220 GAATTTAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.11
18 10 0.37
20 13 0.48
21 1 0.04
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (19 bp):
GAGTATCGATACTCTCCAT
Found at i:5861603 original size:12 final size:12
Alignment explanation
Indices: 5861563--5861595 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5861553 GCAACACTCA
5861563 CTTCTCTCT-TT
1 CTTCTCTCTATT
5861574 CCTTCTCTCTATT
1 -CTTCTCTCTATT
5861587 CTTCTCTCT
1 CTTCTCTCT
5861596 CTTGTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 18 0.90
13 2 0.10
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (12 bp):
CTTCTCTCTATT
Found at i:5866011 original size:31 final size:30
Alignment explanation
Indices: 5865968--5866026 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
5865958 AAAACATAAT
*
5865968 ATATGGTCATTTCGTTTTTATTTGATTAAG
1 ATATGGTCATTTCGTTTTTATTTAATTAAG
*
5865998 ATATGTTCAATTTCGTTTTTATTTAATTA
1 ATATGGTC-ATTTCGTTTTTATTTAATTA
5866027 TGTGGTCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.56
Consensus pattern (30 bp):
ATATGGTCATTTCGTTTTTATTTAATTAAG
Found at i:5876641 original size:24 final size:24
Alignment explanation
Indices: 5876609--5876658 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
5876599 ACAACTTGTA
5876609 GTTGTATGAATCCTCAGAAGAGAG
1 GTTGTATGAATCCTCAGAAGAGAG
5876633 GTTGTATGAATCCTCAGAAGAGAG
1 GTTGTATGAATCCTCAGAAGAGAG
5876657 GT
1 GT
5876659 GTGTTTTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (24 bp):
GTTGTATGAATCCTCAGAAGAGAG
Found at i:5879143 original size:3 final size:3
Alignment explanation
Indices: 5879135--5879160 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5879125 TCTAAATACC
5879135 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5879161 CAATTACGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5880333 original size:29 final size:29
Alignment explanation
Indices: 5880300--5880359 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
5880290 AAATGACTTA
5880300 ATCCATACAACCCAAAAGAGATGGAAGAT
1 ATCCATACAACCCAAAAGAGATGGAAGAT
5880329 ATCCATACAACCCAAAAGAGATGGAAGAT
1 ATCCATACAACCCAAAAGAGATGGAAGAT
5880358 AT
1 AT
5880360 GAGGAGTGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.15
Consensus pattern (29 bp):
ATCCATACAACCCAAAAGAGATGGAAGAT
Found at i:5882352 original size:27 final size:26
Alignment explanation
Indices: 5882316--5882373 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
5882306 AAATTAGATT
* *
5882316 AATATCTTTATAAATATTCTAAATTGA
1 AATATATTTATAAATATT-TAAATTAA
**
5882343 AATATATTTATTTATATTTAAATTAA
1 AATATATTTATAAATATTTAAATTAA
5882369 AATAT
1 AATAT
5882374 TAATAGGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (26 bp):
AATATATTTATAAATATTTAAATTAA
Found at i:5882451 original size:36 final size:36
Alignment explanation
Indices: 5882346--5882456 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 36
5882336 AAATTGAAAT
* * * * *
5882346 ATATTTATT-TATATTTAAATTAAAATATTAATAGG
1 ATATTTATTATCTTTTTAAATTTAAATATTAAAAAG
* * * * *
5882381 ATAATTA-TATCTTTCTAAATAT-CATAGTTTAAAAG
1 ATATTTATTATCTTTTTAAATTTAAATA-TTAAAAAG
5882416 ATATTTATTATCTTTTTAAATTTAAATATTAAAAAG
1 ATATTTATTATCTTTTTAAATTTAAATATTAAAAAG
5882452 ATATT
1 ATATT
5882457 AAAATATATC
Statistics
Matches: 57, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
34 4 0.07
35 25 0.44
36 25 0.44
37 3 0.05
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (36 bp):
ATATTTATTATCTTTTTAAATTTAAATATTAAAAAG
Found at i:5883755 original size:18 final size:18
Alignment explanation
Indices: 5883732--5883778 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
5883722 ATTTTTCGGT
5883732 TCTTCCTTCTTGGGTTCC
1 TCTTCCTTCTTGGGTTCC
5883750 TCTTCCTTCTTGGGTTCC
1 TCTTCCTTCTTGGGTTCC
*
5883768 TCTTCTTTCTT
1 TCTTCCTTCTT
5883779 TGGCTCTTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.13, T:0.55
Consensus pattern (18 bp):
TCTTCCTTCTTGGGTTCC
Found at i:5885832 original size:2 final size:2
Alignment explanation
Indices: 5885825--5885860 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5885815 ATTAAATTAT
5885825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5885861 GTTCGAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5886306 original size:2 final size:2
Alignment explanation
Indices: 5886296--5886325 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5886286 GCGCGCGCGC
*
5886296 AT AT TT 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
5886326 GCAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Done.