Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009014.1 Hibiscus syriacus cultivar Beakdansim tig00112402_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: 3470424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:2403062 original size:21 final size:21
Alignment explanation
Indices: 2403038--2403077 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2403028 GGTAGCTAAA
*
2403038 CTAGTTGAATGGGAGTTGAAC
1 CTAGCTGAATGGGAGTTGAAC
**
2403059 CTAGCTGGGTGGGAGTTGA
1 CTAGCTGAATGGGAGTTGA
2403078 GGACCAAGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.28
Consensus pattern (21 bp):
CTAGCTGAATGGGAGTTGAAC
Found at i:2410545 original size:54 final size:54
Alignment explanation
Indices: 2410465--2410825 Score: 417
Period size: 54 Copynumber: 6.7 Consensus size: 54
2410455 TTTTCATAAC
* * * * * *
2410465 ATTAT-AAGTTCCTTGGGGTGCGCACTTAGT-TCTGATACGATCATTCATAAGCTC
1 ATTATGAA-TTCCGTGGGTTGCACACTTAGTGTC-GATACGATCGTTCATAAACTT
* * * *
2410519 ATTATGAATTCCATGGGTTGCACACTTTGTGTCGATATGGTCGTTCATAAACTT
1 ATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTT
* *
2410573 ATTAGGAATTCCGTGGGTTGCACACTTAGT-ACTGATACGATCGTTCATAAACTT
1 ATTATGAATTCCGTGGGTTGCACACTTAGTGTC-GATACGATCGTTCATAAACTT
* * * * * *
2410627 ATTATGAATTCTGTGGGTTGCACACTTAGT-TCCCATATGGTCCTTCATAAACTA
1 ATTATGAATTCCGTGGGTTGCACACTTAGTGT-CGATACGATCGTTCATAAACTT
** *
2410681 ATTATGAATTTTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
1 ATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTT
** *
2410735 ATTATGAATTATGTGGGTTGCACACTTAGTGTCGATAC-AGTTGTTCATAAACTT
1 ATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATACGA-TCGTTCATAAACTT
*
2410789 ATTATGAATTTCGTGGGTTGCACACTTAGTGTCGATA
1 ATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATA
2410826 GTACACATAA
Statistics
Matches: 268, Mismatches: 33, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
53 1 0.00
54 261 0.97
55 6 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (54 bp):
ATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATACGATCGTTCATAAACTT
Found at i:2410754 original size:162 final size:162
Alignment explanation
Indices: 2410508--2410818 Score: 466
Period size: 162 Copynumber: 1.9 Consensus size: 162
2410498 GATACGATCA
* * * *
2410508 TTCATAAGCTCATTATGAATTCCATGGGTTGCACACTTTGTGTCGATATGGTCGTTCATAAACTT
1 TTCATAAACTAATTATGAATTCCATGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
*
2410573 ATTAGGAATTCCGTGGGTTGCACACTTAGTACT-GATAC-GATCGTTCATAAACTTATTATGAA-
66 ATTAGGAATTACGTGGGTTGCACACTTAGT-CTCGATACAG-TCGTTCATAAACTTATTATGAAT
2410635 TTCTGTGGGTTGCACACTTAGTTCCCATATGGTCC
129 TTC-GTGGGTTGCACACTTAGTTCCCATATGGTCC
***
2410670 TTCATAAACTAATTATGAATTTTGTGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
1 TTCATAAACTAATTATGAATTCCATGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
* * * *
2410735 ATTATGAATTATGTGGGTTGCACACTTAGTGTCGATACAGTTGTTCATAAACTTATTATGAATTT
66 ATTAGGAATTACGTGGGTTGCACACTTAGTCTCGATACAGTCGTTCATAAACTTATTATGAATTT
2410800 CGTGGGTTGCACACTTAGT
131 CGTGGGTTGCACACTTAGT
2410819 GTCGATAGTA
Statistics
Matches: 134, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
161 1 0.01
162 129 0.96
163 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (162 bp):
TTCATAAACTAATTATGAATTCCATGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTT
ATTAGGAATTACGTGGGTTGCACACTTAGTCTCGATACAGTCGTTCATAAACTTATTATGAATTT
CGTGGGTTGCACACTTAGTTCCCATATGGTCC
Found at i:2410825 original size:108 final size:108
Alignment explanation
Indices: 2410478--2410818 Score: 470
Period size: 108 Copynumber: 3.2 Consensus size: 108
2410468 ATAAGTTCCT
* * * * * **
2410478 TGGGGTGCGCACTTAGTTCTGATACGATCATTCATAAGCTCATTATGAATTCCATGGGTTGCACA
1 TGGGTTGCACACTTAGTTCTGATACGATCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
* * *
2410543 CTTTGTGTCGATATGGTCGTTCATAAACTTATTAGGAATTCCG
66 CTTAGTGTCGATATGGTCGTTCATAAACTTATTATGAATTTCG
*
2410586 TGGGTTGCACACTTAGTACTGATACGATCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
1 TGGGTTGCACACTTAGTTCTGATACGATCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
* * * *
2410651 CTTAGT-TCCCATATGGTCCTTCATAAACTAATTATGAATTTTG
66 CTTAGTGT-CGATATGGTCGTTCATAAACTTATTATGAATTTCG
* *
2410694 TGGGTTGCACACTTAGTGTC-GATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGCAC
1 TGGGTTGCACACTTAGT-TCTGATACGATCGTTCATAAACTTATTATGAATTCTGTGGGTTGCAC
** *
2410758 ACTTAGTGTCGATACAGTTGTTCATAAACTTATTATGAATTTCG
65 ACTTAGTGTCGATATGGTCGTTCATAAACTTATTATGAATTTCG
2410802 TGGGTTGCACACTTAGT
1 TGGGTTGCACACTTAGT
2410819 GTCGATAGTA
Statistics
Matches: 205, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
107 1 0.00
108 202 0.99
109 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (108 bp):
TGGGTTGCACACTTAGTTCTGATACGATCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACA
CTTAGTGTCGATATGGTCGTTCATAAACTTATTATGAATTTCG
Found at i:2419976 original size:23 final size:23
Alignment explanation
Indices: 2419950--2420020 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
2419940 GAAAGTGTAC
*
2419950 CGATGCATTCCTTGAATATGCAT
1 CGATGCATTCCTTGAATGTGCAT
* * *
2419973 CGATACA---CTATGAAGGTGCAC
1 CGATGCATTCCT-TGAATGTGCAT
2419994 CGATGCATTCCTTGAATGTGCAT
1 CGATGCATTCCTTGAATGTGCAT
2420017 CGAT
1 CGAT
2420021 ACACTCTGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
20 2 0.05
21 14 0.38
23 19 0.51
24 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (23 bp):
CGATGCATTCCTTGAATGTGCAT
Found at i:2419996 original size:44 final size:44
Alignment explanation
Indices: 2419924--2420025 Score: 177
Period size: 44 Copynumber: 2.3 Consensus size: 44
2419914 TTGTGCAAAG
*
2419924 TGCATCGATACACTATGAAAGTGTACCGATGCATTCCTTGAATA
1 TGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAATA
* *
2419968 TGCATCGATACACTATGAAGGTGCACCGATGCATTCCTTGAATG
1 TGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAATA
2420012 TGCATCGATACACT
1 TGCATCGATACACT
2420026 CTGCAATGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGCACCGATGCATTCCTTGAATA
Found at i:2422809 original size:65 final size:64
Alignment explanation
Indices: 2422677--2422810 Score: 155
Period size: 65 Copynumber: 2.1 Consensus size: 64
2422667 ACACCCTAAT
* * * * *
2422677 TCGAATGCTTTTTATGTACTGATGCACAACCATGCATCGATACACTCTTGATTTTATTGAAACA
1 TCGAAAGCGTTTTATGTACCGATGCACAACAATGCATCGATACACTCTTGATATTATTGAAACA
* * *
2422741 TCGAAAGCGTTTTATGTACCGATGCACAGATAATGCATCGATGCACT-TATGGCTATT-TTGAAA
1 TCGAAAGCGTTTTATGTACCGATGCACA-ACAATGCATCGATACACTCT-T-GATATTATTGAAA
2422804 CA
63 CA
2422806 TCGAA
1 TCGAA
2422811 TGTAATTAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
64 26 0.44
65 29 0.49
66 4 0.07
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (64 bp):
TCGAAAGCGTTTTATGTACCGATGCACAACAATGCATCGATACACTCTTGATATTATTGAAACA
Found at i:2425067 original size:40 final size:40
Alignment explanation
Indices: 2425008--2425093 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
2424998 TTCGACCATG
*
2425008 TTAG-GAAATTGAATTTGATATGAAAGTGATTGTAATTGC
1 TTAGAGAAATTGAAATTGATATGAAAGTGATTGTAATTGC
2425047 TTAGAGAAATTGAAATTGATATGAAAGTGATTGTAATTGC
1 TTAGAGAAATTGAAATTGATATGAAAGTGATTGTAATTGC
2425087 TTAGAGA
1 TTAGAGA
2425094 TGATATTTAG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 4 0.09
40 41 0.91
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.36
Consensus pattern (40 bp):
TTAGAGAAATTGAAATTGATATGAAAGTGATTGTAATTGC
Found at i:2431243 original size:3 final size:3
Alignment explanation
Indices: 2431237--2431301 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
2431227 AAATTAAAGT
* * * *
2431237 TAA TAA TAA TAA TAA TAA TAA TGA TGA TGA -AA TAAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
* *
2431282 TTA -AA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
2431302 ATGTTGTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:2443043 original size:117 final size:117
Alignment explanation
Indices: 2442837--2443075 Score: 451
Period size: 117 Copynumber: 2.0 Consensus size: 117
2442827 TTCAATGATA
*
2442837 TAAAAACATGCTGAGCTAGCCATCTTTACTTCCTTAACCTCATTGGAACATTACAAGTTCTTCAA
1 TAAAAACATGCTGAGCTAGCCATATTTACTTCCTTAACCTCATTGGAACATTACAAGTTCTTCAA
2442902 CATATTTGTGATAGCAAAGAGTTGGGCTGAGATTGAATCCTTAGTATCTAGC
66 CATATTTGTGATAGCAAAGAGTTGGGCTGAGATTGAATCCTTAGTATCTAGC
*
2442954 TAAAAACATGCTGATCTAGCCATATTTACTTCCTTAACCTCATTGGAACATTACAAGTTCTTCAA
1 TAAAAACATGCTGAGCTAGCCATATTTACTTCCTTAACCTCATTGGAACATTACAAGTTCTTCAA
*
2443019 CATATTTGTGATAGCGAAGAGTTGGGCTGAGATTGAATCCTTAGTATCTAGC
66 CATATTTGTGATAGCAAAGAGTTGGGCTGAGATTGAATCCTTAGTATCTAGC
2443071 TAAAA
1 TAAAA
2443076 TGTCCCTATT
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 119 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (117 bp):
TAAAAACATGCTGAGCTAGCCATATTTACTTCCTTAACCTCATTGGAACATTACAAGTTCTTCAA
CATATTTGTGATAGCAAAGAGTTGGGCTGAGATTGAATCCTTAGTATCTAGC
Found at i:2444754 original size:31 final size:31
Alignment explanation
Indices: 2444716--2444777 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
2444706 TGCTCTTATT
*
2444716 GATCTTCACTTAGTTTCTCTCAAACACTAAG
1 GATCTTCAATTAGTTTCTCTCAAACACTAAG
*
2444747 GATCTTCAATTAGTTTCTCTCCAACACTAAG
1 GATCTTCAATTAGTTTCTCTCAAACACTAAG
2444778 TAATTAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (31 bp):
GATCTTCAATTAGTTTCTCTCAAACACTAAG
Found at i:2446046 original size:20 final size:20
Alignment explanation
Indices: 2446023--2446070 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
2446013 ACAAGTTTAG
2446023 AAAATCATTCATATATTACA
1 AAAATCATTCATATATTACA
2446043 AAAATCATTCATATATTACA
1 AAAATCATTCATATATTACA
2446063 AAAATCAT
1 AAAATCAT
2446071 ACAACTTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATCATTCATATATTACA
Found at i:2448663 original size:22 final size:22
Alignment explanation
Indices: 2448635--2448695 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2448625 GGCTGTTTGG
2448635 TCAAAGTCAAGGTCAACACTGA
1 TCAAAGTCAAGGTCAACACTGA
* * * *
2448657 TCAAAGTTAAAGTCAACTCTGG
1 TCAAAGTCAAGGTCAACACTGA
*
2448679 TCAAATTCAACGGTCAA
1 TCAAAGTCAA-GGTCAA
2448696 GTCAATAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (22 bp):
TCAAAGTCAAGGTCAACACTGA
Found at i:2448769 original size:13 final size:14
Alignment explanation
Indices: 2448732--2448769 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2448722 TTGACTGTGT
2448732 TCGAGTTGACTCAA
1 TCGAGTTGACTCAA
2448746 TCG-GTTTGACTCAA
1 TCGAG-TTGACTCAA
2448760 T-GAGTTGACT
1 TCGAGTTGACT
2448770 GAGCTTGATC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (14 bp):
TCGAGTTGACTCAA
Found at i:2455286 original size:26 final size:24
Alignment explanation
Indices: 2455218--2455289 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 24
2455208 CCAAGTCGTG
* *
2455218 AGGGTATTTAGATCATTTCATAAATTG
1 AGGGTATTT-TATCATTT--TAAATTC
*
2455245 AGGGTATGTTATTCATTTTAAATCTC
1 AGGGTATTTTA-TCATTTTAAAT-TC
2455271 AGGGTATTTCTATCATTTT
1 AGGGTATTT-TATCATTTT
2455290 TAATAAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 5 0.13
26 17 0.45
27 16 0.42
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.46
Consensus pattern (24 bp):
AGGGTATTTTATCATTTTAAATTC
Found at i:2456773 original size:23 final size:24
Alignment explanation
Indices: 2456721--2456786 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 24
2456711 TGGCCCGGTT
** *
2456721 TTGACCCGACCCG-TTTGACCCGA
1 TTGACCCGACCCGACCTGACTCGA
*
2456744 TTTACCCGACCCGACCTGACTCG-
1 TTGACCCGACCCGACCTGACTCGA
*
2456767 TTGACCC-ACCCGACCCGACT
1 TTGACCCGACCCGACCTGACT
2456787 GCCCGACCCG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 12 0.33
23 18 0.50
24 6 0.17
ACGTcount: A:0.18, C:0.44, G:0.18, T:0.20
Consensus pattern (24 bp):
TTGACCCGACCCGACCTGACTCGA
Found at i:2459188 original size:22 final size:22
Alignment explanation
Indices: 2459161--2459205 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2459151 GCCTATATTA
2459161 TGATCTGATACTTGACATGGAT
1 TGATCTGATACTTGACATGGAT
*
2459183 TGATCTGATACTTGACCTGGAT
1 TGATCTGATACTTGACATGGAT
2459205 T
1 T
2459206 CTGTTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (22 bp):
TGATCTGATACTTGACATGGAT
Found at i:2461380 original size:17 final size:18
Alignment explanation
Indices: 2461350--2461383 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2461340 TGACCTGACG
2461350 CGTTGACCGACCGTTGAT
1 CGTTGACCGACCGTTGAT
*
2461368 CGTTGATCG-CCGTTGA
1 CGTTGACCGACCGTTGA
2461384 CAAGAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.15, C:0.26, G:0.29, T:0.29
Consensus pattern (18 bp):
CGTTGACCGACCGTTGAT
Found at i:2463755 original size:22 final size:22
Alignment explanation
Indices: 2463729--2463773 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2463719 GCCTATATTC
2463729 TGATCTGATACTTGACATGGAT
1 TGATCTGATACTTGACATGGAT
*
2463751 TGATCTGATACTTGACCTGGAT
1 TGATCTGATACTTGACATGGAT
2463773 T
1 T
2463774 CTGTTATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (22 bp):
TGATCTGATACTTGACATGGAT
Found at i:2463790 original size:24 final size:24
Alignment explanation
Indices: 2463763--2463809 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2463753 ATCTGATACT
* *
2463763 TGACCTGGATTCTGTTATGATTTC
1 TGACCTGAATTATGTTATGATTTC
*
2463787 TGACCTGAATTATGTTTTGATTT
1 TGACCTGAATTATGTTATGATTT
2463810 TTGATATATC
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:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (24 bp):
TGACCTGAATTATGTTATGATTTC
Found at i:2473165 original size:2 final size:2
Alignment explanation
Indices: 2473160--2473206 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
2473150 AAAAAAAAAA
* *
2473160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AG AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2473201 AT AT AT
1 AT AT AT
2473207 GCCAACGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2483365 original size:32 final size:33
Alignment explanation
Indices: 2483310--2483373 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
2483300 GCATCTCTTG
2483310 GATGAAGGTTGATGATTCCAAGCTTCATGTTGA
1 GATGAAGGTTGATGATTCCAAGCTTCATGTTGA
*
2483343 GATGCAGGTTGATG-TTCCAAGCTTCATGTTG
1 GATGAAGGTTGATGATTCCAAGCTTCATGTTG
2483374 TAGTCAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.34
Consensus pattern (33 bp):
GATGAAGGTTGATGATTCCAAGCTTCATGTTGA
Found at i:2486415 original size:8 final size:8
Alignment explanation
Indices: 2486402--2486602 Score: 57
Period size: 8 Copynumber: 26.8 Consensus size: 8
2486392 TTGCAGCCTT
2486402 GATGCATG
1 GATGCATG
2486410 GATGCAT-
1 GATGCATG
2486417 G--GCA-G
1 GATGCATG
*
2486422 GATGCATC
1 GATGCATG
2486430 GATGCAT-
1 GATGCATG
2486437 G--GCA-G
1 GATGCATG
*
2486442 GATGCATC
1 GATGCATG
2486450 GATGCAT-
1 GATGCATG
*
2486457 G--GCAAG
1 GATGCATG
*
2486463 GATGCATC
1 GATGCATG
2486471 GATGCACT-
1 GATGCA-TG
* *
2486479 AATTGCATTC
1 GA-TGCA-TG
**
2486489 GATGTTTG
1 GATGCATG
2486497 GATGCATG
1 GATGCATG
2486505 GATGCATTG
1 GATGCA-TG
*
2486514 CCTGATGCATC
1 ---GATGCATG
2486525 GATGCAT-
1 GATGCATG
*
2486532 TAGTGCA--
1 GA-TGCATG
2486539 GATGCATG
1 GATGCATG
2486547 GATGCAT-
1 GATGCATG
* *
2486554 --TACAGG
1 GATGCATG
2486560 GATGCATG
1 GATGCATG
2486568 GATGCA--
1 GATGCATG
* *
2486574 -CTGCAGG
1 GATGCATG
2486581 GATGCATG
1 GATGCATG
2486589 GATGCATG
1 GATGCATG
2486597 GATGCA
1 GATGCA
2486603 CTTTGACACC
Statistics
Matches: 143, Mismatches: 23, Indels: 54
0.65 0.10 0.25
Matches are distributed among these distances:
5 18 0.13
6 5 0.03
7 11 0.08
8 91 0.64
9 10 0.07
10 1 0.01
11 1 0.01
12 6 0.04
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (8 bp):
GATGCATG
Found at i:2486426 original size:12 final size:12
Alignment explanation
Indices: 2486409--2486469 Score: 57
Period size: 12 Copynumber: 5.7 Consensus size: 12
2486399 CTTGATGCAT
2486409 GGATGCATGGCA
1 GGATGCATGGCA
2486421 GGATGCAT--C-
1 GGATGCATGGCA
2486430 -GATGCATGGCA
1 GGATGCATGGCA
2486441 GGATGCAT--C-
1 GGATGCATGGCA
2486450 -GATGCATGGCAA
1 GGATGCATGGC-A
2486462 GGATGCAT
1 GGATGCAT
2486470 CGATGCACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 17
0.70 0.00 0.30
Matches are distributed among these distances:
8 14 0.35
10 4 0.10
12 15 0.38
13 7 0.17
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.20
Consensus pattern (12 bp):
GGATGCATGGCA
Found at i:2486427 original size:20 final size:20
Alignment explanation
Indices: 2486402--2486597 Score: 117
Period size: 20 Copynumber: 9.8 Consensus size: 20
2486392 TTGCAGCCTT
2486402 GATGCATGGATGCATGGCAG
1 GATGCATGGATGCATGGCAG
*
2486422 GATGCATCGATGCATGGCAG
1 GATGCATGGATGCATGGCAG
*
2486442 GATGCATCGATGCATGGCAAG
1 GATGCATGGATGCATGGC-AG
*
2486463 GATGCATCGATGCA---CTA-
1 GATGCATGGATGCATGGC-AG
***
2486480 -ATTGCAT---T-CGATGTTTG
1 GA-TGCATGGATGC-ATGGCAG
* **
2486497 GATGCATGGATGCATTGCCT
1 GATGCATGGATGCATGGCAG
*
2486517 GATGCATCGATGCATTAGTGCA-
1 GATGCATGGATGCA-T-G-GCAG
**
2486539 GATGCATGGATGCATTACAGG
1 GATGCATGGATGCATGGCA-G
2486560 GATGCATGGATGCACT-GCAGG
1 GATGCATGGATGCA-TGGCA-G
2486581 GATGCATGGATGCATGG
1 GATGCATGGATGCATGG
2486598 ATGCACTTTG
Statistics
Matches: 141, Mismatches: 16, Indels: 37
0.73 0.08 0.19
Matches are distributed among these distances:
13 1 0.01
14 2 0.01
16 1 0.01
17 10 0.07
18 3 0.02
19 2 0.01
20 54 0.38
21 52 0.37
22 14 0.10
23 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (20 bp):
GATGCATGGATGCATGGCAG
Found at i:2486565 original size:21 final size:21
Alignment explanation
Indices: 2486496--2486595 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 21
2486486 TTCGATGTTT
* *
2486496 GGATGCATGGATGCATTGC-C
1 GGATGCATGGATGCATTACAG
* * **
2486516 TGATGCATCGATGCATTAGTG
1 GGATGCATGGATGCATTACAG
*
2486537 CAGATGCATGGATGCATTACAG
1 -GGATGCATGGATGCATTACAG
* *
2486559 GGATGCATGGATGCACTGCAG
1 GGATGCATGGATGCATTACAG
2486580 GGATGCATGGATGCAT
1 GGATGCATGGATGCAT
2486596 GGATGCACTT
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.23
21 33 0.51
22 17 0.26
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (21 bp):
GGATGCATGGATGCATTACAG
Found at i:2486743 original size:30 final size:30
Alignment explanation
Indices: 2486686--2486744 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
2486676 AACTTTGAAT
2486686 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
2486716 AAATTCAATTCAAGTCCAAAAACATTTTG
1 AAATTCAATTCAAATCCAAAAACATTTTG
2486745 TCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:2488137 original size:15 final size:15
Alignment explanation
Indices: 2488119--2488158 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
2488109 TGACTCAACC
2488119 TGAGTTGACTCAGTG
1 TGAGTTGACTCAGTG
*
2488134 TGAGTTGAATCAGTG
1 TGAGTTGACTCAGTG
2488149 -G-GTTGACTCA
1 TGAGTTGACTCA
2488159 CGAGTTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 8 0.35
14 1 0.04
15 14 0.61
ACGTcount: A:0.23, C:0.12, G:0.33, T:0.33
Consensus pattern (15 bp):
TGAGTTGACTCAGTG
Found at i:2494802 original size:15 final size:15
Alignment explanation
Indices: 2494782--2494811 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2494772 TTGATTGGCC
2494782 TGAGTTGACTCAGTG
1 TGAGTTGACTCAGTG
*
2494797 TGAGTTGACTTAGTG
1 TGAGTTGACTCAGTG
2494812 GGTTAACTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.37
Consensus pattern (15 bp):
TGAGTTGACTCAGTG
Found at i:2497238 original size:3 final size:3
Alignment explanation
Indices: 2497230--2497254 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2497220 ATTTATTTAT
2497230 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2497255 ATGTTTTATC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2506856 original size:23 final size:22
Alignment explanation
Indices: 2506791--2506861 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 22
2506781 TCCTTAAAAC
*
2506791 CCTAAAAATCCTAAGAGATAATT
1 CCTAAAAATCC-AAAAGATAATT
* *
2506814 CCTAATAAATGC-AAAGATAACT
1 CCTAA-AAATCCAAAAGATAATT
2506836 CCTAAAAATCACAAAAGATAATT
1 CCTAAAAATC-CAAAAGATAATT
2506859 CCT
1 CCT
2506862 GATAATTGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 4 0.10
22 14 0.35
23 17 0.43
24 5 0.12
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (22 bp):
CCTAAAAATCCAAAAGATAATT
Found at i:2507047 original size:17 final size:18
Alignment explanation
Indices: 2507025--2507059 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2507015 TAAAAGGATA
2507025 AAATAATAAAATA-AAAT
1 AAATAATAAAATATAAAT
*
2507042 AAATAATTAAATATAAAT
1 AAATAATAAAATATAAAT
2507060 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAATAAAATATAAAT
Found at i:2508048 original size:84 final size:82
Alignment explanation
Indices: 2507958--2508127 Score: 268
Period size: 84 Copynumber: 2.0 Consensus size: 82
2507948 AATAAAGAAA
* * * *
2507958 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGCTAAGATAAAA
1 TAAATCCTAATTAAAATAATTAAAACTATTTAAACTAAAATACATAAAACAAAGATAAAAT-AAA
2508023 TATATTTAAAATAATATCC
65 -ATATTTAAAATAATATCC
* *
2508042 TAAATCCTAATTAAAATAATTAAAACTATTTAGACTAAAATACATAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATAATTAAAACTATTTAAACTAAAATACATAAAACAAAGATAAAATAAAA
2508107 TATTTAAAATAATATCC
66 TATTTAAAATAATATCC
2508124 TAAA
1 TAAA
2508128 ATATGAGTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
82 22 0.28
83 2 0.03
84 56 0.70
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.30
Consensus pattern (82 bp):
TAAATCCTAATTAAAATAATTAAAACTATTTAAACTAAAATACATAAAACAAAGATAAAATAAAA
TATTTAAAATAATATCC
Found at i:2509045 original size:35 final size:35
Alignment explanation
Indices: 2509003--2509085 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
2508993 TTCTCTGCTG
**
2509003 TTCGAAACAGTGAACAGTTTTATTTTTTCAATTT-TT
1 TTCGAAACAGTGAACA-ACTT-TTTTTTCAATTTCTT
* *
2509039 TT-GAAACATTGAACAACTTTTTTTTCGATTTCTT
1 TTCGAAACAGTGAACAACTTTTTTTTCAATTTCTT
2509073 TTCGAAACAGTGA
1 TTCGAAACAGTGA
2509086 TTATTTTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
33 11 0.28
34 6 0.15
35 21 0.52
36 2 0.05
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (35 bp):
TTCGAAACAGTGAACAACTTTTTTTTCAATTTCTT
Found at i:2510411 original size:6 final size:6
Alignment explanation
Indices: 2510395--2510467 Score: 74
Period size: 6 Copynumber: 11.3 Consensus size: 6
2510385 AAAAATAAAG
* *
2510395 AAAAAT AAAAAGT AAAAGT GAAAAT AAAAAT AAAAAT AAAAAT AAAAATT
1 AAAAAT AAAAA-T AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA-T
*
2510445 GAACAAACG AAAAAT AAAAAT AA
1 -AA-AAA-T AAAAAT AAAAAT AA
2510468 TAATGAGTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
6 40 0.71
7 9 0.16
8 4 0.07
9 3 0.05
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:2514419 original size:84 final size:81
Alignment explanation
Indices: 2514331--2514499 Score: 266
Period size: 84 Copynumber: 2.0 Consensus size: 81
2514321 AATAAAGAAA
* *
2514331 TAAATCCTAATTAAAATAATTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAGATAAAA
1 TAAATCCTAATTAAAACAATTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAAT-AAA
*
2514396 TATATTTAAAATAATATCT
65 -ATATTT-AAATAATATCC
* *
2514415 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAACAATTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
2514480 TATTTAAATAATATCC
66 TATTTAAATAATATCC
2514496 TAAA
1 TAAA
2514500 ACATGAGTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
81 14 0.17
82 6 0.08
83 2 0.03
84 58 0.73
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (81 bp):
TAAATCCTAATTAAAACAATTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
TATTTAAATAATATCC
Found at i:2527205 original size:55 final size:55
Alignment explanation
Indices: 2527146--2527639 Score: 756
Period size: 55 Copynumber: 9.0 Consensus size: 55
2527136 CCCACTAATA
* * *
2527146 ATACGAAAATTCATATACTTATTATGAATTTCTTATTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* *
2527201 ATACGGAGATTCATAAACTTATTATGAATTTCTTAGCTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* *
2527256 ATACGGAGATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTTCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * *
2527311 ATACGGAGATTCATAAACTTATTATGAATTTCTTCGTTTTGCACACAAAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * * * *
2527366 ATACGGAAATTCATAAAATTGTTATGAATTTCTTAATTTTGCAAACATTA-TGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA-AAGTGCCC
* * *
2527421 ATACAGAAATTTATAAACTTATTATGAATTTCTTAGTTTTTCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * *
2527476 ATATGGAAATTCATAAACTTATTATGAATCTCTTAGTTTTGCACACAAAGTGCTC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
*
2527531 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* *
2527586 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCAAACATAGTGCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCC
2527640 ATTTGGTAAT
Statistics
Matches: 398, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
54 1 0.00
55 396 0.99
56 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (55 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
Found at i:2528085 original size:20 final size:21
Alignment explanation
Indices: 2528060--2528106 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
2528050 CATGGTATCA
* *
2528060 ATACTTCTCTCCTA-GTACCG
1 ATACTTCTATACTAGGTACCG
2528080 ATACTTCTATACTATGGTACCG
1 ATACTTCTATACTA-GGTACCG
2528102 ATACT
1 ATACT
2528107 CCATTACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
22 11 0.48
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.36
Consensus pattern (21 bp):
ATACTTCTATACTAGGTACCG
Found at i:2534526 original size:54 final size:55
Alignment explanation
Indices: 2534317--2534534 Score: 339
Period size: 55 Copynumber: 4.0 Consensus size: 55
2534307 CCCACTAACA
* * * *
2534317 ATACGAAATTTCATATACATATTATGAATTTCTTATTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
*
2534372 ATACGAAAATTCAAAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
2534427 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * * * *
2534482 ATACGGAGATT-ATAAACTTATTATTAATTTCTTAGTTTTTCACACATAGTGCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCC
2534535 ATTTGGTAAT
Statistics
Matches: 152, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
54 39 0.26
55 113 0.74
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (55 bp):
ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
Found at i:2535059 original size:20 final size:20
Alignment explanation
Indices: 2535034--2535083 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2535024 TCTGTATTCT
*
2535034 GTATCAATACCTTCCCCACA
1 GTATCAATACCCTCCCCACA
* *
2535054 GTATCAATACCCTCCTCTCA
1 GTATCAATACCCTCCCCACA
*
2535074 ATATCAATAC
1 GTATCAATAC
2535084 TAATTGCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (20 bp):
GTATCAATACCCTCCCCACA
Found at i:2536523 original size:44 final size:44
Alignment explanation
Indices: 2536469--2536677 Score: 283
Period size: 44 Copynumber: 4.7 Consensus size: 44
2536459 ATACCATCAG
2536469 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* ** *
2536513 TGGTACCTTTCTGCCAATAATGCATTGTCATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * * *
2536557 TGGAATCTTTCTACCAATAATGAACCGTTATGCATTTCCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
2536601 TGACACATTTTATGCCAATAATGCACCGTTATGCATTTTCATTTG
1 TGGCAC-CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
2536646 TGGCACCTTTCTACCAATAATGCACCGTTATG
1 TGGCACCTTTCTGCCAATAATGCACCGTTATG
2536678 TGTTTTAATT
Statistics
Matches: 139, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
44 102 0.73
45 37 0.27
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:2536690 original size:89 final size:88
Alignment explanation
Indices: 2536468--2536677 Score: 294
Period size: 89 Copynumber: 2.4 Consensus size: 88
2536458 AATACCATCA
* ** *
2536468 GTGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGTACCTTTCTGCCAATAA
1 GTGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATGACACCTTTATGCCAATAA
**
2536533 TGCATTGTCATGCATTTTCATTT
66 TGCACCGTCATGCATTTTCATTT
* * * * * *
2536556 ATGGAATCTTTCTACCAATAATGAACCGTTATGCATTTCCATTTATGACACATTTTATGCCAATA
1 GTGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATGACAC-CTTTATGCCAATA
*
2536621 ATGCACCGTTATGCATTTTCATTT
65 ATGCACCGTCATGCATTTTCATTT
2536645 GTGGCACCTTTCTACCAATAATGCACCGTTATG
1 GTGGCACCTTTCTACCAATAATGCACCGTTATG
2536678 TGTTTTAATT
Statistics
Matches: 104, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
88 43 0.41
89 61 0.59
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (88 bp):
GTGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTATGACACCTTTATGCCAATAA
TGCACCGTCATGCATTTTCATTT
Found at i:2540647 original size:20 final size:20
Alignment explanation
Indices: 2540609--2540647 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2540599 AAATCTTACA
* **
2540609 TGGGGGTATTGGTGTCCTCG
1 TGGGGGTATCGGTAACCTCG
2540629 TGGGGGTATCGGTAACCTC
1 TGGGGGTATCGGTAACCTC
2540648 TGGACAATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.10, C:0.18, G:0.41, T:0.31
Consensus pattern (20 bp):
TGGGGGTATCGGTAACCTCG
Found at i:2541248 original size:2 final size:2
Alignment explanation
Indices: 2541241--2541265 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2541231 TAAATCAAAC
2541241 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2541266 AATAAACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2555905 original size:20 final size:21
Alignment explanation
Indices: 2555880--2555918 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2555870 GTTATTGATA
2555880 GGGGGTATCGGTA-CCTCCTT
1 GGGGGTATCGGTATCCTCCTT
*
2555900 GGGGGTATTGGTATCCTCC
1 GGGGGTATCGGTATCCTCC
2555919 GAGCAATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.10, C:0.23, G:0.36, T:0.31
Consensus pattern (21 bp):
GGGGGTATCGGTATCCTCCTT
Found at i:2556730 original size:2 final size:2
Alignment explanation
Indices: 2556723--2556759 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2556713 CGTGCATACC
2556723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2556760 AATGTTTCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2560155 original size:29 final size:29
Alignment explanation
Indices: 2560123--2560203 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
2560113 GTTTGTATTA
*
2560123 TATTGTAATTTATAAAAGGTTTTGTCCTT
1 TATTGTAATTTATAAAAGGTTTTATCCTT
* * * * *
2560152 TATTATGATTTATAAAAAGCTTTATTCTT
1 TATTGTAATTTATAAAAGGTTTTATCCTT
* *
2560181 TAATGCAATTTATAAAAGGTTTT
1 TATTGTAATTTATAAAAGGTTTT
2560204 TTTTTTTGGA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.49
Consensus pattern (29 bp):
TATTGTAATTTATAAAAGGTTTTATCCTT
Found at i:2561073 original size:20 final size:20
Alignment explanation
Indices: 2561050--2561103 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2561040 TGTAAATTTG
*
2561050 ATTTTAAAAATTTTAATTAA
1 ATTTTAAAAAATTTAATTAA
*
2561070 ATTTTAAAAAATTTAATTTA
1 ATTTTAAAAAATTTAATTAA
2561090 ATTTTAAAAAATTT
1 ATTTTAAAAAATTT
2561104 CAATAAAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTAAAAAATTTAATTAA
Found at i:2567584 original size:3 final size:3
Alignment explanation
Indices: 2567576--2567606 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2567566 GTAGGGTAGC
2567576 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2567607 TTTTAAACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2568249 original size:129 final size:128
Alignment explanation
Indices: 2568039--2568275 Score: 330
Period size: 129 Copynumber: 1.8 Consensus size: 128
2568029 AGTTCCTATG
* * * **
2568039 TGATGAAGATGACTGGTTATCTCGGTTGACACAACTCCTACATAGTGAGGAGATCTGGTCGGGTG
1 TGATGAAGATGACTGGTTATCTCGGTTCACACAACTCCTACATAATGAGAAGATCTGGTCAAGTG
* *
2568104 TTGACACGGTTCCTACGTGATGACGACGACAGGCCATCCAAGGTTGATAACACGGTTCGTACA
66 ATGACACGGTTCCTACGCGATGACGACGACAGGCCATCCAAGGTTGATAACACGGTTCGTACA
* * * **
2568167 TGATGAGGATGGCTGGTTATCTGGGGTTCACACAGTTCCTACATAATGAGAAGATCTGGTCAAGT
1 TGATGAAGATGACTGGTTATCT-CGGTTCACACAACTCCTACATAATGAGAAGATCTGGTCAAGT
* * *
2568232 GATGACACGGTTCCTACGCGATGAGGACGGCAGGCCATCTAAGG
65 GATGACACGGTTCCTACGCGATGACGACGACAGGCCATCCAAGG
2568276 GTATTTGGTT
Statistics
Matches: 93, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
128 20 0.22
129 73 0.78
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (128 bp):
TGATGAAGATGACTGGTTATCTCGGTTCACACAACTCCTACATAATGAGAAGATCTGGTCAAGTG
ATGACACGGTTCCTACGCGATGACGACGACAGGCCATCCAAGGTTGATAACACGGTTCGTACA
Found at i:2568558 original size:32 final size:32
Alignment explanation
Indices: 2568517--2568604 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
2568507 TTCACATCAT
*
2568517 GATGTTGAATCCCTAAAGATGCCCCAATATTC
1 GATGTTGAATCCCTAAAGATGCCCCAACATTC
* *
2568549 GTTGTTGAATCTCC-AAAGATGCCCCAACATTT
1 GATGTTGAATC-CCTAAAGATGCCCCAACATTC
*
2568581 GATGTTGAAT-CTTCAAAGATGCCC
1 GATGTTGAATCCCT-AAAGATGCCC
2568605 TCATTTTTCC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
32 45 0.94
33 2 0.04
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCCCTAAAGATGCCCCAACATTC
Found at i:2575972 original size:3 final size:3
Alignment explanation
Indices: 2575964--2575995 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2575954 GTAGGGTAGG
*
2575964 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2575996 TTTTTTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2578330 original size:17 final size:16
Alignment explanation
Indices: 2578308--2578344 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2578298 TATAAGCATC
2578308 CAAATTCAAACAATCCA
1 CAAATTCAAAC-ATCCA
2578325 CAAATTCAAACATCCA
1 CAAATTCAAACATCCA
2578341 -AAAT
1 CAAAT
2578345 GTTAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 11 0.55
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (16 bp):
CAAATTCAAACATCCA
Found at i:2578680 original size:3 final size:3
Alignment explanation
Indices: 2578672--2578712 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
2578662 TTTTAATAGT
*
2578672 TTA TTA TTA TTA TTA TTA -TA TTT TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2578713 ATAAAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2578698 original size:14 final size:14
Alignment explanation
Indices: 2578676--2578712 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2578666 AATAGTTTAT
2578676 TATTATTATTATTA
1 TATTATTATTATTA
*
2578690 TATTTTTATTATTA
1 TATTATTATTATTA
2578704 TTATTATTA
1 -TATTATTA
2578713 ATAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:2578698 original size:17 final size:17
Alignment explanation
Indices: 2578673--2578712 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
2578663 TTTAATAGTT
2578673 TATTATTATTATTATTA
1 TATTATTATTATTATTA
*
2578690 TATTTTTATTATTATTA
1 TATTATTATTATTATTA
2578707 TTATTA
1 -TATTA
2578713 ATAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:2579918 original size:20 final size:23
Alignment explanation
Indices: 2579875--2579919 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2579865 ATAGTTTTAA
*
2579875 TAATTTTTATTTTGATCTAGAAT
1 TAATTTTTATTATGATCTAGAAT
2579898 TAATTTTT-TTATGA-CTA-AAT
1 TAATTTTTATTATGATCTAGAAT
2579918 TA
1 TA
2579920 CAGTATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 5 0.24
23 8 0.38
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (23 bp):
TAATTTTTATTATGATCTAGAAT
Found at i:2580577 original size:4 final size:4
Alignment explanation
Indices: 2580568--2580594 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2580558 ATAATAATAA
2580568 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
2580595 AATATTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2580841 original size:23 final size:22
Alignment explanation
Indices: 2580826--2580867 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2580816 AAATATCTTT
2580826 TTTATAAAAATATAAAATATATA
1 TTTATAAAAATAT-AAATATATA
2580849 TTTATAAAAAT-T-AATATAT
1 TTTATAAAAATATAAATATAT
2580868 TTTCTTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTATAAAAATATAAATATATA
Found at i:2582833 original size:42 final size:43
Alignment explanation
Indices: 2582770--2582854 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 43
2582760 TGGCTTTAGA
* *
2582770 GAAGTTAGGAAGGAAATTTATCCC-TATATGTAATGTTTTGTT
1 GAAGTTAGGAAGGAAAGTTATCCCTTATATGTAAAGTTTTGTT
**
2582812 GAAGTTAGGACTGAAAGTTATCCCTTATATGTAAAGTTTTGTT
1 GAAGTTAGGAAGGAAAGTTATCCCTTATATGTAAAGTTTTGTT
2582855 TGATGCACCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 21 0.55
43 17 0.45
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (43 bp):
GAAGTTAGGAAGGAAAGTTATCCCTTATATGTAAAGTTTTGTT
Found at i:2591525 original size:123 final size:122
Alignment explanation
Indices: 2591100--2591655 Score: 738
Period size: 123 Copynumber: 4.6 Consensus size: 122
2591090 TGCCAGGTAG
* *
2591100 AGTTCATAATGAGAAGAATTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAA-TTGTTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG-TTC
*
2591164 AACCTTTTTC-ATGACTCTATCACAGAAGGAGAT--A-C-GTCA-ACA--TTTCCAGAGA
65 AACCTTTTGCTA-GACTCTATCACAGAAGGAGATAGATCAG-CATACACTTTTCCAGAGA
* * *
2591216 AGTTCATAAAT-ATAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTC
1 AGTTCAT-AATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * *
2591280 AATCTTTTGCTAGACTCTATCACATAAGGAGATAGATCGGCATACACTTTTCCAGAGA
65 AACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATACACTTTTCCAGAGA
* *
2591338 AGTTCATAATGATAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
2591403 ACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATACACTTTTCCAGAGAA
66 ACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATACACTTTTCCAGAG-A
* * * *
2591461 AGATCATAATGAGAAGAACTTATTTGAAGAGGAAGAAGAATTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * **
2591526 ACCTTTTGCTAGACGCTATCACATAATGAGATATATCAGCAT-CAACAATTCCAGAGA
66 ACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATAC-ACTTTTCCAGAGA
* *
2591583 GAGTTCATAACGAGAAGAACTCATCTGAAGAGGAAAAAAAGAAGTTCATAATGAGAAGAACTTGT
1 -AGTTCATAATGAGAAGAACTCATCTGAAGAGG--AAGAAGAAGTTCATAATGAGAAGAACTTGT
*
2591648 CCAACCTT
63 TCAACCTT
2591656 GCCATAATTC
Statistics
Matches: 391, Mismatches: 33, Indels: 23
0.87 0.07 0.05
Matches are distributed among these distances:
116 79 0.20
117 7 0.02
118 1 0.00
119 3 0.01
120 4 0.01
121 3 0.01
122 123 0.31
123 136 0.35
125 35 0.09
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (122 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATACACTTTTCCAGAGA
Found at i:2591696 original size:245 final size:242
Alignment explanation
Indices: 2591098--2591698 Score: 683
Period size: 245 Copynumber: 2.5 Consensus size: 242
2591088 ATTGCCAGGT
* *
2591098 AGAGTTCATAATGAGAAGAATTCATCTGAAGAGG-AAGAAGAAATTCATAATGAGAAGAA-TTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAGAAGAAGTTCATAATGAGAAGAACTTG-
* * * * *
2591161 TTCAACCTTTTTCATGACTCTATCAC-AGAAG-GAGAT--ACGTCAACATTTCCAGAGAAGTTCA
65 TTCAACC-TTTGCATAACTCTATCACAAGAAGTGAGATCAACGAC-ACTTTTCCAGAGAAGATCA
* * *
2591222 TAAATATAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTCAATCTTT
128 TAAATAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * **
2591287 TGCTAGACTCTATCACATAAGGAGATAGATCGGCATACACTTTTCCAGAG
193 TGCTAGACGCTATCACATAAGGAGATAGATCAGCATACACAATTCCAGAG
* *
2591337 A-AGTTCATAATGATAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
2591400 TCAACCTTTTGC-TAGACTCTATCAC-AGAAGGAGATAGATCAGCATACACTTTTCCAGAGAAAG
66 TCAACC-TTTGCATA-ACTCTATCACAAGAA-GTG--AGATCAAC-GACACTTTTCCAGAG-AAG
* * * *
2591463 ATCAT-AATGAGAAGAACTTATTTGAAGAGGAAGAAGAATTTCATAATGAGAAGAACTTGTTCAA
124 ATCATAAAT-AGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* *
2591527 CCTTTTGCTAGACGCTATCACATAATGAGATATATCAGCAT-CAACAATTCCAGAG
188 CCTTTTGCTAGACGCTATCACATAAGGAGATAGATCAGCATAC-ACAATTCCAGAG
* *
2591582 AGAGTTCATAACGAGAAGAACTCATCTGAAGAGGAAAAAAAGAAGTTCATAATGAGAAGAACTTG
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAGG-AAAGAAGAAGTTCATAATGAGAAGAACTTG
* *
2591647 TCCAACC-TTGCCATAATTC-ATCACATATGAAGTTGA-ATCAACGACACTTTTC
65 TTCAACCTTTG-CATAACTCTATCACA-A-GAAG-TGAGATCAACGACACTTTTC
2591699 TTAAAGATCA
Statistics
Matches: 308, Mismatches: 33, Indels: 36
0.82 0.09 0.10
Matches are distributed among these distances:
237 1 0.00
238 79 0.26
239 5 0.02
240 1 0.00
242 4 0.01
244 16 0.05
245 113 0.37
246 42 0.14
247 5 0.02
248 38 0.12
249 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (242 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTGCATAACTCTATCACAAGAAGTGAGATCAACGACACTTTTCCAGAGAAGATCATAA
ATAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
TAGACGCTATCACATAAGGAGATAGATCAGCATACACAATTCCAGAG
Found at i:2592045 original size:22 final size:23
Alignment explanation
Indices: 2592019--2592074 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 23
2592009 TTATCTCGTT
2592019 TTATT-TTAATAGTTTT-TTATTA
1 TTATTATTAATA-TTTTATTATTA
2592041 TTATTATT-ATATTTTATTATTA
1 TTATTATTAATATTTTATTATTA
2592063 TTATTATTAATA
1 TTATTATTAATA
2592075 AAATATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.13
22 22 0.71
23 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTATTATTAATATTTTATTATTA
Found at i:2592055 original size:19 final size:19
Alignment explanation
Indices: 2592033--2592069 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2592023 TTTAATAGTT
2592033 TTTTATTATTATTATTATA
1 TTTTATTATTATTATTATA
2592052 TTTTATTATTATTATTAT
1 TTTTATTATTATTATTAT
2592070 TAATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATTATTATTATTATA
Found at i:2592089 original size:3 final size:3
Alignment explanation
Indices: 2592035--2592071 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
2592025 TAATAGTTTT
2592035 TTA TTA TTA TTA TTA -TA TT- TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2592072 ATAAAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2593953 original size:4 final size:4
Alignment explanation
Indices: 2593946--2593970 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2593936 ATAATAATAA
2593946 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2593971 TAATATTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2594134 original size:9 final size:10
Alignment explanation
Indices: 2594106--2594136 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
2594096 AGAGAAATGT
2594106 TTTATTAATA
1 TTTATTAATA
2594116 TTTATTAATA
1 TTTATTAATA
2594126 TTT-TTAATA
1 TTTATTAATA
2594135 TT
1 TT
2594137 AAGAAAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTATTAATA
Found at i:2594218 original size:23 final size:22
Alignment explanation
Indices: 2594192--2594245 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
2594182 TTCTAAGTAA
*
2594192 ATAAATATCTTATTTATAAAAAT
1 ATAAATAT-ATATTTATAAAAAT
*
2594215 ATAAAATATATATTTATAGAAAT
1 AT-AAATATATATTTATAAAAAT
2594238 -T-AATATAT
1 ATAAATATAT
2594246 TTTCTTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 7 0.25
22 1 0.04
23 14 0.50
24 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATAAATATATATTTATAAAAAT
Found at i:2596303 original size:21 final size:20
Alignment explanation
Indices: 2596259--2596303 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
2596249 CAGAACCCGT
2596259 GGGGGTATCGATTCCCTCCA
1 GGGGGTATCGATTCCCTCCA
2596279 GGGGGTATCGATTCCCTCCA
1 GGGGGTATCGATTCCCTCCA
2596299 GGGGG
1 GGGGG
2596304 AATCAGTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.27, G:0.38, T:0.22
Consensus pattern (20 bp):
GGGGGTATCGATTCCCTCCA
Found at i:2600494 original size:21 final size:21
Alignment explanation
Indices: 2600468--2600542 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
2600458 ACCGTTTAAC
2600468 AGGGGGAATCGGTATTCCCTT
1 AGGGGGAATCGGTATTCCCTT
2600489 AGGGGGAATCGGTATTCCCTT
1 AGGGGGAATCGGTATTCCCTT
* * **
2600510 GGGGGGAATCGATACCCCCTT
1 AGGGGGAATCGGTATTCCCTT
*
2600531 GGGGGGAATCGG
1 AGGGGGAATCGG
2600543 CTCCCTTTGG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.19, C:0.20, G:0.39, T:0.23
Consensus pattern (21 bp):
AGGGGGAATCGGTATTCCCTT
Found at i:2604729 original size:90 final size:89
Alignment explanation
Indices: 2604570--2604746 Score: 282
Period size: 90 Copynumber: 2.0 Consensus size: 89
2604560 CCTAACACAC
* *
2604570 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACACTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
* * *
2604635 TTTAATTTATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
* *
2604659 CCTTTTATATCCAAGTTACACTAATCATATTAGGGATTTTATTGTTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACACTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATATAT
2604724 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
2604747 TTTGGGATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 33 0.41
90 47 0.59
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACACTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATATATA
TTTAATTAATTGAAATTAAATAAT
Found at i:2604733 original size:20 final size:21
Alignment explanation
Indices: 2604708--2604777 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
2604698 TATTGTTTCA
2604708 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* *
2604728 AATTAATTGAAATTAAATATTT
1 AATTAATT-AAAATATATATTT
* *
2604750 GGGATT-ATTAAAACATATATTT
1 --AATTAATTAAAATATATATTT
2604772 AATTAA
1 AATTAA
2604778 CTCTAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 11 0.29
21 1 0.03
22 20 0.53
23 3 0.08
24 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:2610904 original size:90 final size:89
Alignment explanation
Indices: 2610743--2610919 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
2610733 CCTAACACAC
* *
2610743 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTCTTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCAAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
*
2610808 TTTAATTAATTAAAATTTAATAAT
66 TTTAATTAATTAAAATTAAATAAT
*
2610832 CCTTTTATATCAAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCAAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
*
2610897 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTAAAATTAAATA
2610920 TTCGAGATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 33 0.40
90 49 0.60
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCAAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTAAAATTAAATAAT
Found at i:2620433 original size:21 final size:20
Alignment explanation
Indices: 2620385--2620433 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
2620375 TATCAATTTA
2620385 TATGGTATTGACACCAACCC
1 TATGGTATTGACACCAACCC
* *
2620405 T-TCAGTATTGATACCAACCCC
1 TAT-GGTATTGACACCAA-CCC
2620426 TATGGTAT
1 TATGGTAT
2620434 CTATACTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.04
20 13 0.57
21 8 0.35
22 1 0.04
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (20 bp):
TATGGTATTGACACCAACCC
Found at i:2627856 original size:17 final size:17
Alignment explanation
Indices: 2627836--2627868 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2627826 TTTTTCTAAT
2627836 TTTTCTATTTTCTTTTC
1 TTTTCTATTTTCTTTTC
*
2627853 TTTTCTTTTTTCTTTT
1 TTTTCTATTTTCTTTT
2627869 GACAGTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCTATTTTCTTTTC
Found at i:2634740 original size:23 final size:25
Alignment explanation
Indices: 2634693--2634764 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 25
2634683 AAAATAAAAC
2634693 GTAAAATAAAATGAAAATGAA-AAC-TT
1 GTAAAAT-AAA-GAAAA-GAAGAACTTT
2634719 G-AAAATAAAGAAAAGAAGAACTTT
1 GTAAAATAAAGAAAAGAAGAACTTT
2634743 GTAAAACTAGAA-AAAAGAAGAA
1 GTAAAA-TA-AAGAAAAGAAGAA
2634765 TAATGAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
22 3 0.07
23 8 0.20
24 6 0.15
25 9 0.22
26 13 0.32
27 2 0.05
ACGTcount: A:0.64, C:0.04, G:0.15, T:0.17
Consensus pattern (25 bp):
GTAAAATAAAGAAAAGAAGAACTTT
Found at i:2637520 original size:20 final size:20
Alignment explanation
Indices: 2637374--2637522 Score: 174
Period size: 20 Copynumber: 7.5 Consensus size: 20
2637364 GGAAAGAGTA
*
2637374 TCCATATTTTGGTAAAAGTT
1 TCCATACTTTGGTAAAAGTT
2637394 TCCATACTTTGGTAAAAGTT
1 TCCATACTTTGGTAAAAGTT
** *
2637414 TCCATACTTTTTTAAGAGTT
1 TCCATACTTTGGTAAAAGTT
*
2637434 TCCATATTTTGGTAAAAGTT
1 TCCATACTTTGGTAAAAGTT
* *
2637454 TACATACTCTGGTAAGAA-TT
1 TCCATACTTTGGTAA-AAGTT
* * *
2637474 TACATATTTTGGTAAAAGGT
1 TCCATACTTTGGTAAAAGTT
*
2637494 TCCATACTTTGGAAAAAGTT
1 TCCATACTTTGGTAAAAGTT
*
2637514 TCAATACTT
1 TCCATACTT
2637523 CTTCTTAGAG
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
19 2 0.02
20 104 0.96
21 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.42
Consensus pattern (20 bp):
TCCATACTTTGGTAAAAGTT
Found at i:2641930 original size:32 final size:32
Alignment explanation
Indices: 2641870--2641931 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2641860 TTTAAATGAG
* *
2641870 ACATTGACACTATTGTACATTATCTGAATGCA
1 ACATTGACACTATTGTACAATATATGAATGCA
* * *
2641902 ACATTGACTCTGTTGTGCAATATATGAATG
1 ACATTGACACTATTGTACAATATATGAATG
2641932 TCATACTGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
ACATTGACACTATTGTACAATATATGAATGCA
Found at i:2643115 original size:21 final size:21
Alignment explanation
Indices: 2643091--2643144 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
2643081 AAACCTTTTC
2643091 AGTATCGATATTGTTACCCTT
1 AGTATCGATATTGTTACCCTT
2643112 AGTATCGATATTGTTACCCTT
1 AGTATCGATATTGTTACCCTT
2643133 AGTATCGATATT
1 AGTATCGATATT
2643145 AGGGAAACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (21 bp):
AGTATCGATATTGTTACCCTT
Found at i:2643214 original size:20 final size:20
Alignment explanation
Indices: 2643157--2643297 Score: 176
Period size: 20 Copynumber: 7.1 Consensus size: 20
2643147 GGAAACAGTA
* *
2643157 TCCATGCTTTGGTAAAAGTT
1 TCCATACTTTGGTAAGAGTT
*
2643177 TCCATAC-TTGTTAAGAGTT
1 TCCATACTTTGGTAAGAGTT
* *
2643196 TCCATGCTTTGGCAAGAGTT
1 TCCATACTTTGGTAAGAGTT
2643216 TCCATACTTTGGTAAGAGTT
1 TCCATACTTTGGTAAGAGTT
* *
2643236 TCCATACTTTCGTAAGAGTA
1 TCCATACTTTGGTAAGAGTT
* *
2643256 TCAATACTTTGGTAAGAATT
1 TCCATACTTTGGTAAGAGTT
* *
2643276 TTCATACTTTGGAAAGAGTT
1 TCCATACTTTGGTAAGAGTT
2643296 TC
1 TC
2643298 AAAACTTTAG
Statistics
Matches: 101, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
19 16 0.16
20 85 0.84
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (20 bp):
TCCATACTTTGGTAAGAGTT
Found at i:2643283 original size:60 final size:59
Alignment explanation
Indices: 2643157--2643316 Score: 178
Period size: 60 Copynumber: 2.7 Consensus size: 59
2643147 GGAAACAGTA
* * * * * *
2643157 TCCATGCTTTGGTAAAAGTTTCCATAC-TTGTTAAGAGTTTCCATGCTTTGGCAAGAGTT
1 TCCATACTTTGGTAAGAGTTTCCATACTTTG-TAAGAGTATCAATACTTTGGCAAGAATT
*
2643216 TCCATACTTTGGTAAGAGTTTCCATACTTTCGTAAGAGTATCAATACTTTGGTAAGAATT
1 TCCATACTTTGGTAAGAGTTTCCATACTTT-GTAAGAGTATCAATACTTTGGCAAGAATT
* * * * *
2643276 TTCATACTTTGGAAAGAGTTTCAAAACTTTAGCAAGAGTAT
1 TCCATACTTTGGTAAGAGTTTCCATACTTT-GTAAGAGTAT
2643317 TGATACTTCT
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 25 0.29
60 60 0.70
61 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (59 bp):
TCCATACTTTGGTAAGAGTTTCCATACTTTGTAAGAGTATCAATACTTTGGCAAGAATT
Found at i:2643305 original size:40 final size:40
Alignment explanation
Indices: 2643157--2643314 Score: 167
Period size: 40 Copynumber: 4.0 Consensus size: 40
2643147 GGAAACAGTA
* * *
2643157 TCCATGCTTTGGTAAA-AGTTTCCATAC-TTGTTAAGAGTT
1 TCCATACTTTGG-AAAGAGTTTCAATACTTTGGTAAGAGTT
* * *
2643196 TCCATGCTTTGGCAAGAGTTTCCATACTTTGGTAAGAGTT
1 TCCATACTTTGGAAAGAGTTTCAATACTTTGGTAAGAGTT
* * * *
2643236 TCCATACTTTCGTAAGAGTATCAATACTTTGGTAAGAATT
1 TCCATACTTTGGAAAGAGTTTCAATACTTTGGTAAGAGTT
* * * *
2643276 TTCATACTTTGGAAAGAGTTTCAAAACTTTAGCAAGAGT
1 TCCATACTTTGGAAAGAGTTTCAATACTTTGGTAAGAGT
2643315 ATTGATACTT
Statistics
Matches: 101, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
38 2 0.02
39 23 0.23
40 76 0.75
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.37
Consensus pattern (40 bp):
TCCATACTTTGGAAAGAGTTTCAATACTTTGGTAAGAGTT
Found at i:2647517 original size:40 final size:40
Alignment explanation
Indices: 2647462--2647557 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
2647452 TACAGGTTTA
2647462 TAATACACTTCGGTGTATATGGTGAGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGAGCACGACCTTATGTG
* *
2647502 TAATATACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGAGCACGACCTTATGTG
2647542 TAATACACTTCAGGTG
1 TAATACACTTC-GGTG
2647558 GGCACGACCT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 48 0.92
41 4 0.08
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGAGCACGACCTTATGTG
Found at i:2647728 original size:44 final size:47
Alignment explanation
Indices: 2647680--2647791 Score: 158
Period size: 44 Copynumber: 2.4 Consensus size: 47
2647670 ATAACCATGT
2647680 AAATAAGCTTATGAGCTTATGGAA-T-AATGGCAAGTATATTGG-AA
1 AAATAAGCTTATGAGCTTATGGAATTAAATGGCAAGTATATTGGTAA
* * * *
2647724 AAATAAGCTTACGATCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA-TTAAATGGCAAGTATATTGGTAA
2647772 AAATAAGCTTATGAGCTTAT
1 AAATAAGCTTATGAGCTTAT
2647792 AGGGATAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
44 22 0.38
46 1 0.02
47 15 0.26
48 20 0.34
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTATGGAATTAAATGGCAAGTATATTGGTAA
Found at i:2647814 original size:48 final size:45
Alignment explanation
Indices: 2647680--2647807 Score: 168
Period size: 47 Copynumber: 2.8 Consensus size: 45
2647670 ATAACCATGT
* *
2647680 AAATAAGCTTATGAGCTTATGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATTTTGGAA
* *
2647724 AAATAAGCTTACGATCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--TAAATGGTAAGTATTTTGG-AA
*
2647772 AAATAAGCTTATGAGCTTATAGGGATAAATGGTAAG
1 AAATAAGCTTATGAGCTTAT-GGAATAAATGGTAAG
2647808 AAATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
44 22 0.31
46 1 0.01
47 26 0.36
48 20 0.28
49 3 0.04
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATTTTGGAA
Found at i:2648367 original size:36 final size:37
Alignment explanation
Indices: 2648325--2648395 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
2648315 AGAAAAAAAG
2648325 ATGGAAAACATTGATAT-AA-ATAATAGCTCAAGAAAC
1 ATGGAAAACATTGATATGAAGATAA-AGCTCAAGAAAC
* *
2648361 ATGGAAAATATTGATTTGAAGATAAAGCTCAAGAA
1 ATGGAAAACATTGATATGAAGATAAAGCTCAAGAA
2648396 GCACTGGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 15 0.48
37 12 0.39
38 4 0.13
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.24
Consensus pattern (37 bp):
ATGGAAAACATTGATATGAAGATAAAGCTCAAGAAAC
Found at i:2653341 original size:16 final size:16
Alignment explanation
Indices: 2653320--2653358 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2653310 GGTATTACCC
*
2653320 GACCTGTTTTCAACCT
1 GACCTGTTATCAACCT
*
2653336 GACCTGTTATGAACCT
1 GACCTGTTATCAACCT
2653352 GACCTGT
1 GACCTGT
2653359 AATTGACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:2653513 original size:17 final size:17
Alignment explanation
Indices: 2653474--2653513 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
2653464 ATAATAAACT
*
2653474 TATGATAATTAAATTAT
1 TATGATAATTAAATTAA
*
2653491 TTTGATAATTAAATTAA
1 TATGATAATTAAATTAA
2653508 TATGAT
1 TATGAT
2653514 TACTTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
TATGATAATTAAATTAA
Found at i:2653736 original size:15 final size:15
Alignment explanation
Indices: 2653696--2653736 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2653686 AAATTAAATT
* * *
2653696 TAAATATTATCTTAT
1 TAAATTTTATTTTAA
2653711 TAAATTTTATTTTAA
1 TAAATTTTATTTTAA
2653726 TAAATTTTATT
1 TAAATTTTATT
2653737 AATTAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATTTTATTTTAA
Found at i:2656476 original size:2 final size:2
Alignment explanation
Indices: 2656464--2656499 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2656454 AATAAACCAG
2656464 TA TA TA T- 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 TA TA TA TA T
2656500 TAACAACAAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2657858 original size:17 final size:17
Alignment explanation
Indices: 2657813--2657875 Score: 90
Period size: 17 Copynumber: 3.5 Consensus size: 17
2657803 TACAAAATAT
2657813 TAATACTAATAATTATTA
1 TAATA-TAATAATTATTA
2657831 TAATTTATAATAATTATTA
1 TAA--TATAATAATTATTA
*
2657850 TAATATAATGATTATTA
1 TAATATAATAATTATTA
2657867 TAATATAAT
1 TAATATAAT
2657876 TTTTTATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
17 22 0.52
18 3 0.07
19 15 0.36
20 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TAATATAATAATTATTA
Found at i:2657966 original size:18 final size:17
Alignment explanation
Indices: 2657931--2658063 Score: 58
Period size: 18 Copynumber: 7.2 Consensus size: 17
2657921 ATAAAAATAG
*
2657931 TATGTATATATAAG-TCA
1 TATGTAAATAT-AGTTCA
2657948 TATGTAAACTATAGTTCA
1 TATGTAAA-TATAGTTCA
* *
2657966 TATATAAATATCAACTT--
1 TATGTAAATAT--AGTTCA
*
2657983 TA-GTATATATATAGTTCG
1 TATGTA-A-ATATAGTTCA
*
2658001 TATGTAAACTATAGAGTTTA
1 TATGTAAA-TAT--AGTTCA
2658021 TATAGTTTATATATATAGTTCA
1 TAT-G--TA-A-ATATAGTTCA
2658043 TATGTAAACTATAGTTCA
1 TATGTAAA-TATAGTTCA
2658061 TAT
1 TAT
2658064 ATATAGTATA
Statistics
Matches: 90, Mismatches: 8, Indels: 35
0.68 0.06 0.26
Matches are distributed among these distances:
16 5 0.06
17 17 0.19
18 36 0.40
19 8 0.09
20 7 0.08
21 2 0.02
22 8 0.09
23 2 0.02
24 4 0.04
25 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.43
Consensus pattern (17 bp):
TATGTAAATATAGTTCA
Found at i:2658037 original size:13 final size:13
Alignment explanation
Indices: 2658019--2658070 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
2658009 CTATAGAGTT
*
2658019 TATATAGTTTATA
1 TATATAGTTCATA
2658032 TATATAGTTCATA
1 TATATAGTTCATA
2658045 TGTAAACTATAGTTCATA
1 --T--A-TATAGTTCATA
2658063 TATATAGT
1 TATATAGT
2658071 ATATAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
13 18 0.55
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 11 0.33
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (13 bp):
TATATAGTTCATA
Found at i:2658066 original size:42 final size:41
Alignment explanation
Indices: 2657986--2658064 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 41
2657976 TCAACTTTAG
*
2657986 TATATATATAGTTCGTATGTAAACTATAGAGTTTATATAGTT
1 TATATATATAGTTCATATGTAAACTATA-AGTTTATATAGTT
*
2658028 TATATATATAGTTCATATGTAAACTAT-AGTTCATATA
1 TATATATATAGTTCATATGTAAACTATAAGTTTATATA
2658065 TATAGTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 9 0.26
42 26 0.74
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.44
Consensus pattern (41 bp):
TATATATATAGTTCATATGTAAACTATAAGTTTATATAGTT
Found at i:2658073 original size:18 final size:17
Alignment explanation
Indices: 2658028--2658073 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2658018 TTATATAGTT
2658028 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
2658045 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
2658063 TATATAGTATA
1 TATATA-TATA
2658074 TAAATATAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:2658074 original size:42 final size:42
Alignment explanation
Indices: 2657983--2658075 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
2657973 ATATCAACTT
*
2657983 TAGTATATATATAGTTCGTATGTAAACTATAGAGTTTATATAG
1 TAGTATATATATAGTTCATATGTAAACTATA-AGTTTATATAG
*
2658026 T-TTATATATATAGTTCATATGTAAACTAT-AGTTCATATATA-
1 TAGTATATATATAGTTCATATGTAAACTATAAGTT--TATATAG
2658067 TAGTATATA
1 TAGTATATA
2658076 AATATAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
40 4 0.09
41 1 0.02
42 38 0.86
43 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (42 bp):
TAGTATATATATAGTTCATATGTAAACTATAAGTTTATATAG
Found at i:2658088 original size:20 final size:20
Alignment explanation
Indices: 2658064--2658182 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
2658054 TAGTTCATAT
2658064 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
2658084 TTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
2658109 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
2658129 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
2658154 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
2658174 TTATAGTAT
1 ATATAGTAT
2658183 GTAGTTTATA
Statistics
Matches: 84, Mismatches: 5, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
20 30 0.36
21 2 0.02
22 14 0.17
23 14 0.17
24 2 0.02
25 22 0.26
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:2658089 original size:33 final size:33
Alignment explanation
Indices: 2658021--2658113 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
2658011 ATAGAGTTTA
*
2658021 TATAGTTTATATATATAGT-TCAT--ATGTAAAC
1 TATAGTTTATATATATAGTAT-ATAAATATAAAC
* *
2658052 TATAGTTCATATATATAGTATATAAATATAAAT
1 TATAGTTTATATATATAGTATATAAATATAAAC
*
2658085 TATAGTTTATATAAATAGTATA-AAATATA
1 TATAGTTTATATATATAGTATATAAATATA
2658114 GTATATAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
31 20 0.37
32 8 0.15
33 26 0.48
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (33 bp):
TATAGTTTATATATATAGTATATAAATATAAAC
Found at i:2658113 original size:25 final size:23
Alignment explanation
Indices: 2658064--2658169 Score: 116
Period size: 25 Copynumber: 4.7 Consensus size: 23
2658054 TAGTTCATAT
2658064 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
2658084 TTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
2658109 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
2658129 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
2658154 ATATAGTATATAAATA
1 ATATAGTATATAAATA
2658170 TAAATTATAG
Statistics
Matches: 72, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
20 16 0.22
21 1 0.01
22 12 0.17
23 19 0.26
24 2 0.03
25 22 0.31
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.39
Consensus pattern (23 bp):
ATATAGTATATAAATAGTATAAA
Found at i:2658118 original size:45 final size:45
Alignment explanation
Indices: 2658064--2658180 Score: 225
Period size: 45 Copynumber: 2.6 Consensus size: 45
2658054 TAGTTCATAT
2658064 ATATAGTATATAAATATAAATTATAGTTTATATAAATAGTATAAA
1 ATATAGTATATAAATATAAATTATAGTTTATATAAATAGTATAAA
*
2658109 ATATAGTATATAAATATAAACTATAGTTTATATAAATAGTATAAA
1 ATATAGTATATAAATATAAATTATAGTTTATATAAATAGTATAAA
2658154 ATATAGTATATAAATATAAATTATAGT
1 ATATAGTATATAAATATAAATTATAGT
2658181 ATGTAGTTTA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (45 bp):
ATATAGTATATAAATATAAATTATAGTTTATATAAATAGTATAAA
Found at i:2658279 original size:49 final size:49
Alignment explanation
Indices: 2658205--2658298 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
2658195 AATATAAATA
2658205 TAAACCCTAAACCCTAAACCCAACCTACTAAATCATGATCCCTAATCCC
1 TAAACCCTAAACCCTAAACCCAACCTACTAAATCATGATCCCTAATCCC
* * *
2658254 TAAACCCTGATCCCTAAACCTAACCTACTAAATCATGATCCCTAA
1 TAAACCCTAAACCCTAAACCCAACCTACTAAATCATGATCCCTAA
2658299 ACCATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.38, C:0.36, G:0.03, T:0.22
Consensus pattern (49 bp):
TAAACCCTAAACCCTAAACCCAACCTACTAAATCATGATCCCTAATCCC
Found at i:2658522 original size:2 final size:2
Alignment explanation
Indices: 2658517--2658627 Score: 64
Period size: 2 Copynumber: 52.0 Consensus size: 2
2658507 GTATATAGTT
* * *
2658517 TA TA TA TA TA -A TA TA TA GTA TA TA AA TA TA AA CTA TA GCA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA -TA TA
* * * *
2658559 TA TA TA TA TA TA TA TG TCA TA TG TA AA CTA TA TA GTA TA TA AA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA -TA TA TA -TA TA TA TA
2658602 TA TCA -A CTA TA GTA TA TA TA TA TA TA
1 TA T-A TA -TA TA -TA TA TA TA TA TA TA
2658628 GGTCATATGT
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
1 2 0.02
2 70 0.83
3 12 0.14
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (2 bp):
TA
Found at i:2658531 original size:20 final size:20
Alignment explanation
Indices: 2658508--2658790 Score: 98
Period size: 20 Copynumber: 14.9 Consensus size: 20
2658498 TTATACATGG
2658508 TATATAGTTTATATATATAA
1 TATATAGTTTATATATATAA
* *
2658528 TATATAGTATATAAATATAA
1 TATATAGTTTATATATATAA
**
2658548 -ACTATAGCATATATATAT-A
1 TA-TATAGTTTATATATATAA
* *
2658567 TATATA-TGTCATATGTA-AA
1 TATATAGT-TTATATATATAA
* *
2658586 CTATATAGTATATAAATATCAA
1 -TATATAGTTTATATATAT-AA
*
2658608 -CTATAG----TATATAT-A
1 TATATAGTTTATATATATAA
* * *
2658622 TATATAGGTCATATGTA-AA
1 TATATAGTTTATATATATAA
2658641 CTATATAG--T-T-TATAT-A
1 -TATATAGTTTATATATATAA
* *
2658657 TATATAGTTCATATGTA-AA
1 TATATAGTTTATATATATAA
*
2658676 -CTATAG-TTAGTATATA-AA
1 TATATAGTTTA-TATATATAA
*
2658694 CTATATAGTTTATATGTA-AA
1 -TATATAGTTTATATATATAA
* *
2658714 -CTATAGTTCATATATA-AA
1 TATATAGTTTATATATATAA
*
2658732 TATCA-ACTTTAGTATATAT-A
1 TAT-ATAGTTTA-TATATATAA
*
2658752 TATATAGTTCT-TATGTA-AA
1 TATATAGTT-TATATATATAA
2658771 CTATATAGTTTATATATATA
1 -TATATAGTTTATATATATA
2658791 GTTCATATGT
Statistics
Matches: 194, Mismatches: 34, Indels: 69
0.65 0.11 0.23
Matches are distributed among these distances:
14 1 0.01
15 12 0.06
16 10 0.05
17 3 0.02
18 28 0.14
19 36 0.19
20 96 0.49
21 6 0.03
22 2 0.01
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (20 bp):
TATATAGTTTATATATATAA
Found at i:2658643 original size:33 final size:33
Alignment explanation
Indices: 2658606--2658821 Score: 202
Period size: 33 Copynumber: 6.6 Consensus size: 33
2658596 TATAAATATC
*
2658606 AACTATAGTATATATATATATAGGTCATATGTA
1 AACTATAGTATATATATATATAGTTCATATGTA
*
2658639 AACTATATAGTTTATATATATATAGTTCATATGTA
1 AAC--TATAGTATATATATATATAGTTCATATGTA
*
2658674 AACTATAGTTAGTATATAAACTATATAGTTTATATGTA
1 AACTATAG-TA-TATAT--A-TATATAGTTCATATGTA
* *
2658712 AACTATAGT-T-CATATATA-A----ATA--TC
1 AACTATAGTATATATATATATAGTTCATATGTA
* *
2658736 AACTTTAGTATATATATATATAGTTCTTATGTA
1 AACTATAGTATATATATATATAGTTCATATGTA
*
2658769 AACTATA-TAGTTTATATATATAGTTCATATGTA
1 AACTATAGTA-TATATATATATAGTTCATATGTA
2658802 AACTATAGT-TCATATATATA
1 AACTATAGTAT-ATATATATA
2658822 GTATATAAAT
Statistics
Matches: 150, Mismatches: 14, Indels: 38
0.74 0.07 0.19
Matches are distributed among these distances:
24 9 0.06
25 1 0.01
26 10 0.07
27 1 0.01
30 1 0.01
31 6 0.04
32 4 0.03
33 51 0.34
34 4 0.03
35 37 0.25
37 2 0.01
38 24 0.16
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (33 bp):
AACTATAGTATATATATATATAGTTCATATGTA
Found at i:2658643 original size:55 final size:56
Alignment explanation
Indices: 2658528--2658660 Score: 196
Period size: 55 Copynumber: 2.3 Consensus size: 56
2658518 ATATATATAA
*
2658528 TATATAGTATATAAATATAAACTATAGCATATATATATATATATATGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATAG---ATATATATATATATAGGTCATATGTAAAC
*
2658587 TATATAGTATATAAATATCAACTATAG-TATATATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATAGATATATATATATATAGGTCATATGTAAAC
* *
2658642 TATATAGTTTATATATATA
1 TATATAGTATATAAATATA
2658661 TAGTTCATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
55 43 0.62
59 26 0.38
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (56 bp):
TATATAGTATATAAATATAAACTATAGATATATATATATATAGGTCATATGTAAAC
Found at i:2658796 original size:128 final size:128
Alignment explanation
Indices: 2658545--2658828 Score: 395
Period size: 128 Copynumber: 2.2 Consensus size: 128
2658535 TATATAAATA
*
2658545 TAAACTATAG--CATATATATATA-TATATA-TGTCATATGTAAACTATATAGTATATAAATATC
1 TAAACTATAGTTCATATATA-A-ACTATATAGT-TTATATGTAAACTATATAGTATATAAATATC
2658606 AACTATAGTATATATATATATAGGTCATATGTAAACTATATAGTTTATATATATATAGTTCATAT
63 AACTATAGTATATATATATATAGGTCATATGTAAACTATATAGTTTATATATATATAGTTCATAT
2658671 G
128 G
2658672 TAAACTATAGTT-AGTATATAAACTATATAGTTTATATGTAAACTATAGTTCA-TATATAAATAT
1 TAAACTATAGTTCA-TATATAAACTATATAGTTTATATGTAAACTATA--T-AGTATATAAATAT
* * *
2658735 CAACTTTAGTATATATATATATAGTTCTTATGTAAACTATATAG-TT-TATATATATAGTTCATA
62 CAACTATAGTATATATATATATAGGTCATATGTAAACTATATAGTTTATATATATATAGTTCATA
2658798 TG
127 TG
* *
2658800 TAAACTATAGTTCATATATATAGTATATA
1 TAAACTATAGTTCATATATAAACTATATA
2658829 AATATAAACT
Statistics
Matches: 142, Mismatches: 6, Indels: 17
0.86 0.04 0.10
Matches are distributed among these distances:
127 11 0.08
128 67 0.47
129 10 0.07
130 53 0.37
131 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (128 bp):
TAAACTATAGTTCATATATAAACTATATAGTTTATATGTAAACTATATAGTATATAAATATCAAC
TATAGTATATATATATATAGGTCATATGTAAACTATATAGTTTATATATATATAGTTCATATG
Found at i:2658810 original size:18 final size:18
Alignment explanation
Indices: 2658624--2658816 Score: 102
Period size: 18 Copynumber: 10.7 Consensus size: 18
2658614 TATATATATA
*
2658624 TATAGGTCATATGTAAAC
1 TATAGTTCATATGTAAAC
* *
2658642 TATATAGTT--TATATATA-
1 --TATAGTTCATATGTAAAC
2658659 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
*
2658677 TATAGTT-AGTATATAAAC
1 TATAGTTCA-TATGTAAAC
*
2658695 TATATAGTTTATATGTAAAC
1 --TATAGTTCATATGTAAAC
*
2658715 TATAGTTCATATATAAA-
1 TATAGTTCATATGTAAAC
* * *
2658732 TATCAACTTTAGTATATATATA-
1 TAT--AGTTCA-TATGTA-A-AC
*
2658754 TATAGTTCTTATGTAAAC
1 TATAGTTCATATGTAAAC
*
2658772 TATATAGTT--TA--TATA-
1 --TATAGTTCATATGTAAAC
2658787 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
2658805 TATAGTTCATAT
1 TATAGTTCATAT
2658817 ATATAGTATA
Statistics
Matches: 136, Mismatches: 17, Indels: 42
0.70 0.09 0.22
Matches are distributed among these distances:
13 7 0.05
15 9 0.07
16 3 0.02
17 14 0.10
18 51 0.38
19 9 0.07
20 37 0.27
21 2 0.01
22 4 0.03
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:2658837 original size:33 final size:33
Alignment explanation
Indices: 2658724--2658902 Score: 145
Period size: 33 Copynumber: 5.4 Consensus size: 33
2658714 CTATAGTTCA
* *
2658724 TATATAAATATCAACTTTAGTATATATATATATAG
1 TATATAAATATAAACTATAGT-T-TATATATATAG
* * *
2658759 T-TCT-TATGTAAACTATATAGTTTATATATATAG
1 TATATAAATATAAAC--TATAGTTTATATATATAG
* *
2658792 T-TCAT--ATGTAAACTATAGTTCATATATATAG
1 TAT-ATAAATATAAACTATAGTTTATATATATAG
*
2658823 TATATAAATATAAACTATAGTTTATATAAATAG
1 TATATAAATATAAACTATAGTTTATATATATAG
* *
2658856 TATATAAATATAAATTATAGTATGTAGTTTATATA-
1 TATATAAATATAAACTATAGT-T-TA-TATATATAG
*
2658891 AATATAAATATA
1 TATATAAATATA
2658903 CACCCTAAAC
Statistics
Matches: 121, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
31 20 0.17
32 1 0.01
33 70 0.58
34 5 0.04
35 19 0.16
36 6 0.05
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (33 bp):
TATATAAATATAAACTATAGTTTATATATATAG
Found at i:2658841 original size:20 final size:19
Alignment explanation
Indices: 2658817--2658878 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
2658807 TAGTTCATAT
2658817 ATATAGTATATAAATATAA
1 ATATAGTATATAAATATAA
2658836 ACTATAGT-T-T--ATAT-A
1 A-TATAGTATATAAATATAA
2658851 A-ATAGTATATAAATATAA
1 ATATAGTATATAAATATAA
2658869 ATTATAGTAT
1 A-TATAGTAT
2658879 GTAGTTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 15
0.70 0.00 0.30
Matches are distributed among these distances:
13 5 0.14
14 1 0.03
15 3 0.09
16 4 0.11
17 4 0.11
18 3 0.09
19 2 0.06
20 13 0.37
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (19 bp):
ATATAGTATATAAATATAA
Found at i:2658916 original size:7 final size:7
Alignment explanation
Indices: 2658904--2658982 Score: 99
Period size: 7 Copynumber: 11.3 Consensus size: 7
2658894 ATAAATATAC
2658904 ACCCTAA
1 ACCCTAA
2658911 ACCCTAA
1 ACCCTAA
*
2658918 TA-CTTAA
1 -ACCCTAA
2658925 ACCCTAA
1 ACCCTAA
2658932 ACCCTAA
1 ACCCTAA
2658939 ACCCTAA
1 ACCCTAA
2658946 ACCCTAA
1 ACCCTAA
2658953 ACCCTAA
1 ACCCTAA
*
2658960 ACCCTGAT
1 ACCCT-AA
*
2658968 A-CTTAA
1 ACCCTAA
2658974 ACCCTAA
1 ACCCTAA
2658981 AC
1 AC
2658983 TATATATACT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
6 3 0.05
7 56 0.90
8 3 0.05
ACGTcount: A:0.42, C:0.38, G:0.01, T:0.19
Consensus pattern (7 bp):
ACCCTAA
Found at i:2659003 original size:22 final size:22
Alignment explanation
Indices: 2658978--2659034 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
2658968 ACTTAAACCC
2658978 TAAACTATATA-TACTATATATATA
1 TAAACTATATAGT-CTATAT-TA-A
* *
2659002 AAAACTATATAGTTTATATTAA
1 TAAACTATATAGTCTATATTAA
2659024 TAAACTATATA
1 TAAACTATATA
2659035 ATTTATACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 11 0.38
23 2 0.07
24 15 0.52
25 1 0.03
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAACTATATAGTCTATATTAA
Found at i:2659039 original size:22 final size:23
Alignment explanation
Indices: 2658978--2659041 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 23
2658968 ACTTAAACCC
*
2658978 TAAACTATATATACTATATATATAA
1 TAAACTATATA-A-TTTATATATAA
*
2659003 -AAACTATATAGTTTATAT-TAA
1 TAAACTATATAATTTATATATAA
2659024 TAAACTATATAATTTATA
1 TAAACTATATAATTTATA
2659042 CAATATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 3 0.09
22 22 0.63
24 10 0.29
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAACTATATAATTTATATATAA
Found at i:2659070 original size:17 final size:17
Alignment explanation
Indices: 2659032--2659082 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
2659022 AATAAACTAT
*
2659032 ATAATTTATACAATATAT
1 ATAATTTATA-AATATAC
*
2659050 ATAATTTATAATTATAC
1 ATAATTTATAAATATAC
*
2659067 ATAATATATAAATATA
1 ATAATTTATAAATATA
2659083 AATTGTATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATTTATAAATATAC
Found at i:2659073 original size:24 final size:25
Alignment explanation
Indices: 2659031--2659109 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 25
2659021 TAATAAACTA
2659031 TATAATTTATACAATATATATAATT
1 TATAATTTATACAATATATATAATT
*
2659056 TATAA-TTATAC-ATAATATATAA-A
1 TATAATTTATACAAT-ATATATAATT
***
2659079 TATAAATTGTATAGTTTATATATAATT
1 TAT-AATT-TATACAATATATATAATT
2659106 TATA
1 TATA
2659110 TATAAACTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
23 5 0.11
24 16 0.36
25 6 0.14
26 13 0.30
27 4 0.09
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (25 bp):
TATAATTTATACAATATATATAATT
Found at i:2659189 original size:2 final size:2
Alignment explanation
Indices: 2659182--2659309 Score: 84
Period size: 2 Copynumber: 63.0 Consensus size: 2
2659172 TTATACATGG
* * *
2659182 TA TA TA TA GTT TA TA CA TA -A TA TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
2659224 TA TA TA TA TA TA TA AA AA CTA TA TA GT- TA TA TA TA TA -A TA CA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
2659266 TA TA CTT TA TA TA TA AA CTA TA TA GTT TA TA T- TA CA TA TA TA
1 TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
2659308 TA
1 TA
2659310 AAATGAATGC
Statistics
Matches: 98, Mismatches: 18, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
1 4 0.04
2 88 0.90
3 6 0.06
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2659191 original size:20 final size:19
Alignment explanation
Indices: 2659162--2659199 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
2659152 AAACTATATA
2659162 GTATTATAGTTTATACATG
1 GTATTATAGTTTATACATG
2659181 GTATATATAGTTTATACAT
1 GTAT-TATAGTTTATACAT
2659200 AATATGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (19 bp):
GTATTATAGTTTATACATG
Found at i:2659209 original size:20 final size:20
Alignment explanation
Indices: 2659166--2659309 Score: 91
Period size: 20 Copynumber: 7.2 Consensus size: 20
2659156 TATATAGTAT
**
2659166 TATAGTTTATACATGGTATA
1 TATAGTTTATACATAATATA
*
2659186 TATAGTTTATACATAATATG
1 TATAGTTTATACATAATATA
* *
2659206 TATA-TATATATAT-ATATA
1 TATAGTTTATACATAATATA
* * *
2659224 TATA-TATATATATAAAAACTA
1 TATAGTTTATACAT-AATA-TA
* *
2659245 TATAGTTATATATATAATACA
1 TATAGTT-TATACATAATATA
* *
2659266 TATACTTTATATATAA-ACTA
1 TATAGTTTATACATAATA-TA
*
2659286 TATAGTTTATA-TTACATATA
1 TATAGTTTATACATA-ATATA
2659306 TATA
1 TATA
2659310 AAATGAATGC
Statistics
Matches: 102, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
18 17 0.17
19 10 0.10
20 50 0.49
21 14 0.14
22 4 0.04
23 7 0.07
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
TATAGTTTATACATAATATA
Found at i:2659277 original size:41 final size:41
Alignment explanation
Indices: 2659210--2659307 Score: 126
Period size: 41 Copynumber: 2.3 Consensus size: 41
2659200 AATATGTATA
*
2659210 TATATATATATATATATATATATATATAAAAACTATATAGT
1 TATATATATATATACATATATATATATAAAAACTATATAGT
* *
2659251 TATATATATA-ATACATATACTTTATATATAAACTATATAGTT
1 TATATATATATATACATATA-TATATATAAAAACTATATAG-T
*
2659293 TATATTACATATATA
1 TATA-TATATATATA
2659308 TAAAATGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 8 0.16
41 28 0.57
42 5 0.10
43 5 0.10
44 3 0.06
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (41 bp):
TATATATATATATACATATATATATATAAAAACTATATAGT
Found at i:2663873 original size:34 final size:34
Alignment explanation
Indices: 2663830--2663906 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 34
2663820 TAAGTGTGAA
* *
2663830 TATGTGTGGACGAGTGGAGTTATCTCACAGTCCT
1 TATGTGTGGACAAGTGAAGTTATCTCACAGTCCT
* *
2663864 TATGTGTGGACAAGTGAAGTTATCTCGCTGTCCT
1 TATGTGTGGACAAGTGAAGTTATCTCACAGTCCT
*
2663898 TATGCGTGG
1 TATGTGTGG
2663907 TTGATCATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (34 bp):
TATGTGTGGACAAGTGAAGTTATCTCACAGTCCT
Found at i:2678097 original size:25 final size:26
Alignment explanation
Indices: 2678051--2678103 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2678041 TTACATCGGC
2678051 TTCCACCTGCAAATTGACCCCTGAAT
1 TTCCACCTGCAAATTGACCCCTGAAT
* *
2678077 TTCCCCCTGCAATTTGA-CCCTGAAT
1 TTCCACCTGCAAATTGACCCCTGAAT
2678102 TT
1 TT
2678104 AGCTTTGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.23, C:0.34, G:0.11, T:0.32
Consensus pattern (26 bp):
TTCCACCTGCAAATTGACCCCTGAAT
Done.